From da77dde04de70a75a215a7bd0044e757d189352a Mon Sep 17 00:00:00 2001
From: Risto Toijala <risto.toijala@helsinki.fi>
Date: Thu, 4 Apr 2019 14:32:49 +0300
Subject: [PATCH 01/22] MC/fix_bond_break: Use TAGINT_FORMAT where appropriate

---
 src/MC/fix_bond_break.cpp | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index a1c9bb3ab0..05edc0509e 100644
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -800,26 +800,27 @@ void FixBondBreak::print_bb()
   for (int i = 0; i < atom->nlocal; i++) {
     printf("TAG " TAGINT_FORMAT ": %d nbonds: ",atom->tag[i],atom->num_bond[i]);
     for (int j = 0; j < atom->num_bond[i]; j++) {
-      printf(" %d",atom->bond_atom[i][j]);
+      printf(" " TAGINT_FORMAT, atom->bond_atom[i][j]);
     }
     printf("\n");
     printf("TAG " TAGINT_FORMAT ": %d nangles: ",atom->tag[i],atom->num_angle[i]);
     for (int j = 0; j < atom->num_angle[i]; j++) {
-      printf(" %d %d %d,",atom->angle_atom1[i][j],
-             atom->angle_atom2[i][j],atom->angle_atom3[i][j]);
+      printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT ",",
+             atom->angle_atom1[i][j],atom->angle_atom2[i][j],
+             atom->angle_atom3[i][j]);
     }
     printf("\n");
     printf("TAG " TAGINT_FORMAT ": %d ndihedrals: ",atom->tag[i],atom->num_dihedral[i]);
     for (int j = 0; j < atom->num_dihedral[i]; j++) {
-      printf(" %d %d %d %d,",atom->dihedral_atom1[i][j],
-             atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j],
-             atom->dihedral_atom4[i][j]);
+      printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT ",",
+             atom->dihedral_atom1[i][j],atom->dihedral_atom2[i][j],
+             atom->dihedral_atom3[i][j],atom->dihedral_atom4[i][j]);
     }
     printf("\n");
     printf("TAG " TAGINT_FORMAT ": %d %d %d nspecial: ",atom->tag[i],
            atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]);
     for (int j = 0; j < atom->nspecial[i][2]; j++) {
-      printf(" %d",atom->special[i][j]);
+      printf(" " TAGINT_FORMAT, atom->special[i][j]);
     }
     printf("\n");
   }
@@ -830,7 +831,7 @@ void FixBondBreak::print_bb()
 void FixBondBreak::print_copy(const char *str, tagint m,
                               int n1, int n2, int n3, int *v)
 {
-  printf("%s %i: %d %d %d nspecial: ",str,m,n1,n2,n3);
+  printf("%s " TAGINT_FORMAT ": %d %d %d nspecial: ",str,m,n1,n2,n3);
   for (int j = 0; j < n3; j++) printf(" %d",v[j]);
   printf("\n");
 }

From 66794692201d4345cde7aaa5573b4cf4f06cdea7 Mon Sep 17 00:00:00 2001
From: Risto Toijala <risto.toijala@helsinki.fi>
Date: Thu, 4 Apr 2019 15:35:44 +0300
Subject: [PATCH 02/22] USER-MANIFOLD: Use TAGINT_FORMAT where appropriate

---
 src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
index 794a324f03..de134e32ed 100644
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
@@ -559,7 +559,8 @@ void FixNVEManifoldRattle::rattle_manifold_x(double *x, double *v,
 
   if (iters >= max_iter && res > tolerance) {
     char msg[2048];
-    sprintf(msg,"Failed to constrain atom %d (x = (%f, %f, %f)! res = %e, iters = %d\n",
+    sprintf(msg,"Failed to constrain atom " TAGINT_FORMAT
+            " (x = (%f, %f, %f)! res = %e, iters = %d\n",
             tagi, x[0], x[1], x[2], res, iters);
     error->one(FLERR,msg);
   }
@@ -652,7 +653,8 @@ void FixNVEManifoldRattle::rattle_manifold_v(double *v, double *f,
 
   if (iters >= max_iter && res >= tolerance) {
           char msg[2048];
-          sprintf(msg,"Failed to constrain atom %d (x = (%f, %f, %f)! res = %e, iters = %d\n",
+          sprintf(msg,"Failed to constrain atom " TAGINT_FORMAT
+                  " (x = (%f, %f, %f)! res = %e, iters = %d\n",
                   tagi, x[0], x[1], x[2], res, iters);
           error->all(FLERR,msg);
   }

From 2aa7a150b48fbbf080087000d9f7096d8d449e42 Mon Sep 17 00:00:00 2001
From: Risto Toijala <risto.toijala@helsinki.fi>
Date: Thu, 4 Apr 2019 15:38:53 +0300
Subject: [PATCH 03/22] USER-SMD: Use TAGINT_FORMAT where appropriate

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

diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp
index ac67a3279a..1d7bbca780 100644
--- a/src/USER-SMD/pair_smd_tlsph.cpp
+++ b/src/USER-SMD/pair_smd_tlsph.cpp
@@ -308,7 +308,7 @@ void PairTlsph::PreCompute() {
                          */
 
                         if ((detF[i] < DETF_MIN) || (detF[i] > DETF_MAX) || (numNeighsRefConfig[i] == 0)) {
-                                printf("deleting particle [%d] because det(F)=%f is outside stable range %f -- %f \n", tag[i],
+                                printf("deleting particle [" TAGINT_FORMAT "] because det(F)=%f is outside stable range %f -- %f \n", tag[i],
                                                 Fincr[i].determinant(),
                                                 DETF_MIN, DETF_MAX);
                                 printf("nn = %d, damage=%f\n", numNeighsRefConfig[i], damage[i]);

From 81dd96f970250616d4663a0f824bf100a1008f47 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 4 Apr 2019 12:42:54 -0400
Subject: [PATCH 04/22] print more meaningful error message when trying to
 access individual data from a local array produced by a compute */local

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

diff --git a/src/variable.cpp b/src/variable.cpp
index c0e4dae7d0..ed3b41bd00 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -1578,6 +1578,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
           newtree->nextra = 0;
           treestack[ntreestack++] = newtree;
 
+        } else if (nbracket == 1 && compute->local_flag) {
+          print_var_error(FLERR,"Cannot access local data via indexing",ivar);
         } else print_var_error(FLERR,
                                "Mismatched compute in variable formula",ivar);
 

From 265ad4512dfa6f8be1cb0f28abfb4b9d3ffbf4d4 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 4 Apr 2019 13:18:27 -0400
Subject: [PATCH 05/22] add sanity check on plumed pre-installed path location

---
 lib/plumed/Install.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py
index 70296b35d3..2ae5aadd03 100644
--- a/lib/plumed/Install.py
+++ b/lib/plumed/Install.py
@@ -75,6 +75,8 @@ if pathflag:
     if not os.path.isdir(plumedpath):
       sys.exit("Plumed2 path %s does not exist" % plumedpath)
     homedir = fullpath(plumedpath)
+    if not os.path.isdir(os.path.join(homedir, 'include', 'plumed', 'core')):
+      sys.exit("No Plumed2 installation found at %s" % plumedpath)
 
 # download and unpack plumed2 tarball
 

From c52a330a79b674c28cced21879a562fb180c896f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 4 Apr 2019 14:04:12 -0400
Subject: [PATCH 06/22] update USER-PLUMED support for version 2.5.1 and fix
 bug in Install.py script

---
 cmake/CMakeLists.txt  | 11 +++++------
 lib/plumed/Install.py |  6 ++++--
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index fd93814574..b9a93a110e 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -367,7 +367,7 @@ if(PKG_KSPACE)
   endif()
 endif()
 
-if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUIP OR PKG_LATTE)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@@ -577,8 +577,8 @@ if(PKG_USER-PLUMED)
     message(STATUS "PLUMED download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(plumed_build
-      URL https://github.com/plumed/plumed2/releases/download/v2.4.4/plumed-src-2.4.4.tgz
-      URL_MD5 71ed465bdc7c2059e282dbda8d564e71
+      URL https://github.com/plumed/plumed2/releases/download/v2.5.1/plumed-src-2.5.1.tgz
+      URL_MD5 c2a7b519e32197a120cdf47e0f194f81
       BUILD_IN_SOURCE 1
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                                ${CONFIGURE_REQUEST_PIC}
@@ -593,10 +593,9 @@ if(PKG_USER-PLUMED)
     list(APPEND LAMMPS_DEPS plumed_build)
     if(PLUMED_MODE STREQUAL "STATIC")
       add_definitions(-D__PLUMED_WRAPPER_CXX=1)
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o
-        "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS})
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${GSL_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "SHARED")
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS})
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
       add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)
       list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py
index 2ae5aadd03..3623a8cff0 100644
--- a/lib/plumed/Install.py
+++ b/lib/plumed/Install.py
@@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py',
 
 # settings
 
-version = "2.4.4"
+version = "2.5.1"
 mode = "static"
 
 # help message
@@ -43,6 +43,7 @@ checksums = { \
         '2.4.3' : 'b1be7c48971627febc11c61b70767fc5', \
         '2.4.4' : '71ed465bdc7c2059e282dbda8d564e71', \
         '2.5.0' : '6224cd089493661e19ceacccd35cf911', \
+        '2.5.1' : 'c2a7b519e32197a120cdf47e0f194f81', \
         }
 
 # parse and process arguments
@@ -67,6 +68,7 @@ if not args.build and not args.path:
 buildflag = args.build
 pathflag = args.path is not None
 plumedpath = args.path
+mode = args.mode
 
 homepath = fullpath('.')
 homedir = "%s/plumed2" % (homepath)
@@ -129,7 +131,7 @@ if os.path.isfile("Makefile.lammps.%s" % mode):
   lines1 = open(plumedinc, 'r').readlines()
   lines2 = open("Makefile.lammps.%s" % mode, 'r').readlines()
   fp = open("Makefile.lammps", 'w')
-  fp.write(os.path.join("PLUMED_LIBDIR=", homedir, "lib\n"))
+  fp.write("PLUMED_LIBDIR=" + os.path.join(homedir, "lib\n"))
   for line in lines1:
     fp.write(line)
   for line in lines2:

From 78bab6ee395f39fad5374dfdd90d4953353b7c8c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 4 Apr 2019 16:36:57 -0400
Subject: [PATCH 07/22] make format macros in USER-REAXC compatible with
 -DLAMMPS_BIGBIG

---
 src/USER-REAXC/reaxc_traj.h | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/USER-REAXC/reaxc_traj.h b/src/USER-REAXC/reaxc_traj.h
index 72c56637eb..b04a190965 100644
--- a/src/USER-REAXC/reaxc_traj.h
+++ b/src/USER-REAXC/reaxc_traj.h
@@ -42,7 +42,7 @@
 #define SCI_LINE  "%-37s%-24g\n"
 #define REAL3_LINE "%-32s%9.3f,%9.3f,%9.3f\n"
 
-#define INIT_DESC "%9d%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass
+#define INIT_DESC TAGINT_FORMAT "%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass
 #define INIT_DESC_LEN 32
 
 #define SIZE_INFO_LINE2 "%-10d%-10d\n"
@@ -51,21 +51,21 @@
 #define SIZE_INFO_LINE3 "%-10d%-10d%-10d\n"
 #define SIZE_INFO_LEN3 31
 
-#define ATOM_BASIC "%9d%10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge
+#define ATOM_BASIC TAGINT_FORMAT " %10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge
 #define ATOM_BASIC_LEN 50
-#define ATOM_wV    "%9d%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) Charge
+#define ATOM_wV    TAGINT_FORMAT " %10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) Charge
 #define ATOM_wV_LEN 80
-#define ATOM_wF    "%9d%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Fx Fy Fz) Charge
+#define ATOM_wF    TAGINT_FORMAT " %10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Fx Fy Fz) Charge
 #define ATOM_wF_LEN 80
-#define ATOM_FULL  "%9d%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) (Fx Fy Fz) Charge
+#define ATOM_FULL  TAGINT_FORMAT " %10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) (Fx Fy Fz) Charge
 #define ATOM_FULL_LEN 110
 
-#define BOND_BASIC "%9d%9d%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO
+#define BOND_BASIC TAGINT_FORMAT " " TAGINT_FORMAT " %10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO
 #define BOND_BASIC_LEN 39
-#define BOND_FULL  "%9d%9d%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2
+#define BOND_FULL  TAGINT_FORMAT " " TAGINT_FORMAT " %10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2
 #define BOND_FULL_LEN 69
 
-#define ANGLE_BASIC "%9d%9d%9d%10.3f\n" // Atom1 Atom2 Atom3 Theta
+#define ANGLE_BASIC TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " %10.3f\n" // Atom1 Atom2 Atom3 Theta
 #define ANGLE_BASIC_LEN 38
 
 enum ATOM_LINE_OPTS  { OPT_NOATOM = 0, OPT_ATOM_BASIC = 4, OPT_ATOM_wF = 5, OPT_ATOM_wV = 6, OPT_ATOM_FULL = 7, NR_OPT_ATOM = 8 };

From ab5c3b038623b2e77a24470fc3eca9e3eb53eff4 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 4 Apr 2019 16:51:37 -0400
Subject: [PATCH 08/22] protect against possible buffer overflow

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

diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp
index 3e90988cba..0c726985dc 100644
--- a/src/KSPACE/fix_tune_kspace.cpp
+++ b/src/KSPACE/fix_tune_kspace.cpp
@@ -99,8 +99,8 @@ void FixTuneKspace::init()
     error->all(FLERR,"Cannot use fix tune/kspace with dipole long-range solver");
 
   double old_acc = force->kspace->accuracy/force->kspace->two_charge_force;
-  char old_acc_str[12];
-  sprintf(old_acc_str,"%g",old_acc);
+  char old_acc_str[16];
+  snprintf(old_acc_str,16,"%g",old_acc);
   strcpy(new_acc_str,old_acc_str);
 
   int itmp;
@@ -210,8 +210,8 @@ void FixTuneKspace::store_old_kspace_settings()
   strcpy(old_kspace_style,force->kspace_style);
   strcpy(new_kspace_style,old_kspace_style);
   double old_acc = force->kspace->accuracy_relative;
-  char old_acc_str[12];
-  sprintf(old_acc_str,"%g",old_acc);
+  char old_acc_str[16];
+  snprintf(old_acc_str,16,"%g",old_acc);
   strcpy(new_pair_style,force->pair_style);
   strcpy(base_pair_style,force->pair_style);
   char *trunc;

From 4003387fb10e73badd1709fd709fe182d5991999 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 4 Apr 2019 16:51:59 -0400
Subject: [PATCH 09/22] dead code removal

---
 src/REPLICA/fix_hyper_global.cpp | 2 --
 src/REPLICA/fix_hyper_local.cpp  | 8 ++------
 src/REPLICA/hyper.cpp            | 2 +-
 3 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp
index 6924fe2d93..0c76b29911 100644
--- a/src/REPLICA/fix_hyper_global.cpp
+++ b/src/REPLICA/fix_hyper_global.cpp
@@ -191,8 +191,6 @@ void FixHyperGlobal::pre_neighbor()
 
   for (i = 0; i < nall_old; i++) old2now[i] = -1;
 
-  double **x = atom->x;
-
   for (m = 0; m < nblocal; m++) {
     iold = blist[m].iold;
     jold = blist[m].jold;
diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp
index dc7a0b94b9..a6db4419f0 100644
--- a/src/REPLICA/fix_hyper_local.cpp
+++ b/src/REPLICA/fix_hyper_local.cpp
@@ -353,8 +353,6 @@ void FixHyperLocal::pre_neighbor()
 
   for (i = 0; i < nall_old; i++) old2now[i] = -1;
 
-  double **x = atom->x;
-
   for (m = 0; m < nblocal; m++) {
     iold = blist[m].iold;
     jold = blist[m].jold;
@@ -407,7 +405,7 @@ void FixHyperLocal::pre_neighbor()
 void FixHyperLocal::pre_reverse(int /* eflag */, int /* vflag */)
 {
   int i,j,m,ii,jj,inum,jnum,iold,jold,ibond,nbond,ijhalf,ncount;
-  double xtmp,ytmp,ztmp,delx,dely,delz;
+  double delx,dely,delz;
   double r,r0,estrain,emax,ebias,vbias,fbias,fbiasr;
   double halfstrain,selfstrain;
   int *ilist,*jlist,*numneigh,**firstneigh;
@@ -811,7 +809,7 @@ void FixHyperLocal::min_pre_neighbor()
 void FixHyperLocal::build_bond_list(int natom)
 {
   int i,j,ii,jj,m,n,iold,jold,ilocal,jlocal,inum,jnum,nbond;
-  tagint itag,jtag;
+  tagint jtag;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq,distsq,oldcoeff;
   int *ilist,*jlist,*numneigh,**firstneigh;
 
@@ -1006,7 +1004,6 @@ void FixHyperLocal::build_bond_list(int natom)
     ytmp = x[i][1];
     ztmp = x[i][2];
 
-    itag = tag[i];
     tagold[i] = tag[i];
 
     jlist = firstneigh[i];
@@ -1420,7 +1417,6 @@ double FixHyperLocal::compute_vector(int i)
   }
 
   if (i == 4) {
-    const int nlocal = atom->nlocal;
     bigint allneigh,thisneigh;
     thisneigh = listfull->ipage->ndatum;
     MPI_Allreduce(&thisneigh,&allneigh,1,MPI_LMP_BIGINT,MPI_SUM,world);
diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp
index 5d820b2e27..00b91684e9 100644
--- a/src/REPLICA/hyper.cpp
+++ b/src/REPLICA/hyper.cpp
@@ -268,7 +268,7 @@ void Hyper::command(int narg, char **arg)
   double nnewbond,avenbias,avebiascoeff,minbiascoeff,maxbiascoeff;
   double maxbondperatom,neighbondperbond,avebiasnow;
   double tbondbuild,rmaxever,rmaxeverbig,allghost_toofar;
-  double lostbond,lostbondcoeff,biasoverlap;
+  double biasoverlap;
 
   if (hyperenable) {
     t_hyper = fix_hyper->query(1);

From df94e80bb1be510b9c6df8a73059719ae30f8c35 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 4 Apr 2019 16:52:08 -0400
Subject: [PATCH 10/22] silence compiler warnings

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

diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp
index 0e4e151c3d..545ceb7b0e 100644
--- a/src/USER-COLVARS/fix_colvars.cpp
+++ b/src/USER-COLVARS/fix_colvars.cpp
@@ -645,7 +645,7 @@ void FixColvars::setup(int vflag)
 /* ---------------------------------------------------------------------- */
 /* Main colvars handler:
  * Send coodinates and add colvar forces to atoms. */
-void FixColvars::post_force(int vflag)
+void FixColvars::post_force(int /*vflag*/)
 {
   // some housekeeping: update status of the proxy as needed.
   if (me == 0) {
@@ -816,7 +816,7 @@ void FixColvars::min_post_force(int vflag)
 }
 
 /* ---------------------------------------------------------------------- */
-void FixColvars::post_force_respa(int vflag, int ilevel, int iloop)
+void FixColvars::post_force_respa(int vflag, int ilevel, int /*iloop*/)
 {
   /* only process colvar forces on the outmost RESPA level. */
   if (ilevel == nlevels_respa-1) post_force(vflag);

From dbbf198edb4edf36a06550ea20a1a3bf02784864 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 4 Apr 2019 17:10:27 -0400
Subject: [PATCH 11/22] more accurate matching of styles using
 utils::strmatch()

---
 src/info.cpp     | 3 ++-
 src/respa.cpp    | 3 ++-
 src/velocity.cpp | 9 +++++----
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/src/info.cpp b/src/info.cpp
index 3d8a8d7b9e..ac2ee4a96d 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -42,6 +42,7 @@
 #include "variable.h"
 #include "update.h"
 #include "error.h"
+#include "utils.h"
 
 #include <ctime>
 #include <map>
@@ -397,7 +398,7 @@ void Info::command(int narg, char **arg)
     fprintf(out,"Atoms = " BIGINT_FORMAT ",  types = %d,  style = %s\n",
             atom->natoms, atom->ntypes, force->pair_style);
 
-    if (force->pair && strstr(force->pair_style,"hybrid")) {
+    if (force->pair && utils::strmatch(force->pair_style,"^hybrid")) {
       PairHybrid *hybrid = (PairHybrid *)force->pair;
       fprintf(out,"Hybrid sub-styles:");
       for (int i=0; i < hybrid->nstyles; ++i)
diff --git a/src/respa.cpp b/src/respa.cpp
index 26bae5a1cb..6fa9959d78 100644
--- a/src/respa.cpp
+++ b/src/respa.cpp
@@ -38,6 +38,7 @@
 #include "timer.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 #include "pair_hybrid.h"
 
 using namespace LAMMPS_NS;
@@ -120,7 +121,7 @@ Respa::Respa(LAMMPS *lmp, int narg, char **arg) :
       iarg += 2;
     } else if (strcmp(arg[iarg],"hybrid") == 0) {
       // the hybrid keyword requires a hybrid pair style
-      if (!strstr(force->pair_style,"hybrid"))
+      if (!utils::strmatch(force->pair_style,"^hybrid"))
         error->all(FLERR,"Illegal run_style respa command");
       PairHybrid *hybrid = (PairHybrid *) force->pair;
       nhybrid_styles = hybrid->nstyles;
diff --git a/src/velocity.cpp b/src/velocity.cpp
index 6d6027cc3c..32b08708cf 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -33,6 +33,7 @@
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -709,19 +710,19 @@ void Velocity::zero(int /*narg*/, char **arg)
 {
   if (strcmp(arg[0],"linear") == 0) {
     if (rfix < 0) zero_momentum();
-    else if (strcmp(modify->fix[rfix]->style,"rigid/small") == 0) {
+    else if (utils::strmatch(modify->fix[rfix]->style,"^rigid/small")) {
       modify->fix[rfix]->setup_pre_neighbor();
       modify->fix[rfix]->zero_momentum();
-    } else if (strstr(modify->fix[rfix]->style,"rigid")) {
+    } else if (utils::strmatch(modify->fix[rfix]->style,"^rigid")) {
       modify->fix[rfix]->zero_momentum();
     } else error->all(FLERR,"Velocity rigid used with non-rigid fix-ID");
 
   } else if (strcmp(arg[0],"angular") == 0) {
     if (rfix < 0) zero_rotation();
-    else if (strcmp(modify->fix[rfix]->style,"rigid/small") == 0) {
+    else if (utils::strmatch(modify->fix[rfix]->style,"^rigid/small")) {
       modify->fix[rfix]->setup_pre_neighbor();
       modify->fix[rfix]->zero_rotation();
-    } else if (strstr(modify->fix[rfix]->style,"rigid")) {
+    } else if (utils::strmatch(modify->fix[rfix]->style,"^rigid")) {
       modify->fix[rfix]->zero_rotation();
     } else error->all(FLERR,"Velocity rigid used with non-rigid fix-ID");
 

From e359e80118890a6330bb3c3c93e1d6637e16d5ed Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 4 Apr 2019 22:39:58 -0400
Subject: [PATCH 12/22] fix bug reported in issue #1410

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

diff --git a/src/variable.cpp b/src/variable.cpp
index ed3b41bd00..56b66cad0d 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -2181,7 +2181,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
         if (tree) {
           Tree *newtree = new Tree();
           newtree->type = opprevious;
-          if (opprevious == UNARY) {
+          if ((opprevious == UNARY) || (opprevious == NOT)) {
             newtree->first = treestack[--ntreestack];
             newtree->second = NULL;
             newtree->nextra = 0;

From f4159ff5929b1d5ce62a75fd4afe315271160266 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 5 Apr 2019 05:53:19 -0400
Subject: [PATCH 13/22] implement different -DLAMMPS_BIGBIG workaround without
 breaking format

---
 src/USER-REAXC/reaxc_traj.h | 34 +++++++++++++++++++++++++---------
 1 file changed, 25 insertions(+), 9 deletions(-)

diff --git a/src/USER-REAXC/reaxc_traj.h b/src/USER-REAXC/reaxc_traj.h
index b04a190965..4966bf11d8 100644
--- a/src/USER-REAXC/reaxc_traj.h
+++ b/src/USER-REAXC/reaxc_traj.h
@@ -42,7 +42,11 @@
 #define SCI_LINE  "%-37s%-24g\n"
 #define REAL3_LINE "%-32s%9.3f,%9.3f,%9.3f\n"
 
-#define INIT_DESC TAGINT_FORMAT "%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass
+#if defined(LAMMPS_BIGBIG)
+#define INIT_DESC "%9ld%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass
+#else
+#define INIT_DESC "%9d%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass
+#endif
 #define INIT_DESC_LEN 32
 
 #define SIZE_INFO_LINE2 "%-10d%-10d\n"
@@ -51,21 +55,33 @@
 #define SIZE_INFO_LINE3 "%-10d%-10d%-10d\n"
 #define SIZE_INFO_LEN3 31
 
-#define ATOM_BASIC TAGINT_FORMAT " %10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge
+#if defined(LAMMPS_BIGBIG)
+#define ATOM_BASIC "%9ld%10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge
+#define ATOM_wV    "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) Charge
+#define ATOM_wF    "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Fx Fy Fz) Charge
+#define ATOM_FULL  "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) (Fx Fy Fz) Charge
+#else
+#define ATOM_BASIC "%9d%10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge
+#define ATOM_wV    "%9d%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) Charge
+#define ATOM_wF    "%9d%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Fx Fy Fz) Charge
+#define ATOM_FULL  "%9d%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) (Fx Fy Fz) Charge
+#endif
 #define ATOM_BASIC_LEN 50
-#define ATOM_wV    TAGINT_FORMAT " %10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) Charge
 #define ATOM_wV_LEN 80
-#define ATOM_wF    TAGINT_FORMAT " %10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Fx Fy Fz) Charge
 #define ATOM_wF_LEN 80
-#define ATOM_FULL  TAGINT_FORMAT " %10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) (Fx Fy Fz) Charge
 #define ATOM_FULL_LEN 110
 
-#define BOND_BASIC TAGINT_FORMAT " " TAGINT_FORMAT " %10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO
+#if defined(LAMMPS_BIGBIG)
+#define BOND_BASIC "%9ld%9ld%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO
+#define BOND_FULL  "%9ld%9ld%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2
+#define ANGLE_BASIC "%9ld%9ld%9ld%10.3f\n" // Atom1 Atom2 Atom3 Theta
+#else
+#define BOND_BASIC "%9d%9d%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO
+#define BOND_FULL  "%9d%9d%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2
+#define ANGLE_BASIC "%9d%9d%9d%10.3f\n" // Atom1 Atom2 Atom3 Theta
+#endif
 #define BOND_BASIC_LEN 39
-#define BOND_FULL  TAGINT_FORMAT " " TAGINT_FORMAT " %10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2
 #define BOND_FULL_LEN 69
-
-#define ANGLE_BASIC TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " %10.3f\n" // Atom1 Atom2 Atom3 Theta
 #define ANGLE_BASIC_LEN 38
 
 enum ATOM_LINE_OPTS  { OPT_NOATOM = 0, OPT_ATOM_BASIC = 4, OPT_ATOM_wF = 5, OPT_ATOM_wV = 6, OPT_ATOM_FULL = 7, NR_OPT_ATOM = 8 };

From 4f026b9b3830afdbf2ede14fe9d6001be56e5604 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 5 Apr 2019 06:11:06 -0400
Subject: [PATCH 14/22] remove trailing whitespace

---
 src/USER-REAXC/fix_reaxc.cpp         | 2 +-
 src/USER-REAXC/reaxc_ffield.cpp      | 4 ++--
 src/USER-REAXC/reaxc_init_md.cpp     | 8 ++++----
 src/USER-REAXC/reaxc_reset_tools.cpp | 4 ++--
 src/USER-REAXC/reaxc_types.h         | 2 +-
 5 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/USER-REAXC/fix_reaxc.cpp b/src/USER-REAXC/fix_reaxc.cpp
index 361733f3ca..dc67ad6ffb 100644
--- a/src/USER-REAXC/fix_reaxc.cpp
+++ b/src/USER-REAXC/fix_reaxc.cpp
@@ -41,7 +41,7 @@ FixReaxC::FixReaxC(LAMMPS *lmp,int narg, char **arg) :
 {
   // perform initial allocation of atom-based arrays
   // register with atom class
-  
+
   oldnmax = 0;
   num_bonds = NULL;
   num_hbonds = NULL;
diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp
index 13e928ad08..9534637645 100644
--- a/src/USER-REAXC/reaxc_ffield.cpp
+++ b/src/USER-REAXC/reaxc_ffield.cpp
@@ -151,7 +151,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
     /* Sanity checks */
     if (c == 2 && !lgflag)
         control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'");	
-    
+
     if (c < 9) {
       snprintf (errmsg, 1024, "Missing parameter(s) in line %s", s);
       control->error_ptr->all(FLERR, errmsg);
@@ -320,7 +320,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
   if (c == 2 && !lgflag) {
       control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'");
     }
-  
+
   l = atoi(tmp[0]);
 
   /* a line of comments */
diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp
index c1239e0cbb..39b31c38b5 100644
--- a/src/USER-REAXC/reaxc_init_md.cpp
+++ b/src/USER-REAXC/reaxc_init_md.cpp
@@ -236,21 +236,21 @@ void Initialize( reax_system *system, control_params *control,
 
   if (Init_Workspace( system, control, workspace, msg ) ==
       FAILURE) {
-    control->error_ptr->one(FLERR,"Workspace could not be initialized");    
+    control->error_ptr->one(FLERR,"Workspace could not be initialized");
   }
 
   if (Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
       FAILURE) {
-    control->error_ptr->one(FLERR,"Lists could not be initialized");     
+    control->error_ptr->one(FLERR,"Lists could not be initialized");
     }
 
   if (Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) {
-    control->error_ptr->one(FLERR,"Could not open output files"); 
+    control->error_ptr->one(FLERR,"Could not open output files");
   }
 
   if (control->tabulate) {
     if (Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE) {
-    control->error_ptr->one(FLERR,"Lookup table could not be created"); 
+    control->error_ptr->one(FLERR,"Lookup table could not be created");
     }
   }
 
diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp
index 5439ee33a4..e00656694c 100644
--- a/src/USER-REAXC/reaxc_reset_tools.cpp
+++ b/src/USER-REAXC/reaxc_reset_tools.cpp
@@ -144,7 +144,7 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control,
     if (total_bonds >= bonds->num_intrs * DANGER_ZONE) {
       workspace->realloc.bonds = 1;
       if (total_bonds >= bonds->num_intrs) {
-        char errmsg[256]; 
+        char errmsg[256];
         snprintf(errmsg, 256, "Not enough space for bonds! total=%d allocated=%d\n",
                 total_bonds, bonds->num_intrs);
         control->error_ptr->one(FLERR, errmsg);
@@ -170,7 +170,7 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control,
     if (total_hbonds >= hbonds->num_intrs * 0.90/*DANGER_ZONE*/) {
       workspace->realloc.hbonds = 1;
       if (total_hbonds >= hbonds->num_intrs) {
-        char errmsg[256]; 
+        char errmsg[256];
         snprintf(errmsg, 256, "Not enough space for hbonds! total=%d allocated=%d\n",
                 total_hbonds, hbonds->num_intrs);
         control->error_ptr->one(FLERR, errmsg);
diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h
index cdc2916a66..b05f655040 100644
--- a/src/USER-REAXC/reaxc_types.h
+++ b/src/USER-REAXC/reaxc_types.h
@@ -491,7 +491,7 @@ typedef struct
   int lgflag;
   int enobondsflag;
   class LAMMPS_NS::Error *error_ptr;
-  int me; 
+  int me;
 
 } control_params;
 

From 42e8a7613e144e86b8ce0eac302b5fc87323779e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 5 Apr 2019 06:29:38 -0400
Subject: [PATCH 15/22] stop with error or print a warning when the system or
 atom ids get to large for reax/c pair styles

---
 src/USER-OMP/pair_reaxc_omp.cpp   |  9 +++++++++
 src/USER-REAXC/pair_reaxc.cpp     | 11 +++++++++--
 src/USER-REAXC/reaxc_io_tools.cpp |  6 ++----
 3 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp
index 92ba31048d..81e890538a 100644
--- a/src/USER-OMP/pair_reaxc_omp.cpp
+++ b/src/USER-OMP/pair_reaxc_omp.cpp
@@ -343,6 +343,15 @@ void PairReaxCOMP::init_style( )
   if (force->newton_pair == 0)
     error->all(FLERR,"Pair style reax/c/omp requires newton pair on");
 
+ if ((atom->map_max_tag > 99999999) && (comm->me == 0))
+    error->warning(FLERR,"Some Atom-IDs are too large. Pair style reax/c/omp "
+                   "native output files may get misformatted or corrupted");
+
+  // because system->bigN is an int, we cannot have more atoms than MAXSMALLINT
+
+  if (atom->natoms > MAXSMALLINT)
+    error->all(FLERR,"Too many atoms for pair style reax/c/omp");
+
   // need a half neighbor list w/ Newton off and ghost neighbors
   // built whenever re-neighboring occurs
 
diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp
index 6bb2b9a197..3164280872 100644
--- a/src/USER-REAXC/pair_reaxc.cpp
+++ b/src/USER-REAXC/pair_reaxc.cpp
@@ -90,8 +90,7 @@ PairReaxC::PairReaxC(LAMMPS *lmp) : Pair(lmp)
   mpi_data = (mpi_datatypes *)
     memory->smalloc(sizeof(mpi_datatypes),"reax:mpi");
 
-  MPI_Comm_rank(world,&system->my_rank);
-  control->me = system->my_rank;
+  control->me = system->my_rank = comm->me;
 
   system->my_coords[0] = 0;
   system->my_coords[1] = 0;
@@ -383,6 +382,14 @@ void PairReaxC::init_style( )
     error->all(FLERR,"Pair style reax/c requires atom IDs");
   if (force->newton_pair == 0)
     error->all(FLERR,"Pair style reax/c requires newton pair on");
+  if ((atom->map_max_tag > 99999999) && (comm->me == 0))
+    error->warning(FLERR,"Some Atom-IDs are too large. Pair style reax/c "
+                   "native output files may get misformatted or corrupted");
+
+  // because system->bigN is an int, we cannot have more atoms than MAXSMALLINT
+
+  if (atom->natoms > MAXSMALLINT)
+    error->all(FLERR,"Too many atoms for pair style reax/c");
 
   // need a half neighbor list w/ Newton off and ghost neighbors
   // built whenever re-neighboring occurs
diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp
index f71fcbec8e..a4f0db7c7d 100644
--- a/src/USER-REAXC/reaxc_io_tools.cpp
+++ b/src/USER-REAXC/reaxc_io_tools.cpp
@@ -55,8 +55,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
       sprintf( temp, "%s.pot", control->sim_name );
       if ((out_control->pot = fopen( temp, "w" )) != NULL) {
         fflush( out_control->pot );
-      }
-      else {
+      } else {
         strcpy( msg, "init_out_controls: .pot file could not be opened\n" );
         return FAILURE;
       }
@@ -74,8 +73,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
                 "step", "Pint/norm[x]", "Pint/norm[y]", "Pint/norm[z]",
                 "Pext/Ptot[x]", "Pext/Ptot[y]", "Pext/Ptot[z]", "Pkin/V" );
         fflush( out_control->prs );
-      }
-      else {
+      } else {
         strcpy(msg,"init_out_controls: .prs file couldn't be opened\n");
         return FAILURE;
       }

From 8b2a8ad08bd1a2cb22ff3465db810c4735025753 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 5 Apr 2019 06:32:59 -0400
Subject: [PATCH 16/22] fix stupid typo

---
 src/USER-OMP/pair_reaxc_omp.cpp | 2 +-
 src/USER-REAXC/pair_reaxc.cpp   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp
index 81e890538a..a98f7c89d9 100644
--- a/src/USER-OMP/pair_reaxc_omp.cpp
+++ b/src/USER-OMP/pair_reaxc_omp.cpp
@@ -343,7 +343,7 @@ void PairReaxCOMP::init_style( )
   if (force->newton_pair == 0)
     error->all(FLERR,"Pair style reax/c/omp requires newton pair on");
 
- if ((atom->map_max_tag > 99999999) && (comm->me == 0))
+ if ((atom->map_tag_max > 99999999) && (comm->me == 0))
     error->warning(FLERR,"Some Atom-IDs are too large. Pair style reax/c/omp "
                    "native output files may get misformatted or corrupted");
 
diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp
index 3164280872..a65c738766 100644
--- a/src/USER-REAXC/pair_reaxc.cpp
+++ b/src/USER-REAXC/pair_reaxc.cpp
@@ -382,7 +382,7 @@ void PairReaxC::init_style( )
     error->all(FLERR,"Pair style reax/c requires atom IDs");
   if (force->newton_pair == 0)
     error->all(FLERR,"Pair style reax/c requires newton pair on");
-  if ((atom->map_max_tag > 99999999) && (comm->me == 0))
+  if ((atom->map_tag_max > 99999999) && (comm->me == 0))
     error->warning(FLERR,"Some Atom-IDs are too large. Pair style reax/c "
                    "native output files may get misformatted or corrupted");
 

From 383e206cc22fd91f0ed30318b9c8cd0055b8ab42 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 5 Apr 2019 08:00:04 -0400
Subject: [PATCH 17/22] the GCC folks did it again. :-(

---
 src/hashlittle.cpp | 32 +++++++++++---------------------
 1 file changed, 11 insertions(+), 21 deletions(-)

diff --git a/src/hashlittle.cpp b/src/hashlittle.cpp
index 38f192ad76..f612be9eeb 100644
--- a/src/hashlittle.cpp
+++ b/src/hashlittle.cpp
@@ -23,16 +23,6 @@
 # endif
 #endif
 
-// declaration to indicate intended fallthrough cases in switch statements
-// and thus silence the warnings produced by g++ -Wextra
-
-#if defined(__GNUC__)
-#define _fallthrough  __attribute__ ((fallthrough))
-#else
-#define _fallthrough
-#endif
-
-
 #define rot(x,k) (((x)<<(k)) | ((x)>>(32-(k))))
 
 /*
@@ -301,17 +291,17 @@ uint32_t hashlittle( const void *key, size_t length, uint32_t initval)
     /*-------------------------------- last block: affect all 32 bits of (c) */
     switch(length)                   /* all the case statements fall through */
     {
-    case 12: c+=((uint32_t)k[11])<<24; _fallthrough;
-    case 11: c+=((uint32_t)k[10])<<16; _fallthrough;
-    case 10: c+=((uint32_t)k[9])<<8;   _fallthrough;
-    case 9 : c+=k[8];                  _fallthrough;
-    case 8 : b+=((uint32_t)k[7])<<24;  _fallthrough;
-    case 7 : b+=((uint32_t)k[6])<<16;  _fallthrough;
-    case 6 : b+=((uint32_t)k[5])<<8;   _fallthrough;
-    case 5 : b+=k[4];                  _fallthrough;
-    case 4 : a+=((uint32_t)k[3])<<24;  _fallthrough;
-    case 3 : a+=((uint32_t)k[2])<<16;  _fallthrough;
-    case 2 : a+=((uint32_t)k[1])<<8;   _fallthrough;
+    case 12: c+=((uint32_t)k[11])<<24; /* fall through */
+    case 11: c+=((uint32_t)k[10])<<16; /* fall through */
+    case 10: c+=((uint32_t)k[9])<<8;   /* fall through */
+    case 9 : c+=k[8];                  /* fall through */
+    case 8 : b+=((uint32_t)k[7])<<24;  /* fall through */
+    case 7 : b+=((uint32_t)k[6])<<16;  /* fall through */
+    case 6 : b+=((uint32_t)k[5])<<8;   /* fall through */
+    case 5 : b+=k[4];                  /* fall through */
+    case 4 : a+=((uint32_t)k[3])<<24;  /* fall through */
+    case 3 : a+=((uint32_t)k[2])<<16;  /* fall through */
+    case 2 : a+=((uint32_t)k[1])<<8;   /* fall through */
     case 1 : a+=k[0];
              break;
     case 0 : return c;

From 5d3801cb1259ffc50b39a27e08842c9f0488b9de Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Fri, 5 Apr 2019 15:50:58 +0200
Subject: [PATCH 18/22] Include info for COMPASS in the Howto section

---
 doc/src/Howto_bioFF.txt | 29 +++++++++++++++++++++++++++--
 1 file changed, 27 insertions(+), 2 deletions(-)

diff --git a/doc/src/Howto_bioFF.txt b/doc/src/Howto_bioFF.txt
index deb5b31441..ee53420723 100644
--- a/doc/src/Howto_bioFF.txt
+++ b/doc/src/Howto_bioFF.txt
@@ -7,12 +7,12 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-CHARMM, AMBER, and DREIDING force fields :h3
+CHARMM, AMBER, COMPASS and DREIDING force fields :h3
 
 A force field has 2 parts: the formulas that define it and the
 coefficients used for a particular system.  Here we only discuss
 formulas implemented in LAMMPS that correspond to formulas commonly
-used in the CHARMM, AMBER, and DREIDING force fields.  Setting
+used in the CHARMM, AMBER, COMPASS and DREIDING force fields.  Setting
 coefficients is done in the input data file via the
 "read_data"_read_data.html command or in the input script with
 commands like "pair_coeff"_pair_coeff.html or
@@ -50,6 +50,28 @@ older {charmm} styles.  See discussion of the differences on the "pair
 charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
 doc pages.
 
+COMPASS is a general force field for atomistic simulation of 
+common organic molecules, inorganic small molecules, and polymers which
+was developed using ab initio and empirical parametrization techniques.
+See the "Tools"_Tools.html doc page for the msi2lmp tool for creating 
+LAMMPS template input and data files from BIOVIA’s Materias Studio files. 
+See "(Sun)"_#howto-Sun for a description of the COMPASS force field.
+
+These style choices compute force field formulas that are consistent
+with the COMPASS force field.  See each command's
+documentation for the formula it computes.
+
+"bond_style"_bond_class2.html class2
+"angle_style"_angle_class2.html class2
+"dihedral_style"_dihedral_class2.html class2
+"improper_style"_improper_class2.html class2 :ul
+
+"pair_style"_pair_class2.html lj/class2
+"pair_style"_pair_class2.html lj/class2/coul/cut
+"pair_style"_pair_class2.html lj/class2/coul/long :ul
+
+"special_bonds"_special_bonds.html lj/coul 0 0 1 :ul
+
 DREIDING is a generic force field developed by the "Goddard
 group"_http://www.wag.caltech.edu at Caltech and is useful for
 predicting structures and dynamics of organic, biological and
@@ -100,6 +122,9 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
 [(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
 Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
 
+:link(howto-Sun)
+[(Sun)] Sun, J. Phys. Chem. B, 102, 7338–7364 (1998).
+
 :link(howto-Mayo)
 [(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
 (1990).

From 85a0461a48b16c1f383b7cfeb6fc1a69fa9a8bc2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 5 Apr 2019 10:53:23 -0400
Subject: [PATCH 19/22] reword and reformat text in Howto_bioFF.txt a little
 bit. add warnings about msi2lmp's age and lack of maintenance

---
 doc/src/Howto_bioFF.txt | 78 ++++++++++++++++++++++-------------------
 1 file changed, 42 insertions(+), 36 deletions(-)

diff --git a/doc/src/Howto_bioFF.txt b/doc/src/Howto_bioFF.txt
index ee53420723..b6995920ae 100644
--- a/doc/src/Howto_bioFF.txt
+++ b/doc/src/Howto_bioFF.txt
@@ -7,29 +7,31 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-CHARMM, AMBER, COMPASS and DREIDING force fields :h3
+CHARMM, AMBER, COMPASS, and DREIDING force fields :h3
 
 A force field has 2 parts: the formulas that define it and the
 coefficients used for a particular system.  Here we only discuss
 formulas implemented in LAMMPS that correspond to formulas commonly
-used in the CHARMM, AMBER, COMPASS and DREIDING force fields.  Setting
-coefficients is done in the input data file via the
-"read_data"_read_data.html command or in the input script with
+used in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
+coefficients is done either from special sections in an input data file
+via the "read_data"_read_data.html command or in the input script with
 commands like "pair_coeff"_pair_coeff.html or
-"bond_coeff"_bond_coeff.html.  See the "Tools"_Tools.html doc page for
-additional tools that can use CHARMM or AMBER to assign force field
-coefficients and convert their output into LAMMPS input.
+"bond_coeff"_bond_coeff.html and so on.  See the "Tools"_Tools.html doc
+page for additional tools that can use CHARMM, AMBER, or Materials
+Studio generated files to assign force field coefficients and convert
+their output into LAMMPS input.
 
 See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
-field.  See "(Cornell)"_#howto-Cornell for a description of the AMBER force
-field.
+field.  See "(Cornell)"_#howto-Cornell for a description of the AMBER
+force field.  See "(Sun)"_#howto-Sun for a description of the COMPASS
+force field.
 
 :link(charmm,http://www.scripps.edu/brooks)
 :link(amber,http://amber.scripps.edu)
 
-These style choices compute force field formulas that are consistent
-with common options in CHARMM or AMBER.  See each command's
-documentation for the formula it computes.
+The interaction styles listed below compute force field formulas that
+are consistent with common options in CHARMM or AMBER.  See each
+command's documentation for the formula it computes.
 
 "bond_style"_bond_harmonic.html harmonic
 "angle_style"_angle_charmm.html charmm
@@ -44,21 +46,26 @@ documentation for the formula it computes.
 "special_bonds"_special_bonds.html charmm
 "special_bonds"_special_bonds.html amber :ul
 
-NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
-released in March 2017.  We recommend they be used instead of the
-older {charmm} styles.  See discussion of the differences on the "pair
-charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
-doc pages.
+NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were released
+in March 2017.  We recommend they be used instead of the older {charmm}
+styles.  See discussion of the differences on the "pair
+charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html doc
+pages.
 
-COMPASS is a general force field for atomistic simulation of 
-common organic molecules, inorganic small molecules, and polymers which
-was developed using ab initio and empirical parametrization techniques.
-See the "Tools"_Tools.html doc page for the msi2lmp tool for creating 
-LAMMPS template input and data files from BIOVIA’s Materias Studio files. 
-See "(Sun)"_#howto-Sun for a description of the COMPASS force field.
+COMPASS is a general force field for atomistic simulation of common
+organic molecules, inorganic small molecules, and polymers which was
+developed using ab initio and empirical parameterization techniques.
+See the "Tools"_Tools.html doc page for the msi2lmp tool for creating
+LAMMPS template input and data files from BIOVIA’s Materials Studio
+files.  Please note that the msi2lmp tool is very old and largely
+unmaintained, so it does not support all features of Materials Studio
+provided force field files, especially additions during the last decade.
+You should watch the output carefully and compare results, where
+possible.  See "(Sun)"_#howto-Sun for a description of the COMPASS force
+field.
 
-These style choices compute force field formulas that are consistent
-with the COMPASS force field.  See each command's
+These interaction styles listed below compute force field formulas that
+are consistent with the COMPASS force field.  See each command's
 documentation for the formula it computes.
 
 "bond_style"_bond_class2.html class2
@@ -74,20 +81,19 @@ documentation for the formula it computes.
 
 DREIDING is a generic force field developed by the "Goddard
 group"_http://www.wag.caltech.edu at Caltech and is useful for
-predicting structures and dynamics of organic, biological and
-main-group inorganic molecules. The philosophy in DREIDING is to use
-general force constants and geometry parameters based on simple
-hybridization considerations, rather than individual force constants
-and geometric parameters that depend on the particular combinations of
-atoms involved in the bond, angle, or torsion terms. DREIDING has an
-"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
-interactions involving a hydrogen atom on very electronegative atoms
-(N, O, F).
+predicting structures and dynamics of organic, biological and main-group
+inorganic molecules. The philosophy in DREIDING is to use general force
+constants and geometry parameters based on simple hybridization
+considerations, rather than individual force constants and geometric
+parameters that depend on the particular combinations of atoms involved
+in the bond, angle, or torsion terms. DREIDING has an "explicit hydrogen
+bond term"_pair_hbond_dreiding.html to describe interactions involving a
+hydrogen atom on very electronegative atoms (N, O, F).
 
 See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field
 
-These style choices compute force field formulas that are consistent
-with the DREIDING force field.  See each command's
+The interaction styles listed below compute force field formulas that
+are consistent with the DREIDING force field.  See each command's
 documentation for the formula it computes.
 
 "bond_style"_bond_harmonic.html harmonic

From 2757e4e6e6e6ffb61493ae439f2a90efcdac8ae5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 5 Apr 2019 10:53:41 -0400
Subject: [PATCH 20/22] two more false positives

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

diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 8c2ff43c3c..91ae3d6a6c 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -1134,6 +1134,7 @@ infty
 inhomogeneities
 inhomogeneous
 init
+initio
 initializations
 InP
 inregion
@@ -2809,6 +2810,7 @@ unimodal
 unitless
 Universite
 unix
+unmaintained
 unoptimized
 unpadded
 unphysical

From 2e1da2958da1cf362a2185ed51db8902607a1218 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 5 Apr 2019 11:04:11 -0400
Subject: [PATCH 21/22] resolve toctree and paper anchor issues

---
 doc/src/Howto.txt       | 2 +-
 doc/src/Howto_tip3p.txt | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt
index 36f6be7194..0df417af75 100644
--- a/doc/src/Howto.txt
+++ b/doc/src/Howto.txt
@@ -148,7 +148,7 @@ END_RST -->
 
 <!-- HTML_ONLY -->
 
-"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
+"CHARMM, AMBER, COMPASS, and DREIDING force fields"_Howto_bioFF.html
 "TIP3P water model"_Howto_tip3p.html
 "TIP4P water model"_Howto_tip4p.html
 "SPC water model"_Howto_spc.html :all(b)
diff --git a/doc/src/Howto_tip3p.txt b/doc/src/Howto_tip3p.txt
index 942b42aea1..a34577c5e1 100644
--- a/doc/src/Howto_tip3p.txt
+++ b/doc/src/Howto_tip3p.txt
@@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 TIP3P water model :h3
 
 The TIP3P water model as implemented in CHARMM
-"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with
+"(MacKerell)"_#howto-tip3p specifies a 3-site rigid water molecule with
 charges and Lennard-Jones parameters assigned to each of the 3 atoms.
 In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
 the two O-H bonds and the H-O-H angle rigid.  A bond style of
@@ -60,6 +60,10 @@ models"_http://en.wikipedia.org/wiki/Water_model.
 
 :line
 
+:link(howto-tip3p)
+[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+
 :link(Jorgensen1)
 [(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
 Phys, 79, 926 (1983).

From 175f3ee648bf805e233c327eff93a402495e1b80 Mon Sep 17 00:00:00 2001
From: "Ryan S. Elliott" <relliott@umn.edu>
Date: Fri, 5 Apr 2019 10:14:45 -0500
Subject: [PATCH 22/22] Fix pointer assignment in pair_kim

Bug only affects cases where neighbor list needs to be stripped.
Thanks to Mingjian Wen (@mjwen) for finding and reporting this.
---
 src/KIM/pair_kim.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp
index 84842f87cc..ea5f24a67e 100644
--- a/src/KIM/pair_kim.cpp
+++ b/src/KIM/pair_kim.cpp
@@ -481,7 +481,7 @@ void PairKIM::init_style()
       for (int i = 0; i < kim_number_of_neighbor_lists; ++i)
       {
         lmps_stripped_neigh_ptr[i]
-            = &(lmps_stripped_neigh_list[(i-1)*(neighbor->oneatom)]);
+            = &(lmps_stripped_neigh_list[i*(neighbor->oneatom)]);
       }
 
    }