From 8e36364f5ceaa166915ce553aa6b4f8e201fbab8 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 7 Apr 2016 21:04:44 +0000
Subject: [PATCH 01/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@14805
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/ASPHERE/pair_line_lj.cpp             |   4 +-
 src/DEPEND/fastdep.c                     |  85 ++++++---
 src/GRANULAR/pair_gran_hertz_history.cpp |   2 -
 src/GRANULAR/pair_gran_hooke.cpp         |   2 -
 src/GRANULAR/pair_gran_hooke_history.cpp |   2 -
 src/KOKKOS/Install.sh                    |   8 +
 src/KOKKOS/fix_nh_kokkos.cpp             |   1 -
 src/MANYBODY/pair_airebo.cpp             |   1 -
 src/MANYBODY/pair_bop.cpp                |   8 +-
 src/MANYBODY/pair_eim.cpp                |  54 +++---
 src/MANYBODY/pair_polymorphic.cpp        |   2 +
 src/MEAM/pair_meam.cpp                   |   2 +-
 src/Make.py                              | 216 ++++++++++++++++++-----
 src/Makefile                             |   4 +-
 src/QEQ/fix_qeq_fire.cpp                 |   9 +-
 src/REPLICA/temper.cpp                   |  31 +++-
 src/STUBS/Makefile.mingw32-cross         |   2 +-
 src/STUBS/Makefile.mingw64-cross         |   2 +-
 src/USER-OMP/pair_airebo_omp.cpp         |   1 -
 src/compute_chunk_atom.cpp               |   2 +-
 src/domain.cpp                           |  13 +-
 src/dump_image.cpp                       |   1 -
 src/fix_ave_time.cpp                     |   3 +-
 src/math_const.h                         |   1 +
 src/read_data.cpp                        |   2 +-
 src/set.cpp                              |   1 -
 26 files changed, 314 insertions(+), 145 deletions(-)

diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp
index 737aefa18d..aa3493ef47 100644
--- a/src/ASPHERE/pair_line_lj.cpp
+++ b/src/ASPHERE/pair_line_lj.cpp
@@ -69,11 +69,11 @@ PairLineLJ::~PairLineLJ()
 
 void PairLineLJ::compute(int eflag, int vflag)
 {
-  int i,j,ii,jj,inum,jnum,itype,jtype,tmp;
+  int i,j,ii,jj,inum,jnum,itype,jtype;
   int ni,nj,npi,npj,ifirst,jfirst;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
   double rsq,r2inv,r6inv,term1,term2,sig,sig3,forcelj;
-  double xi[2],xj[2],fi[2],fj[2],dxi,dxj,dyi,dyj;
+  double xi[2],xj[2],fi[2],dxi,dxj,dyi,dyj;
   int *ilist,*jlist,*numneigh,**firstneigh;
 
   evdwl = 0.0;
diff --git a/src/DEPEND/fastdep.c b/src/DEPEND/fastdep.c
index 5400e03034..2f4927abce 100644
--- a/src/DEPEND/fastdep.c
+++ b/src/DEPEND/fastdep.c
@@ -33,7 +33,24 @@
 #include <sys/types.h>
 #include <sys/stat.h>
 
-const char version[] = "2.0";
+const char version[] = "2.1";
+
+/* store list of accepted extensions for object targets */
+static const char *extensions[] = { ".cpp", ".c", ".cu" };
+static const int numextensions = sizeof(extensions)/sizeof(const char *);
+
+/* strdup() is not part of ANSI C. provide a replacement for portability */
+static char *my_strdup(const char *src)
+{
+    int len;
+    char *ptr;
+
+    if (src == NULL) return NULL;
+    len = strlen(src);
+    ptr = (char *)malloc(len+1);
+    if (ptr) memcpy(ptr,src,len+1);
+    return ptr;
+}
 
 /************************************************************************
  * utility functions
@@ -198,7 +215,7 @@ static void llist_append(llist_t *ll, const char *key)
     llnode_t *tmp;
     if ((ll == NULL) || (key == NULL)) return;
 
-    ll->tail->key = strdup(key);
+    ll->tail->key = my_strdup(key);
     ll->count ++;
     tmp = (llnode_t *)malloc(sizeof(llnode_t));
     tmp->key = NULL;
@@ -286,7 +303,7 @@ static void set_add(set_t *s, const char *key)
         tmp = tmp->next;
     }
     s->count ++;
-    tmp->key = strdup(key);
+    tmp->key = my_strdup(key);
     tmp->next = (llnode_t *)malloc(sizeof(llnode_t));
     tmp = tmp->next;
     tmp->key = NULL;
@@ -375,7 +392,7 @@ static void map_add(map_t *m, const char *key, const char *val)
     /* add new entry to map */
     if (tmp->next == NULL) {
         m->count ++;
-        tmp->key = strdup(key);
+        tmp->key = my_strdup(key);
         tmp->val = set_init(50); /* XXX: chosen arbitrarily */
         tmp->next = (mapnode_t *)malloc(sizeof(mapnode_t));
         tmp->next->key = NULL;
@@ -547,42 +564,52 @@ static void do_depend(llnode_t *head, map_t *deps)
     set_t *incl;
     const char *source;
     char *target, *ptr;
-    int i,num;
+    int i,num,ext;
 
     tmp = head;
     while (tmp->next != NULL) {
         source = tmp->key;
         target = strrchr(source,'/');
         if (target == NULL) {
-            target = strdup(source);
+            target = my_strdup(source);
         } else {
-            target = strdup(target+1);
+            target = my_strdup(target+1);
         }
 
+        ext = 0;
         ptr = strrchr(target,'.');
         if (ptr != NULL) {
-            ptr[1] = 'o';
-            ptr[2] = '\0';
-        }
-        fputs(target,stdout);
-        fputs(" : ",stdout);
-        fputs(source,stdout);
-        free((void *)target);
-
-        incl = set_init(50);
-        add_depend(source,incl,deps);
-
-        num = incl->nbuckets;
-        for (i = 0; i < num; ++i) {
-            lnk = incl->buckets + i;
-            while (lnk->next != NULL) {
-                fputc(' ',stdout);
-                fputs(lnk->key,stdout);
-                lnk = lnk->next;
+            for (i = 0; i < numextensions; ++i) {
+                if (strcmp(ptr,extensions[i]) == 0) ++ext;
+            }
+            if (ext > 0) {
+                ptr[1] = 'o';
+                ptr[2] = '\0';
             }
         }
-        fputc('\n',stdout);
-        set_free(incl);
+
+        if (ext > 0) {
+            fputs(target,stdout);
+            fputs(" : ",stdout);
+            fputs(source,stdout);
+
+            incl = set_init(50);
+            add_depend(source,incl,deps);
+
+            num = incl->nbuckets;
+            for (i = 0; i < num; ++i) {
+                lnk = incl->buckets + i;
+                while (lnk->next != NULL) {
+                    fputc(' ',stdout);
+                    fputs(lnk->key,stdout);
+                    lnk = lnk->next;
+                }
+            }
+            fputc('\n',stdout);
+            set_free(incl);
+        }
+
+        free((void *)target);
         tmp = tmp->next;
     }
 }
@@ -601,6 +628,8 @@ int main(int argc, char **argv)
         fprintf(stderr,"FastDep v%s for LAMMPS\n"
                 "Usage: %s [-I <path> ...] -- <src1> [<src2> ...]\n",
                 version,argv[0]);
+        fprintf(stderr,"Supported extensions: %d, %s, %s\n",numextensions,
+                extensions[0], extensions[1]);
         return 1;
     }
 
@@ -631,7 +660,7 @@ int main(int argc, char **argv)
             }
         } else if (strcmp(*argv,"--") == 0) {
             break;
-        } // ignore all unrecognized arguments before '--'.
+        } /* ignore all unrecognized arguments before '--'. */
     }
 
     src = llist_init();
diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp
index b32f136726..e14dc7110f 100644
--- a/src/GRANULAR/pair_gran_hertz_history.cpp
+++ b/src/GRANULAR/pair_gran_hertz_history.cpp
@@ -87,7 +87,6 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
   double **torque = atom->torque;
   double *radius = atom->radius;
   double *rmass = atom->rmass;
-  int *type = atom->type;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
@@ -367,7 +366,6 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
   // if I or J is frozen, meff is other particle
 
   double *rmass = atom->rmass;
-  int *type = atom->type;
   int *mask = atom->mask;
 
   mi = rmass[i];
diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp
index b5305c309d..9ff23a7553 100644
--- a/src/GRANULAR/pair_gran_hooke.cpp
+++ b/src/GRANULAR/pair_gran_hooke.cpp
@@ -81,7 +81,6 @@ void PairGranHooke::compute(int eflag, int vflag)
   double **torque = atom->torque;
   double *radius = atom->radius;
   double *rmass = atom->rmass;
-  int *type = atom->type;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
   int newton_pair = force->newton_pair;
@@ -285,7 +284,6 @@ double PairGranHooke::single(int i, int j, int itype, int jtype, double rsq,
   // if I or J is frozen, meff is other particle
 
   double *rmass = atom->rmass;
-  int *type = atom->type;
   int *mask = atom->mask;
 
   mi = rmass[i];
diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp
index c5cca38290..b8b0381d58 100644
--- a/src/GRANULAR/pair_gran_hooke_history.cpp
+++ b/src/GRANULAR/pair_gran_hooke_history.cpp
@@ -129,7 +129,6 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
   double **torque = atom->torque;
   double *radius = atom->radius;
   double *rmass = atom->rmass;
-  int *type = atom->type;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
@@ -670,7 +669,6 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
   // if I or J is frozen, meff is other particle
 
   double *rmass = atom->rmass;
-  int *type = atom->type;
   int *mask = atom->mask;
 
   mi = rmass[i];
diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh
index ad450592be..af77bcd206 100644
--- a/src/KOKKOS/Install.sh
+++ b/src/KOKKOS/Install.sh
@@ -189,6 +189,14 @@ if (test $1 = 1) then
     sed -i -e '5 i \include ..\/..\/lib\/kokkos\/Makefile.kokkos' ../Makefile.package.settings
   fi
 
+  #  comb/omp triggers a persistent bug in nvcc. deleting it.
+  rm -f ../*_comb_omp.*
+
+elif (test $1 = 2) then
+
+  #  comb/omp triggers a persistent bug in nvcc. deleting it.
+  rm -f ../*_comb_omp.*
+
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp
index 28b7ff55b6..8cc06fc52c 100755
--- a/src/KOKKOS/fix_nh_kokkos.cpp
+++ b/src/KOKKOS/fix_nh_kokkos.cpp
@@ -291,7 +291,6 @@ void FixNHKokkos<DeviceType>::final_integrate()
 template<class DeviceType>
 void FixNHKokkos<DeviceType>::remap()
 {
-  int i;
   double oldlo,oldhi;
   double expfac;
 
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index 076848ddf0..12f39bf931 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -2251,7 +2251,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
               ril[1] = rij[1]+rjl[1];
               ril[2] = rij[2]+rjl[2];
               ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
-              rijrjl = 2.0*rijmag*rjlmag;
               rjl2 = rjlmag*rjlmag;
               costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
               tspijl = Sp2(costmp,thmin,thmax,dtsijl);
diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp
index 037f893ea5..219acc50af 100644
--- a/src/MANYBODY/pair_bop.cpp
+++ b/src/MANYBODY/pair_bop.cpp
@@ -993,7 +993,6 @@ void PairBOP::theta()
   int *ilist;
   int *iilist;
   int **firstneigh;
-  int maxn,maxt;
   double rj2,rk2,rsq,ps;
   double rj1k1,rj2k2;
   double **x = atom->x;
@@ -1015,8 +1014,6 @@ void PairBOP::theta()
     itype = map[type[i]]+1;
 
     iilist=firstneigh[i];
-    maxt=0;
-    maxn=0;
     nlisti=BOP_total[i];
     for(jj=0;jj<nlisti;jj++) {
       temp_ij=BOP_index[i]+jj;
@@ -1038,10 +1035,8 @@ void PairBOP::theta()
           +disij[1][temp_ij]*disij[1][temp_ij]
           +disij[2][temp_ij]*disij[2][temp_ij];
       rij[temp_ij]=sqrt(rsq);
-      if(rij[temp_ij]<=rcut[i12]) {
+      if(rij[temp_ij]<=rcut[i12])
         neigh_flag[temp_ij]=1;
-        maxt++;
-      }
       else
         neigh_flag[temp_ij]=0;
       if(rij[temp_ij]<=rcut3[i12])
@@ -1067,7 +1062,6 @@ void PairBOP::theta()
       dRepul[temp_ij]=(pRepul6[i12][ks-1]*ps+pRepul5[i12][ks-1])*ps
           +pRepul4[i12][ks-1];
     }
-    if(maxt>maxn) maxn=maxt;
   }
   for (ii = 0; ii < nall; ii++) {
     n=0;
diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp
index c25f3d92e6..a2807eb78c 100644
--- a/src/MANYBODY/pair_eim.cpp
+++ b/src/MANYBODY/pair_eim.cpp
@@ -921,13 +921,13 @@ int PairEIM::grabsingle(FILE *fptr, int i)
     pch1 = strstr(pch1,"element:");
     if (pch1 != NULL) {
       pch2 = strtok(NULL, " \t\n\r\f");
-      if (pch2 != NULL) data = strtok (NULL, "?");
-      if (strcmp(pch2,elements[i]) == 0) {
-        sscanf(data,"%d %lg %lg %lg %lg %lg %lg",&setfl->ielement[i],
-          &setfl->mass[i],&setfl->negativity[i],&setfl->ra[i],
-          &setfl->ri[i],&setfl->Ec[i],&setfl->q0[i]);
-      } else {
-        pch2 = NULL;
+      if (pch2 != NULL) {
+        data = strtok (NULL, "?");
+        if (strcmp(pch2,elements[i]) == 0) {
+          sscanf(data,"%d %lg %lg %lg %lg %lg %lg",&setfl->ielement[i],
+            &setfl->mass[i],&setfl->negativity[i],&setfl->ra[i],
+            &setfl->ri[i],&setfl->Ec[i],&setfl->q0[i]);
+        } else pch2 = NULL;
       }
     }
   }
@@ -960,25 +960,27 @@ int PairEIM::grabpair(FILE *fptr, int i, int j)
       pch2 = strtok (NULL, " \t\n\r\f");
       if (pch2 != NULL) pch3 = strtok (NULL, " \t\n\r\f");
       if (pch3 != NULL) data = strtok (NULL, "?");
-      if ((strcmp(pch2,elements[i]) == 0 &&
-        strcmp(pch3,elements[j]) == 0) ||
-        (strcmp(pch2,elements[j]) == 0 &&
-        strcmp(pch3,elements[i]) == 0)) {
-        sscanf(data,"%lg %lg %lg %lg %lg",
-          &setfl->rcutphiA[ij],&setfl->rcutphiR[ij],
-          &setfl->Eb[ij],&setfl->r0[ij],&setfl->alpha[ij]);
-        fgets(line,MAXLINE,fptr);
-        sscanf(line,"%lg %lg %lg %lg %lg",
-          &setfl->beta[ij],&setfl->rcutq[ij],&setfl->Asigma[ij],
-          &setfl->rq[ij],&setfl->rcutsigma[ij]);
-        fgets(line,MAXLINE,fptr);
-        sscanf(line,"%lg %lg %lg %d",
-          &setfl->Ac[ij],&setfl->zeta[ij],&setfl->rs[ij],
-          &setfl->tp[ij]);
-      } else {
-         pch1 = NULL;
-         pch2 = NULL;
-         pch3 = NULL;
+      if ((pch2 != NULL) && (pch3 != NULL)) {
+        if ((strcmp(pch2,elements[i]) == 0 &&
+          strcmp(pch3,elements[j]) == 0) ||
+          (strcmp(pch2,elements[j]) == 0 &&
+          strcmp(pch3,elements[i]) == 0)) {
+          sscanf(data,"%lg %lg %lg %lg %lg",
+            &setfl->rcutphiA[ij],&setfl->rcutphiR[ij],
+            &setfl->Eb[ij],&setfl->r0[ij],&setfl->alpha[ij]);
+          fgets(line,MAXLINE,fptr);
+          sscanf(line,"%lg %lg %lg %lg %lg",
+            &setfl->beta[ij],&setfl->rcutq[ij],&setfl->Asigma[ij],
+            &setfl->rq[ij],&setfl->rcutsigma[ij]);
+          fgets(line,MAXLINE,fptr);
+          sscanf(line,"%lg %lg %lg %d",
+            &setfl->Ac[ij],&setfl->zeta[ij],&setfl->rs[ij],
+            &setfl->tp[ij]);
+        } else {
+          pch1 = NULL;
+          pch2 = NULL;
+          pch3 = NULL;
+        }
       }
     }
   }
diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp
index ad53789737..2429dd0638 100755
--- a/src/MANYBODY/pair_polymorphic.cpp
+++ b/src/MANYBODY/pair_polymorphic.cpp
@@ -631,6 +631,8 @@ void PairPolymorphic::read_file(char *file)
   if (ptr) maxX = atof(ptr);
   if (ptr == NULL)
     error->all(FLERR,"Potential file incompatible with this pair style version");
+  if ((ng == 0) || (nr == 0) || (nx == 0))
+    error->all(FLERR,"Error reading potential file header");
 
   npair = nelements*(nelements+1)/2;
   ntriple = nelements*nelements*nelements;
diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp
index a350c66a96..2d14ffa0cf 100644
--- a/src/MEAM/pair_meam.cpp
+++ b/src/MEAM/pair_meam.cpp
@@ -555,7 +555,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
 
     for (i = 0; i < nelements; i++)
       if (strcmp(words[0],elements[i]) == 0) break;
-    if (i == nelements) continue;
+    if (i >= nelements) continue;
 
     // skip if element already appeared
 
diff --git a/src/Make.py b/src/Make.py
index d8be53f13b..6ab41af99a 100755
--- a/src/Make.py
+++ b/src/Make.py
@@ -15,14 +15,14 @@ import sys,os,commands,re,copy,subprocess
 # setargs = makefile settings
 # actionargs = allowed actions (also lib-dir and machine)
 
-abbrevs = "adhjmoprsv"
+abbrevs = "adhjmoprsvz"
 
 switchclasses = ("actions","dir","help","jmake","makefile",
-                 "output","packages","redo","settings","verbose")
+                 "output","packages","redo","settings","verbose","zoutput")
 libclasses = ("atc","awpmd","colvars","cuda","gpu","h5md",
               "meam","poems","python","qmmm","reax","voronoi")
 buildclasses = ("intel","kokkos")
-makeclasses = ("cc","mpi","fft","jpg","png")
+makeclasses = ("cc","flags","mpi","fft","jpg","png")
 
 setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig","smallsmall")
 actionargs = ("lib-all","file","clean","exe")
@@ -137,27 +137,37 @@ class Actions:
     lib-all builds all auxiliary libs needed by installed packages
     lib-dir builds a specific lib whether package installed or not
       dir is any dir in lib directory (atc, cuda, meam, etc) except linalg
-  (2) file = create src/MAKE/MINE/Makefile.auto
-    use -m switch for Makefile.machine to start from,
-      else use existing Makefile.auto
-    adds settings needed for installed accelerator packages
-    existing Makefile.auto is NOT changed unless "file" action is specified
+  (2) file = create a new src/MAKE/MINE/Makefile.auto
+    if file not specified, existing Makefile.auto is NOT changed
+      except by -m switch, which will copy Makefile.machine to Makefile.auto
+      note that exe action can add an -m switch, as described below
+    if file is specified, new Makefile.auto is created
+      if "-m machine" specified (or added by exe),
+        start with existing Makefile.machine, else existing Makefile.auto
+      if "-m none" specified, start Makefile.auto from scratch
+        must use -cc and -mpi switches to specify compiler and MPI
+      settings for these switches will alter Makefile.auto
+        -s, -intel, -kokkos, -cc, -mpi, -fft, -jpg, -png
+      if these accelerator packages are installed, they induce settings
+        that will alter Makefile.auto: opt, user-omp, user-intel, kokkos
+     use -z switch to copy final Makefile.auto to new filename
   (3) clean = invoke "make clean-auto" to insure clean build on current files
     useful if compiler flags have changed
   (4) exe or machine = build LAMMPS
     machine can be any existing Makefile.machine suffix
-      machine is converted to "exe" action, as well as:
+      machine is converted to "exe" action, and additionally:
         "-m machine" is added if -m switch is not specified
         "-o machine" is added if -o switch is not specified
         if either "-m"  or "-o" are specified, they are not overridden
     does not invoke any lib builds, since libs could be previously built
-    exe always builds using src/MAKE/MINE/Makefile.auto
-      if file action also specified, it creates Makefile.auto
+    exe ALWAYS builds using src/MAKE/MINE/Makefile.auto
+      if file action also specified, it creates a new Makefile.auto
       else if -m switch specified,
         existing Makefile.machine is copied to create Makefile.auto
       else Makefile.auto must already exist and is not changed
-    produces src/lmp_auto, or error message if unsuccessful
+    build produces src/lmp_auto, or error message if unsuccessful
       use -o switch to copy src/lmp_auto to new filename
+      use -z switch to copy src/MAKE/MINE/Makefile.auto to new filename
 """
   
   def check(self):
@@ -177,7 +187,7 @@ class Actions:
         cleans.append(one)
       elif one == "exe":
         exes.append(one)
-      # one action can be unknown in case is a machine (checked in setup)
+      # one action can be unknown, must be a machine (checked in setup)
       else:
         exes.append(one)
     if len(set(libs)) != len(libs) or \
@@ -236,9 +246,9 @@ class Actions:
   
   def file(self,caller):
 
-    # if caller = "file", create from mpi or read from makefile.machine or auto
-    # if caller = "exe" and "file" action already invoked, read from auto
-    # if caller = "exe" and no "file" action, read from makefile.machine or auto
+    # if caller="file", create from mpi or read from Makefile.machine or auto
+    # if caller="exe" and "file" action already invoked, read from auto
+    # if caller="exe" and no "file" action, read from Makefile.machine or auto
     
     if caller == "file":
       if makefile and makefile.machine == "none":
@@ -279,7 +289,7 @@ class Actions:
               make.addvar("CC","-cxx=%s" % wrapper)
               make.addvar("LINK","-cxx=%s" % wrapper)
             elif "-lmpi" in txt:
-              make.addvar("OMPI_CXX",wrapper,"cc")
+              make.addvar("export OMPI_CXX",wrapper,"cc")
               precompiler = "env OMPI_CXX=%s " % wrapper
             else: error("Could not add MPI wrapper compiler, " +
                         "did not recognize OpenMPI or MPICH")
@@ -287,8 +297,20 @@ class Actions:
         make.addvar("CCFLAGS","-O3")
         make.setvar("LINKFLAGS","-g")
         make.addvar("LINKFLAGS","-O")
+        
+      # add CC and LINK flags
 
-# add MPI settings
+      if flags:
+        for flag in flags.CC:
+          flag = "-" + flag
+          if flag[:2] == "-O": make.delvar("CCFLAGS","-O*")
+          make.addvar("CCFLAGS",flag)
+        for flag in flags.LINK:
+          flag = "-" + flag
+          if flag[:2] == "-O": make.delvar("LINKFLAGS","-O*")
+          make.addvar("LINKFLAGS",flag)
+
+      # add MPI settings
 
       if mpi:
         make.delvar("MPI_INC","*")
@@ -397,7 +419,7 @@ class Actions:
           make.addvar("KOKKOS_DEVICES","OpenMP","lmp")
           make.addvar("KOKKOS_ARCH","KNC","lmp")
 
-      # add LMP settings
+      # add LMP_INC ifdef settings
       
       if settings:
         list = settings.inlist
@@ -465,12 +487,13 @@ class Actions:
 
     # set self.stubs if Makefile.auto uses STUBS lib in MPI settings
 
-    if "-lmpi_stubs" in make.getvar("MPI_LIB"): self.stubs = 1
+    if make.getvar("MPI_LIB") and "-lmpi_stubs" in make.getvar("MPI_LIB"):
+      self.stubs = 1
     else: self.stubs = 0
     
     # write out Makefile.auto
     # unless caller = "exe" and "file" action already invoked
-
+    
     if caller == "file" or "file" not in self.alist:
       make.write("%s/MAKE/MINE/Makefile.auto" % dir.src,1)
       print "Created src/MAKE/MINE/Makefile.auto"
@@ -510,13 +533,23 @@ class Actions:
         print txt
         error('Unsuccessful "make stubs"')
       print "Created src/STUBS/libmpi_stubs.a"
-    if jmake: str = "cd %s; make -j %d auto" % (dir.src,jmake.n)
-    else: str = "cd %s; make auto" % dir.src
+
+    # special hack for shannon GPU cluster
+    # must use "srun make" if on it and building w/ GPU package, else just make
+    # this is b/c Cuda libs are not all available on host
+
+    make = "make"
+    if "shannon" in os.environ.get("HOST") and packages.final["gpu"]:
+      make = "srun make"
+      
+    if jmake: str = "cd %s; %s -j %d auto" % (dir.src,make,jmake.n)
+    else: str = "cd %s; %s auto" % (dir.src,make)
     
     # if verbose, print output as build proceeds, else only print if fails
 
     if verbose: subprocess.call(str,shell=True)
     else:
+      print str
       try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
       except Exception as e: print e.output
 
@@ -574,8 +607,8 @@ Syntax: Make.py switch args ...
     list one or more actions, in any order
     machine is a Makefile.machine suffix
   one-letter switches:
-    -d (dir), -j (jmake), -m (makefile), -o (output),
-    -p (packages), -r (redo), -s (settings), -v (verbose)
+    -d (dir), -j (jmake), -m (makefile), -o (output), -p (packages),
+    -r (redo), -s (settings), -v (verbose), -z (makefile output)
   switches for libs:
     -atc, -awpmd, -colvars, -cuda, -gpu, -h5md,
     -meam, -poems, -python, -qmmm, -reax, -voronoi
@@ -898,9 +931,13 @@ class Settings:
   def help(self):
     return """
 -s set1 set2 ...
-  possible settings = gzip smallbig bigbig smallsmall
-  add each setting as LAMMPS setting to created Makefile.auto
-  if -s not specified, no settings are changed in Makefile.auto
+  possible settings = gzip #gzip ffmpeg #ffmpeg smallbig bigbig smallsmall
+  alter LAMMPS ifdef settings in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
+  gzip and #gzip turn on/off LAMMPS_GZIP setting
+  ffmpeg and #ffmpeg turn on/off LAMMPS_FFMPEG setting
+  smallbig, bigbig, smallsmall turn on LAMMPS_SMALLBIG, etc
+    and turn off other two
 """
   
   def check(self):
@@ -924,6 +961,23 @@ class Verbose:
   def check(self):
     if len(self.inlist): error("-v args are invalid")
 
+# zoutput switch for making copy of final Makefile.auto
+
+class Zoutput:
+  def __init__(self,list):
+    self.inlist = copy.copy(list)
+
+  def help(self):
+    return """
+-z machine
+  copy created/used src/MAKE/MINE/Makefile.auto to Makefile.machine in same dir
+  this can be used to preserve the machine makefile
+"""
+
+  def check(self):
+    if len(self.inlist) != 1: error("-z args are invalid")
+    self.machine = self.inlist[0]
+
 # ----------------------------------------------------------------
 # lib classes, one per LAMMPS auxiliary lib
 # ----------------------------------------------------------------
@@ -1087,15 +1141,15 @@ class CUDA:
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.mode = "double"
-    self.arch = "31"
+    self.arch = "35"
 
   def help(self):
     return """
--cuda mode=double arch=31
+-cuda mode=double arch=35
   all args are optional and can be in any order
   mode = double or mixed or single (def = double)
-  arch = M (def = 31)
-    M = 31 for Kepler
+  arch = M (def = 35)
+    M = 31,35,37,etc for Kepler
     M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470)
     M = 21 for CC2.1 (GF104/114,  e.g. GTX560, GTX460, GTX450)
     M = 13 for CC1.3 (GF200, e.g. C1060, GTX285)
@@ -1144,16 +1198,18 @@ class GPU:
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.make = "linux.double"
-    self.lammpsflag = self.modeflag = self.archflag = 0
+    self.lammpsflag = self.modeflag = self.archflag = self.homeflag = 0
 
   def help(self):
     return """
--gpu make=suffix lammps=suffix2 mode=double arch=N
+-gpu make=suffix lammps=suffix2 mode=double arch=N home=path
   all args are optional and can be in any order
   make = use Makefile.suffix (def = linux.double)
   lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
   mode = double or mixed or single (def = CUDA_PREC in makefile)
-  arch = 31 (Kepler) or 21 (Fermi) (def = CUDA_ARCH in makefile)
+  arch = 3x (x = digit for Kepler) or 2x (x = digit for Fermi)
+         (def = CUDA_ARCH in makefile)
+  home = path to Cuda, e.g. /usr/local/cuda (def = CUDA_HOME in makefile)
 """
 
   def check(self):
@@ -1172,6 +1228,9 @@ class GPU:
       elif words[0] == "arch":
         self.arch = words[1]
         self.archflag = 1
+      elif words[0] == "home":
+        self.home = words[1]
+        self.homeflag = 1
       else: error("-gpu args are invalid")
       if self.modeflag and (self.mode != "double" and
                             self.mode != "mixed" and
@@ -1192,13 +1251,22 @@ class GPU:
         make.setvar("CUDA_PRECISION","-D_SINGLE_SINGLE")
     if self.archflag:
       make.setvar("CUDA_ARCH","-arch=sm_%s" % self.arch)
+    if self.homeflag:
+      make.setvar("CUDA_HOME",self.home)
     if self.lammpsflag:
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
-    if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
-    else: str = "cd %s; make -f Makefile.auto" % libdir
+    # special hack for shannon GPU cluster
+    # must use "srun make" if on it, else just make
+    # this is b/c Cuda libs are not all available on host
+
+    make = "make"
+    if "shannon" in os.environ.get("HOST"): make = "srun make"
+    
+    commands.getoutput("cd %s; %s -f Makefile.auto clean" % (libdir,make))
+    if jmake: str = "cd %s; %s -j %d -f Makefile.auto" % (libdir,make,jmake.n)
+    else: str = "cd %s; %s -f Makefile.auto" % (libdir,make)
 
     # if verbose, print output as build proceeds, else only print if fails
 
@@ -1574,14 +1642,16 @@ class Kokkos:
   mode is not optional, arch is optional
   mode = omp or cuda or phi (def = KOKKOS_DEVICES setting in Makefile )
     build Kokkos package for omp or cuda or phi
-    set KOKKOS_DEVICES to "OpenMP" (omp, phi) or "Cuda, OpenMP" (cuda)
-  arch = 31 (Kepler) or 21 (Fermi) (def = -arch setting in Makefile)
+    sets KOKKOS_DEVICES to "OpenMP" (omp, phi) or "Cuda, OpenMP" (cuda)
+  arch = number like 35 (Kepler) or 21 (Fermi)
+    sets KOKKOS_ARCH to appropriate value
 """
 
   def check(self):
+    print self.inlist
     if self.inlist != None and len(self.inlist) == 0:
       error("-kokkos args are invalid")
-
+      
     if self.inlist == None: return
     if len(self.inlist) < 1: error("-kokkos args are invalid")
     self.mode = self.inlist[0]
@@ -1596,7 +1666,7 @@ class Kokkos:
       else: error("-kokkos args are invalid")
       
 # ----------------------------------------------------------------
-# makefile classes for CC, MPI, JPG, PNG, FFT settings
+# makefile classes for CC, FLAGS, MPI, JPG, PNG, FFT settings
 # ----------------------------------------------------------------
 
 # Cc class
@@ -1610,7 +1680,8 @@ class Cc:
   def help(self):
     return """
 -cc compiler wrap=wcompiler
-  change CC setting in makefile
+  alter CC setting in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
   compiler is required, all other args are optional
   compiler = any string with g++ or icc or icpc
              or mpi (or mpicxx, mpiCC, mpiicpc, etc)
@@ -1644,6 +1715,41 @@ class Cc:
         self.wrap = words[1]
       else: error("-cc args are invalid")
 
+# Flags class
+
+class Flags:
+  def __init__(self,list):
+    self.inlist = copy.copy(list)
+    self.CC = []
+    self.LINK = []
+    
+  def help(self):
+    return """
+-flags flag f1 f2 ... flag f1 f2 ... 
+  alter CCFLAGS or LINKFLAGS settings in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
+  flag = CC or LINK
+    one or both can be specified
+  f1,f2,etc = flag to add or replace
+    "-" char will be prepended to each
+    for example: g, O3, xHost, "fp-model fast=2"
+    will become: -g, -O3, -xHost, -fp-model fast=2
+    for -O,-O2,-O3,etc: existing -O* will first be removed
+"""
+
+  def check(self):
+    if len(self.inlist) < 1: error("-flags args are invalid")
+    self.CC = []     # necessary?
+    self.LINK = []
+    mode = ""
+    for one in self.inlist:
+      if one == "CC": mode = "CC"
+      elif one == "LINK": mode = "LINK"
+      else:
+        if not mode: error("-flags args are invalid")
+        if mode == "CC": self.CC.append(one)
+        elif mode == "LINK": self.LINK.append(one)
+    
 # Mpi class
 
 class Mpi:
@@ -1654,7 +1760,8 @@ class Mpi:
   def help(self):
     return """
 -mpi style dir=path
-  change MPI settings in makefile
+  alter MPI settings in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
   style is required, all other args are optional
   style = mpi or mpich or ompi or serial
     mpi = no MPI settings (assume compiler is MPI wrapper)
@@ -1687,9 +1794,10 @@ class Fft:
   def help(self):
     return """
 -fft mode lib=libname dir=homedir idir=incdir ldir=libdir
-  change FFT settings in makefile
+  alter FFT settings in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
   mode is required, all other args are optional
-  removes all current FFT variable settings
+  first removes all current FFT variable settings
   mode = none or fftw or fftw3 or ...
     adds -DFFT_MODE setting
   lib = name of FFT library to link with (def is libname = mode)
@@ -1727,6 +1835,8 @@ class Jpg:
   def help(self):
     return """
 -jpg flag dir=homedir idir=incdir ldir=libdir
+  alter JPG settings in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
   change JPG settings in makefile
   all args are optional, flag must come first if specified
   flag = yes or no (def = yes)
@@ -1764,7 +1874,8 @@ class Png:
   def help(self):
     return """
 -png flag dir=homedir idir=incdir ldir=libdir
-  change PNG settings in makefile
+  alter PNG settings in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
   all args are optional, flag must come first if specified
   flag = yes or no (def = yes)
     include or exclude PNG support
@@ -2143,13 +2254,22 @@ while 1:
 
   packages.uninstall()
   
-  # create output file if requested and exe action performed
+  # create copy of executable if requested, and exe action performed
 
   if output and actions and "exe" in actions.alist:
     txt = "cp %s/lmp_auto %s/lmp_%s" % (dir.src,dir.cwd,output.machine)
     commands.getoutput(txt)
     print "Created lmp_%s in %s" % (output.machine,dir.cwd)
 
+  # create copy of Makefile.auto if requested, and file or exe action performed
+
+  if zoutput and actions and \
+        ("file" in actions.alist or "exe" in actions.alist):
+    txt = "cp %s/MAKE/MINE/Makefile.auto %s/MAKE/MINE/Makefile.%s" % \
+        (dir.src,dir.src,zoutput.machine)
+    commands.getoutput(txt)
+    print "Created Makefile.%s in %s/MAKE/MINE" % (zoutput.machine,dir.src)
+
   # write current Make.py command to src/Make.py.last
 
   fp = open("%s/Make.py.last" % dir.src,'w')
diff --git a/src/Makefile b/src/Makefile
index a0d9cc822d..8938c2e72a 100755
--- a/src/Makefile
+++ b/src/Makefile
@@ -205,8 +205,8 @@ install-python:
 tar:
 	@cd STUBS; $(MAKE) clean
 	@cd ..; tar cvzf src/$(ROOT)_src.tar.gz \
-	  src/Make* src/Package.sh src/Depend.sh \
-	  src/MAKE src/*.cpp src/*.h src/STUBS \
+	  src/Make* src/Package.sh src/Depend.sh src/Install.sh \
+	  src/MAKE src/DEPEND src/*.cpp src/*.h src/STUBS \
 	  $(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \
           --exclude=*/.svn
 	@cd STUBS; $(MAKE)
diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp
index af9ca65eef..2404ae536d 100644
--- a/src/QEQ/fix_qeq_fire.cpp
+++ b/src/QEQ/fix_qeq_fire.cpp
@@ -107,17 +107,16 @@ void FixQEqFire::init()
 void FixQEqFire::pre_force(int vflag)
 {
   int inum, *ilist;
-  int i,ii,iloop,loopmax;
-  int *mask = atom->mask;
+  int i,ii,iloop;
 
   double *q = atom->q;
   double vmax,vdotf,vdotfall,vdotv,vdotvall,fdotf,fdotfall;
   double scale1,scale2;
   double dtvone,dtv;
-  double enegtot,enegchk,enegmax;
+  double enegtot,enegchk;
   double alpha = qdamp;
   double dt, dtmax;
-  double enegchkall,enegmaxall;
+  double enegchkall;
   bigint ntimestep = update->ntimestep;
   bigint last_negative = 0;
 
@@ -225,7 +224,7 @@ void FixQEqFire::pre_force(int vflag)
   if (comm->me == 0) {
     if (iloop == maxiter) {
       char str[128];
-      sprintf(str,"Charges did not converge at step "BIGINT_FORMAT
+      sprintf(str,"Charges did not converge at step " BIGINT_FORMAT
 		  ": %lg",update->ntimestep,enegchk);
       error->warning(FLERR,str);
     }
diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp
index 17c2c30fca..5b6c310911 100644
--- a/src/REPLICA/temper.cpp
+++ b/src/REPLICA/temper.cpp
@@ -93,13 +93,38 @@ void Temper::command(int narg, char **arg)
   if (nswaps*nevery != nsteps)
     error->universe_all(FLERR,"Non integer # of swaps in temper command");
 
-  // fix style must be appropriate for temperature control
+  // fix style must be appropriate for temperature control, i.e. it needs
+  // to provide a working Fix::reset_target() and must not change the volume.
 
   if ((strcmp(modify->fix[whichfix]->style,"nvt") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/asphere") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/asphere/omp") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/body") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/eff") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/intel") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/kk") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/kk/host") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/kk/device") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/omp") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/sphere") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/sphere/omp") != 0) &&
       (strcmp(modify->fix[whichfix]->style,"langevin") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"langevin/drude") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"langevin/eff") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"gld") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"gle") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"rigid/nvt") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"rigid/nvt/small") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"rigid/nvt/omp") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"rigid/nvt/small/omp") != 0) &&
       (strcmp(modify->fix[whichfix]->style,"temp/berendsen") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0))
-    error->universe_all(FLERR,"Tempering temperature fix is not valid");
+      (strcmp(modify->fix[whichfix]->style,"temp/berendsen/cuda") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"temp/csvr") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"temp/csld") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"temp/rescale/cuda") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"temp/rescale/eff") != 0))
+    error->universe_all(FLERR,"Tempering temperature fix is not supported");
 
   // setup for long tempering run
 
diff --git a/src/STUBS/Makefile.mingw32-cross b/src/STUBS/Makefile.mingw32-cross
index 8bc6d62135..4144954ec7 100644
--- a/src/STUBS/Makefile.mingw32-cross
+++ b/src/STUBS/Makefile.mingw32-cross
@@ -16,7 +16,7 @@ OBJ = 		$(SRC:%.c=%_mingw32.o)
 # System-specific settings
 
 CC =	        i686-w64-mingw32-gcc
-CCFLAGS =	-O2 -Wall -march=i686 -mtune=generic -mfpmath=387 -mpc64
+CCFLAGS =	-O2 -Wall -march=i686 -mtune=generic -mfpmath=387 -mpc64 -I.
 ARCHIVE =	i686-w64-mingw32-ar
 ARCHFLAG =	rs
 
diff --git a/src/STUBS/Makefile.mingw64-cross b/src/STUBS/Makefile.mingw64-cross
index 2ef8d7fd6e..70b971f262 100644
--- a/src/STUBS/Makefile.mingw64-cross
+++ b/src/STUBS/Makefile.mingw64-cross
@@ -16,7 +16,7 @@ OBJ = 		$(SRC:%.c=%_mingw64.o)
 # System-specific settings
 
 CC =	        x86_64-w64-mingw32-gcc
-CCFLAGS =	-O2 -Wall -march=core2 -mtune=core2 -msse2 -mpc64
+CCFLAGS =	-O2 -Wall -march=core2 -mtune=core2 -msse2 -mpc64 -I.
 ARCHIVE =	x86_64-w64-mingw32-ar
 ARCHFLAG =	rs
 
diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp
index fc6ba17f1c..eeb3e134f6 100644
--- a/src/USER-OMP/pair_airebo_omp.cpp
+++ b/src/USER-OMP/pair_airebo_omp.cpp
@@ -1097,7 +1097,6 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
               ril[1] = rij[1]+rjl[1];
               ril[2] = rij[2]+rjl[2];
               ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
-              rijrjl = 2.0*rijmag*rjlmag;
               rjl2 = rjlmag*rjlmag;
               costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
               tspijl = Sp2(costmp,thmin,thmax,dtsijl);
diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp
index 3a9f043ed9..5412817d59 100644
--- a/src/compute_chunk_atom.cpp
+++ b/src/compute_chunk_atom.cpp
@@ -398,7 +398,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
     double scale;
     if (which == BIN1D || which == BIN2D || which == BIN3D || 
         which == BINCYLINDER) {
-      if (which == BIN1D || BINCYLINDER) ndim = 1;
+      if (which == BIN1D || which == BINCYLINDER) ndim = 1;
       if (which == BIN2D) ndim = 2;
       if (which == BIN3D) ndim = 3;
       for (int idim = 0; idim < ndim; idim++) {
diff --git a/src/domain.cpp b/src/domain.cpp
index ee6d2c1bc5..f47be0c6d5 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -503,13 +503,12 @@ void Domain::pbc()
 
   double *coord;
   int n3 = 3*nlocal;
-  if (x) {
-    coord = &x[0][0];
-    int flag = 0;
-    for (i = 0; i < n3; i++)
-      if (!ISFINITE(*coord++)) flag = 1;
-    if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable");
-  }
+  coord = &x[0][0];  // note: x is always initialzed to at least one element.
+  int flag = 0;
+  for (i = 0; i < n3; i++)
+    if (!ISFINITE(*coord++)) flag = 1;
+  if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable");
+
   // setup for PBC checks
 
   if (triclinic == 0) {
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index de0db88777..2ab9e84467 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -850,7 +850,6 @@ void DumpImage::create_image()
 
   if (bodyflag) {
     Body *bptr = avec_body->bptr;
-    double **x = atom->x;
     int *body = atom->body;
 
     m = 0;
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index 3537e36d54..588aca4738 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -23,7 +23,6 @@
 #include "force.h"
 #include "modify.h"
 #include "compute.h"
-#include "group.h"
 #include "input.h"
 #include "variable.h"
 #include "memory.h"
@@ -55,6 +54,8 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
 
   global_freq = nfreq;
 
+  dynamic_group_allow = 1;
+
   // scan values to count them
   // then read options so know mode = SCALAR/VECTOR before re-reading values
 
diff --git a/src/math_const.h b/src/math_const.h
index c0b81bdf8a..d94f783aa5 100644
--- a/src/math_const.h
+++ b/src/math_const.h
@@ -25,6 +25,7 @@ namespace MathConst {
   static const double MY_PI2 = 1.57079632679489661923; // pi/2
   static const double MY_PI4 = 0.78539816339744830962; // pi/4
   static const double MY_PIS = 1.77245385090551602729; // sqrt(pi)
+  static const double MY_ISPI4 = 1.12837916709551257389; // 1/sqrt(pi/4)
   static const double MY_SQRT2 = 1.41421356237309504880; // sqrt(2)
   static const double MY_CBRT2 = 1.25992104989487316476; // 2*(1/3)
 }
diff --git a/src/read_data.cpp b/src/read_data.cpp
index 5a7484dea8..4b790f343c 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -1468,7 +1468,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
 
 void ReadData::bodies(int firstpass)
 {
-  int i,m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp;
+  int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp;
   char *eof;
 
   int mapflag = 0;
diff --git a/src/set.cpp b/src/set.cpp
index a0bd6c2b65..37a0e815c4 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -917,7 +917,6 @@ void Set::setrandom(int keyword)
 
   } else if (keyword == THETA_RANDOM) {
     int nlocal = atom->nlocal;
-    double theta;
     for (i = 0; i < nlocal; i++) {
       if (select[i]) {
 	if (atom->line[i] < 0)

From 1e180da83007d97c696b6b1ee40c7d726e2f99e4 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 7 Apr 2016 21:05:09 +0000
Subject: [PATCH 02/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@14806
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/GPU/Install.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh
index e4f901c329..0ff436e95d 100644
--- a/src/GPU/Install.sh
+++ b/src/GPU/Install.sh
@@ -113,6 +113,10 @@ action pair_table_gpu.cpp pair_table.cpp
 action pair_table_gpu.h pair_table.cpp
 action pair_tersoff_gpu.cpp pair_tersoff.cpp
 action pair_tersoff_gpu.h pair_tersoff.cpp
+action pair_tersoff_mod_gpu.cpp pair_tersoff_mod.cpp
+action pair_tersoff_mod_gpu.h pair_tersoff_mod.cpp
+action pair_tersoff_zbl_gpu.cpp pair_tersoff_zbl.cpp
+action pair_tersoff_zbl_gpu.h pair_tersoff_zbl.cpp
 action pair_yukawa_colloid_gpu.cpp pair_yukawa_colloid.cpp
 action pair_yukawa_colloid_gpu.h pair_yukawa_colloid.cpp
 action pair_yukawa_gpu.cpp pair_yukawa.cpp

From 67a4004f23533fce1af932a7547c51c3cdd296fe Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 7 Apr 2016 21:05:19 +0000
Subject: [PATCH 03/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@14807
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 lib/gpu/Nvidia.makefile     | 28 +++++++++++++++++
 lib/gpu/Opencl.makefile     | 23 +++++++++++++-
 lib/gpu/lal_sw.cpp          |  6 ++--
 lib/gpu/lal_sw.cu           |  2 +-
 lib/gpu/lal_tersoff.cpp     |  2 +-
 lib/gpu/lal_tersoff.cu      | 60 ++++++++++++++++++-------------------
 lib/gpu/lal_tersoff.h       |  2 +-
 lib/gpu/lal_tersoff_extra.h |  8 ++---
 8 files changed, 91 insertions(+), 40 deletions(-)

diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile
index 004b387649..18efbda55a 100644
--- a/lib/gpu/Nvidia.makefile
+++ b/lib/gpu/Nvidia.makefile
@@ -70,6 +70,8 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \
        $(OBJ_DIR)/lal_lj_gromacs.o $(OBJ_DIR)/lal_lj_gromacs_ext.o \
        $(OBJ_DIR)/lal_dpd.o $(OBJ_DIR)/lal_dpd_ext.o \
        $(OBJ_DIR)/lal_tersoff.o $(OBJ_DIR)/lal_tersoff_ext.o \
+       $(OBJ_DIR)/lal_tersoff_zbl.o $(OBJ_DIR)/lal_tersoff_zbl_ext.o \
+       $(OBJ_DIR)/lal_tersoff_mod.o $(OBJ_DIR)/lal_tersoff_mod_ext.o \
        $(OBJ_DIR)/lal_coul.o $(OBJ_DIR)/lal_coul_ext.o \
        $(OBJ_DIR)/lal_coul_debye.o $(OBJ_DIR)/lal_coul_debye_ext.o \
        $(OBJ_DIR)/lal_zbl.o $(OBJ_DIR)/lal_zbl_ext.o \
@@ -122,6 +124,8 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
        $(OBJ_DIR)/lj_gromacs.cubin $(OBJ_DIR)/lj_gromacs_cubin.h \
        $(OBJ_DIR)/dpd.cubin $(OBJ_DIR)/dpd_cubin.h \
        $(OBJ_DIR)/tersoff.cubin $(OBJ_DIR)/tersoff_cubin.h \
+       $(OBJ_DIR)/tersoff_zbl.cubin $(OBJ_DIR)/tersoff_zbl_cubin.h \
+       $(OBJ_DIR)/tersoff_mod.cubin $(OBJ_DIR)/tersoff_mod_cubin.h \
        $(OBJ_DIR)/coul.cubin $(OBJ_DIR)/coul_cubin.h \
        $(OBJ_DIR)/coul_debye.cubin $(OBJ_DIR)/coul_debye_cubin.h \
        $(OBJ_DIR)/zbl.cubin $(OBJ_DIR)/zbl_cubin.h \
@@ -705,6 +709,30 @@ $(OBJ_DIR)/lal_tersoff.o: $(ALL_H) lal_tersoff.h lal_tersoff.cpp $(OBJ_DIR)/ters
 $(OBJ_DIR)/lal_tersoff_ext.o: $(ALL_H) lal_tersoff.h lal_tersoff_ext.cpp lal_base_three.h
 	$(CUDR) -o $@ -c lal_tersoff_ext.cpp -I$(OBJ_DIR)
 
+$(OBJ_DIR)/tersoff_zbl.cubin: lal_tersoff_zbl.cu lal_precision.h lal_tersoff_zbl_extra.h lal_preprocessor.h
+	$(CUDA) --cubin -DNV_KERNEL -o $@ lal_tersoff_zbl.cu
+
+$(OBJ_DIR)/tersoff_zbl_cubin.h: $(OBJ_DIR)/tersoff_zbl.cubin $(OBJ_DIR)/tersoff_zbl.cubin
+	$(BIN2C) -c -n tersoff_zbl $(OBJ_DIR)/tersoff_zbl.cubin > $(OBJ_DIR)/tersoff_zbl_cubin.h
+
+$(OBJ_DIR)/lal_tersoff_zbl.o: $(ALL_H) lal_tersoff_zbl.h lal_tersoff_zbl.cpp $(OBJ_DIR)/tersoff_zbl_cubin.h $(OBJ_DIR)/lal_base_three.o
+	$(CUDR) -o $@ -c lal_tersoff_zbl.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_tersoff_zbl_ext.o: $(ALL_H) lal_tersoff_zbl.h lal_tersoff_zbl_ext.cpp lal_base_three.h
+	$(CUDR) -o $@ -c lal_tersoff_zbl_ext.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/tersoff_mod.cubin: lal_tersoff_mod.cu lal_precision.h lal_tersoff_mod_extra.h lal_preprocessor.h
+	$(CUDA) --cubin -DNV_KERNEL -o $@ lal_tersoff_mod.cu
+
+$(OBJ_DIR)/tersoff_mod_cubin.h: $(OBJ_DIR)/tersoff_mod.cubin $(OBJ_DIR)/tersoff_mod.cubin
+	$(BIN2C) -c -n tersoff_mod $(OBJ_DIR)/tersoff_mod.cubin > $(OBJ_DIR)/tersoff_mod_cubin.h
+
+$(OBJ_DIR)/lal_tersoff_mod.o: $(ALL_H) lal_tersoff_mod.h lal_tersoff_mod.cpp $(OBJ_DIR)/tersoff_mod_cubin.h $(OBJ_DIR)/lal_base_three.o
+	$(CUDR) -o $@ -c lal_tersoff_mod.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_tersoff_mod_ext.o: $(ALL_H) lal_tersoff_mod.h lal_tersoff_mod_ext.cpp lal_base_three.h
+	$(CUDR) -o $@ -c lal_tersoff_mod_ext.cpp -I$(OBJ_DIR)
+
 $(OBJ_DIR)/coul.cubin: lal_coul.cu lal_precision.h lal_preprocessor.h
 	$(CUDA) --cubin -DNV_KERNEL -o $@ lal_coul.cu
 
diff --git a/lib/gpu/Opencl.makefile b/lib/gpu/Opencl.makefile
index d7bae0f494..b33a392242 100644
--- a/lib/gpu/Opencl.makefile
+++ b/lib/gpu/Opencl.makefile
@@ -59,6 +59,8 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_answer.o \
        $(OBJ_DIR)/lal_lj_gromacs.o $(OBJ_DIR)/lal_lj_gromacs_ext.o \
        $(OBJ_DIR)/lal_dpd.o $(OBJ_DIR)/lal_dpd_ext.o \
        $(OBJ_DIR)/lal_tersoff.o $(OBJ_DIR)/lal_tersoff_ext.o \
+       $(OBJ_DIR)/lal_tersoff_zbl.o $(OBJ_DIR)/lal_tersoff_zbl_ext.o \
+       $(OBJ_DIR)/lal_tersoff_mod.o $(OBJ_DIR)/lal_tersoff_mod_ext.o \
        $(OBJ_DIR)/lal_coul.o $(OBJ_DIR)/lal_coul_ext.o \
        $(OBJ_DIR)/lal_coul_debye.o $(OBJ_DIR)/lal_coul_debye_ext.o \
        $(OBJ_DIR)/lal_zbl.o $(OBJ_DIR)/lal_zbl_ext.o \
@@ -87,7 +89,8 @@ KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \
        $(OBJ_DIR)/soft_cl.h $(OBJ_DIR)/lj_coul_msm_cl.h \
        $(OBJ_DIR)/lj_gromacs_cl.h $(OBJ_DIR)/dpd_cl.h \
        $(OBJ_DIR)/lj_gauss_cl.h $(OBJ_DIR)/dzugutov_cl.h \
-       $(OBJ_DIR)/tersoff_cl.h $(OBJ_DIR)/coul_cl.h \
+       $(OBJ_DIR)/tersoff_cl.h $(OBJ_DIR)/tersoff_zbl_cl.h \
+       $(OBJ_DIR)/tersoff_mod_cl.h $(OBJ_DIR)/coul_cl.h \
        $(OBJ_DIR)/coul_debye_cl.h $(OBJ_DIR)/zbl_cl.h \
        $(OBJ_DIR)/lj_cubic_cl.h
 
@@ -510,6 +513,24 @@ $(OBJ_DIR)/lal_tersoff.o: $(ALL_H) lal_tersoff.h lal_tersoff.cpp  $(OBJ_DIR)/ter
 $(OBJ_DIR)/lal_tersoff_ext.o: $(ALL_H) lal_tersoff.h lal_tersoff_ext.cpp lal_base_three.h
 	$(OCL) -o $@ -c lal_tersoff_ext.cpp -I$(OBJ_DIR)
 
+$(OBJ_DIR)/tersoff_zbl_cl.h: lal_tersoff_zbl.cu lal_tersoff_zbl_extra.h $(PRE1_H)
+	$(BSH) ./geryon/file_to_cstr.sh tersoff_zbl $(PRE1_H) lal_tersoff_zbl_extra.h lal_tersoff_zbl.cu $(OBJ_DIR)/tersoff_zbl_cl.h;
+
+$(OBJ_DIR)/lal_tersoff_zbl.o: $(ALL_H) lal_tersoff_zbl.h lal_tersoff_zbl.cpp  $(OBJ_DIR)/tersoff_zbl_cl.h $(OBJ_DIR)/tersoff_zbl_cl.h $(OBJ_DIR)/lal_base_three.o
+	$(OCL) -o $@ -c lal_tersoff_zbl.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_tersoff_zbl_ext.o: $(ALL_H) lal_tersoff_zbl.h lal_tersoff_zbl_ext.cpp lal_base_three.h
+	$(OCL) -o $@ -c lal_tersoff_zbl_ext.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/tersoff_mod_cl.h: lal_tersoff_mod.cu lal_tersoff_mod_extra.h $(PRE1_H)
+	$(BSH) ./geryon/file_to_cstr.sh tersoff_mod $(PRE1_H) lal_tersoff_mod_extra.h lal_tersoff_mod.cu $(OBJ_DIR)/tersoff_mod_cl.h;
+
+$(OBJ_DIR)/lal_tersoff_mod.o: $(ALL_H) lal_tersoff_mod.h lal_tersoff_mod.cpp  $(OBJ_DIR)/tersoff_mod_cl.h $(OBJ_DIR)/tersoff_mod_cl.h $(OBJ_DIR)/lal_base_three.o
+	$(OCL) -o $@ -c lal_tersoff_mod.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_tersoff_mod_ext.o: $(ALL_H) lal_tersoff_mod.h lal_tersoff_mod_ext.cpp lal_base_three.h
+	$(OCL) -o $@ -c lal_tersoff_mod_ext.cpp -I$(OBJ_DIR)
+
 $(OBJ_DIR)/coul_cl.h: lal_coul.cu $(PRE1_H)
 	$(BSH) ./geryon/file_to_cstr.sh coul $(PRE1_H) lal_coul.cu $(OBJ_DIR)/coul_cl.h;
 
diff --git a/lib/gpu/lal_sw.cpp b/lib/gpu/lal_sw.cpp
index f14b0a3438..1f68616b0e 100644
--- a/lib/gpu/lal_sw.cpp
+++ b/lib/gpu/lal_sw.cpp
@@ -142,7 +142,7 @@ int SWT::init(const int ntypes, const int nlocal, const int nall, const int max_
   ucl_copy(elem2param,dview_elem2param,false);
 
   UCL_H_Vec<int> dview_map(lj_types, *(this->ucl_device), UCL_WRITE_ONLY);
-  for (int i = 0; i < lj_types; i++)
+  for (int i = 0; i < ntypes; i++)
     dview_map[i] = host_map[i];
 
   map.alloc(lj_types,*(this->ucl_device), UCL_READ_ONLY);
@@ -196,13 +196,15 @@ void SWT::loop(const bool _eflag, const bool _vflag, const int evatom) {
   int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
                                (BX/this->_threads_per_atom)));
 
+  // this->_nbor_data == nbor->dev_packed for gpu_nbor == 0 and tpa == 1 
+  // this->_nbor_data == nbor->dev_nbor for gpu_nbor == 1
   int ainum=this->ans->inum();
   int nbor_pitch=this->nbor->nbor_pitch();
   this->time_pair.start();
   this->k_pair.set_size(GX,BX);
   this->k_pair.run(&this->atom->x, &sw1, &sw2, &sw3, 
                    &map, &elem2param, &_nelements,
-                   &this->nbor->dev_nbor, &this->_nbor_data->begin(), 
+                   &this->nbor->dev_nbor, &this->_nbor_data->begin(),
                    &this->ans->force, &this->ans->engv, 
                    &eflag, &vflag, &ainum, &nbor_pitch, 
                    &this->_threads_per_atom);
diff --git a/lib/gpu/lal_sw.cu b/lib/gpu/lal_sw.cu
index 4492e5f60a..1e358fb6f7 100644
--- a/lib/gpu/lal_sw.cu
+++ b/lib/gpu/lal_sw.cu
@@ -35,7 +35,7 @@ texture<int4> sw3_tex;
 #define sw3_tex sw3
 #endif
 
-#define THIRD (numtyp)0.66666667
+#define THIRD (numtyp)0.66666666666666666667
 
 //#define THREE_CONCURRENT
 
diff --git a/lib/gpu/lal_tersoff.cpp b/lib/gpu/lal_tersoff.cpp
index fc7ebc4f08..bc89c53765 100644
--- a/lib/gpu/lal_tersoff.cpp
+++ b/lib/gpu/lal_tersoff.cpp
@@ -178,7 +178,7 @@ int TersoffT::init(const int ntypes, const int nlocal, const int nall, const int
   ucl_copy(elem2param,dview_elem2param,false);
 
   UCL_H_Vec<int> dview_map(lj_types, *(this->ucl_device), UCL_WRITE_ONLY);
-  for (int i = 0; i < lj_types; i++)
+  for (int i = 0; i < ntypes; i++)
     dview_map[i] = host_map[i];
 
   map.alloc(lj_types,*(this->ucl_device), UCL_READ_ONLY);
diff --git a/lib/gpu/lal_tersoff.cu b/lib/gpu/lal_tersoff.cu
index 50202c0ee7..e98a454f58 100644
--- a/lib/gpu/lal_tersoff.cu
+++ b/lib/gpu/lal_tersoff.cu
@@ -43,7 +43,7 @@ texture<int4> ts5_tex;
 
 //#define THREE_CONCURRENT
 
-#define THIRD (numtyp)0.66666667
+#define TWOTHIRD (numtyp)0.66666666666666666667
 
 #define zeta_idx(nbor_mem, packed_mem, nbor_pitch, n_stride, t_per_atom,    \
                  i, nbor_j, offset_j, idx)                                  \
@@ -108,6 +108,7 @@ texture<int4> ts5_tex;
 
 #define store_zeta(z, tid, t_per_atom, offset)                              \
   if (t_per_atom>1) {                                                       \
+    __local acctyp red_acc[BLOCK_PAIR];                                     \
     red_acc[tid]=z;                                                         \
     for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                         \
       if (offset < s) {                                                     \
@@ -180,7 +181,7 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_,
                              const __global int *restrict map,
                              const __global int *restrict elem2param,
                              const int nelements, const int nparams,
-                             __global numtyp4 * zetaij,
+                             __global acctyp4 * zetaij,
                              const __global int * dev_nbor,
                              const __global int * dev_packed,
                              const int eflag, const int nall, const int inum,
@@ -205,9 +206,7 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_,
     ts5[tid]=ts5_in[tid];
   }
 
-  numtyp z = (numtyp)0;
-  __local numtyp red_acc[BLOCK_PAIR];
-  if (tid<BLOCK_PAIR) red_acc[tid] = (numtyp)0;
+  acctyp z = (acctyp)0;
 
   __syncthreads();
 
@@ -245,7 +244,7 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_,
       if (rsq1 > cutsq[ijparam]) continue;
 
       // compute zeta_ij
-      z = (numtyp)0;
+      z = (acctyp)0;
 
       int nbor_k = nborj_start-offset_j+offset_k;
       for ( ; nbor_k < nbor_end; nbor_k+=n_stride) {
@@ -310,7 +309,7 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_,
         force_zeta(ijparam_bigb, ijparam_bigr, ijparam_bigd, ijparam_lam2,
                    ijparam_beta, ijparam_powern, ijparam_c1, ijparam_c2, ijparam_c3,
                    ijparam_c4, rsq1, z, eflag, fpfeng);
-        numtyp4 zij;
+        acctyp4 zij;
         zij.x = fpfeng[0];
         zij.y = fpfeng[1];
         zij.z = fpfeng[2];
@@ -426,7 +425,7 @@ __kernel void k_tersoff_three_center(const __global numtyp4 *restrict x_,
                                      const __global int *restrict map,
                                      const __global int *restrict elem2param,
                                      const int nelements, const int nparams,
-                                     const __global numtyp4 *restrict zetaij,
+                                     const __global acctyp4 *restrict zetaij,
                                      const __global int * dev_nbor,
                                      const __global int * dev_packed,
                                      __global acctyp4 *restrict ans,
@@ -501,7 +500,7 @@ __kernel void k_tersoff_three_center(const __global numtyp4 *restrict x_,
       int idx;
       zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
                i, nbor_j, offset_j, idx);
-      numtyp4 zeta_ij = zetaij[idx]; // fetch(zeta_ij,idx,zeta_tex);
+      acctyp4 zeta_ij = zetaij[idx]; // fetch(zeta_ij,idx,zeta_tex);
       numtyp force = zeta_ij.x*tpainv;
       numtyp prefactor = zeta_ij.y;
       f.x += delr1[0]*force;
@@ -568,7 +567,7 @@ __kernel void k_tersoff_three_center(const __global numtyp4 *restrict x_,
         if (vflag>0) {
           acctyp v[6];
           numtyp pre = (numtyp)2.0;
-          if (evatom==1) pre = THIRD;
+          if (evatom==1) pre = TWOTHIRD;
           v[0] = pre*(delr1[0]*fj[0] + delr2[0]*fk[0]);
           v[1] = pre*(delr1[1]*fj[1] + delr2[1]*fk[1]);
           v[2] = pre*(delr1[2]*fj[2] + delr2[2]*fk[2]);
@@ -595,7 +594,7 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
                                   const __global int *restrict map,
                                   const __global int *restrict elem2param,
                                   const int nelements, const int nparams,
-                                  const __global numtyp4 *restrict zetaij,
+                                  const __global acctyp4 *restrict zetaij,
                                   const __global int * dev_nbor,
                                   const __global int * dev_packed,
                                   __global acctyp4 *restrict ans,
@@ -710,7 +709,7 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
       int idx;
       zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
                j, ijnum, offset_kf, idx);
-      numtyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex);
+      acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex);
       numtyp force = zeta_ji.x*tpainv;
       numtyp prefactor_ji = zeta_ji.y;
       f.x += delr1[0]*force;
@@ -776,7 +775,7 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
         int idx;
         zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
                  j, nbor_k, offset_k, idx);
-        numtyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
+        acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
         numtyp prefactor_jk = zeta_jk.y;
         int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype];
         ts1_param = ts1[jkiparam]; //fetch4(ts1_jkiparam,jkiparam,ts1_tex);
@@ -816,7 +815,7 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
                                         const __global int *restrict map,
                                         const __global int *restrict elem2param,
                                         const int nelements, const int nparams,
-                                        const __global numtyp4 *restrict zetaij,
+                                        const __global acctyp4 *restrict zetaij,
                                         const __global int * dev_nbor,
                                         const __global int * dev_packed,
                                         __global acctyp4 *restrict ans,
@@ -931,9 +930,9 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
       int idx;
       zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
                j, ijnum, offset_kf, idx);
-      numtyp4 zeta_ji = zetaij[idx]; //  fetch(zeta_ji,idx,zeta_tex);
+      acctyp4 zeta_ji = zetaij[idx]; //  fetch(zeta_ji,idx,zeta_tex);
       numtyp force = zeta_ji.x*tpainv;
-      numtyp prefactor = zeta_ji.y;
+      numtyp prefactor_ji = zeta_ji.y;
       f.x += delr1[0]*force;
       f.y += delr1[1]*force;
       f.z += delr1[2]*force;
@@ -987,24 +986,24 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
         h = ts4_param.z;
         gamma = ts4_param.w;
         attractive(bigr, bigd, powermint, lam3, c, d, h, gamma,
-                   prefactor, r1, r1inv, r2, r2inv, mdelr1, delr2, fi, fj, fk);
+                   prefactor_ji, r1, r1inv, r2, r2inv, mdelr1, delr2, fi, fj, fk);
         f.x += fj[0];
         f.y += fj[1];
         f.z += fj[2];
 
-        virial[0] += THIRD*(mdelr1[0]*fj[0] + delr2[0]*fk[0]);
-        virial[1] += THIRD*(mdelr1[1]*fj[1] + delr2[1]*fk[1]);
-        virial[2] += THIRD*(mdelr1[2]*fj[2] + delr2[2]*fk[2]);
-        virial[3] += THIRD*(mdelr1[0]*fj[1] + delr2[0]*fk[1]);
-        virial[4] += THIRD*(mdelr1[0]*fj[2] + delr2[0]*fk[2]);
-        virial[5] += THIRD*(mdelr1[1]*fj[2] + delr2[1]*fk[2]);
+        virial[0] += TWOTHIRD*(mdelr1[0]*fj[0] + delr2[0]*fk[0]);
+        virial[1] += TWOTHIRD*(mdelr1[1]*fj[1] + delr2[1]*fk[1]);
+        virial[2] += TWOTHIRD*(mdelr1[2]*fj[2] + delr2[2]*fk[2]);
+        virial[3] += TWOTHIRD*(mdelr1[0]*fj[1] + delr2[0]*fk[1]);
+        virial[4] += TWOTHIRD*(mdelr1[0]*fj[2] + delr2[0]*fk[2]);
+        virial[5] += TWOTHIRD*(mdelr1[1]*fj[2] + delr2[1]*fk[2]);
 
         //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;
         //int idx = kk*n_stride + j*t_per_atom + offset_k;
         int idx;
         zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
                  j, nbor_k, offset_k, idx);
-        numtyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
+        acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
         numtyp prefactor_jk = zeta_jk.y;
 
         int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype];
@@ -1025,12 +1024,13 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
         f.y += fk[1];
         f.z += fk[2];
 
-        virial[0] += THIRD*(delr2[0]*fj[0] + mdelr1[0]*fk[0]);
-        virial[1] += THIRD*(delr2[1]*fj[1] + mdelr1[1]*fk[1]);
-        virial[2] += THIRD*(delr2[2]*fj[2] + mdelr1[2]*fk[2]);
-        virial[3] += THIRD*(delr2[0]*fj[1] + mdelr1[0]*fk[1]);
-        virial[4] += THIRD*(delr2[0]*fj[2] + mdelr1[0]*fk[2]);
-        virial[5] += THIRD*(delr2[1]*fj[2] + mdelr1[1]*fk[2]);
+        virial[0] += TWOTHIRD*(delr2[0]*fj[0] + mdelr1[0]*fk[0]);
+        virial[1] += TWOTHIRD*(delr2[1]*fj[1] + mdelr1[1]*fk[1]);
+        virial[2] += TWOTHIRD*(delr2[2]*fj[2] + mdelr1[2]*fk[2]);
+        virial[3] += TWOTHIRD*(delr2[0]*fj[1] + mdelr1[0]*fk[1]);
+        virial[4] += TWOTHIRD*(delr2[0]*fj[2] + mdelr1[0]*fk[2]);
+        virial[5] += TWOTHIRD*(delr2[1]*fj[2] + mdelr1[1]*fk[2]);
+
       }
     } // for nbor
 
diff --git a/lib/gpu/lal_tersoff.h b/lib/gpu/lal_tersoff.h
index beae6f5e08..c72ebd7286 100644
--- a/lib/gpu/lal_tersoff.h
+++ b/lib/gpu/lal_tersoff.h
@@ -100,7 +100,7 @@ class Tersoff : public BaseThree<numtyp, acctyp> {
   /// Per-atom arrays:
   /// zetaij.x = force, zetaij.y = prefactor, zetaij.z = evdwl,
   /// zetaij.w = zetaij
-  UCL_D_Vec<numtyp4>   _zetaij;
+  UCL_D_Vec<acctyp4>   _zetaij;
 
   UCL_Kernel k_zeta;
   UCL_Texture ts1_tex, ts2_tex, ts3_tex, ts4_tex, ts5_tex;
diff --git a/lib/gpu/lal_tersoff_extra.h b/lib/gpu/lal_tersoff_extra.h
index 672a767783..21a0315f71 100644
--- a/lib/gpu/lal_tersoff_extra.h
+++ b/lib/gpu/lal_tersoff_extra.h
@@ -227,7 +227,7 @@ ucl_inline void ters_zetaterm_d(const numtyp prefactor,
   if ((int)param_powermint == 3) tmp = t*t*t;
   else tmp = t;
 
-  if (tmp > (numtyp)69.0776) ex_delr = (acctyp)1.e30;
+  if (tmp > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
   else if (tmp < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
   else ex_delr = ucl_exp(tmp);
 
@@ -295,7 +295,7 @@ ucl_inline void ters_zetaterm_d_fi(const numtyp prefactor,
   if ((int)param_powermint == 3) tmp = t*t*t;
   else tmp = t;
 
-  if (tmp > (numtyp)69.0776) ex_delr = (acctyp)1.e30;
+  if (tmp > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
   else if (tmp < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
   else ex_delr = ucl_exp(tmp);
 
@@ -344,7 +344,7 @@ ucl_inline void ters_zetaterm_d_fj(const numtyp prefactor,
   if ((int)param_powermint == 3) tmp = t*t*t;
   else tmp = t;
 
-  if (tmp > (numtyp)69.0776) ex_delr = (acctyp)1.e30;
+  if (tmp > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
   else if (tmp < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
   else ex_delr = ucl_exp(tmp);
 
@@ -391,7 +391,7 @@ ucl_inline void ters_zetaterm_d_fk(const numtyp prefactor,
   if ((int)param_powermint == 3) tmp = t*t*t;
   else tmp = t;
 
-  if (tmp > (numtyp)69.0776) ex_delr = (acctyp)1.e30;
+  if (tmp > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
   else if (tmp < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
   else ex_delr = ucl_exp(tmp);
 

From 008896a77d6cb6ea989ef81ef712c7ce0329c49f Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 7 Apr 2016 21:10:37 +0000
Subject: [PATCH 04/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@14808
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 lib/gpu/lal_tersoff_mod.cpp     |  456 +++++++++++++
 lib/gpu/lal_tersoff_mod.cu      | 1070 +++++++++++++++++++++++++++++++
 lib/gpu/lal_tersoff_mod.h       |  118 ++++
 lib/gpu/lal_tersoff_mod_ext.cpp |  135 ++++
 lib/gpu/lal_tersoff_mod_extra.h |  627 ++++++++++++++++++
 lib/gpu/lal_tersoff_zbl.cpp     |  482 ++++++++++++++
 lib/gpu/lal_tersoff_zbl.cu      | 1065 ++++++++++++++++++++++++++++++
 lib/gpu/lal_tersoff_zbl.h       |  123 ++++
 lib/gpu/lal_tersoff_zbl_ext.cpp |  146 +++++
 lib/gpu/lal_tersoff_zbl_extra.h |  690 ++++++++++++++++++++
 10 files changed, 4912 insertions(+)
 create mode 100644 lib/gpu/lal_tersoff_mod.cpp
 create mode 100644 lib/gpu/lal_tersoff_mod.cu
 create mode 100644 lib/gpu/lal_tersoff_mod.h
 create mode 100644 lib/gpu/lal_tersoff_mod_ext.cpp
 create mode 100644 lib/gpu/lal_tersoff_mod_extra.h
 create mode 100644 lib/gpu/lal_tersoff_zbl.cpp
 create mode 100644 lib/gpu/lal_tersoff_zbl.cu
 create mode 100644 lib/gpu/lal_tersoff_zbl.h
 create mode 100644 lib/gpu/lal_tersoff_zbl_ext.cpp
 create mode 100644 lib/gpu/lal_tersoff_zbl_extra.h

diff --git a/lib/gpu/lal_tersoff_mod.cpp b/lib/gpu/lal_tersoff_mod.cpp
new file mode 100644
index 0000000000..bfcc9c3bd3
--- /dev/null
+++ b/lib/gpu/lal_tersoff_mod.cpp
@@ -0,0 +1,456 @@
+/***************************************************************************
+                               tersoff_mod.cpp
+                             -------------------
+                               Trung Dac Nguyen
+
+  Class for acceleration of the tersoff pair style.
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                :
+    email                : ndactrung@gmail.com
+ ***************************************************************************/
+
+#if defined(USE_OPENCL)
+#include "tersoff_mod_cl.h"
+#elif defined(USE_CUDART)
+const char *tersoff_mod=0;
+#else
+#include "tersoff_mod_cubin.h"
+#endif
+
+#include "lal_tersoff_mod.h"
+#include <cassert>
+using namespace LAMMPS_AL;
+#define TersoffMT TersoffMod<numtyp, acctyp>
+
+extern Device<PRECISION,ACC_PRECISION> device;
+
+template <class numtyp, class acctyp>
+TersoffMT::TersoffMod() : BaseThree<numtyp,acctyp>(), _allocated(false) {
+}
+
+template <class numtyp, class acctyp>
+TersoffMT::~TersoffMod() {
+  clear();
+}
+
+template <class numtyp, class acctyp>
+int TersoffMT::bytes_per_atom(const int max_nbors) const {
+  return this->bytes_per_atom_atomic(max_nbors);
+}
+
+template <class numtyp, class acctyp>
+int TersoffMT::init(const int ntypes, const int nlocal, const int nall, const int max_nbors,
+                   const double cell_size, const double gpu_split, FILE *_screen,
+                   int* host_map, const int nelements, int*** host_elem2param, const int nparams,
+                   const double* lam1, const double* lam2, const double* lam3,const double* powermint,
+                   const double* biga, const double* bigb, const double* bigr, const double* bigd,
+                   const double* c1, const double* c2, const double* c3, const double* c4,
+                   const double* c5, const double* h, const double* beta, const double* powern,
+                   const double* powern_del, const double* ca1, const double* host_cutsq)
+{
+  int success;
+  success=this->init_three(nlocal,nall,max_nbors,0,cell_size,gpu_split,
+                           _screen,tersoff_mod,"k_tersoff_mod_repulsive",
+                           "k_tersoff_mod_three_center", "k_tersoff_mod_three_end");
+  if (success!=0)
+    return success;
+
+  int ef_nall=nall;
+  if (ef_nall==0)
+    ef_nall=2000;
+  _zetaij.alloc(ef_nall*max_nbors,*(this->ucl_device),UCL_READ_WRITE);
+
+  k_zeta.set_function(*(this->pair_program),"k_tersoff_mod_zeta");
+
+  // If atom type constants fit in shared memory use fast kernel
+  int lj_types=ntypes;
+  shared_types=false;
+  int max_shared_types=this->device->max_shared_types();
+  if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
+    lj_types=max_shared_types;
+    shared_types=true;
+  }
+  _lj_types=lj_types;
+
+  _nparams = nparams;
+  _nelements = nelements;
+
+  UCL_H_Vec<numtyp4> dview(nparams,*(this->ucl_device),
+                           UCL_WRITE_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=(numtyp)0;
+    dview[i].y=(numtyp)0;
+    dview[i].z=(numtyp)0;
+    dview[i].w=(numtyp)0;
+  }
+
+  // pack coefficients into arrays
+  ts1.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=static_cast<numtyp>(lam1[i]);
+    dview[i].y=static_cast<numtyp>(lam2[i]);
+    dview[i].z=static_cast<numtyp>(lam3[i]);
+    dview[i].w=static_cast<numtyp>(powermint[i]);
+  }
+
+  ucl_copy(ts1,dview,false);
+  ts1_tex.get_texture(*(this->pair_program),"ts1_tex");
+  ts1_tex.bind_float(ts1,4);
+
+  ts2.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=static_cast<numtyp>(biga[i]);
+    dview[i].y=static_cast<numtyp>(bigb[i]);
+    dview[i].z=static_cast<numtyp>(bigr[i]);
+    dview[i].w=static_cast<numtyp>(bigd[i]);
+  }
+
+  ucl_copy(ts2,dview,false);
+  ts2_tex.get_texture(*(this->pair_program),"ts2_tex");
+  ts2_tex.bind_float(ts2,4);
+
+  ts3.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=static_cast<numtyp>(beta[i]);
+    dview[i].y=static_cast<numtyp>(powern[i]);
+    dview[i].z=static_cast<numtyp>(powern_del[i]);
+    dview[i].w=static_cast<numtyp>(ca1[i]);
+  }
+
+  ucl_copy(ts3,dview,false);
+  ts3_tex.get_texture(*(this->pair_program),"ts3_tex");
+  ts3_tex.bind_float(ts3,4);
+
+  ts4.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=static_cast<numtyp>(c1[i]);
+    dview[i].y=static_cast<numtyp>(c2[i]);
+    dview[i].z=static_cast<numtyp>(c3[i]);
+    dview[i].w=static_cast<numtyp>(c4[i]);
+  }
+
+  ucl_copy(ts4,dview,false);
+  ts4_tex.get_texture(*(this->pair_program),"ts4_tex");
+  ts4_tex.bind_float(ts4,4);
+
+  ts5.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=static_cast<numtyp>(c5[i]);
+    dview[i].y=static_cast<numtyp>(h[i]);
+    dview[i].z=(numtyp)0;
+    dview[i].w=(numtyp)0;
+  }
+
+  ucl_copy(ts5,dview,false);
+  ts5_tex.get_texture(*(this->pair_program),"ts5_tex");
+  ts5_tex.bind_float(ts5,4);
+
+  UCL_H_Vec<numtyp> cutsq_view(nparams,*(this->ucl_device),
+                               UCL_WRITE_ONLY);
+  for (int i=0; i<nparams; i++)
+    cutsq_view[i]=static_cast<numtyp>(host_cutsq[i]);
+  cutsq.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+  ucl_copy(cutsq,cutsq_view,false);
+
+  UCL_H_Vec<int> dview_elem2param(nelements*nelements*nelements,
+                           *(this->ucl_device), UCL_WRITE_ONLY);
+
+  elem2param.alloc(nelements*nelements*nelements,*(this->ucl_device),
+                   UCL_READ_ONLY);
+
+  for (int i = 0; i < nelements; i++)
+    for (int j = 0; j < nelements; j++)
+      for (int k = 0; k < nelements; k++) {
+         int idx = i*nelements*nelements+j*nelements+k;
+         dview_elem2param[idx] = host_elem2param[i][j][k];
+      }
+
+  ucl_copy(elem2param,dview_elem2param,false);
+
+  UCL_H_Vec<int> dview_map(lj_types, *(this->ucl_device), UCL_WRITE_ONLY);
+  for (int i = 0; i < ntypes; i++)
+    dview_map[i] = host_map[i];
+
+  map.alloc(lj_types,*(this->ucl_device), UCL_READ_ONLY);
+  ucl_copy(map,dview_map,false);
+
+  _allocated=true;
+  this->_max_bytes=ts1.row_bytes()+ts2.row_bytes()+ts3.row_bytes()+
+    ts4.row_bytes()+cutsq.row_bytes()+
+    map.row_bytes()+elem2param.row_bytes()+_zetaij.row_bytes();
+  return 0;
+}
+
+template <class numtyp, class acctyp>
+void TersoffMT::clear() {
+  if (!_allocated)
+    return;
+  _allocated=false;
+
+  ts1.clear();
+  ts2.clear();
+  ts3.clear();
+  ts4.clear();
+  ts5.clear();
+  cutsq.clear();
+  map.clear();
+  elem2param.clear();
+  _zetaij.clear();
+
+  k_zeta.clear();
+
+  this->clear_atomic();
+}
+
+template <class numtyp, class acctyp>
+double TersoffMT::host_memory_usage() const {
+  return this->host_memory_usage_atomic()+sizeof(TersoffMod<numtyp,acctyp>);
+}
+
+#define KTHREADS this->_threads_per_atom
+#define JTHREADS this->_threads_per_atom
+// ---------------------------------------------------------------------------
+// Copy nbor list from host if necessary and then calculate forces, virials,..
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+void TersoffMT::compute(const int f_ago, const int nlocal, const int nall,
+                       const int nlist, double **host_x, int *host_type,
+                       int *ilist, int *numj, int **firstneigh,
+                       const bool eflag, const bool vflag, const bool eatom,
+                       const bool vatom, int &host_start,
+                       const double cpu_time, bool &success) {
+  this->acc_timers();
+  if (nlist==0) {
+    host_start=0;
+    // Make sure textures are correct if realloc by a different hybrid style
+    this->resize_atom(0,nall,success);
+    this->zero_timers();
+    return;
+  }
+
+  int ago=this->hd_balancer.ago_first(f_ago);
+  int inum=this->hd_balancer.balance(ago,nlocal,cpu_time);
+  this->ans->inum(inum);
+  #ifdef THREE_CONCURRENT
+  this->ans2->inum(inum);
+  #endif
+  host_start=inum;
+
+  if (ago==0) {
+    this->reset_nbors(nall, inum, nlist, ilist, numj, firstneigh, success);
+    if (!success)
+      return;
+    _max_nbors = this->nbor->max_nbor_loop(nlist,numj,ilist);
+  }
+
+  this->atom->cast_x_data(host_x,host_type);
+  this->hd_balancer.start_timer();
+  this->atom->add_x_data(host_x,host_type);
+
+  // re-allocate zetaij if necessary
+  if (nall*_max_nbors > _zetaij.cols()) {
+    int _nmax=static_cast<int>(static_cast<double>(nall)*1.10);
+    _zetaij.resize(_max_nbors*_nmax);
+  }
+
+  int _eflag;
+  if (eflag)
+    _eflag=1;
+  else
+    _eflag=0;
+
+  int ainum=nall;
+  int nbor_pitch=this->nbor->nbor_pitch();
+  int BX=this->block_pair();
+  int GX=static_cast<int>(ceil(static_cast<double>(ainum)/
+                               (BX/(JTHREADS*KTHREADS))));
+
+  this->k_zeta.set_size(GX,BX);
+  this->k_zeta.run(&this->atom->x, &ts1, &ts2, &ts3, &ts4, &ts5, &cutsq,
+                   &map, &elem2param, &_nelements, &_nparams, &_zetaij,
+                   &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                   &_eflag, &nall, &ainum, &nbor_pitch, &this->_threads_per_atom);
+
+  int evatom=0;
+  if (eatom || vatom)
+    evatom=1;
+  #ifdef THREE_CONCURRENT
+  this->ucl_device->sync();
+  #endif
+  loop(eflag,vflag,evatom);
+  this->ans->copy_answers(eflag,vflag,eatom,vatom,ilist);
+  this->device->add_ans_object(this->ans);
+  #ifdef THREE_CONCURRENT
+  this->ans2->copy_answers(eflag,vflag,eatom,vatom,ilist);
+  this->device->add_ans_object(this->ans2);
+  #endif
+  this->hd_balancer.stop_timer();
+}
+
+// ---------------------------------------------------------------------------
+// Reneighbor on GPU if necessary and then compute forces, virials, energies
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+int ** TersoffMT::compute(const int ago, const int inum_full,
+                         const int nall, double **host_x, int *host_type,
+                         double *sublo, double *subhi, tagint *tag,
+                         int **nspecial, tagint **special, const bool eflag,
+                         const bool vflag, const bool eatom,
+                         const bool vatom, int &host_start,
+                         int **ilist, int **jnum,
+                         const double cpu_time, bool &success) {
+  this->acc_timers();
+
+  if (inum_full==0) {
+    host_start=0;
+    // Make sure textures are correct if realloc by a different hybrid style
+    this->resize_atom(0,nall,success);
+    this->zero_timers();
+    return NULL;
+  }
+
+  this->hd_balancer.balance(cpu_time);
+  int inum=this->hd_balancer.get_gpu_count(ago,inum_full);
+  this->ans->inum(inum);
+  #ifdef THREE_CONCURRENT
+  this->ans2->inum(inum);
+  #endif
+  host_start=inum;
+
+  // Build neighbor list on GPU if necessary
+  if (ago==0) {
+    _max_nbors = this->build_nbor_list(inum, inum_full-inum, nall, host_x, host_type,
+                    sublo, subhi, tag, nspecial, special, success);
+    if (!success)
+      return NULL;
+    this->hd_balancer.start_timer();
+  } else {
+    this->atom->cast_x_data(host_x,host_type);
+    this->hd_balancer.start_timer();
+    this->atom->add_x_data(host_x,host_type);
+  }
+  *ilist=this->nbor->host_ilist.begin();
+  *jnum=this->nbor->host_acc.begin();
+
+  // re-allocate zetaij if necessary
+  if (nall*_max_nbors > _zetaij.cols()) {
+    int _nmax=static_cast<int>(static_cast<double>(nall)*1.10);
+    _zetaij.resize(_max_nbors*_nmax);
+  }
+
+  int _eflag;
+  if (eflag)
+    _eflag=1;
+  else
+    _eflag=0;
+
+  int ainum=nall;
+  int nbor_pitch=this->nbor->nbor_pitch();
+  int BX=this->block_pair();
+  int GX=static_cast<int>(ceil(static_cast<double>(ainum)/
+                               (BX/(JTHREADS*KTHREADS))));
+
+  this->k_zeta.set_size(GX,BX);
+  this->k_zeta.run(&this->atom->x, &ts1, &ts2, &ts3, &ts4, &ts5, &cutsq,
+                   &map, &elem2param, &_nelements, &_nparams, &_zetaij,
+                   &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                   &_eflag, &nall, &ainum, &nbor_pitch, &this->_threads_per_atom);
+
+  int evatom=0;
+  if (eatom || vatom)
+    evatom=1;
+  #ifdef THREE_CONCURRENT
+  this->ucl_device->sync();
+  #endif
+  loop(eflag,vflag,evatom);
+  this->ans->copy_answers(eflag,vflag,eatom,vatom);
+  this->device->add_ans_object(this->ans);
+  #ifdef THREE_CONCURRENT
+  this->ans2->copy_answers(eflag,vflag,eatom,vatom);
+  this->device->add_ans_object(this->ans2);
+  #endif
+  this->hd_balancer.stop_timer();
+
+  return this->nbor->host_jlist.begin()-host_start;
+}
+
+// ---------------------------------------------------------------------------
+// Calculate energies, forces, and torques
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+void TersoffMT::loop(const bool _eflag, const bool _vflag, const int evatom) {
+  // Compute the block size and grid size to keep all cores busy
+  int BX=this->block_pair();
+  int eflag, vflag;
+  if (_eflag)
+    eflag=1;
+  else
+    eflag=0;
+
+  if (_vflag)
+    vflag=1;
+  else
+    vflag=0;
+
+  int ainum=this->ans->inum();
+  int nbor_pitch=this->nbor->nbor_pitch();
+  int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
+                               (BX/this->_threads_per_atom)));
+
+  this->time_pair.start();
+  this->k_pair.set_size(GX,BX);
+  this->k_pair.run(&this->atom->x, &ts1, &ts2, &cutsq,
+                   &map, &elem2param, &_nelements, &_nparams,
+                   &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                   &this->ans->force, &this->ans->engv,
+                   &eflag, &vflag, &ainum, &nbor_pitch,
+                   &this->_threads_per_atom);
+
+  BX=this->block_size();
+  GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
+                           (BX/(KTHREADS*JTHREADS))));
+  this->k_three_center.set_size(GX,BX);
+  this->k_three_center.run(&this->atom->x, &ts1, &ts2, &ts4, &ts5, &cutsq,
+                           &map, &elem2param, &_nelements, &_nparams, &_zetaij,
+                           &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                           &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum,
+                           &nbor_pitch, &this->_threads_per_atom, &evatom);
+
+  Answer<numtyp,acctyp> *end_ans;
+  #ifdef THREE_CONCURRENT
+  end_ans=this->ans2;
+  #else
+  end_ans=this->ans;
+  #endif
+  if (evatom!=0) {
+    this->k_three_end_vatom.set_size(GX,BX);
+    this->k_three_end_vatom.run(&this->atom->x, &ts1, &ts2, &ts4, &ts5, &cutsq,
+                          &map, &elem2param, &_nelements, &_nparams, &_zetaij,
+                          &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                          &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum,
+                          &nbor_pitch, &this->_threads_per_atom);
+
+  } else {
+    this->k_three_end.set_size(GX,BX);
+    this->k_three_end.run(&this->atom->x, &ts1, &ts2, &ts4, &ts5, &cutsq,
+                          &map, &elem2param, &_nelements, &_nparams, &_zetaij,
+                          &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                          &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum,
+                          &nbor_pitch, &this->_threads_per_atom);
+  }
+
+  this->time_pair.stop();
+}
+
+template class TersoffMod<PRECISION,ACC_PRECISION>;
+
diff --git a/lib/gpu/lal_tersoff_mod.cu b/lib/gpu/lal_tersoff_mod.cu
new file mode 100644
index 0000000000..ba4ad32005
--- /dev/null
+++ b/lib/gpu/lal_tersoff_mod.cu
@@ -0,0 +1,1070 @@
+// **************************************************************************
+//                               tersoff_mod.cu
+//                             -------------------
+//                              Trung Dac Nguyen
+//
+//  Device code for acceleration of the tersoff pair style
+//
+// __________________________________________________________________________
+//    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+// __________________________________________________________________________
+//
+//       begin                :
+//       email                : ndactrung@gmail.com
+// ***************************************************************************/
+
+#ifdef NV_KERNEL
+#include "lal_tersoff_mod_extra.h"
+
+#ifndef _DOUBLE_DOUBLE
+texture<float4> pos_tex;
+texture<float4> ts1_tex;
+texture<float4> ts2_tex;
+texture<float4> ts3_tex;
+texture<float4> ts4_tex;
+texture<float4> ts5_tex;
+#else
+texture<int4,1> pos_tex;
+texture<int4> ts1_tex;
+texture<int4> ts2_tex;
+texture<int4> ts3_tex;
+texture<int4> ts4_tex;
+texture<int4> ts5_tex;
+#endif
+
+#else
+#define pos_tex x_
+#define ts1_tex ts1
+#define ts2_tex ts2
+#define ts3_tex ts3
+#define ts4_tex ts4
+#define ts5_tex ts5
+#endif
+
+//#define THREE_CONCURRENT
+
+#define TWOTHIRD (numtyp)0.66666666666666666667
+
+#define zeta_idx(nbor_mem, packed_mem, nbor_pitch, n_stride, t_per_atom,    \
+                 i, nbor_j, offset_j, idx)                                  \
+  if (nbor_mem==packed_mem) {                                               \
+    int jj = (nbor_j-offset_j-2*nbor_pitch)/n_stride;                       \
+    idx = jj*n_stride + i*t_per_atom + offset_j;                            \
+  } else {                                                                  \
+    idx = nbor_j;                                                           \
+  }
+
+#if (ARCH < 300)
+
+#define store_answers_p(f, energy, virial, ii, inum, tid, t_per_atom,       \
+                        offset, eflag, vflag, ans, engv)                    \
+  if (t_per_atom>1) {                                                       \
+    __local acctyp red_acc[6][BLOCK_PAIR];                                  \
+    red_acc[0][tid]=f.x;                                                    \
+    red_acc[1][tid]=f.y;                                                    \
+    red_acc[2][tid]=f.z;                                                    \
+    red_acc[3][tid]=energy;                                                 \
+    for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                         \
+      if (offset < s) {                                                     \
+        for (int r=0; r<4; r++)                                             \
+          red_acc[r][tid] += red_acc[r][tid+s];                             \
+      }                                                                     \
+    }                                                                       \
+    f.x=red_acc[0][tid];                                                    \
+    f.y=red_acc[1][tid];                                                    \
+    f.z=red_acc[2][tid];                                                    \
+    energy=red_acc[3][tid];                                                 \
+    if (vflag>0) {                                                          \
+      for (int r=0; r<6; r++)                                               \
+        red_acc[r][tid]=virial[r];                                          \
+      for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                       \
+        if (offset < s) {                                                   \
+          for (int r=0; r<6; r++)                                           \
+            red_acc[r][tid] += red_acc[r][tid+s];                           \
+        }                                                                   \
+      }                                                                     \
+      for (int r=0; r<6; r++)                                               \
+        virial[r]=red_acc[r][tid];                                          \
+    }                                                                       \
+  }                                                                         \
+  if (offset==0) {                                                          \
+    int ei=ii;                                                              \
+    if (eflag>0) {                                                          \
+      engv[ei]+=energy*(acctyp)0.5;                                         \
+      ei+=inum;                                                             \
+    }                                                                       \
+    if (vflag>0) {                                                          \
+      for (int i=0; i<6; i++) {                                             \
+        engv[ei]+=virial[i]*(acctyp)0.5;                                    \
+        ei+=inum;                                                           \
+      }                                                                     \
+    }                                                                       \
+    acctyp4 old=ans[ii];                                                    \
+    old.x+=f.x;                                                             \
+    old.y+=f.y;                                                             \
+    old.z+=f.z;                                                             \
+    ans[ii]=old;                                                            \
+  }
+
+#define store_zeta(z, tid, t_per_atom, offset)                              \
+  if (t_per_atom>1) {                                                       \
+    __local acctyp red_acc[BLOCK_PAIR];                                     \
+    red_acc[tid]=z;                                                         \
+    for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                         \
+      if (offset < s) {                                                     \
+        red_acc[tid] += red_acc[tid+s];                                     \
+      }                                                                     \
+    }                                                                       \
+    z=red_acc[tid];                                                         \
+  }
+
+#else
+
+#define store_answers_p(f, energy, virial, ii, inum, tid, t_per_atom,       \
+                        offset, eflag, vflag, ans, engv)                    \
+  if (t_per_atom>1) {                                                       \
+    for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                         \
+      f.x += shfl_xor(f.x, s, t_per_atom);                                  \
+      f.y += shfl_xor(f.y, s, t_per_atom);                                  \
+      f.z += shfl_xor(f.z, s, t_per_atom);                                  \
+      energy += shfl_xor(energy, s, t_per_atom);                            \
+    }                                                                       \
+    if (vflag>0) {                                                          \
+      for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                       \
+          for (int r=0; r<6; r++)                                           \
+            virial[r] += shfl_xor(virial[r], s, t_per_atom);                \
+      }                                                                     \
+    }                                                                       \
+  }                                                                         \
+  if (offset==0) {                                                          \
+    int ei=ii;                                                              \
+    if (eflag>0) {                                                          \
+      engv[ei]+=energy*(acctyp)0.5;                                         \
+      ei+=inum;                                                             \
+    }                                                                       \
+    if (vflag>0) {                                                          \
+      for (int i=0; i<6; i++) {                                             \
+        engv[ei]+=virial[i]*(acctyp)0.5;                                    \
+        ei+=inum;                                                           \
+      }                                                                     \
+    }                                                                       \
+    acctyp4 old=ans[ii];                                                    \
+    old.x+=f.x;                                                             \
+    old.y+=f.y;                                                             \
+    old.z+=f.z;                                                             \
+    ans[ii]=old;                                                            \
+  }
+
+#define store_zeta(z, tid, t_per_atom, offset)                              \
+  if (t_per_atom>1) {                                                       \
+    for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                         \
+      z += shfl_xor(z, s, t_per_atom);                                      \
+    }                                                                       \
+  }
+
+#endif
+
+// Tersoff is currently used for 3 elements at most: 3*3*3 = 27 entries
+// while the block size should never be less than 32.
+// SHARED_SIZE = 32 for now to reduce the pressure on the shared memory per block
+// must be increased if there will be more than 3 elements in the future.
+
+#define SHARED_SIZE 32
+
+__kernel void k_tersoff_mod_zeta(const __global numtyp4 *restrict x_,
+                             const __global numtyp4 *restrict ts1_in,
+                             const __global numtyp4 *restrict ts2_in,
+                             const __global numtyp4 *restrict ts3_in,
+                             const __global numtyp4 *restrict ts4_in,
+                             const __global numtyp4 *restrict ts5_in,
+                             const __global numtyp *restrict cutsq,
+                             const __global int *restrict map,
+                             const __global int *restrict elem2param,
+                             const int nelements, const int nparams,
+                             __global acctyp4 * zetaij,
+                             const __global int * dev_nbor,
+                             const __global int * dev_packed,
+                             const int eflag, const int nall, const int inum,
+                             const int nbor_pitch, const int t_per_atom) {
+  __local int tpa_sq,n_stride;
+  tpa_sq = fast_mul(t_per_atom,t_per_atom);
+
+  int tid, ii, offset;
+  atom_info(tpa_sq,ii,tid,offset);
+
+  // must be increased if there will be more than 3 elements in the future.
+  __local numtyp4 ts1[SHARED_SIZE];
+  __local numtyp4 ts2[SHARED_SIZE];
+  __local numtyp4 ts3[SHARED_SIZE];
+  __local numtyp4 ts4[SHARED_SIZE];
+  __local numtyp4 ts5[SHARED_SIZE];
+  if (tid<nparams) {
+    ts1[tid]=ts1_in[tid];
+    ts2[tid]=ts2_in[tid];
+    ts3[tid]=ts3_in[tid];
+    ts4[tid]=ts4_in[tid];
+    ts5[tid]=ts5_in[tid];
+  }
+
+  acctyp z = (acctyp)0;
+
+  __syncthreads();
+
+  if (ii<nall) {
+    int nbor_j, nbor_end;
+    int i, numj;
+
+    int offset_j=offset/t_per_atom;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
+              n_stride,nbor_end,nbor_j);
+    int offset_k=tid & (t_per_atom-1);
+    int nborj_start = nbor_j;
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype=ix.w;
+    itype=map[itype];
+
+    for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
+
+      int j=dev_packed[nbor_j];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype=jx.w;
+      jtype=map[jtype];
+      int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
+
+      // Compute rij
+      numtyp4 delr1, delr2;
+      delr1.x = jx.x-ix.x;
+      delr1.y = jx.y-ix.y;
+      delr1.z = jx.z-ix.z;
+      numtyp rsq1 = delr1.x*delr1.x+delr1.y*delr1.y+delr1.z*delr1.z;
+
+      if (rsq1 > cutsq[ijparam]) continue;
+
+      // compute zeta_ij
+      z = (numtyp)0;
+
+      int nbor_k = nborj_start-offset_j+offset_k;
+      for ( ; nbor_k < nbor_end; nbor_k+=n_stride) {
+        int k=dev_packed[nbor_k];
+        k &= NEIGHMASK;
+
+        if (k == j) continue;
+
+        numtyp4 kx; fetch4(kx,k,pos_tex); //x_[k];
+        int ktype=kx.w;
+        ktype=map[ktype];
+        int ijkparam=elem2param[itype*nelements*nelements+jtype*nelements+ktype];
+
+        // Compute rik
+        delr2.x = kx.x-ix.x;
+        delr2.y = kx.y-ix.y;
+        delr2.z = kx.z-ix.z;
+        numtyp rsq2 = delr2.x*delr2.x+delr2.y*delr2.y+delr2.z*delr2.z;
+
+        if (rsq2 > cutsq[ijkparam]) continue;
+
+        numtyp4 ts1_ijkparam = ts1[ijkparam]; //fetch4(ts1_ijkparam,ijkparam,ts1_tex);
+        numtyp ijkparam_lam3 = ts1_ijkparam.z;
+        numtyp ijkparam_powermint = ts1_ijkparam.w;
+        numtyp4 ts2_ijkparam = ts2[ijkparam]; //fetch4(ts2_ijkparam,ijkparam,ts2_tex);
+        numtyp ijkparam_bigr = ts2_ijkparam.z;
+        numtyp ijkparam_bigd = ts2_ijkparam.w;
+        numtyp4 ts4_ijkparam = ts4[ijkparam]; //fetch4(ts4_ijkparam,ijkparam,ts4_tex);
+        numtyp ijkparam_c1 = ts4_ijkparam.x;
+        numtyp ijkparam_c2 = ts4_ijkparam.y;
+        numtyp ijkparam_c3 = ts4_ijkparam.z;
+        numtyp ijkparam_c4 = ts4_ijkparam.w;
+        numtyp4 ts5_ijkparam = ts5[ijkparam]; //fetch4(ts4_ijkparam,ijkparam,ts4_tex);
+        numtyp ijkparam_c5 = ts5_ijkparam.x;
+        numtyp ijkparam_h = ts5_ijkparam.y;
+        z += zeta(ijkparam_powermint, ijkparam_lam3, ijkparam_bigr, ijkparam_bigd,
+                  ijkparam_h, ijkparam_c1, ijkparam_c2, ijkparam_c3, ijkparam_c4,
+                  ijkparam_c5, rsq1, rsq2, delr1, delr2);
+      }
+
+      //int jj = (nbor_j-offset_j-2*nbor_pitch)/n_stride;
+      //int idx = jj*n_stride + i*t_per_atom + offset_j;
+      int idx;
+      zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
+               i, nbor_j, offset_j, idx);
+      store_zeta(z, tid, t_per_atom, offset_k);
+
+      numtyp4 ts1_ijparam = ts1[ijparam]; //fetch4(ts1_ijparam,ijparam,ts1_tex);
+      numtyp ijparam_lam2 = ts1_ijparam.y;
+      numtyp4 ts2_ijparam = ts2[ijparam]; //fetch4(ts2_ijparam,ijparam,ts2_tex);
+      numtyp ijparam_bigb = ts2_ijparam.y;
+      numtyp ijparam_bigr = ts2_ijparam.z;
+      numtyp ijparam_bigd = ts2_ijparam.w;
+      numtyp4 ts3_ijparam = ts3[ijparam]; //fetch4(ts3_ijparam,ijparam,ts3_tex);
+      numtyp ijparam_beta = ts3_ijparam.x;
+      numtyp ijparam_powern = ts3_ijparam.y;
+      numtyp ijparam_powern_del = ts3_ijparam.z;
+      numtyp ijparam_ca1 = ts3_ijparam.w;
+      numtyp ijparam_ca4 = ucl_recip(ts3_ijparam.w);
+
+      if (offset_k == 0) {
+        numtyp fpfeng[4];
+        force_zeta(ijparam_bigb, ijparam_bigr, ijparam_bigd, ijparam_lam2,
+                   ijparam_beta, ijparam_powern, ijparam_powern_del, ijparam_ca1,
+                   ijparam_ca4, rsq1, z, eflag, fpfeng);
+        acctyp4 zij;
+        zij.x = fpfeng[0];
+        zij.y = fpfeng[1];
+        zij.z = fpfeng[2];
+        zij.w = z;
+        zetaij[idx] = zij;
+      }
+
+    } // for nbor
+  } // if ii
+}
+
+__kernel void k_tersoff_mod_repulsive(const __global numtyp4 *restrict x_,
+                                  const __global numtyp4 *restrict ts1_in,
+                                  const __global numtyp4 *restrict ts2_in,
+                                  const __global numtyp *restrict cutsq,
+                                  const __global int *restrict map,
+                                  const __global int *restrict elem2param,
+                                  const int nelements, const int nparams,
+                                  const __global int * dev_nbor,
+                                  const __global int * dev_packed,
+                                  __global acctyp4 *restrict ans,
+                                  __global acctyp *restrict engv,
+                                  const int eflag, const int vflag,
+                                  const int inum, const int nbor_pitch,
+                                  const int t_per_atom) {
+  __local int n_stride;
+  int tid, ii, offset;
+  atom_info(t_per_atom,ii,tid,offset);
+
+  __local numtyp4 ts1[SHARED_SIZE];
+  __local numtyp4 ts2[SHARED_SIZE];
+  if (tid<nparams) {
+    ts1[tid]=ts1_in[tid];
+    ts2[tid]=ts2_in[tid];
+  }
+
+  acctyp energy=(acctyp)0;
+  acctyp4 f;
+  f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+  acctyp virial[6];
+  for (int i=0; i<6; i++)
+    virial[i]=(acctyp)0;
+
+  __syncthreads();
+
+  if (ii<inum) {
+    int nbor, nbor_end;
+    int i, numj;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
+              n_stride,nbor_end,nbor);
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype=ix.w;
+    itype=map[itype];
+
+    for ( ; nbor<nbor_end; nbor+=n_stride) {
+
+      int j=dev_packed[nbor];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype=jx.w;
+      jtype=map[jtype];
+      int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
+
+      // Compute r12
+
+      numtyp delx = ix.x-jx.x;
+      numtyp dely = ix.y-jx.y;
+      numtyp delz = ix.z-jx.z;
+      numtyp rsq = delx*delx+dely*dely+delz*delz;
+
+      if (rsq<cutsq[ijparam]) {
+        numtyp feng[2];
+        numtyp ijparam_lam1 = ts1[ijparam].x;
+        numtyp4 ts2_ijparam = ts2[ijparam];
+        numtyp ijparam_biga = ts2_ijparam.x;
+        numtyp ijparam_bigr = ts2_ijparam.z;
+        numtyp ijparam_bigd = ts2_ijparam.w;
+
+        repulsive(ijparam_bigr, ijparam_bigd, ijparam_lam1, ijparam_biga,
+                  rsq, eflag, feng);
+
+        numtyp force = feng[0];
+        f.x+=delx*force;
+        f.y+=dely*force;
+        f.z+=delz*force;
+
+        if (eflag>0)
+          energy+=feng[1];
+        if (vflag>0) {
+          virial[0] += delx*delx*force;
+          virial[1] += dely*dely*force;
+          virial[2] += delz*delz*force;
+          virial[3] += delx*dely*force;
+          virial[4] += delx*delz*force;
+          virial[5] += dely*delz*force;
+        }
+      }
+    } // for nbor
+
+    store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
+                  ans,engv);
+  } // if ii
+
+}
+
+__kernel void k_tersoff_mod_three_center(const __global numtyp4 *restrict x_,
+                                     const __global numtyp4 *restrict ts1_in,
+                                     const __global numtyp4 *restrict ts2_in,
+                                     const __global numtyp4 *restrict ts4_in,
+                                     const __global numtyp4 *restrict ts5_in,
+                                     const __global numtyp *restrict cutsq,
+                                     const __global int *restrict map,
+                                     const __global int *restrict elem2param,
+                                     const int nelements, const int nparams,
+                                     const __global acctyp4 *restrict zetaij,
+                                     const __global int * dev_nbor,
+                                     const __global int * dev_packed,
+                                     __global acctyp4 *restrict ans,
+                                     __global acctyp *restrict engv,
+                                     const int eflag, const int vflag,
+                                     const int inum,  const int nbor_pitch,
+                                     const int t_per_atom, const int evatom) {
+  __local int tpa_sq, n_stride;
+  tpa_sq=fast_mul(t_per_atom,t_per_atom);
+  numtyp lam3, powermint, bigr, bigd, c1, c2, c3, c4, c5, h;
+
+  int tid, ii, offset;
+  atom_info(tpa_sq,ii,tid,offset); // offset ranges from 0 to tpa_sq-1
+
+  __local numtyp4 ts1[SHARED_SIZE];
+  __local numtyp4 ts2[SHARED_SIZE];
+  __local numtyp4 ts4[SHARED_SIZE];
+  __local numtyp4 ts5[SHARED_SIZE];
+  if (tid<nparams) {
+    ts1[tid]=ts1_in[tid];
+    ts2[tid]=ts2_in[tid];
+    ts4[tid]=ts4_in[tid];
+    ts5[tid]=ts5_in[tid];
+  }
+
+  acctyp energy=(acctyp)0;
+  acctyp4 f;
+  f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+  acctyp virial[6];
+  for (int i=0; i<6; i++)
+    virial[i]=(acctyp)0;
+  numtyp tpainv = ucl_recip((numtyp)t_per_atom);
+
+  __syncthreads();
+
+  if (ii<inum) {
+    int i, numj, nbor_j, nbor_end;
+
+    int offset_j=offset/t_per_atom;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
+              n_stride,nbor_end,nbor_j);
+    int offset_k=tid & (t_per_atom-1);
+    int nborj_start = nbor_j;
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype=ix.w;
+    itype=map[itype];
+
+    for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
+
+      int j=dev_packed[nbor_j];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype=jx.w;
+      jtype=map[jtype];
+      int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
+
+      // Compute r12
+      numtyp delr1[3];
+      delr1[0] = jx.x-ix.x;
+      delr1[1] = jx.y-ix.y;
+      delr1[2] = jx.z-ix.z;
+      numtyp rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
+
+      if (rsq1 > cutsq[ijparam]) continue;
+      numtyp r1 = ucl_sqrt(rsq1);
+      numtyp r1inv = ucl_rsqrt(rsq1);
+
+      // look up for zeta_ij
+
+      //int jj = (nbor_j-offset_j-2*nbor_pitch) / n_stride;
+      //int idx = jj*n_stride + i*t_per_atom + offset_j;
+      int idx;
+      zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
+               i, nbor_j, offset_j, idx);
+      acctyp4 zeta_ij = zetaij[idx]; // fetch(zeta_ij,idx,zeta_tex);
+      numtyp force = zeta_ij.x*tpainv;
+      numtyp prefactor = zeta_ij.y;
+      f.x += delr1[0]*force;
+      f.y += delr1[1]*force;
+      f.z += delr1[2]*force;
+
+      if (eflag>0) {
+        energy+=zeta_ij.z*tpainv;
+      }
+      if (vflag>0) {
+        numtyp mforce = -force;
+        virial[0] += delr1[0]*delr1[0]*mforce;
+        virial[1] += delr1[1]*delr1[1]*mforce;
+        virial[2] += delr1[2]*delr1[2]*mforce;
+        virial[3] += delr1[0]*delr1[1]*mforce;
+        virial[4] += delr1[0]*delr1[2]*mforce;
+        virial[5] += delr1[1]*delr1[2]*mforce;
+      }
+
+      int nbor_k=nborj_start-offset_j+offset_k;
+      for ( ; nbor_k<nbor_end; nbor_k+=n_stride) {
+        int k=dev_packed[nbor_k];
+        k &= NEIGHMASK;
+
+        if (j == k) continue;
+
+        numtyp4 kx; fetch4(kx,k,pos_tex);
+        int ktype=kx.w;
+        ktype=map[ktype];
+        int ijkparam=elem2param[itype*nelements*nelements+jtype*nelements+ktype];
+
+        numtyp delr2[3];
+        delr2[0] = kx.x-ix.x;
+        delr2[1] = kx.y-ix.y;
+        delr2[2] = kx.z-ix.z;
+        numtyp rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+
+        if (rsq2 > cutsq[ijkparam]) continue;
+        numtyp r2 = ucl_sqrt(rsq2);
+        numtyp r2inv = ucl_rsqrt(rsq2);
+
+        numtyp fi[3], fj[3], fk[3];
+        numtyp4 ts1_ijkparam = ts1[ijkparam]; //fetch4(ts1_ijkparam,ijkparam,ts1_tex);
+        lam3 = ts1_ijkparam.z;
+        powermint = ts1_ijkparam.w;
+        numtyp4 ts2_ijkparam = ts2[ijkparam]; //fetch4(ts2_ijkparam,ijkparam,ts2_tex);
+        bigr = ts2_ijkparam.z;
+        bigd = ts2_ijkparam.w;
+        numtyp4 ts4_ijkparam = ts4[ijkparam]; //fetch4(ts4_ijkparam,ijkparam,ts4_tex);
+        c1 = ts4_ijkparam.x;
+        c2 = ts4_ijkparam.y;
+        c3 = ts4_ijkparam.z;
+        c4 = ts4_ijkparam.w;
+        numtyp4 ts5_ijkparam = ts5[ijkparam]; //fetch4(ts5_ijkparam,ijkparam,ts5_tex);
+        c5 = ts5_ijkparam.x;
+        h = ts5_ijkparam.y;
+        if (vflag>0)
+          attractive(bigr, bigd, powermint, lam3, h, c1, c2, c3, c4, c5,
+                     prefactor, r1, r1inv, r2, r2inv, delr1, delr2, fi, fj, fk);
+        else
+          attractive_fi(bigr, bigd, powermint, lam3, h, c1, c2, c3, c4, c5,
+                        prefactor, r1, r1inv, r2, r2inv, delr1, delr2, fi);
+        f.x += fi[0];
+        f.y += fi[1];
+        f.z += fi[2];
+
+        if (vflag>0) {
+          acctyp v[6];
+          numtyp pre = (numtyp)2.0;
+          if (evatom==1) pre = TWOTHIRD;
+          v[0] = pre*(delr1[0]*fj[0] + delr2[0]*fk[0]);
+          v[1] = pre*(delr1[1]*fj[1] + delr2[1]*fk[1]);
+          v[2] = pre*(delr1[2]*fj[2] + delr2[2]*fk[2]);
+          v[3] = pre*(delr1[0]*fj[1] + delr2[0]*fk[1]);
+          v[4] = pre*(delr1[0]*fj[2] + delr2[0]*fk[2]);
+          v[5] = pre*(delr1[1]*fj[2] + delr2[1]*fk[2]);
+
+          virial[0] += v[0]; virial[1] += v[1]; virial[2] += v[2];
+          virial[3] += v[3]; virial[4] += v[4]; virial[5] += v[5];
+        }
+      } // nbor_k
+    } // for nbor_j
+
+    store_answers_p(f,energy,virial,ii,inum,tid,tpa_sq,
+                     offset,eflag,vflag,ans,engv);
+  } // if ii
+}
+
+__kernel void k_tersoff_mod_three_end(const __global numtyp4 *restrict x_,
+                                  const __global numtyp4 *restrict ts1_in,
+                                  const __global numtyp4 *restrict ts2_in,
+                                  const __global numtyp4 *restrict ts4_in,
+                                  const __global numtyp4 *restrict ts5_in,
+                                  const __global numtyp *restrict cutsq,
+                                  const __global int *restrict map,
+                                  const __global int *restrict elem2param,
+                                  const int nelements, const int nparams,
+                                  const __global acctyp4 *restrict zetaij,
+                                  const __global int * dev_nbor,
+                                  const __global int * dev_packed,
+                                  __global acctyp4 *restrict ans,
+                                  __global acctyp *restrict engv,
+                                  const int eflag, const int vflag,
+                                  const int inum,  const int nbor_pitch,
+                                  const int t_per_atom) {
+  __local int tpa_sq, n_stride;
+  tpa_sq=fast_mul(t_per_atom,t_per_atom);
+  numtyp lam3, powermint, bigr, bigd, c1, c2, c3, c4, c5, h;
+
+  int tid, ii, offset;
+  atom_info(tpa_sq,ii,tid,offset);
+
+  __local numtyp4 ts1[SHARED_SIZE];
+  __local numtyp4 ts2[SHARED_SIZE];
+  __local numtyp4 ts4[SHARED_SIZE];
+  __local numtyp4 ts5[SHARED_SIZE];
+  if (tid<nparams) {
+    ts1[tid]=ts1_in[tid];
+    ts2[tid]=ts2_in[tid];
+    ts4[tid]=ts4_in[tid];
+    ts5[tid]=ts5_in[tid];
+  }
+
+  acctyp energy=(acctyp)0;
+  acctyp4 f;
+  f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+  acctyp virial[6];
+  for (int i=0; i<6; i++)
+    virial[i]=(acctyp)0;
+
+  __local int red_acc[2*BLOCK_PAIR];
+
+  __syncthreads();
+
+  if (ii<inum) {
+    int i, numj, nbor_j, nbor_end, k_end;
+
+    int offset_j=offset/t_per_atom;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
+              n_stride,nbor_end,nbor_j);
+    int offset_k=tid & (t_per_atom-1);
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype=ix.w;
+    itype=map[itype];
+
+    numtyp tpainv = ucl_recip((numtyp)t_per_atom);
+    for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
+
+      int j=dev_packed[nbor_j];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype=jx.w;
+      jtype=map[jtype];
+      int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
+
+      // Compute r12
+      numtyp delr1[3];
+      delr1[0] = jx.x-ix.x;
+      delr1[1] = jx.y-ix.y;
+      delr1[2] = jx.z-ix.z;
+      numtyp rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
+
+      if (rsq1 > cutsq[ijparam]) continue;
+
+      numtyp mdelr1[3];
+      mdelr1[0] = -delr1[0];
+      mdelr1[1] = -delr1[1];
+      mdelr1[2] = -delr1[2];
+
+      int nbor_k=j+nbor_pitch;
+      int numk=dev_nbor[nbor_k];
+      if (dev_nbor==dev_packed) {
+        nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1);
+        k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1));
+        nbor_k+=offset_k;
+      } else {
+        nbor_k+=nbor_pitch;
+        nbor_k=dev_nbor[nbor_k];
+        k_end=nbor_k+numk;
+        nbor_k+=offset_k;
+      }
+      int nbork_start = nbor_k;
+
+      // look up for zeta_ji: find i in the j's neighbor list
+      int m = tid / t_per_atom;
+      int ijnum = -1;
+      for ( ; nbor_k<k_end; nbor_k+=n_stride) {
+        int k=dev_packed[nbor_k];
+        k &= NEIGHMASK;
+        if (k == i) {
+          ijnum = nbor_k;
+          red_acc[2*m+0] = ijnum;
+          red_acc[2*m+1] = offset_k;
+          break;
+        }
+      }
+
+      numtyp r1 = ucl_sqrt(rsq1);
+      numtyp r1inv = ucl_rsqrt(rsq1);
+      int offset_kf;
+      if (ijnum >= 0) {
+        offset_kf = offset_k;
+      } else {
+        ijnum = red_acc[2*m+0];
+        offset_kf = red_acc[2*m+1];
+      }
+
+      //int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride;
+      //int idx = iix*n_stride + j*t_per_atom + offset_kf;
+      int idx;
+      zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
+               j, ijnum, offset_kf, idx);
+      acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex);
+      numtyp force = zeta_ji.x*tpainv;
+      numtyp prefactor_ji = zeta_ji.y;
+      f.x += delr1[0]*force;
+      f.y += delr1[1]*force;
+      f.z += delr1[2]*force;
+
+      if (eflag>0) {
+        energy+=zeta_ji.z*tpainv;
+      }
+      if (vflag>0) {
+        numtyp mforce = -force;
+        virial[0] += mdelr1[0]*mdelr1[0]*mforce;
+        virial[1] += mdelr1[1]*mdelr1[1]*mforce;
+        virial[2] += mdelr1[2]*mdelr1[2]*mforce;
+        virial[3] += mdelr1[0]*mdelr1[1]*mforce;
+        virial[4] += mdelr1[0]*mdelr1[2]*mforce;
+        virial[5] += mdelr1[1]*mdelr1[2]*mforce;
+      }
+
+      // attractive forces
+      for (nbor_k = nbork_start ; nbor_k<k_end; nbor_k+=n_stride) {
+        int k=dev_packed[nbor_k];
+        k &= NEIGHMASK;
+
+        if (k == i) continue;
+
+        numtyp4 kx; fetch4(kx,k,pos_tex);
+        int ktype=kx.w;
+        ktype=map[ktype];
+        int jikparam=elem2param[jtype*nelements*nelements+itype*nelements+ktype];
+
+        numtyp delr2[3];
+        delr2[0] = kx.x-jx.x;
+        delr2[1] = kx.y-jx.y;
+        delr2[2] = kx.z-jx.z;
+        numtyp rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+
+        if (rsq2 > cutsq[jikparam]) continue;
+        numtyp r2 = ucl_sqrt(rsq2);
+        numtyp r2inv = ucl_rsqrt(rsq2);
+        numtyp4 ts1_param, ts2_param, ts4_param, ts5_param;
+        numtyp fi[3];
+
+        ts1_param = ts1[jikparam]; //fetch4(ts1_jikparam,jikparam,ts1_tex);
+        lam3 = ts1_param.z;
+        powermint = ts1_param.w;
+        ts2_param = ts2[jikparam]; //fetch4(ts2_jikparam,jikparam,ts2_tex);
+        bigr = ts2_param.z;
+        bigd = ts2_param.w;
+        ts4_param = ts4[jikparam]; //fetch4(ts4_jikparam,jikparam,ts4_tex);
+        c1 = ts4_param.x;
+        c2 = ts4_param.y;
+        c3 = ts4_param.z;
+        c4 = ts4_param.w;
+        ts5_param = ts5[jikparam]; //fetch4(ts5_jikparam,jikparam,ts5_tex);
+        c5 = ts5_param.x;
+        h = ts5_param.y;
+        attractive_fj(bigr, bigd, powermint, lam3, h, c1, c2, c3, c4, c5,
+                      prefactor_ji, r1, r1inv, r2, r2inv, mdelr1, delr2, fi);
+        f.x += fi[0];
+        f.y += fi[1];
+        f.z += fi[2];
+
+        //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;
+        //int idx = kk*n_stride + j*t_per_atom + offset_k;
+        int idx;
+        zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
+                 j, nbor_k, offset_k, idx);
+        acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
+        numtyp prefactor_jk = zeta_jk.y;
+        int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype];
+        ts1_param = ts1[jkiparam]; //fetch4(ts1_jkiparam,jkiparam,ts1_tex);
+        lam3 = ts1_param.z;
+        powermint = ts1_param.w;
+        ts2_param = ts2[jkiparam]; //fetch4(ts2_jkiparam,jkiparam,ts2_tex);
+        bigr = ts2_param.z;
+        bigd = ts2_param.w;
+        ts4_param = ts4[jkiparam]; //fetch4(ts4_jkiparam,jkiparam,ts4_tex);
+        c1 = ts4_param.x;
+        c2 = ts4_param.y;
+        c3 = ts4_param.z;
+        c4 = ts4_param.w;
+        ts5_param = ts5[jkiparam]; //fetch4(ts5_ikiparam,jkiparam,ts5_tex);
+        c5 = ts5_param.x;
+        h = ts5_param.y;
+        attractive_fk(bigr, bigd, powermint, lam3, h, c1, c2, c3, c4, c5,
+                      prefactor_jk, r2, r2inv, r1, r1inv, delr2, mdelr1, fi);
+        f.x += fi[0];
+        f.y += fi[1];
+        f.z += fi[2];
+      } // for nbor_k
+    } // for nbor_j
+
+    #ifdef THREE_CONCURRENT
+    store_answers(f,energy,virial,ii,inum,tid,tpa_sq,offset,
+                  eflag,vflag,ans,engv);
+    #else
+    store_answers_p(f,energy,virial,ii,inum,tid,tpa_sq,offset,
+                    eflag,vflag,ans,engv);
+    #endif
+  } // if ii
+}
+
+__kernel void k_tersoff_mod_three_end_vatom(const __global numtyp4 *restrict x_,
+                                        const __global numtyp4 *restrict ts1_in,
+                                        const __global numtyp4 *restrict ts2_in,
+      	                                const __global numtyp4 *restrict ts4_in,
+      	                                const __global numtyp4 *restrict ts5_in,
+                                        const __global numtyp *restrict cutsq,
+                                        const __global int *restrict map,
+                                        const __global int *restrict elem2param,
+                                        const int nelements, const int nparams,
+                                        const __global acctyp4 *restrict zetaij,
+                                        const __global int * dev_nbor,
+                                        const __global int * dev_packed,
+                                        __global acctyp4 *restrict ans,
+                                        __global acctyp *restrict engv,
+                                        const int eflag, const int vflag,
+                                        const int inum,  const int nbor_pitch,
+                                        const int t_per_atom) {
+  __local int tpa_sq, n_stride;
+  tpa_sq=fast_mul(t_per_atom,t_per_atom);
+  numtyp lam3, powermint, bigr, bigd, c1, c2, c3, c4, c5, h;
+
+  int tid, ii, offset;
+  atom_info(tpa_sq,ii,tid,offset);
+
+  __local numtyp4 ts1[SHARED_SIZE];
+  __local numtyp4 ts2[SHARED_SIZE];
+  __local numtyp4 ts4[SHARED_SIZE];
+  __local numtyp4 ts5[SHARED_SIZE];
+  if (tid<nparams) {
+    ts1[tid]=ts1_in[tid];
+    ts2[tid]=ts2_in[tid];
+    ts4[tid]=ts4_in[tid];
+    ts5[tid]=ts5_in[tid];
+  }
+
+  acctyp energy=(acctyp)0;
+  acctyp4 f;
+  f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+  acctyp virial[6];
+  for (int i=0; i<6; i++)
+    virial[i]=(acctyp)0;
+
+  __local int red_acc[2*BLOCK_PAIR];
+
+  __syncthreads();
+
+  if (ii<inum) {
+    int i, numj, nbor_j, nbor_end, k_end;
+
+    int offset_j=offset/t_per_atom;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
+              n_stride,nbor_end,nbor_j);
+    int offset_k=tid & (t_per_atom-1);
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype=ix.w;
+    itype=map[itype];
+
+    numtyp tpainv = ucl_recip((numtyp)t_per_atom);
+    for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
+
+      int j=dev_packed[nbor_j];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype=jx.w;
+      jtype=map[jtype];
+      int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
+
+      // Compute r12
+      numtyp delr1[3];
+      delr1[0] = jx.x-ix.x;
+      delr1[1] = jx.y-ix.y;
+      delr1[2] = jx.z-ix.z;
+      numtyp rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
+
+      if (rsq1 > cutsq[ijparam]) continue;
+
+      numtyp mdelr1[3];
+      mdelr1[0] = -delr1[0];
+      mdelr1[1] = -delr1[1];
+      mdelr1[2] = -delr1[2];
+
+      int nbor_k=j+nbor_pitch;
+      int numk=dev_nbor[nbor_k];
+      if (dev_nbor==dev_packed) {
+        nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1);
+        k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1));
+        nbor_k+=offset_k;
+      } else {
+        nbor_k+=nbor_pitch;
+        nbor_k=dev_nbor[nbor_k];
+        k_end=nbor_k+numk;
+        nbor_k+=offset_k;
+      }
+      int nbork_start = nbor_k;
+
+      // look up for zeta_ji
+      int m = tid / t_per_atom;
+      int ijnum = -1;
+      for ( ; nbor_k<k_end; nbor_k+=n_stride) {
+        int k=dev_packed[nbor_k];
+        k &= NEIGHMASK;
+        if (k == i) {
+          ijnum = nbor_k;
+          red_acc[2*m+0] = ijnum;
+          red_acc[2*m+1] = offset_k;
+          break;
+        }
+      }
+
+      numtyp r1 = ucl_sqrt(rsq1);
+      numtyp r1inv = ucl_rsqrt(rsq1);
+      int offset_kf;
+      if (ijnum >= 0) {
+        offset_kf = offset_k;
+      } else {
+        ijnum = red_acc[2*m+0];
+        offset_kf = red_acc[2*m+1];
+      }
+
+      //int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride;
+      //int idx = iix*n_stride + j*t_per_atom + offset_kf;
+      int idx;
+      zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
+               j, ijnum, offset_kf, idx);
+      acctyp4 zeta_ji = zetaij[idx]; //  fetch(zeta_ji,idx,zeta_tex);
+      numtyp force = zeta_ji.x*tpainv;
+      numtyp prefactor_ji = zeta_ji.y;
+      f.x += delr1[0]*force;
+      f.y += delr1[1]*force;
+      f.z += delr1[2]*force;
+
+      if (eflag>0) {
+        energy+=zeta_ji.z*tpainv;
+      }
+      if (vflag>0) {
+        numtyp mforce = -force;
+        virial[0] += mdelr1[0]*mdelr1[0]*mforce;
+        virial[1] += mdelr1[1]*mdelr1[1]*mforce;
+        virial[2] += mdelr1[2]*mdelr1[2]*mforce;
+        virial[3] += mdelr1[0]*mdelr1[1]*mforce;
+        virial[4] += mdelr1[0]*mdelr1[2]*mforce;
+        virial[5] += mdelr1[1]*mdelr1[2]*mforce;
+      }
+
+      // attractive forces
+      for (nbor_k = nbork_start; nbor_k<k_end; nbor_k+=n_stride) {
+        int k=dev_packed[nbor_k];
+        k &= NEIGHMASK;
+
+        if (k == i) continue;
+
+        numtyp4 kx; fetch4(kx,k,pos_tex);
+        int ktype=kx.w;
+        ktype=map[ktype];
+        int jikparam=elem2param[jtype*nelements*nelements+itype*nelements+ktype];
+
+        numtyp delr2[3];
+        delr2[0] = kx.x-jx.x;
+      	delr2[1] = kx.y-jx.y;
+        delr2[2] = kx.z-jx.z;
+        numtyp rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+
+        if (rsq2 > cutsq[jikparam]) continue;
+        numtyp r2 = ucl_sqrt(rsq2);
+        numtyp r2inv = ucl_rsqrt(rsq2);
+
+        numtyp fi[3], fj[3], fk[3];
+        numtyp4 ts1_param, ts2_param, ts4_param, ts5_param;
+        ts1_param = ts1[jikparam]; //fetch4(ts1_jikparam,jikparam,ts1_tex);
+        lam3 = ts1_param.z;
+        powermint = ts1_param.w;
+        ts2_param = ts2[jikparam]; //fetch4(ts2_jikparam,jikparam,ts2_tex);
+        bigr = ts2_param.z;
+        bigd = ts2_param.w;
+        ts4_param = ts4[jikparam]; //fetch4(ts4_jikparam,jikparam,ts4_tex);
+        c1 = ts4_param.x;
+        c2 = ts4_param.y;
+        c3 = ts4_param.z;
+        c4 = ts4_param.w;
+        ts5_param = ts5[jikparam]; //fetch4(ts5_jijparam,jikparam,ts5_tex);
+        c5 = ts5_param.x;
+        h = ts5_param.y;
+        attractive(bigr, bigd, powermint, lam3, h, c1, c2, c3, c4, c5,
+                   prefactor_ji, r1, r1inv, r2, r2inv, mdelr1, delr2, fi, fj, fk);
+        f.x += fj[0];
+        f.y += fj[1];
+        f.z += fj[2];
+
+        virial[0] += TWOTHIRD*(mdelr1[0]*fj[0] + delr2[0]*fk[0]);
+        virial[1] += TWOTHIRD*(mdelr1[1]*fj[1] + delr2[1]*fk[1]);
+        virial[2] += TWOTHIRD*(mdelr1[2]*fj[2] + delr2[2]*fk[2]);
+        virial[3] += TWOTHIRD*(mdelr1[0]*fj[1] + delr2[0]*fk[1]);
+        virial[4] += TWOTHIRD*(mdelr1[0]*fj[2] + delr2[0]*fk[2]);
+        virial[5] += TWOTHIRD*(mdelr1[1]*fj[2] + delr2[1]*fk[2]);
+
+        //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;
+        //int idx = kk*n_stride + j*t_per_atom + offset_k;
+        int idx;
+        zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
+                 j, nbor_k, offset_k, idx);
+        acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
+        numtyp prefactor_jk = zeta_jk.y;
+
+        int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype];
+        ts1_param = ts1[jkiparam]; //fetch4(ts1_jkiparam,jkiparam,ts1_tex);
+        lam3 = ts1_param.z;
+        powermint = ts1_param.w;
+        ts2_param = ts2[jkiparam]; //fetch4(ts2_jkiparam,jkiparam,ts2_tex);
+        bigr = ts2_param.z;
+        bigd = ts2_param.w;
+        ts4_param = ts4[jkiparam]; //fetch4(ts4_jkiparam,jkiparam,ts4_tex);
+        c1 = ts4_param.x;
+        c2 = ts4_param.y;
+        c3 = ts4_param.z;
+        c4 = ts4_param.w;
+        ts5_param = ts5[jkiparam]; //fetch4(ts5_ikiparam,jkiparam,ts5_tex);
+        c5 = ts5_param.x;
+        h = ts5_param.y;
+        attractive(bigr, bigd, powermint, lam3, h, c1, c2, c3, c4, c5,
+                   prefactor_jk, r2, r2inv, r1, r1inv, delr2, mdelr1, fi, fj, fk);
+        f.x += fk[0];
+        f.y += fk[1];
+        f.z += fk[2];
+
+        virial[0] += TWOTHIRD*(delr2[0]*fj[0] + mdelr1[0]*fk[0]);
+        virial[1] += TWOTHIRD*(delr2[1]*fj[1] + mdelr1[1]*fk[1]);
+        virial[2] += TWOTHIRD*(delr2[2]*fj[2] + mdelr1[2]*fk[2]);
+        virial[3] += TWOTHIRD*(delr2[0]*fj[1] + mdelr1[0]*fk[1]);
+        virial[4] += TWOTHIRD*(delr2[0]*fj[2] + mdelr1[0]*fk[2]);
+        virial[5] += TWOTHIRD*(delr2[1]*fj[2] + mdelr1[1]*fk[2]);
+      }
+    } // for nbor
+
+    #ifdef THREE_CONCURRENT
+    store_answers(f,energy,virial,ii,inum,tid,tpa_sq,offset,
+                  eflag,vflag,ans,engv);
+    #else
+    store_answers_p(f,energy,virial,ii,inum,tid,tpa_sq,offset,
+                    eflag,vflag,ans,engv);
+    #endif
+  } // if ii
+}
+
diff --git a/lib/gpu/lal_tersoff_mod.h b/lib/gpu/lal_tersoff_mod.h
new file mode 100644
index 0000000000..9a05c66009
--- /dev/null
+++ b/lib/gpu/lal_tersoff_mod.h
@@ -0,0 +1,118 @@
+/***************************************************************************
+                                tersoff_mod.h
+                             -------------------
+                              Trung Dac Nguyen
+
+  Class for acceleration of the tersoff/mod pair style.
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                :
+    email                : ndactrung@gmail.com
+ ***************************************************************************/
+
+#ifndef LAL_TERSOFF_MOD_H
+#define LAL_TERSOFF_MOD_H
+
+#include "lal_base_three.h"
+
+namespace LAMMPS_AL {
+
+template <class numtyp, class acctyp>
+class TersoffMod : public BaseThree<numtyp, acctyp> {
+ public:
+  TersoffMod();
+  ~TersoffMod();
+
+  /// Clear any previous data and set up for a new LAMMPS run for generic systems
+  /** \param max_nbors initial number of rows in the neighbor matrix
+    * \param cell_size cutoff + skin
+    * \param gpu_split fraction of particles handled by device
+    *
+    * Returns:
+    * -  0 if successfull
+    * - -1 if fix gpu not found
+    * - -3 if there is an out of memory error
+    * - -4 if the GPU library was not compiled for GPU
+    * - -5 Double precision is not supported on card **/
+  int init(const int ntypes, const int nlocal, const int nall, const int max_nbors,
+           const double cell_size, const double gpu_split, FILE *screen,
+           int* host_map, const int nelements, int*** host_elem2param, const int nparams,
+           const double* lam1, const double* lam2, const double* lam3,
+           const double* powermint, const double* biga, const double* bigb,
+           const double* bigr, const double* bigd, const double* c1, const double* c2,
+           const double* c3, const double* c4, const double* c5,
+           const double* h, const double* beta, const double* powern,
+           const double* powern_del, const double* ca1, const double* cutsq);
+
+  /// Pair loop with host neighboring
+  void compute(const int f_ago, const int inum_full, const int nall,
+               const int nlist, double **host_x, int *host_type,
+               int *ilist, int *numj, int **firstneigh, const bool eflag,
+               const bool vflag, const bool eatom, const bool vatom,
+               int &host_start, const double cpu_time, bool &success);
+
+  /// Pair loop with device neighboring
+  int ** compute(const int ago, const int inum_full,
+                 const int nall, double **host_x, int *host_type, double *sublo,
+                 double *subhi, tagint *tag, int **nspecial,
+                 tagint **special, const bool eflag, const bool vflag,
+                 const bool eatom, const bool vatom, int &host_start,
+                 int **ilist, int **numj, const double cpu_time, bool &success);
+
+  /// Clear all host and device data
+  /** \note This is called at the beginning of the init() routine **/
+  void clear();
+
+  /// Returns memory usage on device per atom
+  int bytes_per_atom(const int max_nbors) const;
+
+  /// Total host memory used by library for pair style
+  double host_memory_usage() const;
+
+  // --------------------------- TYPE DATA --------------------------
+
+  /// If atom type constants fit in shared memory, use fast kernels
+  bool shared_types;
+
+  /// Number of atom types
+  int _lj_types;
+
+  /// ts1.x = lam1, ts1.y = lam2,  ts1.z = lam3, ts1.w = powermint
+  UCL_D_Vec<numtyp4> ts1;
+  /// ts2.x = biga, ts2.y = bigb,  ts2.z = bigr, ts2.w = bigd
+  UCL_D_Vec<numtyp4> ts2;
+  /// ts3.x = beta, ts3.y = powern, ts3.z = powern_del, ts3.w = ca1
+  UCL_D_Vec<numtyp4> ts3;
+  /// ts4.x = c1,    ts4.y = c2,     ts4.z = c3,    ts4.w = c4
+  UCL_D_Vec<numtyp4> ts4;
+  /// ts5.x = c5, ts5.y = h
+  UCL_D_Vec<numtyp4> ts5;
+
+  UCL_D_Vec<numtyp> cutsq;
+
+  UCL_D_Vec<int> elem2param;
+  UCL_D_Vec<int> map;
+  int _nparams,_nelements;
+
+  /// Per-atom arrays:
+  /// zetaij.x = force, zetaij.y = prefactor, zetaij.z = evdwl,
+  /// zetaij.w = zetaij
+  UCL_D_Vec<acctyp4>   _zetaij;
+
+  UCL_Kernel k_zeta;
+  UCL_Texture ts1_tex, ts2_tex, ts3_tex, ts4_tex, ts5_tex;
+
+  int _max_nbors;
+
+ private:
+  bool _allocated;
+  void loop(const bool _eflag, const bool _vflag, const int evatom);
+};
+
+}
+
+#endif
+
diff --git a/lib/gpu/lal_tersoff_mod_ext.cpp b/lib/gpu/lal_tersoff_mod_ext.cpp
new file mode 100644
index 0000000000..7817e7d08d
--- /dev/null
+++ b/lib/gpu/lal_tersoff_mod_ext.cpp
@@ -0,0 +1,135 @@
+/***************************************************************************
+                             tersoff_mod_ext.cpp
+                             -------------------
+                              Trung Dac Nguyen
+
+  Functions for LAMMPS access to tersoff acceleration routines.
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                : Thu April 17, 2014
+    email                : ndactrung@gmail.com
+ ***************************************************************************/
+
+#include <iostream>
+#include <cassert>
+#include <math.h>
+
+#include "lal_tersoff_mod.h"
+
+using namespace std;
+using namespace LAMMPS_AL;
+
+static TersoffMod<PRECISION,ACC_PRECISION> TSMMF;
+
+// ---------------------------------------------------------------------------
+// Allocate memory on host and device and copy constants to device
+// ---------------------------------------------------------------------------
+int tersoff_mod_gpu_init(const int ntypes, const int inum, const int nall,
+       const int max_nbors, const double cell_size, int &gpu_mode, FILE *screen,
+       int* host_map, const int nelements, int*** host_elem2param, const int nparams,
+       const double* ts_lam1, const double* ts_lam2, const double* ts_lam3,
+       const double* ts_powermint, const double* ts_biga, const double* ts_bigb,
+       const double* ts_bigr, const double* ts_bigd, const double* ts_c1,
+       const double* ts_c2, const double* ts_c3, const double* ts_c4,
+       const double* ts_c5, const double* ts_h, const double* ts_beta,
+       const double* ts_powern, const double* ts_powern_del,
+       const double* ts_ca1, const double* ts_cutsq) {
+  TSMMF.clear();
+  gpu_mode=TSMMF.device->gpu_mode();
+  double gpu_split=TSMMF.device->particle_split();
+  int first_gpu=TSMMF.device->first_device();
+  int last_gpu=TSMMF.device->last_device();
+  int world_me=TSMMF.device->world_me();
+  int gpu_rank=TSMMF.device->gpu_rank();
+  int procs_per_gpu=TSMMF.device->procs_per_gpu();
+
+  // disable host/device split for now
+  if (gpu_split != 1.0)
+    return -8;
+
+  TSMMF.device->init_message(screen,"tersoff/mod/gpu",first_gpu,last_gpu);
+
+  bool message=false;
+  if (TSMMF.device->replica_me()==0 && screen)
+    message=true;
+
+  if (message) {
+    fprintf(screen,"Initializing Device and compiling on process 0...");
+    fflush(screen);
+  }
+
+  int init_ok=0;
+  if (world_me==0)
+    init_ok=TSMMF.init(ntypes, inum, nall, 300, cell_size, gpu_split, screen,
+                      host_map, nelements, host_elem2param, nparams,
+                      ts_lam1, ts_lam2, ts_lam3, ts_powermint,
+                      ts_biga, ts_bigb, ts_bigr, ts_bigd, ts_c1, ts_c2,
+                      ts_c3, ts_c4, ts_c5, ts_h, ts_beta, ts_powern,
+                      ts_powern_del, ts_ca1, ts_cutsq);
+
+  TSMMF.device->world_barrier();
+  if (message)
+    fprintf(screen,"Done.\n");
+
+  for (int i=0; i<procs_per_gpu; i++) {
+    if (message) {
+      if (last_gpu-first_gpu==0)
+        fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
+      else
+        fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
+                last_gpu,i);
+      fflush(screen);
+    }
+    if (gpu_rank==i && world_me!=0)
+      init_ok=TSMMF.init(ntypes, inum, nall, 300, cell_size, gpu_split, screen,
+                        host_map, nelements, host_elem2param, nparams,
+                        ts_lam1, ts_lam2, ts_lam3, ts_powermint,
+                        ts_biga, ts_bigb, ts_bigr, ts_bigd, ts_c1, ts_c2,
+                        ts_c3, ts_c4, ts_c5, ts_h, ts_beta, ts_powern,
+                        ts_powern_del, ts_ca1, ts_cutsq);
+
+    TSMMF.device->gpu_barrier();
+    if (message)
+      fprintf(screen,"Done.\n");
+  }
+  if (message)
+    fprintf(screen,"\n");
+
+  if (init_ok==0)
+    TSMMF.estimate_gpu_overhead();
+  return init_ok;
+}
+
+void tersoff_mod_gpu_clear() {
+  TSMMF.clear();
+}
+
+int ** tersoff_mod_gpu_compute_n(const int ago, const int inum_full,
+                        const int nall, double **host_x, int *host_type,
+                        double *sublo, double *subhi, tagint *tag, int **nspecial,
+                        tagint **special, const bool eflag, const bool vflag,
+                        const bool eatom, const bool vatom, int &host_start,
+                        int **ilist, int **jnum, const double cpu_time,
+                        bool &success) {
+  return TSMMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
+                       subhi, tag, nspecial, special, eflag, vflag, eatom,
+                       vatom, host_start, ilist, jnum, cpu_time, success);
+}
+			
+void tersoff_mod_gpu_compute(const int ago, const int nlocal, const int nall,
+                    const int nlist, double **host_x, int *host_type,
+                    int *ilist, int *numj, int **firstneigh, const bool eflag,
+                    const bool vflag, const bool eatom, const bool vatom,
+                    int &host_start, const double cpu_time, bool &success) {
+  TSMMF.compute(ago,nlocal,nall,nlist,host_x,host_type,ilist,numj,
+               firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success);
+}
+
+double tersoff_mod_gpu_bytes() {
+  return TSMMF.host_memory_usage();
+}
+
+
diff --git a/lib/gpu/lal_tersoff_mod_extra.h b/lib/gpu/lal_tersoff_mod_extra.h
new file mode 100644
index 0000000000..370aceb634
--- /dev/null
+++ b/lib/gpu/lal_tersoff_mod_extra.h
@@ -0,0 +1,627 @@
+/// **************************************************************************
+//                             tersoff_mod_extra.h
+//                             -------------------
+//                              Trung Dac Nguyen
+//
+//  Device code for Tersoff math routines
+//
+// __________________________________________________________________________
+//    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+// __________________________________________________________________________
+//
+//    begin                :
+//    email                : ndactrung@gmail.com
+// ***************************************************************************/*
+
+#ifndef LAL_TERSOFF_MOD_EXTRA_H
+#define LAL_TERSOFF_MOD_EXTRA_H
+
+#ifdef NV_KERNEL
+#include "lal_aux_fun1.h"
+#else
+#endif
+
+#define MY_PI2 (numtyp)1.57079632679489661923
+#define MY_PI4 (numtyp)0.78539816339744830962
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp vec3_dot(const numtyp x[3], const numtyp y[3])
+{
+  return (x[0]*y[0] + x[1]*y[1] + x[2]*y[2]);
+}
+
+ucl_inline void vec3_add(const numtyp x[3], const numtyp y[3], numtyp z[3])
+{
+  z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
+}
+
+ucl_inline void vec3_scale(const numtyp k, const numtyp x[3], numtyp y[3])
+{
+  y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
+}
+
+ucl_inline void vec3_scaleadd(const numtyp k, const numtyp x[3],
+                              const numtyp y[3], numtyp z[3])
+{
+  z[0] = k*x[0]+y[0]; z[1] = k*x[1]+y[1]; z[2] = k*x[2]+y[2];
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_gijk_mod(const numtyp costheta,
+                                const numtyp param_c1,
+                                const numtyp param_c2,
+                                const numtyp param_c3,
+                                const numtyp param_c4,
+                                const numtyp param_c5,
+                                const numtyp param_h)
+{
+  const numtyp tmp_h = (param_h - costheta)*(param_h - costheta);
+  return param_c1 + (param_c2*tmp_h/(param_c3 + tmp_h)) *
+    ((numtyp)1.0 + param_c4*ucl_exp(-param_c5*tmp_h));
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_gijk_d_mod(const numtyp costheta,
+                                  const numtyp param_c2,
+                                  const numtyp param_c3,
+                                  const numtyp param_c4,
+                                  const numtyp param_c5,
+                                  const numtyp param_h)
+{
+  const numtyp tmp_h = (param_h - costheta)*(param_h - costheta);
+  const numtyp g1 = (param_h - costheta)/(param_c3 + tmp_h);
+  const numtyp g2 = ucl_exp(-param_c5*tmp_h);
+  return (numtyp)-2.0*param_c2*g1*((1 + param_c4*g2) *
+         (1 + g1*(costheta - param_h)) - tmp_h*param_c4*param_c5*g2);
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline void costheta_d(const numtyp rij_hat[3],
+                           const numtyp rij,
+                           const numtyp rik_hat[3],
+                           const numtyp rik,
+                           numtyp *dri,
+                           numtyp *drj,
+                           numtyp *drk)
+{
+  // first element is derivative wrt Ri, second wrt Rj, third wrt Rk
+
+  numtyp cos_theta = vec3_dot(rij_hat,rik_hat);
+
+  vec3_scaleadd(-cos_theta,rij_hat,rik_hat,drj);
+  vec3_scale(ucl_recip(rij),drj,drj);
+  vec3_scaleadd(-cos_theta,rik_hat,rij_hat,drk);
+  vec3_scale(ucl_recip(rik),drk,drk);
+  vec3_add(drj,drk,dri);
+  vec3_scale((numtyp)-1.0,dri,dri);
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_fc(const numtyp r,
+                          const numtyp param_bigr,
+                          const numtyp param_bigd)
+{
+  if (r < param_bigr-param_bigd) return (numtyp)1.0;
+  if (r > param_bigr+param_bigd) return (numtyp)0.0;
+  return (numtyp)0.5*((numtyp)1.0 -
+         (numtyp)1.125*sin(MY_PI2*(r - param_bigr)/param_bigd) -
+         (numtyp)0.125*sin(3*MY_PI2*(r - param_bigr)/param_bigd));
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_fc_d(const numtyp r,
+                            const numtyp param_bigr,
+                            const numtyp param_bigd)
+{
+  if (r < param_bigr-param_bigd) return (numtyp)0.0;
+  if (r > param_bigr+param_bigd) return (numtyp)0.0;
+  return -((numtyp)0.375*MY_PI4/param_bigd) *
+           ((numtyp)3*cos(MY_PI2*(r - param_bigr)/param_bigd) +
+            cos((numtyp)3*MY_PI2*(r - param_bigr)/param_bigd));
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_fa(const numtyp r,
+                          const numtyp param_bigb,
+                          const numtyp param_bigr,
+                          const numtyp param_bigd,
+                          const numtyp param_lam2)
+{
+  if (r > param_bigr + param_bigd) return (numtyp)0.0;
+  return -param_bigb * ucl_exp(-param_lam2 * r) *
+    ters_fc(r,param_bigr,param_bigd);
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_fa_d(const numtyp r,
+                            const numtyp param_bigb,
+                            const numtyp param_bigr,
+                            const numtyp param_bigd,
+                            const numtyp param_lam2)
+{
+  if (r > param_bigr + param_bigd) return (numtyp)0.0;
+  return param_bigb * ucl_exp(-param_lam2 * r) * (param_lam2 *
+    ters_fc(r,param_bigr,param_bigd) - ters_fc_d(r,param_bigr,param_bigd));
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_bij(const numtyp zeta,
+                           const numtyp param_beta,
+                           const numtyp param_powern,
+                           const numtyp param_powern_del,
+                           const numtyp param_ca1,
+                           const numtyp param_ca4)
+{
+  numtyp tmp = param_beta * zeta;
+  if (tmp > param_ca1)
+    return ucl_powr(tmp, -param_powern/((numtyp)2.0*param_powern_del));
+  if (tmp < param_ca4) return (numtyp)1.0;
+  return ucl_powr((numtyp)1.0 + ucl_powr(tmp,param_powern),
+    (numtyp)-1.0/((numtyp)2.0*param_powern_del));
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_bij_d(const numtyp zeta,
+                             const numtyp param_beta,
+                             const numtyp param_powern,
+                             const numtyp param_powern_del,
+                             const numtyp param_ca1,
+                             const numtyp param_ca4)
+{
+  numtyp tmp = param_beta * zeta;
+  if (tmp > param_ca1) return (numtyp)-0.5*(param_powern/param_powern_del) *
+	  ucl_powr(tmp,(numtyp)-0.5*(param_powern/param_powern_del)) / zeta;
+  if (tmp < param_ca4) return (numtyp)0.0;
+
+  numtyp tmp_n = ucl_powr(tmp,param_powern);
+  return (numtyp)-0.5 *(param_powern/param_powern_del) *
+	  ucl_powr((numtyp)1.0+tmp_n, (numtyp)-1.0-((numtyp)1.0 /
+    ((numtyp)2.0*param_powern_del)))*tmp_n / zeta;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline void ters_zetaterm_d(const numtyp prefactor,
+                                const numtyp rij_hat[3],
+                                const numtyp rij,
+                                const numtyp rik_hat[3],
+                                const numtyp rik,
+                                const numtyp param_bigr,
+                                const numtyp param_bigd,
+                                const numtyp param_powermint,
+                                const numtyp param_lam3,
+                                const numtyp param_h,
+                                const numtyp param_c1,
+                                const numtyp param_c2,
+                                const numtyp param_c3,
+                                const numtyp param_c4,
+                                const numtyp param_c5,
+                                numtyp dri[3],
+                                numtyp drj[3],
+                                numtyp drk[3])
+{
+  numtyp gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
+  numtyp dcosdri[3],dcosdrj[3],dcosdrk[3];
+
+  fc = ters_fc(rik,param_bigr,param_bigd);
+  dfc = ters_fc_d(rik,param_bigr,param_bigd);
+
+  numtyp t = param_lam3*(rij-rik);
+  if ((int)param_powermint == 3) tmp = t*t*t;
+  else tmp = t;
+
+  if (tmp > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
+  else if (tmp < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
+  else ex_delr = ucl_exp(tmp);
+
+  if ((int)param_powermint == 3)
+    ex_delr_d = (numtyp)3.0*param_lam3*t*t*ex_delr;
+  else ex_delr_d = param_lam3 * ex_delr;
+
+  cos_theta = vec3_dot(rij_hat,rik_hat);
+  gijk = ters_gijk_mod(cos_theta,param_c1,param_c2,param_c3,param_c4,param_c5,param_h);
+  gijk_d = ters_gijk_d_mod(cos_theta,param_c2,param_c3,param_c4,param_c5,param_h);
+  costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
+
+  // compute the derivative wrt Ri
+  // dri = -dfc*gijk*ex_delr*rik_hat;
+  // dri += fc*gijk_d*ex_delr*dcosdri;
+  // dri += fc*gijk*ex_delr_d*(rik_hat - rij_hat);
+
+  vec3_scale(-dfc*gijk*ex_delr,rik_hat,dri);
+  vec3_scaleadd(fc*gijk_d*ex_delr,dcosdri,dri,dri);
+  vec3_scaleadd(fc*gijk*ex_delr_d,rik_hat,dri,dri);
+  vec3_scaleadd(-fc*gijk*ex_delr_d,rij_hat,dri,dri);
+  vec3_scale(prefactor,dri,dri);
+
+  // compute the derivative wrt Rj
+  // drj = fc*gijk_d*ex_delr*dcosdrj;
+  // drj += fc*gijk*ex_delr_d*rij_hat;
+
+  vec3_scale(fc*gijk_d*ex_delr,dcosdrj,drj);
+  vec3_scaleadd(fc*gijk*ex_delr_d,rij_hat,drj,drj);
+  vec3_scale(prefactor,drj,drj);
+
+  // compute the derivative wrt Rk
+  // drk = dfc*gijk*ex_delr*rik_hat;
+  // drk += fc*gijk_d*ex_delr*dcosdrk;
+  // drk += -fc*gijk*ex_delr_d*rik_hat;
+
+  vec3_scale(dfc*gijk*ex_delr,rik_hat,drk);
+  vec3_scaleadd(fc*gijk_d*ex_delr,dcosdrk,drk,drk);
+  vec3_scaleadd(-fc*gijk*ex_delr_d,rik_hat,drk,drk);
+  vec3_scale(prefactor,drk,drk);
+}
+
+ucl_inline void ters_zetaterm_d_fi(const numtyp prefactor,
+                                   const numtyp rij_hat[3],
+                                   const numtyp rij,
+                                   const numtyp rik_hat[3],
+                                   const numtyp rik,
+                                   const numtyp param_bigr,
+                                   const numtyp param_bigd,
+                                   const numtyp param_powermint,
+                                   const numtyp param_lam3,
+                                   const numtyp param_h,
+                                   const numtyp param_c1,
+                                   const numtyp param_c2,
+                                   const numtyp param_c3,
+                                   const numtyp param_c4,
+                                   const numtyp param_c5,
+                                   numtyp dri[3])
+{
+  numtyp gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
+  numtyp dcosdri[3],dcosdrj[3],dcosdrk[3];
+
+  fc = ters_fc(rik,param_bigr,param_bigd);
+  dfc = ters_fc_d(rik,param_bigr,param_bigd);
+
+  numtyp t = param_lam3*(rij-rik);
+  if ((int)param_powermint == 3) tmp = t*t*t;
+  else tmp = t;
+
+  if (tmp > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
+  else if (tmp < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
+  else ex_delr = ucl_exp(tmp);
+
+  if ((int)param_powermint == 3)
+    ex_delr_d = (numtyp)3.0*param_lam3*t*t*ex_delr;
+  else ex_delr_d = param_lam3 * ex_delr;
+
+  cos_theta = vec3_dot(rij_hat,rik_hat);
+  gijk = ters_gijk_mod(cos_theta,param_c1,param_c2,param_c3,param_c4,param_c5,param_h);
+  gijk_d = ters_gijk_d_mod(cos_theta,param_c2,param_c3,param_c4,param_c5,param_h);
+  costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
+
+  // compute the derivative wrt Ri
+  // dri = -dfc*gijk*ex_delr*rik_hat;
+  // dri += fc*gijk_d*ex_delr*dcosdri;
+  // dri += fc*gijk*ex_delr_d*(rik_hat - rij_hat);
+
+  vec3_scale(-dfc*gijk*ex_delr,rik_hat,dri);
+  vec3_scaleadd(fc*gijk_d*ex_delr,dcosdri,dri,dri);
+  vec3_scaleadd(fc*gijk*ex_delr_d,rik_hat,dri,dri);
+  vec3_scaleadd(-fc*gijk*ex_delr_d,rij_hat,dri,dri);
+  vec3_scale(prefactor,dri,dri);
+}
+
+ucl_inline void ters_zetaterm_d_fj(const numtyp prefactor,
+                                   const numtyp rij_hat[3],
+                                   const numtyp rij,
+                                   const numtyp rik_hat[3],
+                                   const numtyp rik,
+                                   const numtyp param_bigr,
+                                   const numtyp param_bigd,
+                                   const numtyp param_powermint,
+                                   const numtyp param_lam3,
+                                   const numtyp param_h,
+                                   const numtyp param_c1,
+                                   const numtyp param_c2,
+                                   const numtyp param_c3,
+                                   const numtyp param_c4,
+                                   const numtyp param_c5,
+                                   numtyp drj[3])
+{
+  numtyp gijk,gijk_d,ex_delr,ex_delr_d,fc,cos_theta,tmp;
+  numtyp dcosdri[3],dcosdrj[3],dcosdrk[3];
+
+  fc = ters_fc(rik,param_bigr,param_bigd);
+
+  numtyp t = param_lam3*(rij-rik);
+  if ((int)param_powermint == 3) tmp = t*t*t;
+  else tmp = t;
+
+  if (tmp > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
+  else if (tmp < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
+  else ex_delr = ucl_exp(tmp);
+
+  if ((int)param_powermint == 3)
+    ex_delr_d = (numtyp)3.0*param_lam3*t*t*ex_delr;
+  else ex_delr_d = param_lam3 * ex_delr;
+
+  cos_theta = vec3_dot(rij_hat,rik_hat);
+  gijk = ters_gijk_mod(cos_theta,param_c1,param_c2,param_c3,param_c4,param_c5,param_h);
+  gijk_d = ters_gijk_d_mod(cos_theta,param_c2,param_c3,param_c4,param_c5,param_h);
+  costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
+
+  // compute the derivative wrt Rj
+  // drj = fc*gijk_d*ex_delr*dcosdrj;
+  // drj += fc*gijk*ex_delr_d*rij_hat;
+
+  vec3_scale(fc*gijk_d*ex_delr,dcosdrj,drj);
+  vec3_scaleadd(fc*gijk*ex_delr_d,rij_hat,drj,drj);
+  vec3_scale(prefactor,drj,drj);
+}
+
+ucl_inline void ters_zetaterm_d_fk(const numtyp prefactor,
+                                   const numtyp rij_hat[3],
+                                   const numtyp rij,
+                                   const numtyp rik_hat[3],
+                                   const numtyp rik,
+                                   const numtyp param_bigr,
+                                   const numtyp param_bigd,
+                                   const numtyp param_powermint,
+                                   const numtyp param_lam3,
+                                   const numtyp param_h,
+                                   const numtyp param_c1,
+                                   const numtyp param_c2,
+                                   const numtyp param_c3,
+                                   const numtyp param_c4,
+                                   const numtyp param_c5,
+                                   numtyp drk[3])
+{
+  numtyp gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
+  numtyp dcosdri[3],dcosdrj[3],dcosdrk[3];
+
+  fc = ters_fc(rik,param_bigr,param_bigd);
+  dfc = ters_fc_d(rik,param_bigr,param_bigd);
+
+  numtyp t = param_lam3*(rij-rik);
+  if ((int)param_powermint == 3) tmp = t*t*t;
+  else tmp = t;
+
+  if (tmp > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
+  else if (tmp < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
+  else ex_delr = ucl_exp(tmp);
+
+  if ((int)param_powermint == 3)
+    ex_delr_d = (numtyp)3.0*param_lam3*t*t*ex_delr;
+  else ex_delr_d = param_lam3 * ex_delr;
+
+  cos_theta = vec3_dot(rij_hat,rik_hat);
+  gijk = ters_gijk_mod(cos_theta,param_c1,param_c2,param_c3,param_c4,param_c5,param_h);
+  gijk_d = ters_gijk_d_mod(cos_theta,param_c2,param_c3,param_c4,param_c5,param_h);
+  costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
+
+  // compute the derivative wrt Rk
+  // drk = dfc*gijk*ex_delr*rik_hat;
+  // drk += fc*gijk_d*ex_delr*dcosdrk;
+  // drk += -fc*gijk*ex_delr_d*rik_hat;
+
+  vec3_scale(dfc*gijk*ex_delr,rik_hat,drk);
+  vec3_scaleadd(fc*gijk_d*ex_delr,dcosdrk,drk,drk);
+  vec3_scaleadd(-fc*gijk*ex_delr_d,rik_hat,drk,drk);
+  vec3_scale(prefactor,drk,drk);
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline void repulsive(const numtyp param_bigr,
+                          const numtyp param_bigd,
+                          const numtyp param_lam1,
+                          const numtyp param_biga,
+                          const numtyp rsq,
+                          const int eflag,
+                          numtyp *ans)
+{
+  numtyp r,tmp_fc,tmp_fc_d,tmp_exp;
+  r = ucl_sqrt(rsq);
+  tmp_fc = ters_fc(r,param_bigr,param_bigd);
+  tmp_fc_d = ters_fc_d(r,param_bigr,param_bigd);
+  tmp_exp = ucl_exp(-param_lam1 * r);
+  // fforce
+  ans[0] = -param_biga*tmp_exp*(tmp_fc_d - tmp_fc*param_lam1)*ucl_recip(r);
+  // eng
+  if (eflag) ans[1] = tmp_fc * param_biga * tmp_exp;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp zeta(const numtyp param_powermint,
+                       const numtyp param_lam3,
+                       const numtyp param_bigr,
+                       const numtyp param_bigd,
+                       const numtyp param_h,
+                       const numtyp param_c1,
+                       const numtyp param_c2,
+                       const numtyp param_c3,
+                       const numtyp param_c4,
+                       const numtyp param_c5,
+                       const numtyp rsqij,
+                       const numtyp rsqik,
+                       const numtyp4 delrij,
+                       const numtyp4 delrik)
+{
+  numtyp rij,rik,costheta,arg,ex_delr;
+
+  rij = ucl_sqrt(rsqij);
+  rik = ucl_sqrt(rsqik);
+  costheta = (delrij.x*delrik.x + delrij.y*delrik.y +
+              delrij.z*delrik.z) / (rij*rik);
+
+  numtyp t = param_lam3*(rij-rik);
+  if ((int)param_powermint == 3) arg = t*t*t;
+  else arg = t;
+
+  if (arg > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
+  else if (arg < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
+  else ex_delr = ucl_exp(arg);
+
+  return ters_fc(rik,param_bigr,param_bigd) *
+    ters_gijk_mod(costheta,param_c1,param_c2,param_c3,param_c4,param_c5,
+                  param_h) * ex_delr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline void force_zeta(const numtyp param_bigb,
+                           const numtyp param_bigr,
+                           const numtyp param_bigd,
+                           const numtyp param_lam2,
+                           const numtyp param_beta,
+                           const numtyp param_powern,
+                           const numtyp param_powern_del,
+                           const numtyp param_ca1,
+                           const numtyp param_ca4,
+                           const numtyp rsq,
+                           const numtyp zeta_ij,
+                           const int eflag,
+                           numtyp fpfeng[4])
+{
+  numtyp r,fa,fa_d,bij;
+
+  r = ucl_sqrt(rsq);
+  fa = ters_fa(r,param_bigb,param_bigr,param_bigd,param_lam2);
+  fa_d = ters_fa_d(r,param_bigb,param_bigr,param_bigd,param_lam2);
+  bij = ters_bij(zeta_ij,param_beta,param_powern,
+                 param_powern_del,param_ca1,param_ca4);
+  fpfeng[0] = (numtyp)0.5*bij*fa_d * ucl_recip(r); // fforce
+  fpfeng[1] = (numtyp)-0.5*fa * ters_bij_d(zeta_ij,param_beta, param_powern,
+           param_powern_del,param_ca1,param_ca4); // prefactor
+  if (eflag) fpfeng[2] = (numtyp)0.5*bij*fa; // eng
+}
+
+/* ----------------------------------------------------------------------
+   attractive term
+   use param_ij cutoff for rij test
+   use param_ijk cutoff for rik test
+------------------------------------------------------------------------- */
+
+ucl_inline void attractive(const numtyp param_bigr,
+                           const numtyp param_bigd,
+                           const numtyp param_powermint,
+                           const numtyp param_lam3,
+                           const numtyp param_h,
+                           const numtyp param_c1,
+                           const numtyp param_c2,
+                           const numtyp param_c3,
+                           const numtyp param_c4,
+                           const numtyp param_c5,
+                           const numtyp prefactor,
+                           const numtyp rij,
+                           const numtyp rijinv,
+                           const numtyp rik,
+                           const numtyp rikinv,
+                           const numtyp delrij[3],
+                           const numtyp delrik[3],
+                           numtyp fi[3],
+                           numtyp fj[3],
+                           numtyp fk[3])
+{
+  numtyp rij_hat[3],rik_hat[3];
+  vec3_scale(rijinv,delrij,rij_hat);
+  vec3_scale(rikinv,delrik,rik_hat);
+  ters_zetaterm_d(prefactor,rij_hat,rij,rik_hat,rik,
+                  param_bigr, param_bigd, param_powermint, param_lam3,
+                  param_h, param_c1, param_c2, param_c3, param_c4, param_c5,
+                  fi, fj, fk);
+}
+
+ucl_inline void attractive_fi(const numtyp param_bigr,
+                              const numtyp param_bigd,
+                              const numtyp param_powermint,
+                              const numtyp param_lam3,
+                              const numtyp param_h,
+                              const numtyp param_c1,
+                              const numtyp param_c2,
+                              const numtyp param_c3,
+                              const numtyp param_c4,
+                              const numtyp param_c5,
+                              const numtyp prefactor,
+                              const numtyp rij,
+                              const numtyp rijinv,
+                              const numtyp rik,
+                              const numtyp rikinv,
+                              const numtyp delrij[3],
+                              const numtyp delrik[3],
+                              numtyp fi[3])
+{
+  numtyp rij_hat[3],rik_hat[3];
+  vec3_scale(rijinv,delrij,rij_hat);
+  vec3_scale(rikinv,delrik,rik_hat);
+  ters_zetaterm_d_fi(prefactor,rij_hat,rij,rik_hat,rik,
+                  param_bigr, param_bigd, param_powermint, param_lam3,
+                  param_h, param_c1, param_c2, param_c3, param_c4, param_c5,
+                  fi);
+}
+
+ucl_inline void attractive_fj(const numtyp param_bigr,
+                              const numtyp param_bigd,
+                              const numtyp param_powermint,
+                              const numtyp param_lam3,
+                              const numtyp param_h,
+                              const numtyp param_c1,
+                              const numtyp param_c2,
+                              const numtyp param_c3,
+                              const numtyp param_c4,
+                              const numtyp param_c5,
+                              const numtyp prefactor,
+                              const numtyp rij,
+                              const numtyp rijinv,
+                              const numtyp rik,
+                              const numtyp rikinv,
+                              const numtyp delrij[3],
+                              const numtyp delrik[3],
+                              numtyp fj[3])
+{
+  numtyp rij_hat[3],rik_hat[3];
+  vec3_scale(rijinv,delrij,rij_hat);
+  vec3_scale(rikinv,delrik,rik_hat);
+  ters_zetaterm_d_fj(prefactor,rij_hat,rij,rik_hat,rik,
+                     param_bigr, param_bigd, param_powermint, param_lam3,
+                     param_h, param_c1, param_c2, param_c3, param_c4, param_c5,
+                     fj);
+}
+
+ucl_inline void attractive_fk(const numtyp param_bigr,
+                              const numtyp param_bigd,
+                              const numtyp param_powermint,
+                              const numtyp param_lam3,
+                              const numtyp param_h,
+                              const numtyp param_c1,
+                              const numtyp param_c2,
+                              const numtyp param_c3,
+                              const numtyp param_c4,
+                              const numtyp param_c5,
+                              const numtyp prefactor,
+                              const numtyp rij,
+                              const numtyp rijinv,
+                              const numtyp rik,
+                              const numtyp rikinv,
+                              const numtyp delrij[3],
+                              const numtyp delrik[3],
+                              numtyp fk[3])
+{
+  numtyp rij_hat[3],rik_hat[3];
+  vec3_scale(rijinv,delrij,rij_hat);
+  vec3_scale(rikinv,delrik,rik_hat);
+  ters_zetaterm_d_fk(prefactor,rij_hat,rij,rik_hat,rik,
+                     param_bigr, param_bigd, param_powermint, param_lam3,
+                     param_h, param_c1, param_c2, param_c3, param_c4, param_c5,
+                     fk);
+}
+
+
+#endif
+
+
diff --git a/lib/gpu/lal_tersoff_zbl.cpp b/lib/gpu/lal_tersoff_zbl.cpp
new file mode 100644
index 0000000000..57688f53ab
--- /dev/null
+++ b/lib/gpu/lal_tersoff_zbl.cpp
@@ -0,0 +1,482 @@
+/***************************************************************************
+                               tersoff_zbl.cpp
+                             -------------------
+                               Trung Dac Nguyen
+
+  Class for acceleration of the tersoff/zbl pair style.
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                :
+    email                : ndactrung@gmail.com
+ ***************************************************************************/
+
+#if defined(USE_OPENCL)
+#include "tersoff_zbl_cl.h"
+#elif defined(USE_CUDART)
+const char *tersoff_zbl=0;
+#else
+#include "tersoff_zbl_cubin.h"
+#endif
+
+#include "lal_tersoff_zbl.h"
+#include <cassert>
+using namespace LAMMPS_AL;
+#define TersoffZT TersoffZBL<numtyp, acctyp>
+
+extern Device<PRECISION,ACC_PRECISION> device;
+
+template <class numtyp, class acctyp>
+TersoffZT::TersoffZBL() : BaseThree<numtyp,acctyp>(), _allocated(false) {
+}
+
+template <class numtyp, class acctyp>
+TersoffZT::~TersoffZBL() {
+  clear();
+}
+
+template <class numtyp, class acctyp>
+int TersoffZT::bytes_per_atom(const int max_nbors) const {
+  return this->bytes_per_atom_atomic(max_nbors);
+}
+
+template <class numtyp, class acctyp>
+int TersoffZT::init(const int ntypes, const int nlocal, const int nall,
+                    const int max_nbors, const double cell_size,
+                    const double gpu_split, FILE *_screen, int* host_map,
+                    const int nelements, int*** host_elem2param,
+                    const int nparams, const double* lam1, const double* lam2,
+                    const double* lam3, const double* powermint,
+                    const double* biga, const double* bigb, const double* bigr,
+                    const double* bigd, const double* c1, const double* c2,
+                    const double* c3, const double* c4, const double* c,
+                    const double* d, const double* h, const double* gamma,
+                    const double* beta, const double* powern, const double* Z_i,
+                    const double* Z_j, const double* ZBLcut,
+                    const double* ZBLexpscale, const double global_e,
+                    const double global_a_0, const double global_epsilon_0,
+                    const double* host_cutsq)
+{
+  int success;
+  success=this->init_three(nlocal,nall,max_nbors,0,cell_size,gpu_split,
+                           _screen,tersoff_zbl,"k_tersoff_zbl_repulsive",
+                           "k_tersoff_zbl_three_center", "k_tersoff_zbl_three_end");
+  if (success!=0)
+    return success;
+
+  int ef_nall=nall;
+  if (ef_nall==0)
+    ef_nall=2000;
+  _zetaij.alloc(ef_nall*max_nbors,*(this->ucl_device),UCL_READ_WRITE);
+
+  k_zeta.set_function(*(this->pair_program),"k_tersoff_zbl_zeta");
+
+  // If atom type constants fit in shared memory use fast kernel
+  int lj_types=ntypes;
+  shared_types=false;
+  int max_shared_types=this->device->max_shared_types();
+  if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
+    lj_types=max_shared_types;
+    shared_types=true;
+  }
+  _lj_types=lj_types;
+
+  _nparams = nparams;
+  _nelements = nelements;
+
+  UCL_H_Vec<numtyp4> dview(nparams,*(this->ucl_device),
+                           UCL_WRITE_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=(numtyp)0;
+    dview[i].y=(numtyp)0;
+    dview[i].z=(numtyp)0;
+    dview[i].w=(numtyp)0;
+  }
+
+  // pack coefficients into arrays
+  ts1.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=static_cast<numtyp>(lam1[i]);
+    dview[i].y=static_cast<numtyp>(lam2[i]);
+    dview[i].z=static_cast<numtyp>(lam3[i]);
+    dview[i].w=static_cast<numtyp>(powermint[i]);
+  }
+
+  ucl_copy(ts1,dview,false);
+  ts1_tex.get_texture(*(this->pair_program),"ts1_tex");
+  ts1_tex.bind_float(ts1,4);
+
+  ts2.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=static_cast<numtyp>(biga[i]);
+    dview[i].y=static_cast<numtyp>(bigb[i]);
+    dview[i].z=static_cast<numtyp>(bigr[i]);
+    dview[i].w=static_cast<numtyp>(bigd[i]);
+  }
+
+  ucl_copy(ts2,dview,false);
+  ts2_tex.get_texture(*(this->pair_program),"ts2_tex");
+  ts2_tex.bind_float(ts2,4);
+
+  ts3.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=static_cast<numtyp>(c1[i]);
+    dview[i].y=static_cast<numtyp>(c2[i]);
+    dview[i].z=static_cast<numtyp>(c3[i]);
+    dview[i].w=static_cast<numtyp>(c4[i]);
+  }
+
+  ucl_copy(ts3,dview,false);
+  ts3_tex.get_texture(*(this->pair_program),"ts3_tex");
+  ts3_tex.bind_float(ts3,4);
+
+  ts4.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=static_cast<numtyp>(c[i]);
+    dview[i].y=static_cast<numtyp>(d[i]);
+    dview[i].z=static_cast<numtyp>(h[i]);
+    dview[i].w=static_cast<numtyp>(gamma[i]);
+  }
+
+  ucl_copy(ts4,dview,false);
+  ts4_tex.get_texture(*(this->pair_program),"ts4_tex");
+  ts4_tex.bind_float(ts4,4);
+
+  ts5.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=static_cast<numtyp>(beta[i]);
+    dview[i].y=static_cast<numtyp>(powern[i]);
+    dview[i].z=(numtyp)0;
+    dview[i].w=(numtyp)0;
+  }
+
+  ucl_copy(ts5,dview,false);
+  ts5_tex.get_texture(*(this->pair_program),"ts5_tex");
+  ts5_tex.bind_float(ts5,4);
+
+  ts6.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+
+  for (int i=0; i<nparams; i++) {
+    dview[i].x=static_cast<numtyp>(Z_i[i]);
+    dview[i].y=static_cast<numtyp>(Z_j[i]);
+    dview[i].z=static_cast<numtyp>(ZBLcut[i]);
+    dview[i].w=static_cast<numtyp>(ZBLexpscale[i]);
+  }
+
+  ucl_copy(ts6,dview,false);
+  ts6_tex.get_texture(*(this->pair_program),"ts6_tex");
+  ts6_tex.bind_float(ts6,4);
+
+  UCL_H_Vec<numtyp> cutsq_view(nparams,*(this->ucl_device),
+                               UCL_WRITE_ONLY);
+  for (int i=0; i<nparams; i++)
+    cutsq_view[i]=static_cast<numtyp>(host_cutsq[i]);
+  cutsq.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
+  ucl_copy(cutsq,cutsq_view,false);
+
+  UCL_H_Vec<int> dview_elem2param(nelements*nelements*nelements,
+                           *(this->ucl_device), UCL_WRITE_ONLY);
+
+  elem2param.alloc(nelements*nelements*nelements,*(this->ucl_device),
+                   UCL_READ_ONLY);
+
+  for (int i = 0; i < nelements; i++)
+    for (int j = 0; j < nelements; j++)
+      for (int k = 0; k < nelements; k++) {
+         int idx = i*nelements*nelements+j*nelements+k;
+         dview_elem2param[idx] = host_elem2param[i][j][k];
+      }
+
+  ucl_copy(elem2param,dview_elem2param,false);
+
+  UCL_H_Vec<int> dview_map(lj_types, *(this->ucl_device), UCL_WRITE_ONLY);
+  for (int i = 0; i < ntypes; i++)
+    dview_map[i] = host_map[i];
+
+  map.alloc(lj_types,*(this->ucl_device), UCL_READ_ONLY);
+  ucl_copy(map,dview_map,false);
+
+  _global_e = global_e;
+  _global_a_0 = global_a_0;
+  _global_epsilon_0 = global_epsilon_0;
+
+  _allocated=true;
+  this->_max_bytes=ts1.row_bytes()+ts2.row_bytes()+ts3.row_bytes()+
+    ts4.row_bytes()+ts5.row_bytes()+cutsq.row_bytes()+
+    map.row_bytes()+elem2param.row_bytes()+_zetaij.row_bytes();
+  return 0;
+}
+
+template <class numtyp, class acctyp>
+void TersoffZT::clear() {
+  if (!_allocated)
+    return;
+  _allocated=false;
+
+  ts1.clear();
+  ts2.clear();
+  ts3.clear();
+  ts4.clear();
+  ts5.clear();
+  ts6.clear();
+  cutsq.clear();
+  map.clear();
+  elem2param.clear();
+  _zetaij.clear();
+
+  k_zeta.clear();
+
+  this->clear_atomic();
+}
+
+template <class numtyp, class acctyp>
+double TersoffZT::host_memory_usage() const {
+  return this->host_memory_usage_atomic()+sizeof(TersoffZBL<numtyp,acctyp>);
+}
+
+#define KTHREADS this->_threads_per_atom
+#define JTHREADS this->_threads_per_atom
+// ---------------------------------------------------------------------------
+// Copy nbor list from host if necessary and then calculate forces, virials,..
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+void TersoffZT::compute(const int f_ago, const int nlocal, const int nall,
+                       const int nlist, double **host_x, int *host_type,
+                       int *ilist, int *numj, int **firstneigh,
+                       const bool eflag, const bool vflag, const bool eatom,
+                       const bool vatom, int &host_start,
+                       const double cpu_time, bool &success) {
+  this->acc_timers();
+  if (nlist==0) {
+    host_start=0;
+    // Make sure textures are correct if realloc by a different hybrid style
+    this->resize_atom(0,nall,success);
+    this->zero_timers();
+    return;
+  }
+
+  int ago=this->hd_balancer.ago_first(f_ago);
+  int inum=this->hd_balancer.balance(ago,nlocal,cpu_time);
+  this->ans->inum(inum);
+  #ifdef THREE_CONCURRENT
+  this->ans2->inum(inum);
+  #endif
+  host_start=inum;
+
+  if (ago==0) {
+    this->reset_nbors(nall, inum, nlist, ilist, numj, firstneigh, success);
+    if (!success)
+      return;
+    _max_nbors = this->nbor->max_nbor_loop(nlist,numj,ilist);
+  }
+
+  this->atom->cast_x_data(host_x,host_type);
+  this->hd_balancer.start_timer();
+  this->atom->add_x_data(host_x,host_type);
+
+  // re-allocate zetaij if necessary
+  if (nall*_max_nbors > _zetaij.cols()) {
+    int _nmax=static_cast<int>(static_cast<double>(nall)*1.10);
+    _zetaij.resize(_max_nbors*_nmax);
+  }
+
+  int _eflag;
+  if (eflag)
+    _eflag=1;
+  else
+    _eflag=0;
+
+  int ainum=nall;
+  int nbor_pitch=this->nbor->nbor_pitch();
+  int BX=this->block_pair();
+  int GX=static_cast<int>(ceil(static_cast<double>(ainum)/
+                               (BX/(JTHREADS*KTHREADS))));
+
+  this->k_zeta.set_size(GX,BX);
+  this->k_zeta.run(&this->atom->x, &ts1, &ts2, &ts3, &ts4, &ts5, &ts6, &cutsq,
+                   &map, &elem2param, &_nelements, &_nparams, &_zetaij,
+                   &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                   &_eflag, &nall, &ainum, &nbor_pitch, &this->_threads_per_atom);
+
+  int evatom=0;
+  if (eatom || vatom)
+    evatom=1;
+  #ifdef THREE_CONCURRENT
+  this->ucl_device->sync();
+  #endif
+  loop(eflag,vflag,evatom);
+  this->ans->copy_answers(eflag,vflag,eatom,vatom,ilist);
+  this->device->add_ans_object(this->ans);
+  #ifdef THREE_CONCURRENT
+  this->ans2->copy_answers(eflag,vflag,eatom,vatom,ilist);
+  this->device->add_ans_object(this->ans2);
+  #endif
+  this->hd_balancer.stop_timer();
+}
+
+// ---------------------------------------------------------------------------
+// Reneighbor on GPU if necessary and then compute forces, virials, energies
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+int ** TersoffZT::compute(const int ago, const int inum_full,
+                         const int nall, double **host_x, int *host_type,
+                         double *sublo, double *subhi, tagint *tag,
+                         int **nspecial, tagint **special, const bool eflag,
+                         const bool vflag, const bool eatom,
+                         const bool vatom, int &host_start,
+                         int **ilist, int **jnum,
+                         const double cpu_time, bool &success) {
+  this->acc_timers();
+
+  if (inum_full==0) {
+    host_start=0;
+    // Make sure textures are correct if realloc by a different hybrid style
+    this->resize_atom(0,nall,success);
+    this->zero_timers();
+    return NULL;
+  }
+
+  this->hd_balancer.balance(cpu_time);
+  int inum=this->hd_balancer.get_gpu_count(ago,inum_full);
+  this->ans->inum(inum);
+  #ifdef THREE_CONCURRENT
+  this->ans2->inum(inum);
+  #endif
+  host_start=inum;
+
+  // Build neighbor list on GPU if necessary
+  if (ago==0) {
+    _max_nbors = this->build_nbor_list(inum, inum_full-inum, nall, host_x, host_type,
+                    sublo, subhi, tag, nspecial, special, success);
+    if (!success)
+      return NULL;
+    this->hd_balancer.start_timer();
+  } else {
+    this->atom->cast_x_data(host_x,host_type);
+    this->hd_balancer.start_timer();
+    this->atom->add_x_data(host_x,host_type);
+  }
+  *ilist=this->nbor->host_ilist.begin();
+  *jnum=this->nbor->host_acc.begin();
+
+  // re-allocate zetaij if necessary
+  if (nall*_max_nbors > _zetaij.cols()) {
+    int _nmax=static_cast<int>(static_cast<double>(nall)*1.10);
+    _zetaij.resize(_max_nbors*_nmax);
+  }
+
+  int _eflag;
+  if (eflag)
+    _eflag=1;
+  else
+    _eflag=0;
+
+  int ainum=nall;
+  int nbor_pitch=this->nbor->nbor_pitch();
+  int BX=this->block_pair();
+  int GX=static_cast<int>(ceil(static_cast<double>(ainum)/
+                               (BX/(JTHREADS*KTHREADS))));
+
+  this->k_zeta.set_size(GX,BX);
+  this->k_zeta.run(&this->atom->x, &ts1, &ts2, &ts3, &ts4, &ts5, &ts6, &cutsq,
+                   &map, &elem2param, &_nelements, &_nparams, &_zetaij,
+                   &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                   &_eflag, &nall, &ainum, &nbor_pitch, &this->_threads_per_atom);
+
+  int evatom=0;
+  if (eatom || vatom)
+    evatom=1;
+  #ifdef THREE_CONCURRENT
+  this->ucl_device->sync();
+  #endif
+  loop(eflag,vflag,evatom);
+  this->ans->copy_answers(eflag,vflag,eatom,vatom);
+  this->device->add_ans_object(this->ans);
+  #ifdef THREE_CONCURRENT
+  this->ans2->copy_answers(eflag,vflag,eatom,vatom);
+  this->device->add_ans_object(this->ans2);
+  #endif
+  this->hd_balancer.stop_timer();
+
+  return this->nbor->host_jlist.begin()-host_start;
+}
+
+// ---------------------------------------------------------------------------
+// Calculate energies, forces, and torques
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+void TersoffZT::loop(const bool _eflag, const bool _vflag, const int evatom) {
+  // Compute the block size and grid size to keep all cores busy
+  int BX=this->block_pair();
+  int eflag, vflag;
+  if (_eflag)
+    eflag=1;
+  else
+    eflag=0;
+
+  if (_vflag)
+    vflag=1;
+  else
+    vflag=0;
+
+  int ainum=this->ans->inum();
+  int nbor_pitch=this->nbor->nbor_pitch();
+  int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
+                               (BX/this->_threads_per_atom)));
+
+  this->time_pair.start();
+  this->k_pair.set_size(GX,BX);
+  this->k_pair.run(&this->atom->x, &ts1, &ts2, &ts6,
+                   &_global_e, &_global_a_0, &_global_epsilon_0, &cutsq,
+                   &map, &elem2param, &_nelements, &_nparams,
+                   &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                   &this->ans->force, &this->ans->engv,
+                   &eflag, &vflag, &ainum, &nbor_pitch,
+                   &this->_threads_per_atom);
+
+  BX=this->block_size();
+  GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
+                           (BX/(KTHREADS*JTHREADS))));
+  this->k_three_center.set_size(GX,BX);
+  this->k_three_center.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq,
+                           &map, &elem2param, &_nelements, &_nparams, &_zetaij,
+                           &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                           &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum,
+                           &nbor_pitch, &this->_threads_per_atom, &evatom);
+
+  Answer<numtyp,acctyp> *end_ans;
+  #ifdef THREE_CONCURRENT
+  end_ans=this->ans2;
+  #else
+  end_ans=this->ans;
+  #endif
+  if (evatom!=0) {
+    this->k_three_end_vatom.set_size(GX,BX);
+    this->k_three_end_vatom.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq,
+                          &map, &elem2param, &_nelements, &_nparams, &_zetaij,
+                          &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                          &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum,
+                          &nbor_pitch, &this->_threads_per_atom);
+
+  } else {
+    this->k_three_end.set_size(GX,BX);
+    this->k_three_end.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq,
+                          &map, &elem2param, &_nelements, &_nparams, &_zetaij,
+                          &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                          &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum,
+                          &nbor_pitch, &this->_threads_per_atom);
+  }
+
+  this->time_pair.stop();
+}
+
+template class TersoffZBL<PRECISION,ACC_PRECISION>;
+
diff --git a/lib/gpu/lal_tersoff_zbl.cu b/lib/gpu/lal_tersoff_zbl.cu
new file mode 100644
index 0000000000..0d6c5a38d6
--- /dev/null
+++ b/lib/gpu/lal_tersoff_zbl.cu
@@ -0,0 +1,1065 @@
+// **************************************************************************
+//                               tersoff_zbl.cu
+//                             -------------------
+//                              Trung Dac Nguyen
+//
+//  Device code for acceleration of the tersoff/zbl pair style
+//
+// __________________________________________________________________________
+//    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+// __________________________________________________________________________
+//
+//       begin                :
+//       email                : ndactrung@gmail.com
+// ***************************************************************************/
+
+#ifdef NV_KERNEL
+#include "lal_tersoff_zbl_extra.h"
+
+#ifndef _DOUBLE_DOUBLE
+texture<float4> pos_tex;
+texture<float4> ts1_tex;
+texture<float4> ts2_tex;
+texture<float4> ts3_tex;
+texture<float4> ts4_tex;
+texture<float4> ts5_tex;
+texture<float4> ts6_tex;
+#else
+texture<int4,1> pos_tex;
+texture<int4> ts1_tex;
+texture<int4> ts2_tex;
+texture<int4> ts3_tex;
+texture<int4> ts4_tex;
+texture<int4> ts5_tex;
+texture<int4> ts6_tex;
+#endif
+
+#else
+#define pos_tex x_
+#define ts1_tex ts1
+#define ts2_tex ts2
+#define ts3_tex ts3
+#define ts4_tex ts4
+#define ts5_tex ts5
+#define ts6_tex ts6
+#endif
+
+//#define THREE_CONCURRENT
+
+#define TWOTHIRD (numtyp)0.66666666666666666667
+
+#define zeta_idx(nbor_mem, packed_mem, nbor_pitch, n_stride, t_per_atom,    \
+                 i, nbor_j, offset_j, idx)                                  \
+  if (nbor_mem==packed_mem) {                                               \
+    int jj = (nbor_j-offset_j-2*nbor_pitch)/n_stride;                       \
+    idx = jj*n_stride + i*t_per_atom + offset_j;                            \
+  } else {                                                                  \
+    idx = nbor_j;                                                           \
+  }
+
+#if (ARCH < 300)
+
+#define store_answers_p(f, energy, virial, ii, inum, tid, t_per_atom,       \
+                        offset, eflag, vflag, ans, engv)                    \
+  if (t_per_atom>1) {                                                       \
+    __local acctyp red_acc[6][BLOCK_PAIR];                                  \
+    red_acc[0][tid]=f.x;                                                    \
+    red_acc[1][tid]=f.y;                                                    \
+    red_acc[2][tid]=f.z;                                                    \
+    red_acc[3][tid]=energy;                                                 \
+    for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                         \
+      if (offset < s) {                                                     \
+        for (int r=0; r<4; r++)                                             \
+          red_acc[r][tid] += red_acc[r][tid+s];                             \
+      }                                                                     \
+    }                                                                       \
+    f.x=red_acc[0][tid];                                                    \
+    f.y=red_acc[1][tid];                                                    \
+    f.z=red_acc[2][tid];                                                    \
+    energy=red_acc[3][tid];                                                 \
+    if (vflag>0) {                                                          \
+      for (int r=0; r<6; r++)                                               \
+        red_acc[r][tid]=virial[r];                                          \
+      for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                       \
+        if (offset < s) {                                                   \
+          for (int r=0; r<6; r++)                                           \
+            red_acc[r][tid] += red_acc[r][tid+s];                           \
+        }                                                                   \
+      }                                                                     \
+      for (int r=0; r<6; r++)                                               \
+        virial[r]=red_acc[r][tid];                                          \
+    }                                                                       \
+  }                                                                         \
+  if (offset==0) {                                                          \
+    int ei=ii;                                                              \
+    if (eflag>0) {                                                          \
+      engv[ei]+=energy*(acctyp)0.5;                                         \
+      ei+=inum;                                                             \
+    }                                                                       \
+    if (vflag>0) {                                                          \
+      for (int i=0; i<6; i++) {                                             \
+        engv[ei]+=virial[i]*(acctyp)0.5;                                    \
+        ei+=inum;                                                           \
+      }                                                                     \
+    }                                                                       \
+    acctyp4 old=ans[ii];                                                    \
+    old.x+=f.x;                                                             \
+    old.y+=f.y;                                                             \
+    old.z+=f.z;                                                             \
+    ans[ii]=old;                                                            \
+  }
+
+#define store_zeta(z, tid, t_per_atom, offset)                              \
+  if (t_per_atom>1) {                                                       \
+    __local acctyp red_acc[BLOCK_PAIR];                                     \
+    red_acc[tid]=z;                                                         \
+    for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                         \
+      if (offset < s) {                                                     \
+        red_acc[tid] += red_acc[tid+s];                                     \
+      }                                                                     \
+    }                                                                       \
+    z=red_acc[tid];                                                         \
+  }
+
+#else
+
+#define store_answers_p(f, energy, virial, ii, inum, tid, t_per_atom,       \
+                        offset, eflag, vflag, ans, engv)                    \
+  if (t_per_atom>1) {                                                       \
+    for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                         \
+      f.x += shfl_xor(f.x, s, t_per_atom);                                  \
+      f.y += shfl_xor(f.y, s, t_per_atom);                                  \
+      f.z += shfl_xor(f.z, s, t_per_atom);                                  \
+      energy += shfl_xor(energy, s, t_per_atom);                            \
+    }                                                                       \
+    if (vflag>0) {                                                          \
+      for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                       \
+          for (int r=0; r<6; r++)                                           \
+            virial[r] += shfl_xor(virial[r], s, t_per_atom);                \
+      }                                                                     \
+    }                                                                       \
+  }                                                                         \
+  if (offset==0) {                                                          \
+    int ei=ii;                                                              \
+    if (eflag>0) {                                                          \
+      engv[ei]+=energy*(acctyp)0.5;                                         \
+      ei+=inum;                                                             \
+    }                                                                       \
+    if (vflag>0) {                                                          \
+      for (int i=0; i<6; i++) {                                             \
+        engv[ei]+=virial[i]*(acctyp)0.5;                                    \
+        ei+=inum;                                                           \
+      }                                                                     \
+    }                                                                       \
+    acctyp4 old=ans[ii];                                                    \
+    old.x+=f.x;                                                             \
+    old.y+=f.y;                                                             \
+    old.z+=f.z;                                                             \
+    ans[ii]=old;                                                            \
+  }
+
+#define store_zeta(z, tid, t_per_atom, offset)                              \
+  if (t_per_atom>1) {                                                       \
+    for (unsigned int s=t_per_atom/2; s>0; s>>=1) {                         \
+      z += shfl_xor(z, s, t_per_atom);                                      \
+    }                                                                       \
+  }
+
+#endif
+
+// Tersoff is currently used for 3 elements at most: 3*3*3 = 27 entries
+// while the block size should never be less than 32.
+// SHARED_SIZE = 32 for now to reduce the pressure on the shared memory per block
+// must be increased if there will be more than 3 elements in the future.
+
+#define SHARED_SIZE 32
+
+__kernel void k_tersoff_zbl_zeta(const __global numtyp4 *restrict x_,
+                             const __global numtyp4 *restrict ts1_in,
+                             const __global numtyp4 *restrict ts2_in,
+                             const __global numtyp4 *restrict ts3_in,
+                             const __global numtyp4 *restrict ts4_in,
+                             const __global numtyp4 *restrict ts5_in,
+                             const __global numtyp4 *restrict ts6_in,
+                             const __global numtyp *restrict cutsq,
+                             const __global int *restrict map,
+                             const __global int *restrict elem2param,
+                             const int nelements, const int nparams,
+                             __global acctyp4 * zetaij,
+                             const __global int * dev_nbor,
+                             const __global int * dev_packed,
+                             const int eflag, const int nall, const int inum,
+                             const int nbor_pitch, const int t_per_atom) {
+  __local int tpa_sq,n_stride;
+  tpa_sq = fast_mul(t_per_atom,t_per_atom);
+
+  int tid, ii, offset;
+  atom_info(tpa_sq,ii,tid,offset);
+
+  // must be increased if there will be more than 3 elements in the future.
+  __local numtyp4 ts1[SHARED_SIZE];
+  __local numtyp4 ts2[SHARED_SIZE];
+  __local numtyp4 ts3[SHARED_SIZE];
+  __local numtyp4 ts4[SHARED_SIZE];
+  __local numtyp4 ts5[SHARED_SIZE];
+  __local numtyp4 ts6[SHARED_SIZE];
+  if (tid<nparams) {
+    ts1[tid]=ts1_in[tid];
+    ts2[tid]=ts2_in[tid];
+    ts3[tid]=ts3_in[tid];
+    ts4[tid]=ts4_in[tid];
+    ts5[tid]=ts5_in[tid];
+    ts6[tid]=ts6_in[tid];
+  }
+
+  acctyp z = (acctyp)0;
+
+  __syncthreads();
+
+  if (ii<nall) {
+    int nbor_j, nbor_end;
+    int i, numj;
+
+    int offset_j=offset/t_per_atom;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
+              n_stride,nbor_end,nbor_j);
+    int offset_k=tid & (t_per_atom-1);
+    int nborj_start = nbor_j;
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype=ix.w;
+    itype=map[itype];
+
+    for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
+
+      int j=dev_packed[nbor_j];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype=jx.w;
+      jtype=map[jtype];
+      int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
+
+      // Compute rij
+      numtyp4 delr1, delr2;
+      delr1.x = jx.x-ix.x;
+      delr1.y = jx.y-ix.y;
+      delr1.z = jx.z-ix.z;
+      numtyp rsq1 = delr1.x*delr1.x+delr1.y*delr1.y+delr1.z*delr1.z;
+
+      if (rsq1 > cutsq[ijparam]) continue;
+
+      // compute zeta_ij
+      z = (acctyp)0;
+
+      int nbor_k = nborj_start-offset_j+offset_k;
+      for ( ; nbor_k < nbor_end; nbor_k+=n_stride) {
+        int k=dev_packed[nbor_k];
+        k &= NEIGHMASK;
+
+        if (k == j) continue;
+
+        numtyp4 kx; fetch4(kx,k,pos_tex); //x_[k];
+        int ktype=kx.w;
+        ktype=map[ktype];
+        int ijkparam=elem2param[itype*nelements*nelements+jtype*nelements+ktype];
+
+        // Compute rik
+        delr2.x = kx.x-ix.x;
+        delr2.y = kx.y-ix.y;
+        delr2.z = kx.z-ix.z;
+        numtyp rsq2 = delr2.x*delr2.x+delr2.y*delr2.y+delr2.z*delr2.z;
+
+        if (rsq2 > cutsq[ijkparam]) continue;
+
+        numtyp4 ts1_ijkparam = ts1[ijkparam]; //fetch4(ts1_ijkparam,ijkparam,ts1_tex);
+        numtyp ijkparam_lam3 = ts1_ijkparam.z;
+        numtyp ijkparam_powermint = ts1_ijkparam.w;
+        numtyp4 ts2_ijkparam = ts2[ijkparam]; //fetch4(ts2_ijkparam,ijkparam,ts2_tex);
+        numtyp ijkparam_bigr = ts2_ijkparam.z;
+        numtyp ijkparam_bigd = ts2_ijkparam.w;
+        numtyp4 ts4_ijkparam = ts4[ijkparam]; //fetch4(ts4_ijkparam,ijkparam,ts4_tex);
+        numtyp ijkparam_c = ts4_ijkparam.x;
+        numtyp ijkparam_d = ts4_ijkparam.y;
+        numtyp ijkparam_h = ts4_ijkparam.z;
+        numtyp ijkparam_gamma = ts4_ijkparam.w;
+        z += zeta(ijkparam_powermint, ijkparam_lam3, ijkparam_bigr, ijkparam_bigd,
+                  ijkparam_c, ijkparam_d, ijkparam_h, ijkparam_gamma,
+                  rsq1, rsq2, delr1, delr2);
+      }
+
+      //int jj = (nbor_j-offset_j-2*nbor_pitch)/n_stride;
+      //int idx = jj*n_stride + i*t_per_atom + offset_j;
+      int idx;
+      zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
+               i, nbor_j, offset_j, idx);
+      store_zeta(z, tid, t_per_atom, offset_k);
+
+      numtyp4 ts1_ijparam = ts1[ijparam]; //fetch4(ts1_ijparam,ijparam,ts1_tex);
+      numtyp ijparam_lam2 = ts1_ijparam.y;
+      numtyp4 ts2_ijparam = ts2[ijparam]; //fetch4(ts2_ijparam,ijparam,ts2_tex);
+      numtyp ijparam_bigb = ts2_ijparam.y;
+      numtyp ijparam_bigr = ts2_ijparam.z;
+      numtyp ijparam_bigd = ts2_ijparam.w;
+      numtyp4 ts3_ijparam = ts3[ijparam]; //fetch4(ts3_ijparam,ijparam,ts3_tex);
+      numtyp ijparam_c1 = ts3_ijparam.x;
+      numtyp ijparam_c2 = ts3_ijparam.y;
+      numtyp ijparam_c3 = ts3_ijparam.z;
+      numtyp ijparam_c4 = ts3_ijparam.w;
+      numtyp4 ts5_ijparam = ts5[ijparam]; //fetch4(ts5_ijparam,ijparam,ts5_tex);
+      numtyp ijparam_beta = ts5_ijparam.x;
+      numtyp ijparam_powern = ts5_ijparam.y;
+      numtyp4 ts6_ijparam = ts6[ijparam]; //fetch4(ts6_ijparam,ijparam,ts6_tex);
+      numtyp ijparam_ZBLcut = ts6_ijparam.z;
+      numtyp ijparam_ZBLexpscale = ts6_ijparam.w;
+
+      if (offset_k == 0) {
+        numtyp fpfeng[4];
+        force_zeta(ijparam_bigb, ijparam_bigr, ijparam_bigd, ijparam_lam2,
+                   ijparam_beta, ijparam_powern, ijparam_c1, ijparam_c2, ijparam_c3,
+                   ijparam_c4, ijparam_ZBLcut, ijparam_ZBLexpscale, rsq1, z, eflag, fpfeng);
+        acctyp4 zij;
+        zij.x = fpfeng[0];
+        zij.y = fpfeng[1];
+        zij.z = fpfeng[2];
+        zij.w = z;
+        zetaij[idx] = zij;
+      }
+
+    } // for nbor
+  } // if ii
+}
+
+__kernel void k_tersoff_zbl_repulsive(const __global numtyp4 *restrict x_,
+                                  const __global numtyp4 *restrict ts1_in,
+                                  const __global numtyp4 *restrict ts2_in,
+                                  const __global numtyp4 *restrict ts6_in,
+                                  const numtyp global_e, const numtyp global_a_0,
+                                  const numtyp global_epsilon_0,
+                                  const __global numtyp *restrict cutsq,
+                                  const __global int *restrict map,
+                                  const __global int *restrict elem2param,
+                                  const int nelements, const int nparams,
+                                  const __global int * dev_nbor,
+                                  const __global int * dev_packed,
+                                  __global acctyp4 *restrict ans,
+                                  __global acctyp *restrict engv,
+                                  const int eflag, const int vflag,
+                                  const int inum, const int nbor_pitch,
+                                  const int t_per_atom) {
+  __local int n_stride;
+  int tid, ii, offset;
+  atom_info(t_per_atom,ii,tid,offset);
+
+  __local numtyp4 ts1[SHARED_SIZE];
+  __local numtyp4 ts2[SHARED_SIZE];
+  __local numtyp4 ts6[SHARED_SIZE];
+  if (tid<nparams) {
+    ts1[tid]=ts1_in[tid];
+    ts2[tid]=ts2_in[tid];
+    ts6[tid]=ts6_in[tid];
+  }
+
+  acctyp energy=(acctyp)0;
+  acctyp4 f;
+  f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+  acctyp virial[6];
+  for (int i=0; i<6; i++)
+    virial[i]=(acctyp)0;
+
+  __syncthreads();
+
+  if (ii<inum) {
+    int nbor, nbor_end;
+    int i, numj;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
+              n_stride,nbor_end,nbor);
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype=ix.w;
+    itype=map[itype];
+
+    for ( ; nbor<nbor_end; nbor+=n_stride) {
+
+      int j=dev_packed[nbor];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype=jx.w;
+      jtype=map[jtype];
+      int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
+
+      // Compute r12
+
+      numtyp delx = ix.x-jx.x;
+      numtyp dely = ix.y-jx.y;
+      numtyp delz = ix.z-jx.z;
+      numtyp rsq = delx*delx+dely*dely+delz*delz;
+
+      if (rsq<cutsq[ijparam]) {
+        numtyp feng[2];
+        numtyp ijparam_lam1 = ts1[ijparam].x;
+        numtyp4 ts2_ijparam = ts2[ijparam];
+        numtyp ijparam_biga = ts2_ijparam.x;
+        numtyp ijparam_bigr = ts2_ijparam.z;
+        numtyp ijparam_bigd = ts2_ijparam.w;
+        numtyp4 ts6_ijparam = ts6[ijparam];
+        numtyp ijparam_Z_i = ts6_ijparam.x;
+        numtyp ijparam_Z_j = ts6_ijparam.y;
+        numtyp ijparam_ZBLcut = ts6_ijparam.z;
+        numtyp ijparam_ZBLexpscale = ts6_ijparam.w;
+
+        repulsive(ijparam_bigr, ijparam_bigd, ijparam_lam1, ijparam_biga,
+                  ijparam_Z_i, ijparam_Z_j, ijparam_ZBLcut, ijparam_ZBLexpscale,
+                  global_e, global_a_0, global_epsilon_0, rsq, eflag, feng);
+
+        numtyp force = feng[0];
+        f.x+=delx*force;
+        f.y+=dely*force;
+        f.z+=delz*force;
+
+        if (eflag>0)
+          energy+=feng[1];
+        if (vflag>0) {
+          virial[0] += delx*delx*force;
+          virial[1] += dely*dely*force;
+          virial[2] += delz*delz*force;
+          virial[3] += delx*dely*force;
+          virial[4] += delx*delz*force;
+          virial[5] += dely*delz*force;
+        }
+      }
+    } // for nbor
+
+    store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
+                  ans,engv);
+  } // if ii
+
+}
+
+__kernel void k_tersoff_zbl_three_center(const __global numtyp4 *restrict x_,
+                                     const __global numtyp4 *restrict ts1_in,
+                                     const __global numtyp4 *restrict ts2_in,
+                                     const __global numtyp4 *restrict ts4_in,
+                                     const __global numtyp *restrict cutsq,
+                                     const __global int *restrict map,
+                                     const __global int *restrict elem2param,
+                                     const int nelements, const int nparams,
+                                     const __global acctyp4 *restrict zetaij,
+                                     const __global int * dev_nbor,
+                                     const __global int * dev_packed,
+                                     __global acctyp4 *restrict ans,
+                                     __global acctyp *restrict engv,
+                                     const int eflag, const int vflag,
+                                     const int inum,  const int nbor_pitch,
+                                     const int t_per_atom, const int evatom) {
+  __local int tpa_sq, n_stride;
+  tpa_sq=fast_mul(t_per_atom,t_per_atom);
+  numtyp lam3, powermint, bigr, bigd, c, d, h, gamma;
+
+  int tid, ii, offset;
+  atom_info(tpa_sq,ii,tid,offset); // offset ranges from 0 to tpa_sq-1
+
+  __local numtyp4 ts1[SHARED_SIZE];
+  __local numtyp4 ts2[SHARED_SIZE];
+  __local numtyp4 ts4[SHARED_SIZE];
+  if (tid<nparams) {
+    ts1[tid]=ts1_in[tid];
+    ts2[tid]=ts2_in[tid];
+    ts4[tid]=ts4_in[tid];
+  }
+
+  acctyp energy=(acctyp)0;
+  acctyp4 f;
+  f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+  acctyp virial[6];
+  for (int i=0; i<6; i++)
+    virial[i]=(acctyp)0;
+  numtyp tpainv = ucl_recip((numtyp)t_per_atom);
+
+  __syncthreads();
+
+  if (ii<inum) {
+    int i, numj, nbor_j, nbor_end;
+
+    int offset_j=offset/t_per_atom;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
+              n_stride,nbor_end,nbor_j);
+    int offset_k=tid & (t_per_atom-1);
+    int nborj_start = nbor_j;
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype=ix.w;
+    itype=map[itype];
+
+    for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
+
+      int j=dev_packed[nbor_j];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype=jx.w;
+      jtype=map[jtype];
+      int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
+
+      // Compute r12
+      numtyp delr1[3];
+      delr1[0] = jx.x-ix.x;
+      delr1[1] = jx.y-ix.y;
+      delr1[2] = jx.z-ix.z;
+      numtyp rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
+
+      if (rsq1 > cutsq[ijparam]) continue;
+      numtyp r1 = ucl_sqrt(rsq1);
+      numtyp r1inv = ucl_rsqrt(rsq1);
+
+      // look up for zeta_ij
+
+      //int jj = (nbor_j-offset_j-2*nbor_pitch) / n_stride;
+      //int idx = jj*n_stride + i*t_per_atom + offset_j;
+      int idx;
+      zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
+               i, nbor_j, offset_j, idx);
+      acctyp4 zeta_ij = zetaij[idx]; // fetch(zeta_ij,idx,zeta_tex);
+      numtyp force = zeta_ij.x*tpainv;
+      numtyp prefactor = zeta_ij.y;
+      f.x += delr1[0]*force;
+      f.y += delr1[1]*force;
+      f.z += delr1[2]*force;
+
+      if (eflag>0) {
+        energy+=zeta_ij.z*tpainv;
+      }
+      if (vflag>0) {
+        numtyp mforce = -force;
+        virial[0] += delr1[0]*delr1[0]*mforce;
+        virial[1] += delr1[1]*delr1[1]*mforce;
+        virial[2] += delr1[2]*delr1[2]*mforce;
+        virial[3] += delr1[0]*delr1[1]*mforce;
+        virial[4] += delr1[0]*delr1[2]*mforce;
+        virial[5] += delr1[1]*delr1[2]*mforce;
+      }
+
+      int nbor_k=nborj_start-offset_j+offset_k;
+      for ( ; nbor_k<nbor_end; nbor_k+=n_stride) {
+        int k=dev_packed[nbor_k];
+        k &= NEIGHMASK;
+
+        if (j == k) continue;
+
+        numtyp4 kx; fetch4(kx,k,pos_tex);
+        int ktype=kx.w;
+        ktype=map[ktype];
+        int ijkparam=elem2param[itype*nelements*nelements+jtype*nelements+ktype];
+
+        numtyp delr2[3];
+        delr2[0] = kx.x-ix.x;
+        delr2[1] = kx.y-ix.y;
+        delr2[2] = kx.z-ix.z;
+        numtyp rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+
+        if (rsq2 > cutsq[ijkparam]) continue;
+        numtyp r2 = ucl_sqrt(rsq2);
+        numtyp r2inv = ucl_rsqrt(rsq2);
+
+        numtyp fi[3], fj[3], fk[3];
+        numtyp4 ts1_ijkparam = ts1[ijkparam]; //fetch4(ts1_ijkparam,ijkparam,ts1_tex);
+        lam3 = ts1_ijkparam.z;
+        powermint = ts1_ijkparam.w;
+        numtyp4 ts2_ijkparam = ts2[ijkparam]; //fetch4(ts2_ijkparam,ijkparam,ts2_tex);
+        bigr = ts2_ijkparam.z;
+        bigd = ts2_ijkparam.w;
+        numtyp4 ts4_ijkparam = ts4[ijkparam]; //fetch4(ts4_ijkparam,ijkparam,ts4_tex);
+        c = ts4_ijkparam.x;
+        d = ts4_ijkparam.y;
+        h = ts4_ijkparam.z;
+        gamma = ts4_ijkparam.w;
+        if (vflag>0)
+          attractive(bigr, bigd, powermint, lam3, c, d, h, gamma,
+                     prefactor, r1, r1inv, r2, r2inv, delr1, delr2, fi, fj, fk);
+        else
+          attractive_fi(bigr, bigd, powermint, lam3, c, d, h, gamma,
+                        prefactor, r1, r1inv, r2, r2inv, delr1, delr2, fi);
+        f.x += fi[0];
+        f.y += fi[1];
+        f.z += fi[2];
+
+        if (vflag>0) {
+          acctyp v[6];
+          numtyp pre = (numtyp)2.0;
+          if (evatom==1) pre = TWOTHIRD;
+          v[0] = pre*(delr1[0]*fj[0] + delr2[0]*fk[0]);
+          v[1] = pre*(delr1[1]*fj[1] + delr2[1]*fk[1]);
+          v[2] = pre*(delr1[2]*fj[2] + delr2[2]*fk[2]);
+          v[3] = pre*(delr1[0]*fj[1] + delr2[0]*fk[1]);
+          v[4] = pre*(delr1[0]*fj[2] + delr2[0]*fk[2]);
+          v[5] = pre*(delr1[1]*fj[2] + delr2[1]*fk[2]);
+
+          virial[0] += v[0]; virial[1] += v[1]; virial[2] += v[2];
+          virial[3] += v[3]; virial[4] += v[4]; virial[5] += v[5];
+        }
+      } // nbor_k
+    } // for nbor_j
+
+    store_answers_p(f,energy,virial,ii,inum,tid,tpa_sq,
+                     offset,eflag,vflag,ans,engv);
+  } // if ii
+}
+
+__kernel void k_tersoff_zbl_three_end(const __global numtyp4 *restrict x_,
+                                  const __global numtyp4 *restrict ts1_in,
+                                  const __global numtyp4 *restrict ts2_in,
+                                  const __global numtyp4 *restrict ts4_in,
+                                  const __global numtyp *restrict cutsq,
+                                  const __global int *restrict map,
+                                  const __global int *restrict elem2param,
+                                  const int nelements, const int nparams,
+                                  const __global acctyp4 *restrict zetaij,
+                                  const __global int * dev_nbor,
+                                  const __global int * dev_packed,
+                                  __global acctyp4 *restrict ans,
+                                  __global acctyp *restrict engv,
+                                  const int eflag, const int vflag,
+                                  const int inum,  const int nbor_pitch,
+                                  const int t_per_atom) {
+  __local int tpa_sq, n_stride;
+  tpa_sq=fast_mul(t_per_atom,t_per_atom);
+  numtyp lam3, powermint, bigr, bigd, c, d, h, gamma;
+
+  int tid, ii, offset;
+  atom_info(tpa_sq,ii,tid,offset);
+
+  __local numtyp4 ts1[SHARED_SIZE];
+  __local numtyp4 ts2[SHARED_SIZE];
+  __local numtyp4 ts4[SHARED_SIZE];
+  if (tid<nparams) {
+    ts1[tid]=ts1_in[tid];
+    ts2[tid]=ts2_in[tid];
+    ts4[tid]=ts4_in[tid];
+  }
+
+  acctyp energy=(acctyp)0;
+  acctyp4 f;
+  f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+  acctyp virial[6];
+  for (int i=0; i<6; i++)
+    virial[i]=(acctyp)0;
+
+  __local int red_acc[2*BLOCK_PAIR];
+
+  __syncthreads();
+
+  if (ii<inum) {
+    int i, numj, nbor_j, nbor_end, k_end;
+
+    int offset_j=offset/t_per_atom;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
+              n_stride,nbor_end,nbor_j);
+    int offset_k=tid & (t_per_atom-1);
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype=ix.w;
+    itype=map[itype];
+
+    numtyp tpainv = ucl_recip((numtyp)t_per_atom);
+    for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
+
+      int j=dev_packed[nbor_j];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype=jx.w;
+      jtype=map[jtype];
+      int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
+
+      // Compute r12
+      numtyp delr1[3];
+      delr1[0] = jx.x-ix.x;
+      delr1[1] = jx.y-ix.y;
+      delr1[2] = jx.z-ix.z;
+      numtyp rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
+
+      if (rsq1 > cutsq[ijparam]) continue;
+
+      numtyp mdelr1[3];
+      mdelr1[0] = -delr1[0];
+      mdelr1[1] = -delr1[1];
+      mdelr1[2] = -delr1[2];
+
+      int nbor_k=j+nbor_pitch;
+      int numk=dev_nbor[nbor_k];
+      if (dev_nbor==dev_packed) {
+        nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1);
+        k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1));
+        nbor_k+=offset_k;
+      } else {
+        nbor_k+=nbor_pitch;
+        nbor_k=dev_nbor[nbor_k];
+        k_end=nbor_k+numk;
+        nbor_k+=offset_k;
+      }
+      int nbork_start = nbor_k;
+
+      // look up for zeta_ji: find i in the j's neighbor list
+      int m = tid / t_per_atom;
+      int ijnum = -1;
+      for ( ; nbor_k<k_end; nbor_k+=n_stride) {
+        int k=dev_packed[nbor_k];
+        k &= NEIGHMASK;
+        if (k == i) {
+          ijnum = nbor_k;
+          red_acc[2*m+0] = ijnum;
+          red_acc[2*m+1] = offset_k;
+          break;
+        }
+      }
+
+      numtyp r1 = ucl_sqrt(rsq1);
+      numtyp r1inv = ucl_rsqrt(rsq1);
+      int offset_kf;
+      if (ijnum >= 0) {
+        offset_kf = offset_k;
+      } else {
+        ijnum = red_acc[2*m+0];
+        offset_kf = red_acc[2*m+1];
+      }
+
+      //int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride;
+      //int idx = iix*n_stride + j*t_per_atom + offset_kf;
+      int idx;
+      zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
+               j, ijnum, offset_kf, idx);
+      acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex);
+      numtyp force = zeta_ji.x*tpainv;
+      numtyp prefactor_ji = zeta_ji.y;
+      f.x += delr1[0]*force;
+      f.y += delr1[1]*force;
+      f.z += delr1[2]*force;
+
+      if (eflag>0) {
+        energy+=zeta_ji.z*tpainv;
+      }
+      if (vflag>0) {
+        numtyp mforce = -force;
+        virial[0] += mdelr1[0]*mdelr1[0]*mforce;
+        virial[1] += mdelr1[1]*mdelr1[1]*mforce;
+        virial[2] += mdelr1[2]*mdelr1[2]*mforce;
+        virial[3] += mdelr1[0]*mdelr1[1]*mforce;
+        virial[4] += mdelr1[0]*mdelr1[2]*mforce;
+        virial[5] += mdelr1[1]*mdelr1[2]*mforce;
+      }
+
+      // attractive forces
+      for (nbor_k = nbork_start ; nbor_k<k_end; nbor_k+=n_stride) {
+        int k=dev_packed[nbor_k];
+        k &= NEIGHMASK;
+
+        if (k == i) continue;
+
+        numtyp4 kx; fetch4(kx,k,pos_tex);
+        int ktype=kx.w;
+        ktype=map[ktype];
+        int jikparam=elem2param[jtype*nelements*nelements+itype*nelements+ktype];
+
+        numtyp delr2[3];
+        delr2[0] = kx.x-jx.x;
+        delr2[1] = kx.y-jx.y;
+        delr2[2] = kx.z-jx.z;
+        numtyp rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+
+        if (rsq2 > cutsq[jikparam]) continue;
+        numtyp r2 = ucl_sqrt(rsq2);
+        numtyp r2inv = ucl_rsqrt(rsq2);
+        numtyp4 ts1_param, ts2_param, ts4_param;
+        numtyp fi[3];
+
+        ts1_param = ts1[jikparam]; //fetch4(ts1_jikparam,jikparam,ts1_tex);
+        lam3 = ts1_param.z;
+        powermint = ts1_param.w;
+        ts2_param = ts2[jikparam]; //fetch4(ts2_jikparam,jikparam,ts2_tex);
+        bigr = ts2_param.z;
+        bigd = ts2_param.w;
+        ts4_param = ts4[jikparam]; //fetch4(ts4_jikparam,jikparam,ts4_tex);
+        c = ts4_param.x;
+        d = ts4_param.y;
+        h = ts4_param.z;
+        gamma = ts4_param.w;
+        attractive_fj(bigr, bigd, powermint, lam3, c, d, h, gamma,
+                      prefactor_ji, r1, r1inv, r2, r2inv, mdelr1, delr2, fi);
+        f.x += fi[0];
+        f.y += fi[1];
+        f.z += fi[2];
+
+        //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;
+        //int idx = kk*n_stride + j*t_per_atom + offset_k;
+        int idx;
+        zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
+                 j, nbor_k, offset_k, idx);
+        acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
+        numtyp prefactor_jk = zeta_jk.y;
+        int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype];
+        ts1_param = ts1[jkiparam]; //fetch4(ts1_jkiparam,jkiparam,ts1_tex);
+        lam3 = ts1_param.z;
+        powermint = ts1_param.w;
+        ts2_param = ts2[jkiparam]; //fetch4(ts2_jkiparam,jkiparam,ts2_tex);
+        bigr = ts2_param.z;
+        bigd = ts2_param.w;
+        ts4_param = ts4[jkiparam]; //fetch4(ts4_jkiparam,jkiparam,ts4_tex);
+        c = ts4_param.x;
+        d = ts4_param.y;
+        h = ts4_param.z;
+        gamma = ts4_param.w;
+        attractive_fk(bigr, bigd, powermint, lam3, c, d, h, gamma,
+                      prefactor_jk, r2, r2inv, r1, r1inv, delr2, mdelr1, fi);
+        f.x += fi[0];
+        f.y += fi[1];
+        f.z += fi[2];
+      } // for nbor_k
+    } // for nbor_j
+
+    #ifdef THREE_CONCURRENT
+    store_answers(f,energy,virial,ii,inum,tid,tpa_sq,offset,
+                  eflag,vflag,ans,engv);
+    #else
+    store_answers_p(f,energy,virial,ii,inum,tid,tpa_sq,offset,
+                    eflag,vflag,ans,engv);
+    #endif
+  } // if ii
+}
+
+__kernel void k_tersoff_zbl_three_end_vatom(const __global numtyp4 *restrict x_,
+                                        const __global numtyp4 *restrict ts1_in,
+                                        const __global numtyp4 *restrict ts2_in,
+      	                                const __global numtyp4 *restrict ts4_in,
+                                        const __global numtyp *restrict cutsq,
+                                        const __global int *restrict map,
+                                        const __global int *restrict elem2param,
+                                        const int nelements, const int nparams,
+                                        const __global acctyp4 *restrict zetaij,
+                                        const __global int * dev_nbor,
+                                        const __global int * dev_packed,
+                                        __global acctyp4 *restrict ans,
+                                        __global acctyp *restrict engv,
+                                        const int eflag, const int vflag,
+                                        const int inum,  const int nbor_pitch,
+                                        const int t_per_atom) {
+  __local int tpa_sq, n_stride;
+  tpa_sq=fast_mul(t_per_atom,t_per_atom);
+  numtyp lam3, powermint, bigr, bigd, c, d, h, gamma;
+
+  int tid, ii, offset;
+  atom_info(tpa_sq,ii,tid,offset);
+
+  __local numtyp4 ts1[SHARED_SIZE];
+  __local numtyp4 ts2[SHARED_SIZE];
+  __local numtyp4 ts4[SHARED_SIZE];
+  if (tid<nparams) {
+    ts1[tid]=ts1_in[tid];
+    ts2[tid]=ts2_in[tid];
+    ts4[tid]=ts4_in[tid];
+  }
+
+  acctyp energy=(acctyp)0;
+  acctyp4 f;
+  f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+  acctyp virial[6];
+  for (int i=0; i<6; i++)
+    virial[i]=(acctyp)0;
+
+  __local int red_acc[2*BLOCK_PAIR];
+
+  __syncthreads();
+
+  if (ii<inum) {
+    int i, numj, nbor_j, nbor_end, k_end;
+
+    int offset_j=offset/t_per_atom;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
+              n_stride,nbor_end,nbor_j);
+    int offset_k=tid & (t_per_atom-1);
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype=ix.w;
+    itype=map[itype];
+
+    numtyp tpainv = ucl_recip((numtyp)t_per_atom);
+    for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
+
+      int j=dev_packed[nbor_j];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype=jx.w;
+      jtype=map[jtype];
+      int ijparam=elem2param[itype*nelements*nelements+jtype*nelements+jtype];
+
+      // Compute r12
+      numtyp delr1[3];
+      delr1[0] = jx.x-ix.x;
+      delr1[1] = jx.y-ix.y;
+      delr1[2] = jx.z-ix.z;
+      numtyp rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
+
+      if (rsq1 > cutsq[ijparam]) continue;
+
+      numtyp mdelr1[3];
+      mdelr1[0] = -delr1[0];
+      mdelr1[1] = -delr1[1];
+      mdelr1[2] = -delr1[2];
+
+      int nbor_k=j+nbor_pitch;
+      int numk=dev_nbor[nbor_k];
+      if (dev_nbor==dev_packed) {
+        nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1);
+        k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1));
+        nbor_k+=offset_k;
+      } else {
+        nbor_k+=nbor_pitch;
+        nbor_k=dev_nbor[nbor_k];
+        k_end=nbor_k+numk;
+        nbor_k+=offset_k;
+      }
+      int nbork_start = nbor_k;
+
+      // look up for zeta_ji
+      int m = tid / t_per_atom;
+      int ijnum = -1;
+      for ( ; nbor_k<k_end; nbor_k+=n_stride) {
+        int k=dev_packed[nbor_k];
+        k &= NEIGHMASK;
+        if (k == i) {
+          ijnum = nbor_k;
+          red_acc[2*m+0] = ijnum;
+          red_acc[2*m+1] = offset_k;
+          break;
+        }
+      }
+
+      numtyp r1 = ucl_sqrt(rsq1);
+      numtyp r1inv = ucl_rsqrt(rsq1);
+      int offset_kf;
+      if (ijnum >= 0) {
+        offset_kf = offset_k;
+      } else {
+        ijnum = red_acc[2*m+0];
+        offset_kf = red_acc[2*m+1];
+      }
+
+      //int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride;
+      //int idx = iix*n_stride + j*t_per_atom + offset_kf;
+      int idx;
+      zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
+               j, ijnum, offset_kf, idx);
+      acctyp4 zeta_ji = zetaij[idx]; //  fetch(zeta_ji,idx,zeta_tex);
+      numtyp force = zeta_ji.x*tpainv;
+      numtyp prefactor_ji = zeta_ji.y;
+      f.x += delr1[0]*force;
+      f.y += delr1[1]*force;
+      f.z += delr1[2]*force;
+
+      if (eflag>0) {
+        energy+=zeta_ji.z*tpainv;
+      }
+      if (vflag>0) {
+        numtyp mforce = -force;
+        virial[0] += mdelr1[0]*mdelr1[0]*mforce;
+        virial[1] += mdelr1[1]*mdelr1[1]*mforce;
+        virial[2] += mdelr1[2]*mdelr1[2]*mforce;
+        virial[3] += mdelr1[0]*mdelr1[1]*mforce;
+        virial[4] += mdelr1[0]*mdelr1[2]*mforce;
+        virial[5] += mdelr1[1]*mdelr1[2]*mforce;
+      }
+
+      // attractive forces
+      for (nbor_k = nbork_start; nbor_k<k_end; nbor_k+=n_stride) {
+        int k=dev_packed[nbor_k];
+        k &= NEIGHMASK;
+
+        if (k == i) continue;
+
+        numtyp4 kx; fetch4(kx,k,pos_tex);
+        int ktype=kx.w;
+        ktype=map[ktype];
+        int jikparam=elem2param[jtype*nelements*nelements+itype*nelements+ktype];
+
+        numtyp delr2[3];
+        delr2[0] = kx.x-jx.x;
+      	delr2[1] = kx.y-jx.y;
+        delr2[2] = kx.z-jx.z;
+        numtyp rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+
+        if (rsq2 > cutsq[jikparam]) continue;
+        numtyp r2 = ucl_sqrt(rsq2);
+        numtyp r2inv = ucl_rsqrt(rsq2);
+
+        numtyp fi[3], fj[3], fk[3];
+        numtyp4 ts1_param, ts2_param, ts4_param;
+        ts1_param = ts1[jikparam]; //fetch4(ts1_jikparam,jikparam,ts1_tex);
+        lam3 = ts1_param.z;
+        powermint = ts1_param.w;
+        ts2_param = ts2[jikparam]; //fetch4(ts2_jikparam,jikparam,ts2_tex);
+        bigr = ts2_param.z;
+        bigd = ts2_param.w;
+        ts4_param = ts4[jikparam]; //fetch4(ts4_jikparam,jikparam,ts4_tex);
+        c = ts4_param.x;
+        d = ts4_param.y;
+        h = ts4_param.z;
+        gamma = ts4_param.w;
+        attractive(bigr, bigd, powermint, lam3, c, d, h, gamma,
+                   prefactor_ji, r1, r1inv, r2, r2inv, mdelr1, delr2, fi, fj, fk);
+        f.x += fj[0];
+        f.y += fj[1];
+        f.z += fj[2];
+
+        virial[0] += TWOTHIRD*(mdelr1[0]*fj[0] + delr2[0]*fk[0]);
+        virial[1] += TWOTHIRD*(mdelr1[1]*fj[1] + delr2[1]*fk[1]);
+        virial[2] += TWOTHIRD*(mdelr1[2]*fj[2] + delr2[2]*fk[2]);
+        virial[3] += TWOTHIRD*(mdelr1[0]*fj[1] + delr2[0]*fk[1]);
+        virial[4] += TWOTHIRD*(mdelr1[0]*fj[2] + delr2[0]*fk[2]);
+        virial[5] += TWOTHIRD*(mdelr1[1]*fj[2] + delr2[1]*fk[2]);
+
+        //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;
+        //int idx = kk*n_stride + j*t_per_atom + offset_k;
+        int idx;
+        zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
+                 j, nbor_k, offset_k, idx);
+        acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
+        numtyp prefactor_jk = zeta_jk.y;
+
+        int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype];
+        ts1_param = ts1[jkiparam]; //fetch4(ts1_jkiparam,jkiparam,ts1_tex);
+        lam3 = ts1_param.z;
+        powermint = ts1_param.w;
+        ts2_param = ts2[jkiparam]; //fetch4(ts2_jkiparam,jkiparam,ts2_tex);
+        bigr = ts2_param.z;
+        bigd = ts2_param.w;
+        ts4_param = ts4[jkiparam]; //fetch4(ts4_jkiparam,jkiparam,ts4_tex);
+        c = ts4_param.x;
+        d = ts4_param.y;
+        h = ts4_param.z;
+        gamma = ts4_param.w;
+        attractive(bigr, bigd, powermint, lam3, c, d, h, gamma,
+                   prefactor_jk, r2, r2inv, r1, r1inv, delr2, mdelr1, fi, fj, fk);
+        f.x += fk[0];
+        f.y += fk[1];
+        f.z += fk[2];
+
+        virial[0] += TWOTHIRD*(delr2[0]*fj[0] + mdelr1[0]*fk[0]);
+        virial[1] += TWOTHIRD*(delr2[1]*fj[1] + mdelr1[1]*fk[1]);
+        virial[2] += TWOTHIRD*(delr2[2]*fj[2] + mdelr1[2]*fk[2]);
+        virial[3] += TWOTHIRD*(delr2[0]*fj[1] + mdelr1[0]*fk[1]);
+        virial[4] += TWOTHIRD*(delr2[0]*fj[2] + mdelr1[0]*fk[2]);
+        virial[5] += TWOTHIRD*(delr2[1]*fj[2] + mdelr1[1]*fk[2]);
+      }
+    } // for nbor
+
+    #ifdef THREE_CONCURRENT
+    store_answers(f,energy,virial,ii,inum,tid,tpa_sq,offset,
+                  eflag,vflag,ans,engv);
+    #else
+    store_answers_p(f,energy,virial,ii,inum,tid,tpa_sq,offset,
+                    eflag,vflag,ans,engv);
+    #endif
+  } // if ii
+}
+
diff --git a/lib/gpu/lal_tersoff_zbl.h b/lib/gpu/lal_tersoff_zbl.h
new file mode 100644
index 0000000000..cc0b848845
--- /dev/null
+++ b/lib/gpu/lal_tersoff_zbl.h
@@ -0,0 +1,123 @@
+/***************************************************************************
+                               tersoff_zbl.h
+                             -------------------
+                              Trung Dac Nguyen
+
+  Class for acceleration of the tersoff pair style.
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                :
+    email                : ndactrung@gmail.com
+ ***************************************************************************/
+
+#ifndef LAL_TERSOFF_ZBL_H
+#define LAL_TERSOFF_ZBL_H
+
+#include "lal_base_three.h"
+
+namespace LAMMPS_AL {
+
+template <class numtyp, class acctyp>
+class TersoffZBL : public BaseThree<numtyp, acctyp> {
+ public:
+  TersoffZBL();
+  ~TersoffZBL();
+
+  /// Clear any previous data and set up for a new LAMMPS run for generic systems
+  /** \param max_nbors initial number of rows in the neighbor matrix
+    * \param cell_size cutoff + skin
+    * \param gpu_split fraction of particles handled by device
+    *
+    * Returns:
+    * -  0 if successfull
+    * - -1 if fix gpu not found
+    * - -3 if there is an out of memory error
+    * - -4 if the GPU library was not compiled for GPU
+    * - -5 Double precision is not supported on card **/
+  int init(const int ntypes, const int nlocal, const int nall, const int max_nbors,
+           const double cell_size, const double gpu_split, FILE *screen,
+           int* host_map, const int nelements, int*** host_elem2param, const int nparams,
+           const double* lam1, const double* lam2, const double* lam3,
+           const double* powermint, const double* biga, const double* bigb,
+           const double* bigr, const double* bigd, const double* c1, const double* c2,
+           const double* c3, const double* c4, const double* c, const double* d,
+           const double* h, const double* gamma, const double* beta,
+           const double* powern, const double* Z_i, const double* Z_j,
+           const double* ZBLcut, const double* ZBLexpscale, const double global_e,
+           const double global_a_0, const double global_epsilon_0, const double* cutsq);
+
+  /// Pair loop with host neighboring
+  void compute(const int f_ago, const int inum_full, const int nall,
+               const int nlist, double **host_x, int *host_type,
+               int *ilist, int *numj, int **firstneigh, const bool eflag,
+               const bool vflag, const bool eatom, const bool vatom,
+               int &host_start, const double cpu_time, bool &success);
+
+  /// Pair loop with device neighboring
+  int ** compute(const int ago, const int inum_full,
+                 const int nall, double **host_x, int *host_type, double *sublo,
+                 double *subhi, tagint *tag, int **nspecial,
+                 tagint **special, const bool eflag, const bool vflag,
+                 const bool eatom, const bool vatom, int &host_start,
+                 int **ilist, int **numj, const double cpu_time, bool &success);
+
+  /// Clear all host and device data
+  /** \note This is called at the beginning of the init() routine **/
+  void clear();
+
+  /// Returns memory usage on device per atom
+  int bytes_per_atom(const int max_nbors) const;
+
+  /// Total host memory used by library for pair style
+  double host_memory_usage() const;
+
+  // --------------------------- TYPE DATA --------------------------
+
+  /// If atom type constants fit in shared memory, use fast kernels
+  bool shared_types;
+
+  /// Number of atom types
+  int _lj_types;
+
+  /// ts1.x = lam1, ts1.y = lam2,  ts1.z = lam3, ts1.w = powermint
+  UCL_D_Vec<numtyp4> ts1;
+  /// ts2.x = biga, ts2.y = bigb,  ts2.z = bigr, ts2.w = bigd
+  UCL_D_Vec<numtyp4> ts2;
+  /// ts3.x = c1,   ts3.y = c2,    ts3.z = c3,   ts3.w = c4
+  UCL_D_Vec<numtyp4> ts3;
+  /// ts4.x = c,    ts4.y = d,     ts4.z = h,    ts4.w = gamma
+  UCL_D_Vec<numtyp4> ts4;
+  /// ts5.x = beta, ts5.y = powern
+  UCL_D_Vec<numtyp4> ts5;
+  /// ts6.x = Z_i, ts6.y = Z_j, ts6.z = ZBLcut, ts6.w = ZBLexpscale
+  UCL_D_Vec<numtyp4> ts6;
+
+  UCL_D_Vec<numtyp> cutsq;
+
+  UCL_D_Vec<int> elem2param;
+  UCL_D_Vec<int> map;
+  int _nparams,_nelements;
+
+  /// Per-atom arrays:
+  /// zetaij.x = force, zetaij.y = prefactor, zetaij.z = evdwl,
+  /// zetaij.w = zetaij
+  UCL_D_Vec<acctyp4>   _zetaij;
+
+  UCL_Kernel k_zeta;
+  UCL_Texture ts1_tex, ts2_tex, ts3_tex, ts4_tex, ts5_tex, ts6_tex;
+
+  int _max_nbors;
+  numtyp _global_e,_global_a_0,_global_epsilon_0;
+
+ private:
+  bool _allocated;
+  void loop(const bool _eflag, const bool _vflag, const int evatom);
+};
+
+}
+
+#endif
+
diff --git a/lib/gpu/lal_tersoff_zbl_ext.cpp b/lib/gpu/lal_tersoff_zbl_ext.cpp
new file mode 100644
index 0000000000..fce240f8fe
--- /dev/null
+++ b/lib/gpu/lal_tersoff_zbl_ext.cpp
@@ -0,0 +1,146 @@
+/***************************************************************************
+                             tersoff_zbl_ext.cpp
+                             -------------------
+                              Trung Dac Nguyen
+
+  Functions for LAMMPS access to tersoff/zbl acceleration routines.
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                :
+    email                : ndactrung@gmail.com
+ ***************************************************************************/
+
+#include <iostream>
+#include <cassert>
+#include <math.h>
+
+#include "lal_tersoff_zbl.h"
+
+using namespace std;
+using namespace LAMMPS_AL;
+
+static TersoffZBL<PRECISION,ACC_PRECISION> TSZMF;
+
+// ---------------------------------------------------------------------------
+// Allocate memory on host and device and copy constants to device
+// ---------------------------------------------------------------------------
+int tersoff_zbl_gpu_init(const int ntypes, const int inum, const int nall,
+                     const int max_nbors, const double cell_size, int &gpu_mode,
+                     FILE *screen, int* host_map, const int nelements,
+                     int*** host_elem2param, const int nparams,
+                     const double* ts_lam1, const double* ts_lam2,
+                     const double* ts_lam3, const double* ts_powermint,
+                     const double* ts_biga, const double* ts_bigb,
+                     const double* ts_bigr, const double* ts_bigd,
+                     const double* ts_c1, const double* ts_c2,
+                     const double* ts_c3, const double* ts_c4,
+                     const double* ts_c, const double* ts_d, const double* ts_h,
+                     const double* ts_gamma, const double* ts_beta,
+                     const double* ts_powern, const double* ts_Z_i,
+                     const double* ts_Z_j, const double* ts_ZBLcut,
+                     const double* ts_ZBLexpscale, const double global_e,
+                     const double global_a_0, const double global_epsilon_0,
+                     const double* ts_cutsq) {
+  TSZMF.clear();
+  gpu_mode=TSZMF.device->gpu_mode();
+  double gpu_split=TSZMF.device->particle_split();
+  int first_gpu=TSZMF.device->first_device();
+  int last_gpu=TSZMF.device->last_device();
+  int world_me=TSZMF.device->world_me();
+  int gpu_rank=TSZMF.device->gpu_rank();
+  int procs_per_gpu=TSZMF.device->procs_per_gpu();
+
+  // disable host/device split for now
+  if (gpu_split != 1.0)
+    return -8;
+
+  TSZMF.device->init_message(screen,"tersoff/zbl/gpu",first_gpu,last_gpu);
+
+  bool message=false;
+  if (TSZMF.device->replica_me()==0 && screen)
+    message=true;
+
+  if (message) {
+    fprintf(screen,"Initializing Device and compiling on process 0...");
+    fflush(screen);
+  }
+
+  int init_ok=0;
+  if (world_me==0)
+    init_ok=TSZMF.init(ntypes, inum, nall, 300, cell_size, gpu_split, screen,
+                      host_map, nelements, host_elem2param, nparams,
+                      ts_lam1, ts_lam2, ts_lam3, ts_powermint,
+                      ts_biga, ts_bigb, ts_bigr, ts_bigd,
+                      ts_c1, ts_c2, ts_c3, ts_c4, ts_c, ts_d, ts_h,
+                      ts_gamma, ts_beta, ts_powern, ts_Z_i, ts_Z_j,
+                      ts_ZBLcut, ts_ZBLexpscale, global_e, global_a_0,
+                      global_epsilon_0, ts_cutsq);
+
+  TSZMF.device->world_barrier();
+  if (message)
+    fprintf(screen,"Done.\n");
+
+  for (int i=0; i<procs_per_gpu; i++) {
+    if (message) {
+      if (last_gpu-first_gpu==0)
+        fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
+      else
+        fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
+                last_gpu,i);
+      fflush(screen);
+    }
+    if (gpu_rank==i && world_me!=0)
+      init_ok=TSZMF.init(ntypes, inum, nall, 300, cell_size, gpu_split, screen,
+                        host_map, nelements, host_elem2param, nparams,
+                        ts_lam1, ts_lam2, ts_lam3, ts_powermint,
+                        ts_biga, ts_bigb, ts_bigr, ts_bigd,
+                        ts_c1, ts_c2, ts_c3, ts_c4, ts_c, ts_d, ts_h,
+                        ts_gamma, ts_beta, ts_powern, ts_Z_i, ts_Z_j,
+                        ts_ZBLcut, ts_ZBLexpscale, global_e, global_a_0,
+                        global_epsilon_0, ts_cutsq);
+
+    TSZMF.device->gpu_barrier();
+    if (message)
+      fprintf(screen,"Done.\n");
+  }
+  if (message)
+    fprintf(screen,"\n");
+
+  if (init_ok==0)
+    TSZMF.estimate_gpu_overhead();
+  return init_ok;
+}
+
+void tersoff_zbl_gpu_clear() {
+  TSZMF.clear();
+}
+
+int ** tersoff_zbl_gpu_compute_n(const int ago, const int inum_full,
+                        const int nall, double **host_x, int *host_type,
+                        double *sublo, double *subhi, tagint *tag, int **nspecial,
+                        tagint **special, const bool eflag, const bool vflag,
+                        const bool eatom, const bool vatom, int &host_start,
+                        int **ilist, int **jnum, const double cpu_time,
+                        bool &success) {
+  return TSZMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
+                       subhi, tag, nspecial, special, eflag, vflag, eatom,
+                       vatom, host_start, ilist, jnum, cpu_time, success);
+}
+			
+void tersoff_zbl_gpu_compute(const int ago, const int nlocal, const int nall,
+                    const int nlist, double **host_x, int *host_type,
+                    int *ilist, int *numj, int **firstneigh, const bool eflag,
+                    const bool vflag, const bool eatom, const bool vatom,
+                    int &host_start, const double cpu_time, bool &success) {
+  TSZMF.compute(ago,nlocal,nall,nlist,host_x,host_type,ilist,numj,
+               firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success);
+}
+
+double tersoff_zbl_gpu_bytes() {
+  return TSZMF.host_memory_usage();
+}
+
+
diff --git a/lib/gpu/lal_tersoff_zbl_extra.h b/lib/gpu/lal_tersoff_zbl_extra.h
new file mode 100644
index 0000000000..79afb4de82
--- /dev/null
+++ b/lib/gpu/lal_tersoff_zbl_extra.h
@@ -0,0 +1,690 @@
+/// **************************************************************************
+//                             tersoff_zbl_extra.h
+//                             -------------------
+//                              Trung Dac Nguyen
+//
+//  Device code for Tersoff math routines
+//
+// __________________________________________________________________________
+//    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+// __________________________________________________________________________
+//
+//    begin                :
+//    email                : ndactrung@gmail.com
+// ***************************************************************************/*
+
+#ifndef LAL_TERSOFF_ZBL_EXTRA_H
+#define LAL_TERSOFF_ZBL_EXTRA_H
+
+#ifdef NV_KERNEL
+#include "lal_aux_fun1.h"
+#else
+#endif
+
+#define MY_PI (numtyp)3.14159265358979323846
+#define MY_PI2 (numtyp)1.57079632679489661923
+#define MY_PI4 (numtyp)0.78539816339744830962
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp vec3_dot(const numtyp x[3], const numtyp y[3])
+{
+  return (x[0]*y[0] + x[1]*y[1] + x[2]*y[2]);
+}
+
+ucl_inline void vec3_add(const numtyp x[3], const numtyp y[3], numtyp z[3])
+{
+  z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
+}
+
+ucl_inline void vec3_scale(const numtyp k, const numtyp x[3], numtyp y[3])
+{
+  y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
+}
+
+ucl_inline void vec3_scaleadd(const numtyp k, const numtyp x[3],
+                              const numtyp y[3], numtyp z[3])
+{
+  z[0] = k*x[0]+y[0]; z[1] = k*x[1]+y[1]; z[2] = k*x[2]+y[2];
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_gijk(const numtyp costheta,
+                            const numtyp param_c,
+                            const numtyp param_d,
+                            const numtyp param_h,
+                            const numtyp param_gamma)
+{
+  const numtyp ters_c = param_c * param_c;
+  const numtyp ters_d = param_d * param_d;
+  const numtyp hcth = param_h - costheta;
+  return param_gamma*((numtyp)1.0 + ters_c*ucl_recip(ters_d) -
+         ters_c *ucl_recip(ters_d + hcth*hcth));
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_gijk_d(const numtyp costheta,
+                              const numtyp param_c,
+                              const numtyp param_d,
+                              const numtyp param_h,
+                              const numtyp param_gamma)
+{
+  const numtyp ters_c = param_c * param_c;
+  const numtyp ters_d = param_d * param_d;
+  const numtyp hcth = param_h - costheta;
+  const numtyp numerator = (numtyp)-2.0 * ters_c * hcth;
+  const numtyp denominator = ucl_recip(ters_d + hcth*hcth);
+  return param_gamma*numerator*denominator*denominator;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline void costheta_d(const numtyp rij_hat[3],
+                           const numtyp rij,
+                           const numtyp rik_hat[3],
+                           const numtyp rik,
+                           numtyp *dri,
+                           numtyp *drj,
+                           numtyp *drk)
+{
+  // first element is derivative wrt Ri, second wrt Rj, third wrt Rk
+
+  numtyp cos_theta = vec3_dot(rij_hat,rik_hat);
+
+  vec3_scaleadd(-cos_theta,rij_hat,rik_hat,drj);
+  vec3_scale(ucl_recip(rij),drj,drj);
+  vec3_scaleadd(-cos_theta,rik_hat,rij_hat,drk);
+  vec3_scale(ucl_recip(rik),drk,drk);
+  vec3_add(drj,drk,dri);
+  vec3_scale((numtyp)-1.0,dri,dri);
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_fc(const numtyp r,
+                          const numtyp param_bigr,
+                          const numtyp param_bigd)
+{
+  if (r < param_bigr-param_bigd) return (numtyp)1.0;
+  if (r > param_bigr+param_bigd) return (numtyp)0.0;
+  return (numtyp)0.5*((numtyp)1.0 - sin(MY_PI2*(r - param_bigr)/param_bigd));
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_fc_d(const numtyp r,
+                            const numtyp param_bigr,
+                            const numtyp param_bigd)
+{
+  if (r < param_bigr-param_bigd) return (numtyp)0.0;
+  if (r > param_bigr+param_bigd) return (numtyp)0.0;
+  return -(MY_PI4/param_bigd) * cos(MY_PI2*(r - param_bigr)/param_bigd);
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp F_fermi(const numtyp r, const numtyp param_ZBLcut,
+                          const numtyp param_ZBLexpscale)
+{
+  return ucl_recip((numtyp)1.0+ucl_exp(-param_ZBLexpscale*(r-param_ZBLcut)));
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp F_fermi_d(const numtyp r, const numtyp param_ZBLcut,
+                            const numtyp param_ZBLexpscale)
+{
+  numtyp a = ucl_exp(-param_ZBLexpscale*(r-param_ZBLcut));
+  numtyp b = (numtyp)1.0 + a;
+  return param_ZBLexpscale*a*ucl_recip(b*b);
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_fa(const numtyp r,
+                          const numtyp param_bigb,
+                          const numtyp param_bigr,
+                          const numtyp param_bigd,
+                          const numtyp param_lam2,
+                          const numtyp param_ZBLcut,
+                          const numtyp param_ZBLexpscale)
+{
+  if (r > param_bigr + param_bigd) return (numtyp)0.0;
+  return -param_bigb * ucl_exp(-param_lam2 * r) *
+    ters_fc(r,param_bigr,param_bigd)*F_fermi(r,param_ZBLcut,param_ZBLexpscale);
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_fa_d(const numtyp r,
+                            const numtyp param_bigb,
+                            const numtyp param_bigr,
+                            const numtyp param_bigd,
+                            const numtyp param_lam2,
+                            const numtyp param_ZBLcut,
+                            const numtyp param_ZBLexpscale)
+{
+  if (r > param_bigr + param_bigd) return (numtyp)0.0;
+  numtyp f = F_fermi(r,param_ZBLcut,param_ZBLexpscale);
+  return param_bigb * ucl_exp(-param_lam2 * r) *
+    (param_lam2 * ters_fc(r,param_bigr,param_bigd) * f -
+    ters_fc_d(r,param_bigr,param_bigd) * f -
+    ters_fc(r,param_bigr,param_bigd) * F_fermi_d(r,param_ZBLcut,param_ZBLexpscale));
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_bij(const numtyp zeta,
+                           const numtyp param_beta,
+                           const numtyp param_powern,
+                           const numtyp param_c1,
+                           const numtyp param_c2,
+                           const numtyp param_c3,
+                           const numtyp param_c4)
+{
+  numtyp tmp = param_beta * zeta;
+  if (tmp > param_c1) return ucl_rsqrt(tmp);
+  if (tmp > param_c2)
+    return ((numtyp)1.0 - ucl_powr(tmp,-param_powern) /
+      ((numtyp)2.0*param_powern))*ucl_rsqrt(tmp);
+  if (tmp < param_c4) return (numtyp)1.0;
+  if (tmp < param_c3)
+    return (numtyp)1.0 - ucl_powr(tmp,param_powern)/((numtyp)2.0*param_powern);
+  return ucl_powr((numtyp)1.0 + ucl_powr(tmp,param_powern),
+    (numtyp)-1.0/((numtyp)2.0*param_powern));
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp ters_bij_d(const numtyp zeta,
+                             const numtyp param_beta,
+                             const numtyp param_powern,
+                             const numtyp param_c1,
+                             const numtyp param_c2,
+                             const numtyp param_c3,
+                             const numtyp param_c4)
+{
+  numtyp tmp = param_beta * zeta;
+  if (tmp > param_c1)
+    return param_beta * (numtyp)-0.5*ucl_powr(tmp,(numtyp)-1.5);
+  if (tmp > param_c2)
+    return param_beta * ((numtyp)-0.5*ucl_powr(tmp,(numtyp)-1.5) *
+    // error in negligible 2nd term fixed 9/30/2015
+		// (1.0 - 0.5*(1.0 +  1.0/(2.0*param->powern)) *
+      ((numtyp)1.0 - ((numtyp)1.0 + (numtyp)1.0 /((numtyp)2.0 * param_powern)) *
+       ucl_powr(tmp,-param_powern)));
+  if (tmp < param_c4) return (numtyp)0.0;
+  if (tmp < param_c3)
+    return (numtyp)-0.5*param_beta * ucl_powr(tmp,param_powern-(numtyp)1.0);
+
+  numtyp tmp_n = ucl_powr(tmp,param_powern);
+  return (numtyp)-0.5 * ucl_powr((numtyp)1.0+tmp_n, (numtyp) -
+    (numtyp)1.0-((numtyp)1.0 / ((numtyp)2.0 * param_powern)))*tmp_n / zeta;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline void ters_zetaterm_d(const numtyp prefactor,
+                                const numtyp rij_hat[3],
+                                const numtyp rij,
+                                const numtyp rik_hat[3],
+                                const numtyp rik,
+                                const numtyp param_bigr,
+                                const numtyp param_bigd,
+                                const numtyp param_powermint,
+                                const numtyp param_lam3,
+                                const numtyp param_c,
+                                const numtyp param_d,
+                                const numtyp param_h,
+                                const numtyp param_gamma,
+                                numtyp dri[3],
+                                numtyp drj[3],
+                                numtyp drk[3])
+{
+  numtyp gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
+  numtyp dcosdri[3],dcosdrj[3],dcosdrk[3];
+
+  fc = ters_fc(rik,param_bigr,param_bigd);
+  dfc = ters_fc_d(rik,param_bigr,param_bigd);
+
+  numtyp t = param_lam3*(rij-rik);
+  if ((int)param_powermint == 3) tmp = t*t*t;
+  else tmp = t;
+
+  if (tmp > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
+  else if (tmp < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
+  else ex_delr = ucl_exp(tmp);
+
+  if ((int)param_powermint == 3)
+    ex_delr_d = (numtyp)3.0*param_lam3*t*t*ex_delr;
+  else ex_delr_d = param_lam3 * ex_delr;
+
+  cos_theta = vec3_dot(rij_hat,rik_hat);
+  gijk = ters_gijk(cos_theta,param_c,param_d,param_h,param_gamma);
+  gijk_d = ters_gijk_d(cos_theta,param_c,param_d,param_h,param_gamma);
+  costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
+
+  // compute the derivative wrt Ri
+  // dri = -dfc*gijk*ex_delr*rik_hat;
+  // dri += fc*gijk_d*ex_delr*dcosdri;
+  // dri += fc*gijk*ex_delr_d*(rik_hat - rij_hat);
+
+  vec3_scale(-dfc*gijk*ex_delr,rik_hat,dri);
+  vec3_scaleadd(fc*gijk_d*ex_delr,dcosdri,dri,dri);
+  vec3_scaleadd(fc*gijk*ex_delr_d,rik_hat,dri,dri);
+  vec3_scaleadd(-fc*gijk*ex_delr_d,rij_hat,dri,dri);
+  vec3_scale(prefactor,dri,dri);
+
+  // compute the derivative wrt Rj
+  // drj = fc*gijk_d*ex_delr*dcosdrj;
+  // drj += fc*gijk*ex_delr_d*rij_hat;
+
+  vec3_scale(fc*gijk_d*ex_delr,dcosdrj,drj);
+  vec3_scaleadd(fc*gijk*ex_delr_d,rij_hat,drj,drj);
+  vec3_scale(prefactor,drj,drj);
+
+  // compute the derivative wrt Rk
+  // drk = dfc*gijk*ex_delr*rik_hat;
+  // drk += fc*gijk_d*ex_delr*dcosdrk;
+  // drk += -fc*gijk*ex_delr_d*rik_hat;
+
+  vec3_scale(dfc*gijk*ex_delr,rik_hat,drk);
+  vec3_scaleadd(fc*gijk_d*ex_delr,dcosdrk,drk,drk);
+  vec3_scaleadd(-fc*gijk*ex_delr_d,rik_hat,drk,drk);
+  vec3_scale(prefactor,drk,drk);
+}
+
+ucl_inline void ters_zetaterm_d_fi(const numtyp prefactor,
+                                   const numtyp rij_hat[3],
+                                   const numtyp rij,
+                                   const numtyp rik_hat[3],
+                                   const numtyp rik,
+                                   const numtyp param_bigr,
+                                   const numtyp param_bigd,
+                                   const numtyp param_powermint,
+                                   const numtyp param_lam3,
+                                   const numtyp param_c,
+                                   const numtyp param_d,
+                                   const numtyp param_h,
+                                   const numtyp param_gamma,
+                                   numtyp dri[3])
+{
+  numtyp gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
+  numtyp dcosdri[3],dcosdrj[3],dcosdrk[3];
+
+  fc = ters_fc(rik,param_bigr,param_bigd);
+  dfc = ters_fc_d(rik,param_bigr,param_bigd);
+
+  numtyp t = param_lam3*(rij-rik);
+  if ((int)param_powermint == 3) tmp = t*t*t;
+  else tmp = t;
+
+  if (tmp > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
+  else if (tmp < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
+  else ex_delr = ucl_exp(tmp);
+
+  if ((int)param_powermint == 3)
+    ex_delr_d = (numtyp)3.0*param_lam3*t*t*ex_delr;
+  else ex_delr_d = param_lam3 * ex_delr;
+
+  cos_theta = vec3_dot(rij_hat,rik_hat);
+  gijk = ters_gijk(cos_theta,param_c,param_d,param_h,param_gamma);
+  gijk_d = ters_gijk_d(cos_theta,param_c,param_d,param_h,param_gamma);
+  costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
+
+  // compute the derivative wrt Ri
+  // dri = -dfc*gijk*ex_delr*rik_hat;
+  // dri += fc*gijk_d*ex_delr*dcosdri;
+  // dri += fc*gijk*ex_delr_d*(rik_hat - rij_hat);
+
+  vec3_scale(-dfc*gijk*ex_delr,rik_hat,dri);
+  vec3_scaleadd(fc*gijk_d*ex_delr,dcosdri,dri,dri);
+  vec3_scaleadd(fc*gijk*ex_delr_d,rik_hat,dri,dri);
+  vec3_scaleadd(-fc*gijk*ex_delr_d,rij_hat,dri,dri);
+  vec3_scale(prefactor,dri,dri);
+}
+
+ucl_inline void ters_zetaterm_d_fj(const numtyp prefactor,
+                                   const numtyp rij_hat[3],
+                                   const numtyp rij,
+                                   const numtyp rik_hat[3],
+                                   const numtyp rik,
+                                   const numtyp param_bigr,
+                                   const numtyp param_bigd,
+                                   const numtyp param_powermint,
+                                   const numtyp param_lam3,
+                                   const numtyp param_c,
+                                   const numtyp param_d,
+                                   const numtyp param_h,
+                                   const numtyp param_gamma,
+                                   numtyp drj[3])
+{
+  numtyp gijk,gijk_d,ex_delr,ex_delr_d,fc,cos_theta,tmp;
+  numtyp dcosdri[3],dcosdrj[3],dcosdrk[3];
+
+  fc = ters_fc(rik,param_bigr,param_bigd);
+
+  numtyp t = param_lam3*(rij-rik);
+  if ((int)param_powermint == 3) tmp = t*t*t;
+  else tmp = t;
+
+  if (tmp > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
+  else if (tmp < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
+  else ex_delr = ucl_exp(tmp);
+
+  if ((int)param_powermint == 3)
+    ex_delr_d = (numtyp)3.0*param_lam3*t*t*ex_delr;
+  else ex_delr_d = param_lam3 * ex_delr;
+
+  cos_theta = vec3_dot(rij_hat,rik_hat);
+  gijk = ters_gijk(cos_theta,param_c,param_d,param_h,param_gamma);
+  gijk_d = ters_gijk_d(cos_theta,param_c,param_d,param_h,param_gamma);
+  costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
+
+  // compute the derivative wrt Rj
+  // drj = fc*gijk_d*ex_delr*dcosdrj;
+  // drj += fc*gijk*ex_delr_d*rij_hat;
+
+  vec3_scale(fc*gijk_d*ex_delr,dcosdrj,drj);
+  vec3_scaleadd(fc*gijk*ex_delr_d,rij_hat,drj,drj);
+  vec3_scale(prefactor,drj,drj);
+}
+
+ucl_inline void ters_zetaterm_d_fk(const numtyp prefactor,
+                                   const numtyp rij_hat[3],
+                                   const numtyp rij,
+                                   const numtyp rik_hat[3],
+                                   const numtyp rik,
+                                   const numtyp param_bigr,
+                                   const numtyp param_bigd,
+                                   const numtyp param_powermint,
+                                   const numtyp param_lam3,
+                                   const numtyp param_c,
+                                   const numtyp param_d,
+                                   const numtyp param_h,
+                                   const numtyp param_gamma,
+                                   numtyp drk[3])
+{
+  numtyp gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
+  numtyp dcosdri[3],dcosdrj[3],dcosdrk[3];
+
+  fc = ters_fc(rik,param_bigr,param_bigd);
+  dfc = ters_fc_d(rik,param_bigr,param_bigd);
+
+  numtyp t = param_lam3*(rij-rik);
+  if ((int)param_powermint == 3) tmp = t*t*t;
+  else tmp = t;
+
+  if (tmp > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
+  else if (tmp < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
+  else ex_delr = ucl_exp(tmp);
+
+  if ((int)param_powermint == 3)
+    ex_delr_d = (numtyp)3.0*param_lam3*t*t*ex_delr;
+  else ex_delr_d = param_lam3 * ex_delr;
+
+  cos_theta = vec3_dot(rij_hat,rik_hat);
+  gijk = ters_gijk(cos_theta,param_c,param_d,param_h,param_gamma);
+  gijk_d = ters_gijk_d(cos_theta,param_c,param_d,param_h,param_gamma);
+  costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
+
+  // compute the derivative wrt Rk
+  // drk = dfc*gijk*ex_delr*rik_hat;
+  // drk += fc*gijk_d*ex_delr*dcosdrk;
+  // drk += -fc*gijk*ex_delr_d*rik_hat;
+
+  vec3_scale(dfc*gijk*ex_delr,rik_hat,drk);
+  vec3_scaleadd(fc*gijk_d*ex_delr,dcosdrk,drk,drk);
+  vec3_scaleadd(-fc*gijk*ex_delr_d,rik_hat,drk,drk);
+  vec3_scale(prefactor,drk,drk);
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline void repulsive(const numtyp param_bigr,
+                          const numtyp param_bigd,
+                          const numtyp param_lam1,
+                          const numtyp param_biga,
+                          const numtyp param_Z_i,
+                          const numtyp param_Z_j,
+                          const numtyp param_ZBLcut,
+                          const numtyp param_ZBLexpscale,
+                          const numtyp global_e,
+                          const numtyp global_a_0,
+                          const numtyp global_epsilon_0,
+                          const numtyp rsq,
+                          const int eflag,
+                          numtyp *ans)
+{
+  numtyp r,tmp_fc,tmp_fc_d,tmp_exp;
+
+  // Tersoff repulsive portion
+
+  r = ucl_sqrt(rsq);
+  tmp_fc = ters_fc(r,param_bigr,param_bigd);
+  tmp_fc_d = ters_fc_d(r,param_bigr,param_bigd);
+  tmp_exp = ucl_exp(-param_lam1 * r);
+
+  numtyp fforce_ters = param_biga * tmp_exp * (tmp_fc_d - tmp_fc*param_lam1);
+  numtyp eng_ters = tmp_fc * param_biga * tmp_exp;
+
+  // ZBL repulsive portion
+
+  numtyp esq = global_e*global_e;
+  numtyp a_ij = ((numtyp)0.8854*global_a_0) /
+    (ucl_powr(param_Z_i,(numtyp)0.23) + ucl_powr(param_Z_j,(numtyp)0.23));
+  numtyp premult = (param_Z_i * param_Z_j * esq)/((numtyp)4.0*MY_PI*global_epsilon_0);
+  numtyp r_ov_a = r/a_ij;
+  numtyp t1 = (numtyp)0.1818*ucl_exp((numtyp)-3.2*r_ov_a);
+  numtyp t2 = (numtyp)0.5099*ucl_exp((numtyp)-0.9423*r_ov_a);
+  numtyp t3 = (numtyp)0.2802*ucl_exp((numtyp)-0.4029*r_ov_a);
+  numtyp t4 = (numtyp)0.02817*ucl_exp((numtyp)-0.2016*r_ov_a);
+  numtyp phi = t1 + t2 + t3 + t4;
+  numtyp dphi = (numtyp)-3.2*t1 - (numtyp)0.9423*t2 - (numtyp)0.4029*t3 -
+    (numtyp)0.2016*t4;
+  dphi *= ucl_recip(a_ij);
+/*
+  numtyp phi = (numtyp)0.1818*ucl_exp((numtyp)-3.2*r_ov_a) +
+    (numtyp)0.5099*ucl_exp((numtyp)-0.9423*r_ov_a) +
+    (numtyp)0.2802*ucl_exp((numtyp)-0.4029*r_ov_a) +
+    (numtyp)0.02817*ucl_exp((numtyp)-0.2016*r_ov_a);
+  numtyp dphi = ucl_recip(a_ij) * ((numtyp)-3.2*(numtyp)0.1818*ucl_exp((numtyp)-3.2*r_ov_a) -
+    (numtyp)0.9423*(numtyp)0.5099*ucl_exp((numtyp)-0.9423*r_ov_a) -
+    (numtyp)0.4029*(numtyp)0.2802*ucl_exp((numtyp)-0.4029*r_ov_a) -
+    (numtyp)0.2016*(numtyp)0.02817*ucl_exp((numtyp)-0.2016*r_ov_a));
+*/
+  numtyp rinv = ucl_recip(r);
+  numtyp fforce_ZBL = premult*(-phi)/rsq + premult*dphi*rinv;
+  numtyp eng_ZBL = premult*rinv*phi;
+
+  // combine two parts with smoothing by Fermi-like function
+  // ans[0] = fforce
+  numtyp f = F_fermi(r,param_ZBLcut,param_ZBLexpscale);
+  numtyp f_d = F_fermi_d(r,param_ZBLcut,param_ZBLexpscale);
+  ans[0] = -(-f_d * eng_ZBL + ((numtyp)1.0 - f)*fforce_ZBL + f_d*eng_ters +
+             f*fforce_ters) * rinv;
+
+  // ans[1] = eng
+  if (eflag) ans[1] = ((numtyp)1.0 - f)*eng_ZBL + f*eng_ters;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline numtyp zeta(const numtyp param_powermint,
+                       const numtyp param_lam3,
+                       const numtyp param_bigr,
+                       const numtyp param_bigd,
+                       const numtyp param_c,
+                       const numtyp param_d,
+                       const numtyp param_h,
+                       const numtyp param_gamma,
+                       const numtyp rsqij,
+                       const numtyp rsqik,
+                       const numtyp4 delrij,
+                       const numtyp4 delrik)
+{
+  numtyp rij,rik,costheta,arg,ex_delr;
+
+  rij = ucl_sqrt(rsqij);
+  rik = ucl_sqrt(rsqik);
+  costheta = (delrij.x*delrik.x + delrij.y*delrik.y +
+              delrij.z*delrik.z) / (rij*rik);
+
+  numtyp t = param_lam3*(rij-rik);
+  if ((int)param_powermint == 3) arg = t*t*t;
+  else arg = t;
+
+  if (arg > (numtyp)69.0776) ex_delr = (numtyp)1.e30;
+  else if (arg < (numtyp)-69.0776) ex_delr = (numtyp)0.0;
+  else ex_delr = ucl_exp(arg);
+
+  return ters_fc(rik,param_bigr,param_bigd) *
+         ters_gijk(costheta,param_c, param_d, param_h, param_gamma) * ex_delr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ucl_inline void force_zeta(const numtyp param_bigb,
+                           const numtyp param_bigr,
+                           const numtyp param_bigd,
+                           const numtyp param_lam2,
+                           const numtyp param_beta,
+                           const numtyp param_powern,
+                           const numtyp param_c1,
+                           const numtyp param_c2,
+                           const numtyp param_c3,
+                           const numtyp param_c4,
+                           const numtyp param_ZBLcut,
+                           const numtyp param_ZBLexpscale,
+                           const numtyp rsq,
+                           const numtyp zeta_ij,
+                           const int eflag,
+                           numtyp fpfeng[4])
+{
+  numtyp r,fa,fa_d,bij;
+
+  r = ucl_sqrt(rsq);
+  fa = ters_fa(r,param_bigb,param_bigr,param_bigd,param_lam2,param_ZBLcut,param_ZBLexpscale);
+  fa_d = ters_fa_d(r,param_bigb,param_bigr,param_bigd,param_lam2,param_ZBLcut,param_ZBLexpscale);
+  bij = ters_bij(zeta_ij,param_beta,param_powern,
+                 param_c1,param_c2, param_c3, param_c4);
+  fpfeng[0] = (numtyp)0.5*bij*fa_d * ucl_recip(r); // fforce
+  fpfeng[1] = (numtyp)-0.5*fa * ters_bij_d(zeta_ij,param_beta, param_powern,
+           param_c1,param_c2, param_c3, param_c4); // prefactor
+  if (eflag) fpfeng[2] = (numtyp)0.5*bij*fa; // eng
+}
+
+/* ----------------------------------------------------------------------
+   attractive term
+   use param_ij cutoff for rij test
+   use param_ijk cutoff for rik test
+------------------------------------------------------------------------- */
+
+ucl_inline void attractive(const numtyp param_bigr,
+                           const numtyp param_bigd,
+                           const numtyp param_powermint,
+                           const numtyp param_lam3,
+                           const numtyp param_c,
+                           const numtyp param_d,
+                           const numtyp param_h,
+                           const numtyp param_gamma,
+                           const numtyp prefactor,
+                           const numtyp rij,
+                           const numtyp rijinv,
+                           const numtyp rik,
+                           const numtyp rikinv,
+                           const numtyp delrij[3],
+                           const numtyp delrik[3],
+                           numtyp fi[3],
+                           numtyp fj[3],
+                           numtyp fk[3])
+{
+  numtyp rij_hat[3],rik_hat[3];
+  vec3_scale(rijinv,delrij,rij_hat);
+  vec3_scale(rikinv,delrik,rik_hat);
+  ters_zetaterm_d(prefactor,rij_hat,rij,rik_hat,rik,
+                  param_bigr, param_bigd, param_powermint, param_lam3,
+                  param_c, param_d, param_h, param_gamma, fi, fj, fk);
+}
+
+ucl_inline void attractive_fi(const numtyp param_bigr,
+                              const numtyp param_bigd,
+                              const numtyp param_powermint,
+                              const numtyp param_lam3,
+                              const numtyp param_c,
+                              const numtyp param_d,
+                              const numtyp param_h,
+                              const numtyp param_gamma,
+                              const numtyp prefactor,
+                              const numtyp rij,
+                              const numtyp rijinv,
+                              const numtyp rik,
+                              const numtyp rikinv,
+                              const numtyp delrij[3],
+                              const numtyp delrik[3],
+                              numtyp fi[3])
+{
+  numtyp rij_hat[3],rik_hat[3];
+  vec3_scale(rijinv,delrij,rij_hat);
+  vec3_scale(rikinv,delrik,rik_hat);
+  ters_zetaterm_d_fi(prefactor,rij_hat,rij,rik_hat,rik,
+                  param_bigr, param_bigd, param_powermint, param_lam3,
+                  param_c, param_d, param_h, param_gamma, fi);
+}
+
+ucl_inline void attractive_fj(const numtyp param_bigr,
+                              const numtyp param_bigd,
+                              const numtyp param_powermint,
+                              const numtyp param_lam3,
+                              const numtyp param_c,
+                              const numtyp param_d,
+                              const numtyp param_h,
+                              const numtyp param_gamma,
+                              const numtyp prefactor,
+                              const numtyp rij,
+                              const numtyp rijinv,
+                              const numtyp rik,
+                              const numtyp rikinv,
+                              const numtyp delrij[3],
+                              const numtyp delrik[3],
+                              numtyp fj[3])
+{
+  numtyp rij_hat[3],rik_hat[3];
+  vec3_scale(rijinv,delrij,rij_hat);
+  vec3_scale(rikinv,delrik,rik_hat);
+  ters_zetaterm_d_fj(prefactor,rij_hat,rij,rik_hat,rik,
+                     param_bigr, param_bigd, param_powermint, param_lam3,
+                     param_c, param_d, param_h, param_gamma, fj);
+}
+
+ucl_inline void attractive_fk(const numtyp param_bigr,
+                              const numtyp param_bigd,
+                              const numtyp param_powermint,
+                              const numtyp param_lam3,
+                              const numtyp param_c,
+                              const numtyp param_d,
+                              const numtyp param_h,
+                              const numtyp param_gamma,
+                              const numtyp prefactor,
+                              const numtyp rij,
+                              const numtyp rijinv,
+                              const numtyp rik,
+                              const numtyp rikinv,
+                              const numtyp delrij[3],
+                              const numtyp delrik[3],
+                              numtyp fk[3])
+{
+  numtyp rij_hat[3],rik_hat[3];
+  vec3_scale(rijinv,delrij,rij_hat);
+  vec3_scale(rikinv,delrik,rik_hat);
+  ters_zetaterm_d_fk(prefactor,rij_hat,rij,rik_hat,rik,
+                     param_bigr, param_bigd, param_powermint, param_lam3,
+                     param_c, param_d, param_h, param_gamma, fk);
+}
+
+
+#endif
+
+

From 13c55490099890791a2bed3aff92ced293a53da8 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 7 Apr 2016 21:12:44 +0000
Subject: [PATCH 05/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@14809
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/bond.cpp       | 71 ++++++++++++++++++++++++++++++++++++++++++++++
 src/bond.h         |  2 ++
 src/input.cpp      | 12 ++++++++
 src/input.h        |  1 +
 src/pair.cpp       |  8 +++---
 src/pair_table.cpp | 27 +++++++++++++-----
 6 files changed, 110 insertions(+), 11 deletions(-)

diff --git a/src/bond.cpp b/src/bond.cpp
index 443816418f..5c2622281d 100644
--- a/src/bond.cpp
+++ b/src/bond.cpp
@@ -16,6 +16,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
+#include "neighbor.h"
 #include "suffix.h"
 #include "atom_masks.h"
 #include "memory.h"
@@ -23,6 +24,8 @@
 
 using namespace LAMMPS_NS;
 
+enum{NONE,LINEAR,SPLINE};
+
 /* -----------------------------------------------------------------------
    set bond contribution to Vdwl energy to 0.0
    a particular bond style can override this
@@ -212,6 +215,74 @@ void Bond::ev_tally(int i, int j, int nlocal, int newton_bond,
   }
 }
 
+/* ----------------------------------------------------------------------
+   write a table of bond potential energy/force vs distance to a file
+------------------------------------------------------------------------- */
+
+void Bond::write_file(int narg, char **arg)
+{
+  if (narg != 6 && narg !=8) error->all(FLERR,"Illegal bond_write command");
+
+  // parse optional arguments
+
+  int itype = 0;
+  int jtype = 0;
+  if (narg == 8) {
+    itype = force->inumeric(FLERR,arg[6]);
+    jtype = force->inumeric(FLERR,arg[7]);
+    if (itype < 1 || itype > atom->ntypes || jtype < 1 || jtype > atom->ntypes)
+    error->all(FLERR,"Invalid atom types in bond_write command");
+  }
+
+  int btype = force->inumeric(FLERR,arg[0]);
+  int n = force->inumeric(FLERR,arg[1]);
+  double inner = force->numeric(FLERR,arg[2]);
+  double outer = force->numeric(FLERR,arg[3]);
+  if (inner <= 0.0 || inner >= outer)
+    error->all(FLERR,"Invalid rlo/rhi values in bond_write command");
+
+
+  double r0 = equilibrium_distance(btype);
+
+  // open file in append mode
+  // print header in format used by bond_style table
+
+  int me;
+  MPI_Comm_rank(world,&me);
+  FILE *fp;
+  if (me == 0) {
+    fp = fopen(arg[4],"a");
+    if (fp == NULL) error->one(FLERR,"Cannot open bond_write file");
+  }
+
+  // initialize potentials before evaluating bond potential
+  // insures all bond coeffs are set and force constants
+  // also initialize neighbor so that neighbor requests are processed
+  // NOTE: might be safest to just do lmp->init()
+
+  force->init();
+  neighbor->init();
+
+  if (me == 0) {
+    double r,e,f;
+
+    // evaluate energy and force at each of N distances
+    // note that Bond::single() takes r**2 and returns f/r.
+
+    fprintf(fp,"# Bond potential %s for bond type %d: i,r,energy,force\n",
+            force->bond_style,btype);
+    fprintf(fp,"\n%s\nN %d EQ %.15g\n\n",arg[5],n,r0);
+
+    const double dr = (outer-inner) / static_cast<double>(n-1);
+    for (int i = 0; i < n; i++) {
+      r = inner + dr * static_cast<double>(i);
+      e = single(btype,r*r,itype,jtype,f);
+      fprintf(fp,"%d %.15g %.15g %.15g\n",i+1,r,e,f*r);
+    }
+    fclose(fp);
+  }
+}
+
 /* ---------------------------------------------------------------------- */
 
 double Bond::memory_usage()
diff --git a/src/bond.h b/src/bond.h
index 6841e9362d..d455cda204 100644
--- a/src/bond.h
+++ b/src/bond.h
@@ -54,6 +54,8 @@ class Bond : protected Pointers {
   virtual unsigned int data_mask() {return datamask;}
   virtual unsigned int data_mask_ext() {return datamask_ext;}
 
+  void write_file(int, char**);
+
  protected:
   int suffix_flag;             // suffix compatibility flag
 
diff --git a/src/input.cpp b/src/input.cpp
index 3ceb906911..bcb64effe9 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -644,6 +644,7 @@ int Input::execute_command()
   else if (!strcmp(command,"atom_style")) atom_style();
   else if (!strcmp(command,"bond_coeff")) bond_coeff();
   else if (!strcmp(command,"bond_style")) bond_style();
+  else if (!strcmp(command,"bond_write")) bond_write();
   else if (!strcmp(command,"boundary")) boundary();
   else if (!strcmp(command,"box")) box();
   else if (!strcmp(command,"comm_modify")) comm_modify();
@@ -1281,6 +1282,17 @@ void Input::bond_style()
 
 /* ---------------------------------------------------------------------- */
 
+void Input::bond_write()
+{
+  if (atom->avec->bonds_allow == 0)
+    error->all(FLERR,"Bond_write command when no bonds allowed");
+  if (force->bond == NULL)
+    error->all(FLERR,"Bond_write command before bond_style is defined");
+  else force->bond->write_file(narg,arg);
+}
+
+/* ---------------------------------------------------------------------- */
+
 void Input::boundary()
 {
   if (domain->box_exist)
diff --git a/src/input.h b/src/input.h
index 9bdedabe14..ccda3f49b1 100644
--- a/src/input.h
+++ b/src/input.h
@@ -86,6 +86,7 @@ class Input : protected Pointers {
   void atom_style();
   void bond_coeff();
   void bond_style();
+  void bond_write();
   void boundary();
   void box();
   void comm_modify();
diff --git a/src/pair.cpp b/src/pair.cpp
index 89c5bea380..e3c4a1aa36 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -1574,9 +1574,9 @@ void Pair::write_file(int narg, char **arg)
     fprintf(fp,"# Pair potential %s for atom types %d %d: i,r,energy,force\n",
             force->pair_style,itype,jtype);
     if (style == RLINEAR)
-      fprintf(fp,"\n%s\nN %d R %g %g\n\n",arg[7],n,inner,outer);
+      fprintf(fp,"\n%s\nN %d R %.15g %.15g\n\n",arg[7],n,inner,outer);
     if (style == RSQ)
-      fprintf(fp,"\n%s\nN %d RSQ %g %g\n\n",arg[7],n,inner,outer);
+      fprintf(fp,"\n%s\nN %d RSQ %.15g %.15g\n\n",arg[7],n,inner,outer);
   }
 
   // initialize potentials before evaluating pair potential
@@ -1618,7 +1618,7 @@ void Pair::write_file(int narg, char **arg)
     init_bitmap(inner,outer,n,masklo,maskhi,nmask,nshiftbits);
     int ntable = 1 << n;
     if (me == 0)
-      fprintf(fp,"\n%s\nN %d BITMAP %g %g\n\n",arg[7],ntable,inner,outer);
+      fprintf(fp,"\n%s\nN %d BITMAP %.15g %.15g\n\n",arg[7],ntable,inner,outer);
     n = ntable;
   }
 
@@ -1647,7 +1647,7 @@ void Pair::write_file(int narg, char **arg)
       e = single(0,1,itype,jtype,rsq,1.0,1.0,f);
       f *= r;
     } else e = f = 0.0;
-    if (me == 0) fprintf(fp,"%d %g %g %g\n",i+1,r,e,f);
+    if (me == 0) fprintf(fp,"%d %.15g %.15g %.15g\n",i+1,r,e,f);
   }
 
   // restore original vecs that were swapped in for
diff --git a/src/pair_table.cpp b/src/pair_table.cpp
index 1013bd3677..71b4d49b5f 100644
--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@@ -395,13 +395,16 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
   union_int_float_t rsq_lookup;
 
   int rerror = 0;
+  int cerror = 0;
 
   fgets(line,MAXLINE,fp);
   for (int i = 0; i < tb->ninput; i++) {
-    fgets(line,MAXLINE,fp);
-    sscanf(line,"%d %lg %lg %lg",&itmp,&rfile,&tb->efile[i],&tb->ffile[i]);
-    rnew = rfile;
+    if (NULL == fgets(line,MAXLINE,fp))
+      error->one(FLERR,"Premature end of file in pair table");
+    if (4 != sscanf(line,"%d %lg %lg %lg",
+                    &itmp,&rfile,&tb->efile[i],&tb->ffile[i]))  ++cerror;
 
+    rnew = rfile;
     if (tb->rflag == RLINEAR)
       rnew = tb->rlo + (tb->rhi - tb->rlo)*i/(tb->ninput-1);
     else if (tb->rflag == RSQ) {
@@ -419,6 +422,7 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
     }
 
     if (tb->rflag && fabs(rnew-rfile)/rfile > EPSILONR) rerror++;
+
     tb->rfile[i] = rnew;
   }
 
@@ -452,8 +456,8 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
 
   if (ferror) {
     char str[128];
-    sprintf(str,"%d force values in table are inconsistent with -dE/dr; "
-            "should only be mistakenly flagged at inflection points",ferror);
+    sprintf(str,"%d of %d force values in table are inconsistent with -dE/dr.\n"
+            "  Should only be flagged at inflection points",ferror,tb->ninput);
     error->warning(FLERR,str);
   }
 
@@ -461,8 +465,17 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
 
   if (rerror) {
     char str[128];
-    sprintf(str,"%d distance values in table differ signifcantly "
-            "from re-computed values",rerror);
+    sprintf(str,"%d of %d distance values in table with relative error\n"
+            "  over %g to re-computed values",rerror,tb->ninput,EPSILONR);
+    error->warning(FLERR,str);
+  }
+
+  // warn if data was read incompletely, e.g. columns were missing
+
+  if (cerror) {
+    char str[128];
+    sprintf(str,"%d of %d lines in table were incomplete\n"
+            "  or could not be parsed completely",cerror,tb->ninput);
     error->warning(FLERR,str);
   }
 }

From d8a711e50ea14de5f87bad21531eea0993dc6515 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 7 Apr 2016 21:13:52 +0000
Subject: [PATCH 06/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@14810
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Section_commands.html         |   4 +-
 doc/Section_commands.txt          |   4 +-
 doc/_images/fix_nh1.jpg           | Bin 31088 -> 68243 bytes
 doc/_sources/Manual.txt           |   4 +-
 doc/_sources/Section_commands.txt |   4 +-
 doc/_sources/bond_table.txt       |   2 +-
 doc/_sources/lattice.txt          |   8 +-
 doc/_sources/pair_colloid.txt     |   2 +-
 doc/_sources/pair_dpd.txt         |   2 +-
 doc/_sources/pair_table.txt       |   2 +-
 doc/_sources/pair_tersoff_mod.txt |   3 +
 doc/_sources/pair_tersoff_zbl.txt |   3 +
 doc/_sources/pair_write.txt       |   1 +
 doc/_sources/temper.txt           |   6 +-
 doc/bond_table.html               |   2 +-
 doc/bond_table.txt                |   2 +-
 doc/bond_write.html               | 248 ++++++++++++++++++++++++++++++
 doc/bond_write.txt                |  64 ++++++++
 doc/genindex.html                 |   8 +-
 doc/lattice.html                  |   8 +-
 doc/pair_colloid.html             |   4 +-
 doc/pair_colloid.txt              |   2 +-
 doc/pair_dpd.html                 |   2 +-
 doc/pair_dpd.txt                  |   2 +-
 doc/pair_table.html               |   2 +-
 doc/pair_table.txt                |   2 +-
 doc/pair_tersoff_mod.html         |   3 +
 doc/pair_tersoff_mod.txt          |   1 +
 doc/pair_tersoff_zbl.html         |   3 +
 doc/pair_tersoff_zbl.txt          |   1 +
 doc/pair_write.html               |   3 +-
 doc/pair_write.txt                |   1 +
 doc/searchindex.js                |   2 +-
 doc/temper.html                   |   6 +-
 doc/temper.txt                    |   6 +-
 35 files changed, 379 insertions(+), 38 deletions(-)
 create mode 100644 doc/bond_write.html
 create mode 100644 doc/bond_write.txt

diff --git a/doc/Section_commands.html b/doc/Section_commands.html
index 6f1ec8745b..a0b5680239 100644
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -1157,9 +1157,9 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
 <tr class="row-even"><td><a class="reference internal" href="pair_sw.html"><em>sw (cgkio)</em></a></td>
 <td><a class="reference internal" href="pair_table.html"><em>table (gko)</em></a></td>
 <td><a class="reference internal" href="pair_tersoff.html"><em>tersoff (cgkio)</em></a></td>
-<td><a class="reference internal" href="pair_tersoff_mod.html"><em>tersoff/mod (ko)</em></a></td>
+<td><a class="reference internal" href="pair_tersoff_mod.html"><em>tersoff/mod (gko)</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="pair_tersoff_zbl.html"><em>tersoff/zbl (ko)</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="pair_tersoff_zbl.html"><em>tersoff/zbl (gko)</em></a></td>
 <td><a class="reference internal" href="pair_coul.html"><em>tip4p/cut (o)</em></a></td>
 <td><a class="reference internal" href="pair_coul.html"><em>tip4p/long (o)</em></a></td>
 <td><a class="reference internal" href="pair_tri_lj.html"><em>tri/lj</em></a></td>
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 977993ee4b..d0f5e34bad 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -905,8 +905,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "sw (cgkio)"_pair_sw.html,
 "table (gko)"_pair_table.html,
 "tersoff (cgkio)"_pair_tersoff.html,
-"tersoff/mod (ko)"_pair_tersoff_mod.html,
-"tersoff/zbl (ko)"_pair_tersoff_zbl.html,
+"tersoff/mod (gko)"_pair_tersoff_mod.html,
+"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
 "tip4p/cut (o)"_pair_coul.html,
 "tip4p/long (o)"_pair_coul.html,
 "tri/lj"_pair_tri_lj.html,
diff --git a/doc/_images/fix_nh1.jpg b/doc/_images/fix_nh1.jpg
index db59dbc43e6f922be085465f9837738c468297e5..af07ea3a4b3a197d6b415937d1325a7c2a5a4a00 100644
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diff --git a/doc/_sources/Manual.txt b/doc/_sources/Manual.txt
index 9f3d82bd5c..273536104f 100644
--- a/doc/_sources/Manual.txt
+++ b/doc/_sources/Manual.txt
@@ -5,8 +5,8 @@
 LAMMPS Documentation
 ====================
 
-23 Mar 2016 version
--------------------
+28 Mar20 2016 version
+---------------------
 
 Version info:
 -------------
diff --git a/doc/_sources/Section_commands.txt b/doc/_sources/Section_commands.txt
index 39eb381979..8c872a653f 100644
--- a/doc/_sources/Section_commands.txt
+++ b/doc/_sources/Section_commands.txt
@@ -636,9 +636,9 @@ KOKKOS, o = USER-OMP, t = OPT.
 +-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+
 | :doc:`rebo (o) <pair_airebo>`                             | :doc:`resquared (go) <pair_resquared>`              | :doc:`snap <pair_snap>`                            | :doc:`soft (go) <pair_soft>`                          |
 +-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+
-| :doc:`sw (cgkio) <pair_sw>`                               | :doc:`table (gko) <pair_table>`                     | :doc:`tersoff (cgkio) <pair_tersoff>`              | :doc:`tersoff/mod (ko) <pair_tersoff_mod>`            |
+| :doc:`sw (cgkio) <pair_sw>`                               | :doc:`table (gko) <pair_table>`                     | :doc:`tersoff (cgkio) <pair_tersoff>`              | :doc:`tersoff/mod (gko) <pair_tersoff_mod>`           |
 +-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+
-| :doc:`tersoff/zbl (ko) <pair_tersoff_zbl>`                | :doc:`tip4p/cut (o) <pair_coul>`                    | :doc:`tip4p/long (o) <pair_coul>`                  | :doc:`tri/lj <pair_tri_lj>`                           |
+| :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`               | :doc:`tip4p/cut (o) <pair_coul>`                    | :doc:`tip4p/long (o) <pair_coul>`                  | :doc:`tri/lj <pair_tri_lj>`                           |
 +-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+
 | :doc:`vashishta (o) <pair_vashishta>`                     | :doc:`yukawa (go) <pair_yukawa>`                    | :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`   | :doc:`zbl (go) <pair_zbl>`                            |
 +-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+
diff --git a/doc/_sources/bond_table.txt b/doc/_sources/bond_table.txt
index 11aebc8b72..b6d4bee1a1 100644
--- a/doc/_sources/bond_table.txt
+++ b/doc/_sources/bond_table.txt
@@ -110,7 +110,7 @@ values in the table.
 
 The "EQ" parameter is also optional.  If used, it is followed by a the
 equilibrium bond length, which is used, for example, by the :doc:`fix shake <fix_shake>` command.  If not used, the equilibrium bond
-length is set to 0.0.
+length is to the distance in the table with the lowest potential energy.
 
 Following a blank line, the next N lines list the tabulated values.
 On each line, the 1st value is the index from 1 to N, the 2nd value is
diff --git a/doc/_sources/lattice.txt b/doc/_sources/lattice.txt
index 5b73cda966..1f6c4638da 100644
--- a/doc/_sources/lattice.txt
+++ b/doc/_sources/lattice.txt
@@ -275,7 +275,7 @@ of Aidan Thompson), with its 8 atom unit cell.
    variable 1_6 equal 1.0/6.0
    variable 5_6 equal 5.0/6.0
    variable 1_12 equal 1.0/12.0
-   variable 5_12 equal 5.0/12/0
+   variable 5_12 equal 5.0/12.0
 
 .. parsed-literal::
 
@@ -296,7 +296,11 @@ of Aidan Thompson), with its 8 atom unit cell.
 
    region myreg block 0 1 0 1 0 1
    create_box      2 myreg
-   create_atoms    1 box
+   create_atoms    1 box      &
+           basis   5       2       &
+           basis   6       2       &
+           basis   7       2       &
+           basis   8       2
 
 
 ----------
diff --git a/doc/_sources/pair_colloid.txt b/doc/_sources/pair_colloid.txt
index d2684eb43b..b49fd7f2d7 100644
--- a/doc/_sources/pair_colloid.txt
+++ b/doc/_sources/pair_colloid.txt
@@ -128,7 +128,7 @@ colloid-solvent cutoff in this case.
 
    When using pair_style colloid for a mixture with 2 (or more)
    widely different particles sizes (e.g. sigma=10 colloids in a
-   background sigam=1 LJ fluid), you will likely want to use these
+   background sigma=1 LJ fluid), you will likely want to use these
    commands for efficiency: :doc:`neighbor multi <neighbor>` and
    :doc:`comm_modify multi <comm_modify>`.
 
diff --git a/doc/_sources/pair_dpd.txt b/doc/_sources/pair_dpd.txt
index 0236f22845..1015e66b56 100644
--- a/doc/_sources/pair_dpd.txt
+++ b/doc/_sources/pair_dpd.txt
@@ -58,7 +58,7 @@ field.  This pair-wise thermostat can be used in conjunction with any
 :doc:`pair style <pair_style>`, and in leiu of per-particle thermostats
 like :doc:`fix langevin <fix_langevin>` or ensemble thermostats like
 Nose Hoover as implemented by :doc:`fix nvt <fix_nh>`.  To use
-*dpd/stat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay <pair_hybrid>` command to compute both the desired
+*dpd/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay <pair_hybrid>` command to compute both the desired
 pair interaction and the thermostat for each pair of particles.
 
 For style *dpd*, the force on atom I due to atom J is given as a sum
diff --git a/doc/_sources/pair_table.txt b/doc/_sources/pair_table.txt
index 9d3bad87f4..53fe626aec 100644
--- a/doc/_sources/pair_table.txt
+++ b/doc/_sources/pair_table.txt
@@ -279,7 +279,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`pair_write <pair_write>`
 
 **Default:** none
 
diff --git a/doc/_sources/pair_tersoff_mod.txt b/doc/_sources/pair_tersoff_mod.txt
index 949893a752..8f38096fae 100644
--- a/doc/_sources/pair_tersoff_mod.txt
+++ b/doc/_sources/pair_tersoff_mod.txt
@@ -3,6 +3,9 @@
 pair_style tersoff/mod command
 ==============================
 
+pair_style tersoff/mod/gpu command
+==================================
+
 pair_style tersoff/mod/kk command
 =================================
 
diff --git a/doc/_sources/pair_tersoff_zbl.txt b/doc/_sources/pair_tersoff_zbl.txt
index 9b19956b34..f1f5c3c5aa 100644
--- a/doc/_sources/pair_tersoff_zbl.txt
+++ b/doc/_sources/pair_tersoff_zbl.txt
@@ -3,6 +3,9 @@
 pair_style tersoff/zbl command
 ==============================
 
+pair_style tersoff/zbl/gpu command
+==================================
+
 pair_style tersoff/zbl/kk command
 =================================
 
diff --git a/doc/_sources/pair_write.txt b/doc/_sources/pair_write.txt
index ec6e2a3fb8..94bf06230a 100644
--- a/doc/_sources/pair_write.txt
+++ b/doc/_sources/pair_write.txt
@@ -78,6 +78,7 @@ pairwise portion of the potential, not the embedding portion.
 Related commands
 """"""""""""""""
 
+:doc:`pair_style table <pair_table>`,
 :doc:`pair_style <pair_style>`, :doc:`pair_coeff <pair_coeff>`
 
 **Default:** none
diff --git a/doc/_sources/temper.txt b/doc/_sources/temper.txt
index db8ca2a205..21ddf42a13 100644
--- a/doc/_sources/temper.txt
+++ b/doc/_sources/temper.txt
@@ -43,9 +43,9 @@ would see with one or more physical processors per replica.  See :ref:`this sect
 discussion.
 
 Each replica's temperature is controlled at a different value by a fix
-with *fix-ID* that controls temperature.  Possible fix styles are
-:doc:`nvt <fix_nh>`, :doc:`temp/berendsen <fix_nh>`,
-:doc:`langevin <fix_langevin>` and :doc:`temp/rescale <fix_temp_rescale>`.
+with *fix-ID* that controls temperature. Most thermostat fix styles
+(with and without included time integration) are supported. The command
+will print an error message and abort, if the chosen fix is unsupported.
 The desired temperature is specified by *temp*, which is typically a
 variable previously set in the input script, so that each partition is
 assigned a different temperature.  See the :doc:`variable <variable>`
diff --git a/doc/bond_table.html b/doc/bond_table.html
index 6f506973a6..fa8162a92c 100644
--- a/doc/bond_table.html
+++ b/doc/bond_table.html
@@ -217,7 +217,7 @@ are estimated (less accurately) by the first two and last two force
 values in the table.</p>
 <p>The &#8220;EQ&#8221; parameter is also optional.  If used, it is followed by a the
 equilibrium bond length, which is used, for example, by the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command.  If not used, the equilibrium bond
-length is set to 0.0.</p>
+length is to the distance in the table with the lowest potential energy.</p>
 <p>Following a blank line, the next N lines list the tabulated values.
 On each line, the 1st value is the index from 1 to N, the 2nd value is
 the bond length r (in distance units), the 3rd value is the energy (in
diff --git a/doc/bond_table.txt b/doc/bond_table.txt
index f4235f10ef..7d4191cf7e 100644
--- a/doc/bond_table.txt
+++ b/doc/bond_table.txt
@@ -101,7 +101,7 @@ values in the table.
 The "EQ" parameter is also optional.  If used, it is followed by a the
 equilibrium bond length, which is used, for example, by the "fix
 shake"_fix_shake.html command.  If not used, the equilibrium bond
-length is set to 0.0.
+length is to the distance in the table with the lowest potential energy.
 
 Following a blank line, the next N lines list the tabulated values.
 On each line, the 1st value is the index from 1 to N, the 2nd value is
diff --git a/doc/bond_write.html b/doc/bond_write.html
new file mode 100644
index 0000000000..75966abad2
--- /dev/null
+++ b/doc/bond_write.html
@@ -0,0 +1,248 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
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+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
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+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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+            <a href="Section_commands.html#comm">Commands</a>
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+           <div itemprop="articleBody">
+            
+  <div class="section" id="bond-write-command">
+<span id="index-0"></span><h1>bond_write command<a class="headerlink" href="#bond-write-command" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="syntax">
+<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>bond_write btype N inner outer file keyword itype jtype
+</pre></div>
+</div>
+<ul class="simple">
+<li>btype = bond types</li>
+<li>N = # of values</li>
+<li>inner,outer = inner and outer bond length (distance units)</li>
+<li>file = name of file to write values to</li>
+<li>keyword = section name in file for this set of tabulated values</li>
+<li>itype,jtype = 2 atom types (optional)</li>
+<li></li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>bond_write 1 500 0.5 3.5 table.txt Harmonic_1
+bond_write 3 1000 0.1 6.0 table.txt Morse
+</pre></div>
+</div>
+</div>
+<div class="section" id="description">
+<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
+<p>Write energy and force values to a file as a function of distance for
+the currently defined bond potential.  This is useful for plotting the
+potential function or otherwise debugging its values.  If the file
+already exists, the table of values is appended to the end of the file
+to allow multiple tables of energy and force to be included in one
+file.</p>
+<p>The energy and force values are computed at distances from inner to
+outer for 2 interacting atoms forming a bond of type btype, using the
+appropriate <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> coefficients. N evenly spaced
+distances are used.</p>
+<p>For example, for N = 7, inner = 1.0, and outer = 4.0,
+values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.</p>
+<p>The file is written in the format used as input for the
+<a class="reference internal" href="bond_style.html"><em>bond_style</em></a> <em>table</em> option with <em>keyword</em> as the
+section name.  Each line written to the file lists an index number
+(1-N), a distance (in distance units), an energy (in energy units),
+and a force (in force units).</p>
+</div>
+<div class="section" id="restrictions">
+<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
+<p>All force field coefficients for bond and other kinds of interactions
+must be set before this command can be invoked.</p>
+<p>Due to how the bond force is computed, an inner value &gt; 0.0 must
+be specified even if the potential has a finite value at r = 0.0.</p>
+</div>
+<div class="section" id="related-commands">
+<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference internal" href="bond_table.html"><em>bond_style table</em></a>,
+<a class="reference internal" href="bond_style.html"><em>bond_style</em></a>, <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a></p>
+<p><strong>Default:</strong> none</p>
+</div>
+</div>
+
+
+           </div>
+          </div>
+          <footer>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2013 Sandia Corporation.
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+  
+
+
+  
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+      <script type="text/javascript" src="_static/jquery.js"></script>
+      <script type="text/javascript" src="_static/underscore.js"></script>
+      <script type="text/javascript" src="_static/doctools.js"></script>
+      <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
+
+  
+
+  
+  
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+  
+
+  
+  
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+   
+
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/bond_write.txt b/doc/bond_write.txt
new file mode 100644
index 0000000000..4797d06cb1
--- /dev/null
+++ b/doc/bond_write.txt
@@ -0,0 +1,64 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+bond_write command :h3
+
+[Syntax:]
+
+bond_write btype N inner outer file keyword itype jtype :pre
+
+btype = bond types
+N = # of values
+inner,outer = inner and outer bond length (distance units)
+file = name of file to write values to
+keyword = section name in file for this set of tabulated values
+itype,jtype = 2 atom types (optional)
+:ul
+
+[Examples:]
+
+bond_write 1 500 0.5 3.5 table.txt Harmonic_1
+bond_write 3 1000 0.1 6.0 table.txt Morse :pre
+
+[Description:]
+
+Write energy and force values to a file as a function of distance for
+the currently defined bond potential.  This is useful for plotting the
+potential function or otherwise debugging its values.  If the file
+already exists, the table of values is appended to the end of the file
+to allow multiple tables of energy and force to be included in one
+file.
+
+The energy and force values are computed at distances from inner to
+outer for 2 interacting atoms forming a bond of type btype, using the
+appropriate "bond_coeff"_bond_coeff.html coefficients. N evenly spaced
+distances are used.
+
+For example, for N = 7, inner = 1.0, and outer = 4.0,
+values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.
+
+The file is written in the format used as input for the
+"bond_style"_bond_style.html {table} option with {keyword} as the
+section name.  Each line written to the file lists an index number
+(1-N), a distance (in distance units), an energy (in energy units),
+and a force (in force units).
+
+[Restrictions:]
+
+All force field coefficients for bond and other kinds of interactions
+must be set before this command can be invoked.
+
+Due to how the bond force is computed, an inner value > 0.0 must
+be specified even if the potential has a finite value at r = 0.0.
+
+[Related commands:]
+
+"bond_style table"_bond_table.html,
+"bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html
+
+[Default:] none
diff --git a/doc/genindex.html b/doc/genindex.html
index 73772deeff..593cb434dd 100644
--- a/doc/genindex.html
+++ b/doc/genindex.html
@@ -287,12 +287,12 @@
   <dt><a href="bond_harmonic_shift_cut.html#index-0">bond_style harmonic/shift/cut</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="bond_hybrid.html#index-0">bond_style hybrid</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="bond_morse.html#index-0">bond_style morse</a>
   </dt>
@@ -318,6 +318,10 @@
   </dt>
 
       
+  <dt><a href="bond_write.html#index-0">bond_write</a>
+  </dt>
+
+      
   <dt><a href="boundary.html#index-0">boundary</a>
   </dt>
 
diff --git a/doc/lattice.html b/doc/lattice.html
index 4eecaba347..c4bdaa3334 100644
--- a/doc/lattice.html
+++ b/doc/lattice.html
@@ -359,7 +359,7 @@ variable 2_3 equal 2.0/3.0
 variable 1_6 equal 1.0/6.0
 variable 5_6 equal 5.0/6.0
 variable 1_12 equal 1.0/12.0
-variable 5_12 equal 5.0/12/0
+variable 5_12 equal 5.0/12.0
 </pre></div>
 </div>
 <div class="highlight-python"><div class="highlight"><pre>lattice custom    1.0     &amp;
@@ -378,7 +378,11 @@ variable 5_12 equal 5.0/12/0
 </div>
 <div class="highlight-python"><div class="highlight"><pre>region myreg block 0 1 0 1 0 1
 create_box      2 myreg
-create_atoms    1 box
+create_atoms    1 box      &amp;
+        basis   5       2       &amp;
+        basis   6       2       &amp;
+        basis   7       2       &amp;
+        basis   8       2
 </pre></div>
 </div>
 </div>
diff --git a/doc/pair_colloid.html b/doc/pair_colloid.html
index d009a0fd6b..e2e1987eac 100644
--- a/doc/pair_colloid.html
+++ b/doc/pair_colloid.html
@@ -163,7 +163,7 @@ Lennard-Jones particle of size sigma.</p>
 colloidal particles, and Rc is the cutoff.  This equation results from
 describing each colloidal particle as an integrated collection of
 Lennard-Jones particles of size sigma and is derived in
-<a class="reference internal" href="pair_resquared.html#everaers"><span>(Everaers)</span></a>.</p>
+<a class="reference internal" href="#everaers"><span>(Everaers)</span></a>.</p>
 <p>The colloid-solvent interaction energy is given by</p>
 <img alt="_images/pair_colloid_cs.jpg" class="align-center" src="_images/pair_colloid_cs.jpg" />
 <p>where A_cs is the Hamaker constant, a is the radius of the colloidal
@@ -231,7 +231,7 @@ colloid-solvent cutoff in this case.</p>
 <p class="first admonition-title">Note</p>
 <p class="last">When using pair_style colloid for a mixture with 2 (or more)
 widely different particles sizes (e.g. sigma=10 colloids in a
-background sigam=1 LJ fluid), you will likely want to use these
+background sigma=1 LJ fluid), you will likely want to use these
 commands for efficiency: <a class="reference internal" href="neighbor.html"><em>neighbor multi</em></a> and
 <a class="reference internal" href="comm_modify.html"><em>comm_modify multi</em></a>.</p>
 </div>
diff --git a/doc/pair_colloid.txt b/doc/pair_colloid.txt
index 4fb65f3f82..39b89e710e 100644
--- a/doc/pair_colloid.txt
+++ b/doc/pair_colloid.txt
@@ -118,7 +118,7 @@ colloid-solvent cutoff in this case.
 
 NOTE: When using pair_style colloid for a mixture with 2 (or more)
 widely different particles sizes (e.g. sigma=10 colloids in a
-background sigam=1 LJ fluid), you will likely want to use these
+background sigma=1 LJ fluid), you will likely want to use these
 commands for efficiency: "neighbor multi"_neighbor.html and
 "comm_modify multi"_comm_modify.html.
 
diff --git a/doc/pair_dpd.html b/doc/pair_dpd.html
index 8ee2027f30..efd2360e27 100644
--- a/doc/pair_dpd.html
+++ b/doc/pair_dpd.html
@@ -177,7 +177,7 @@ field.  This pair-wise thermostat can be used in conjunction with any
 <a class="reference internal" href="pair_style.html"><em>pair style</em></a>, and in leiu of per-particle thermostats
 like <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a> or ensemble thermostats like
 Nose Hoover as implemented by <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>.  To use
-<em>dpd/stat</em> as a thermostat for another pair style, use the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> command to compute both the desired
+<em>dpd/tstat</em> as a thermostat for another pair style, use the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> command to compute both the desired
 pair interaction and the thermostat for each pair of particles.</p>
 <p>For style <em>dpd</em>, the force on atom I due to atom J is given as a sum
 of 3 terms</p>
diff --git a/doc/pair_dpd.txt b/doc/pair_dpd.txt
index c0c306eb38..dcfcf27d84 100644
--- a/doc/pair_dpd.txt
+++ b/doc/pair_dpd.txt
@@ -44,7 +44,7 @@ field.  This pair-wise thermostat can be used in conjunction with any
 "pair style"_pair_style.html, and in leiu of per-particle thermostats
 like "fix langevin"_fix_langevin.html or ensemble thermostats like
 Nose Hoover as implemented by "fix nvt"_fix_nh.html.  To use
-{dpd/stat} as a thermostat for another pair style, use the "pair_style
+{dpd/tstat} as a thermostat for another pair style, use the "pair_style
 hybrid/overlay"_pair_hybrid.html command to compute both the desired
 pair interaction and the thermostat for each pair of particles.
 
diff --git a/doc/pair_table.html b/doc/pair_table.html
index 35bf6af10d..db745338dd 100644
--- a/doc/pair_table.html
+++ b/doc/pair_table.html
@@ -359,7 +359,7 @@ commands do need to be specified in the restart input script.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
-<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
+<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="pair_write.html"><em>pair_write</em></a></p>
 <p><strong>Default:</strong> none</p>
 <hr class="docutils" />
 <p id="wolff"><strong>(Wolff)</strong> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).</p>
diff --git a/doc/pair_table.txt b/doc/pair_table.txt
index 0825d00bb2..bffcef4f8a 100644
--- a/doc/pair_table.txt
+++ b/doc/pair_table.txt
@@ -261,7 +261,7 @@ This pair style can only be used via the {pair} keyword of the
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html
+"pair_coeff"_pair_coeff.html, "pair_write"_pair_write.html
 
 [Default:] none
 
diff --git a/doc/pair_tersoff_mod.html b/doc/pair_tersoff_mod.html
index 6bd967f1ee..694bbb5988 100644
--- a/doc/pair_tersoff_mod.html
+++ b/doc/pair_tersoff_mod.html
@@ -127,6 +127,9 @@
   <div class="section" id="pair-style-tersoff-mod-command">
 <span id="index-0"></span><h1>pair_style tersoff/mod command<a class="headerlink" href="#pair-style-tersoff-mod-command" title="Permalink to this headline">¶</a></h1>
 </div>
+<div class="section" id="pair-style-tersoff-mod-gpu-command">
+<h1>pair_style tersoff/mod/gpu command<a class="headerlink" href="#pair-style-tersoff-mod-gpu-command" title="Permalink to this headline">¶</a></h1>
+</div>
 <div class="section" id="pair-style-tersoff-mod-kk-command">
 <h1>pair_style tersoff/mod/kk command<a class="headerlink" href="#pair-style-tersoff-mod-kk-command" title="Permalink to this headline">¶</a></h1>
 </div>
diff --git a/doc/pair_tersoff_mod.txt b/doc/pair_tersoff_mod.txt
index 8e87fa8e89..2b17800140 100644
--- a/doc/pair_tersoff_mod.txt
+++ b/doc/pair_tersoff_mod.txt
@@ -7,6 +7,7 @@
 :line
 
 pair_style tersoff/mod command :h3
+pair_style tersoff/mod/gpu command :h3
 pair_style tersoff/mod/kk command :h3
 pair_style tersoff/mod/omp command :h3
 
diff --git a/doc/pair_tersoff_zbl.html b/doc/pair_tersoff_zbl.html
index 891ac9f5c9..003636dc71 100644
--- a/doc/pair_tersoff_zbl.html
+++ b/doc/pair_tersoff_zbl.html
@@ -127,6 +127,9 @@
   <div class="section" id="pair-style-tersoff-zbl-command">
 <span id="index-0"></span><h1>pair_style tersoff/zbl command<a class="headerlink" href="#pair-style-tersoff-zbl-command" title="Permalink to this headline">¶</a></h1>
 </div>
+<div class="section" id="pair-style-tersoff-zbl-gpu-command">
+<h1>pair_style tersoff/zbl/gpu command<a class="headerlink" href="#pair-style-tersoff-zbl-gpu-command" title="Permalink to this headline">¶</a></h1>
+</div>
 <div class="section" id="pair-style-tersoff-zbl-kk-command">
 <h1>pair_style tersoff/zbl/kk command<a class="headerlink" href="#pair-style-tersoff-zbl-kk-command" title="Permalink to this headline">¶</a></h1>
 </div>
diff --git a/doc/pair_tersoff_zbl.txt b/doc/pair_tersoff_zbl.txt
index b2a8537b27..7b8097dc0c 100644
--- a/doc/pair_tersoff_zbl.txt
+++ b/doc/pair_tersoff_zbl.txt
@@ -7,6 +7,7 @@
 :line
 
 pair_style tersoff/zbl command :h3
+pair_style tersoff/zbl/gpu command :h3
 pair_style tersoff/zbl/kk command :h3
 pair_style tersoff/zbl/omp command :h3
 
diff --git a/doc/pair_write.html b/doc/pair_write.html
index c9e5121789..086cbcd7bf 100644
--- a/doc/pair_write.html
+++ b/doc/pair_write.html
@@ -189,7 +189,8 @@ pairwise portion of the potential, not the embedding portion.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
-<p><a class="reference internal" href="pair_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
+<p><a class="reference internal" href="pair_table.html"><em>pair_style table</em></a>,
+<a class="reference internal" href="pair_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
 <p><strong>Default:</strong> none</p>
 </div>
 </div>
diff --git a/doc/pair_write.txt b/doc/pair_write.txt
index 29ac26ad8a..9f5970fcbc 100644
--- a/doc/pair_write.txt
+++ b/doc/pair_write.txt
@@ -73,6 +73,7 @@ pairwise portion of the potential, not the embedding portion.
 
 [Related commands:]
 
+"pair_style table"_pair_table.html,
 "pair_style"_pair_style.html, "pair_coeff"_pair_coeff.html
 
 [Default:] none
diff --git a/doc/searchindex.js b/doc/searchindex.js
index d0f14a29a8..95721c31ec 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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292,302,304,365,411,413,513],chiefli:446,child:8,chip:[7,9,12,17,18,384,498],chipot:229,chiral:362,chmod:[11,12],cho:434,chocol:[7,204],choic:[3,6,9,12,15,16,18,41,42,55,94,151,154,155,169,180,196,216,220,221,224,227,230,231,245,251,254,265,267,294,302,311,334,363,370,375,376,379,381,384,417,430,439,443,485,494,495,498,499,505,506,511],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,94,127,166,167,203,225,226,227,228,231,240,251,254,265,267,269,270,271,272,273,274,275,297,298,315,327,331,345,369,370,376,474,480,482,494,500],chose:[468,470],chosen:[2,3,6,12,17,150,176,179,188,196,203,209,214,228,231,240,243,244,252,254,265,267,272,294,297,308,327,331,334,335,340,342,343,349,370,371,376,384,405,406,410,414,421,424,450,468,480,494,499,506],chri:174,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[69,79,97,102,113,115,124,156,171,173,216],chute:[4,9,10,246],ciccotti:314,cieplak:[6,182,497],cii:217,cij:217,ciko:2,circl:[43,75,323],circular:[3,6,154,198],circumst:18,circumv:[99,116,306],citat:[],cite:[3,7,8,12,251,455],civ:9,ckio:2,cko:2,cl1:175,clarendon:[29,403],clarifi:[7,468,470],clariti:352,clark:442,class2:[],classic:[0,3,5,6,7,8,9,241,294,301,306,339,364,410],classifi:[465,473],claus:483,clean:[6,12,14,15,17,493],cleanli:[484,515],clear:[],clearli:7,clebsch:150,clermont:[9,13],clever:489,click:[2,11,22,37,45,56,176,184,195,203,248,354,363,379,397,465,507],client:[248,250],climb:[266,379,499],clinic:[7,13],clo:[165,199,513],clock:[12,480,499],clockwis:345,clone:507,close:[3,6,11,12,13,40,42,70,75,151,179,200,226,227,228,245,252,254,267,288,311,314,345,348,368,370,373,375,376,379,384,386,390,400,401,420,434,439,447,451,453,467,470,489,495,506,507,509],closer:[3,10,42,126,174,199,200,224,228,232,336,379],closest:[226,292,311,342,413,449,464,474],cloud:[455,506],clovertown:18,clsuter:76,clump1:[296,311],clump2:[296,311],clump3:[296,311],clump:311,cluster:[],clutter:3,cmap:485,cmatrix:245,cmax:434,cmd:[11,12,294,496],cmdarg:11,cmin:434,cmm:[],cmoput:143,cn1:217,cn2:217,cna:[],cnn:217,cnr:[9,13],cnt:[417,489],co2:[41,175,314,378],coars:[7,9,10,29,36,41,55,188,296,311,327,415,450,494,497],coarser:[370,512],coarsest:150,code:[],coeff:[3,7,8,12,21,22,33,45,51,182,183,184,189,353,354,360,397,417,421,439,452,454,457,485],coeffcient:485,coeffici:[],coefficienct:404,coefficient0:408,coefficient1:408,coeffieci:[6,388,420],coeffincientn:408,coexist:[243,410],cohes:[6,411,434],coincid:[132,348,395,431,432,480],colberg:202,cold:[6,161,243,247,380,506],coldest:335,coleman8:9,coleman:[9,128,175,312],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,69,79,90,97,102,107,113,115,124,156,164,171,173,176,200,201,204,216,229,257,263,296,306,309,311,350,369,378,380,398,485,492,498,504,516],collid:[235,327,349],colliex:175,collinear:[3,296],collis:[3,254,327,345,349,407,414,477],colllis:327,colloid:[],colombo:40,colon:[205,350,486],color1:204,color2:204,color:[3,9,42,200,203,204,224,244,301,306],column:[3,6,9,12,13,43,65,68,69,70,71,73,75,79,81,84,86,88,97,99,101,102,113,115,116,118,120,123,124,125,126,127,129,150,151,156,164,171,173,174,175,196,200,201,204,207,215,216,217,219,220,221,222,257,264,265,301,311,328,329,339,349,412,416,447,448,486,500,502,512],columnar:174,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:384,comb3:[],comb:[],comb_1:303,comb_2:303,combiant:401,combin:[3,6,7,9,11,13,36,41,65,68,73,84,94,101,112,118,125,154,155,169,200,203,213,219,248,257,267,294,300,315,331,340,348,351,353,369,370,372,376,384,398,400,401,406,410,411,417,429,430,456,466,468,470,471,473,476,488,493,498,506,512],come:[],comfort:[12,13],comit:507,comm:[0,3,11,12,63,77,202,248,250,251,370,379,384,404,439,444,467,487],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,182,196,200,239,252,311,339,378,379,385,408,409,411,421,434,441,448,455,456,466,467,468,469,470,473,482,483,485,506,507,512],commerci:7,commit:[9,507],commmand:[3,6,12,61,117,289,420,479,480,482,499,515],common:[],commonli:[3,6,9,12,17,25,59,61,114,116,178,200,203,205,364,415,424,456,468,470,485,488,497],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,60,63,64,75,174,179,180,203,204,224,225,226,228,229,230,248,250,254,256,257,258,267,293,300,302,303,304,311,315,327,339,350,367,369,380,381,382,384,406,407,443,478,482,483,494,495,512,514,516],communc:369,comp:[7,202,250,251,314,370,379,410,439,444,449,463,467,469],compact:[65,207,397,465],compani:[5,7],compar:[1,3,4,6,8,12,17,40,93,120,128,159,175,184,195,204,234,302,350,352,369,370,377,379,434,455,480,499,500,506,511],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,183,184,195,353,354,363,396,465],compat:[3,5,7,8,9,11,12,13,17,18,42,75,127,129,187,200,205,209,215,216,217,219,220,221,222,224,293,305,331,334,341,344,347,369,384,418,437,439,467,482,483,512],compens:[6,225,226,309,380,410],compet:338,competit:370,compil:[3,7,8,9,12,13,14,15,16,17,18,19,174,200,202,203,205,248,338,370,384,437,485,486,490,512],compl:17,complain:[11,12,17],complement:434,complementari:[7,400,422],complet:[3,6,9,11,12,15,42,61,75,204,220,224,229,257,294,297,300,327,338,340,351,352,368,379,384,411,452,454,472,480,485,490,493,497,499,502,506,512],complex:[4,6,8,11,12,13,25,41,43,64,99,116,150,152,164,176,177,254,323,348,367,379,410,437,467,483,485,488,512],compli:[334,338],complic:[6,7,9,12,13,214,243,483],complier:12,compon:[3,6,8,12,63,65,69,70,77,86,95,96,97,98,99,102,103,106,113,114,115,116,117,118,119,120,122,123,127,137,140,141,142,143,146,147,148,150,151,153,154,155,156,157,158,159,160,161,162,163,164,165,166,168,169,171,172,173,199,200,201,203,204,210,211,215,216,217,218,219,220,221,222,223,227,228,230,231,236,241,246,250,251,254,257,259,263,264,266,267,268,272,273,274,275,286,287,288,290,291,293,294,295,298,309,311,313,314,316,320,321,324,327,330,331,332,334,341,342,347,348,349,369,372,376,377,378,379,384,404,410,414,431,432,452,454,455,456,485,486,495,503,512,513],componenet:6,composit:[6,214,254,408],compound:[399,410,411,473],compres:[75,124,216],compress:[],compris:[41,348,449,472],compton:[128,175],comptu:3,compuat:370,comput:[],computation:[3,6,225,226,339,390],computational:506,compute_arrai:8,compute_fep:[209,430],compute_group_group:243,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[128,312],compute_scalar:8,compute_temp:8,compute_ti:209,compute_vector:8,compute_xrd:175,concaten:[2,3,515],concav:348,concentr:[75,408],concept:[6,156,166,216,494],conceptu:[3,6,75,164,228,230,379,400,417,434,490],concern:[6,77,94,202,244],concetr:75,concis:[11,338],conclud:12,concret:8,concurr:[16,370,512],conden:[339,468,470],condens:[6,158,339,386,402,408,422,473],condit:[],conducit:6,conduct:[],cone:488,confer:437,confid:[3,499],config:[12,200,482],configfil:229,configur:[1,2,6,12,15,17,38,61,132,178,196,199,200,203,207,228,229,230,231,235,243,250,251,281,294,302,338,367,377,379,386,390,409,434,437,466,468,470,473,480,485,487,488,499,507],confin:[485,499],conflict:[3,12,41,201,439,483,507],conform:[3,6,13,61,227,228,266,310,316,338,362,379,410,497],confus:[3,473],conjuct:[9,404],conjug:[7,8,251,376,410,447,448],conjunct:[6,7,75,93,94,124,159,164,170,176,180,204,208,209,251,254,258,281,297,298,302,303,304,306,311,315,327,335,342,347,369,370,379,391,393,397,400,404,410,416,422,439,442,450,471,485,488,492,506,516],connect:[3,6,9,94,161,179,227,248,296,311,314,324,379,401,414,447,448,464,470,482,483,485,489,506],conner:386,connor:386,conput:3,consecut:[3,11,12,40,75,176,204,208,209,231,248,249,400,422,426,480,486,488],consequ:[1,6,214,339,421,499],conserv:[],consid:[6,74,75,82,94,125,158,161,162,179,200,201,204,208,209,215,217,220,224,226,227,231,255,268,293,311,334,335,338,339,342,370,397,410,417,448,449,455,464,480,481,483,486,487,488,490,493,495,503,506,512],consider:[6,8,251,252,330,331,332,384,494],consist:[3,6,8,9,11,12,41,43,68,73,84,101,113,118,121,122,125,156,159,161,176,188,199,205,210,211,216,230,231,234,236,241,244,251,252,253,264,267,269,270,271,272,273,274,275,276,277,279,280,281,282,284,285,286,287,288,289,290,298,301,306,308,310,311,330,331,332,333,343,369,370,372,378,379,384,386,390,392,398,400,410,413,417,420,431,432,434,437,439,449,452,454,455,467,474,483,485,486,487,488,489,490,497,506,512],consistent_fe_initi:213,consit:311,constant:[],constitu:[3,6,257,311,344,348,398,449],constitut:[452,454],constrain:[3,6,8,153,154,155,156,157,159,162,163,164,165,166,168,169,207,216,231,243,244,249,257,261,296,297,309,311,314,325,335,342,377,378,410,490,497,506],constraint:[],construct:[6,8,12,14,38,55,57,63,66,70,74,76,77,81,99,116,128,150,175,228,267,293,310,348,380,384,403,437,439,464,466,467,488,489,504,512],constructor:[8,11],consult:448,consum:[1,306,443,512],consumpt:367,contact:[],contact_stiff:[451,453],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,94,98,126,128,150,152,156,164,174,175,176,178,182,184,195,196,200,201,203,204,205,207,208,209,213,215,216,217,219,220,221,222,224,229,231,236,239,245,249,250,251,254,265,281,292,293,296,297,299,301,304,308,311,312,317,327,334,338,339,348,349,352,368,370,378,379,382,383,385,386,387,390,399,400,403,408,409,410,417,418,434,437,441,445,446,447,448,456,466,467,468,469,470,471,473,480,481,482,483,485,486,487,488,490,492,494,497,499,500,502,503,506,507,512,514,516],content:[4,8,9,12,18,448,501,503],context:[3,6,8,12,17,126,127,204,225,226,231,296,308,343,376,476,485,492,501,511,512,513],contibut:74,contigu:482,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,75,86,112,113,172,204,207,208,209,214,216,217,218,219,220,221,222,224,227,228,229,230,231,243,244,245,247,248,249,251,252,253,259,264,265,267,269,270,271,272,273,274,275,286,287,288,289,290,295,297,300,301,311,312,316,326,327,329,336,337,339,345,348,352,368,383,384,390,404,407,424,427,447,448,449,452,454,469,480,483,485,487,488,493,499,500,502,503,512,514],continuum:[6,7,9,213,339,452,454],contour_integr:213,contract:[61,228,230,267,298,311],contradictori:3,contrain:314,contraint:281,contrari:[245,252],contrast:[1,6,43,56,66,158,161,201,230,350,452,454,476,515],contrib:339,contribut:[3,4,5,6,7,8,9,12,13,17,65,67,69,71,72,74,75,78,79,81,83,85,91,94,95,96,97,98,100,102,111,113,115,117,118,119,120,122,124,127,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,209,214,215,216,217,219,220,221,222,228,243,251,254,257,258,262,268,288,289,296,297,305,308,311,312,314,341,369,377,379,387,404,407,408,410,417,431,432,437,439,447,448,455,497,503,506,507],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,94,98,132,150,185,200,201,203,207,213,214,224,228,229,230,247,248,251,252,267,269,270,271,272,273,274,275,298,303,311,318,319,330,331,332,339,343,367,369,381,410,413,437,447,448,451,453,466,470,480,482,494,500,501],control_typ:213,controlfil:448,convect:98,conveni:[6,12,29,200,205,222,312,372,456,471,507,512],convent:[3,8,29,187,194,195,201,204,310,324,351,408,410,512],converg:[3,6,42,95,200,201,203,205,210,224,227,228,236,241,272,301,303,306,310,314,375,376,377,379,399,400,422,455,480,492,499],convers:[3,8,150,203,204,214,217,298,369,400,401,402,410,422,426,430,442,483,499,511],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,75,98,176,183,200,203,204,217,222,265,297,350,353,355,359,362,372,379,385,408,437,468,470,477,483,485,486,487,492,502,506,511,512,514,516],convex:[43,348],convinc:[7,12],cook:9,cooki:7,cool:[7,166,247,309],cooordin:[200,201],cooper:[5,7],coord123:124,coord1:[3,124,216,220,221],coord2:[3,124,216,220,221],coord3:[3,124,216,220,221],coord:[],coordb:455,coordbb:455,coordiat:377,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,69,71,75,78,79,81,86,94,96,97,102,112,113,115,123,124,126,144,150,159,165,171,173,174,176,180,199,200,201,202,203,204,205,207,210,215,216,219,220,221,224,225,226,227,228,229,230,231,234,236,237,241,243,246,247,248,249,250,251,252,264,266,267,269,270,271,273,274,275,288,291,292,293,296,297,298,308,309,311,313,314,316,321,324,325,326,327,329,337,338,339,346,347,349,350,372,377,378,379,384,385,386,389,409,455,480,485,486,487,488,490,493,495,499,506,512,513],coordn:[124,216],coorind:[],copi:[0,3,4,8,9,11,12,15,17,41,129,203,339,379,397,447,483,507],copper:477,coproccesor:16,coprocessor:[1,7,9,16,17,384,498],coproprocessor:17,copy_arrai:8,copyright:[7,8,296],coral:204,core:[],core_shel:158,coreshel:[],cornel:[6,182,497],corner123i:123,corner123x:123,corner123z:123,corner1i:123,corner1x:123,corner1z:123,corner2i:123,corner2x:123,corner2z:123,corner3i:123,corner3x:123,corner3z:123,corner:[3,6,41,123,203,348,349,372,472,485,507],cornflowerblu:204,cornsilk:204,corp:9,corpor:16,corr:399,correct:[3,6,9,11,12,16,17,61,94,95,111,112,117,120,126,158,163,170,201,203,230,243,245,251,267,268,288,296,298,301,338,344,348,369,379,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,401,402,403,404,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,477,478,485,500,503,506,507],correction_max_iter:213,correctli:[3,8,11,17,75,86,111,112,113,153,154,155,157,159,161,162,163,164,165,168,169,172,200,204,210,231,236,241,252,261,267,268,304,311,314,324,326,345,348,379,380,384,402,432,437,482,483,485,495,507,511,513],correl:[],correpond:239,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,74,75,94,105,106,119,122,123,124,125,128,129,137,140,141,142,143,144,146,147,148,150,153,154,163,170,174,175,182,183,184,185,186,187,188,190,191,193,194,196,199,200,201,203,204,208,209,210,216,218,219,220,221,223,226,228,230,237,241,242,246,251,254,255,263,264,265,267,269,270,271,272,273,274,275,276,277,281,284,286,287,288,290,293,294,298,303,311,313,314,330,332,334,343,344,345,347,348,349,351,353,354,355,356,358,359,362,364,370,374,376,378,379,385,386,388,391,392,393,394,395,396,397,398,399,400,403,404,408,409,410,411,412,413,414,415,416,417,420,422,423,424,425,426,427,428,429,430,431,434,435,437,439,440,441,442,444,445,447,448,449,450,455,456,457,466,467,468,469,470,471,473,475,476,477,480,482,483,485,486,488,498,499,500,502,503,506,512],correspondingli:[431,432,494],corrupt:3,cosin:[],cosineshift:27,cosmo:[245,250],cossq:[],cost:[1,6,10,11,12,17,40,42,75,119,128,151,175,203,204,216,220,221,224,225,226,240,267,303,339,369,370,382,400,422,426,437,439,466,482,494],costheta0:[466,468,470,473],costheta:445,costli:[11,95,245,380],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,69,75,79,94,97,102,113,115,119,122,124,156,166,171,173,189,200,201,203,204,208,209,216,217,220,224,230,241,250,300,301,302,306,309,311,313,327,328,334,338,339,340,344,348,350,352,360,366,368,375,377,380,384,387,412,416,417,420,447,448,481,482,483,485,487,489,492,493,500,501,506,512,513],coulomb:[3,5,6,7,8,9,10,12,14,15,18,76,95,117,118,126,151,177,181,302,304,340,369,370,377,384,391,393,394,395,396,399,400,401,402,403,410,414,415,417,422,426,430,433,439,442,447,448,450,455,465,470,471,473,476,490,497,503,506,511],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,65,71,81,98,124,126,127,164,174,180,210,211,214,216,219,220,221,223,224,231,236,240,243,249,267,281,297,314,330,331,348,370,377,378,379,381,384,412,416,439,503,512],counter:[3,345,480,491,493,499],counteract:243,counterbal:247,counterbalanc:29,counterpart:[200,311,480],counterproduct:18,coupl:[],courant:317,cours:[3,8,136,138,170,200,208,209,244,310,324,338,344,346,347,349,350,370,431,457,482,485,498,506,512,514],courtesi:372,cov:455,coval:[6,9,29,410,434,455,506],covari:245,cover:[6,75,196,204,213,254,410,472],coverag:[75,220],cpc:250,cpp:[1,3,6,8,9,11,12,13,94,200,208,209,241,314],cpu:[1,3,9,10,12,14,15,16,17,18,65,75,204,218,234,252,340,367,370,384,397,465,480,498,499,502,503,504,512],cpuremain:503,cr2:175,cr3:175,crack:[4,380],crada:[5,7],crai:[5,7,13,18,200],crash:[3,12,380,506],craympi:384,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:213,create_faceset:213,create_group:202,create_nodeset:213,createatom:[],creation:[],crimson:204,critchlei:296,criteria:[3,126,177,203,204,225,226,227,262,377,444,472,487,490,512],criterion:[12,42,131,176,179,214,224,227,243,281,303,317,345,350,377,379,399,410,414,455,490,499,500],criterioni:499,critic:[6,49,50,265,334,339,377],crmax:75,crmin:75,cross:[3,12,22,75,96,154,174,184,200,201,203,215,220,226,230,264,266,288,311,320,324,326,335,342,354,372,379,395,404,407,408,415,416,417,422,424,426,445,450,452,454,468,470,477,485,489,495,514],crossov:1,crossterm:485,crozier:[0,7,13],crucial:301,crystal:[3,4,6,13,77,116,292,293,337,372,380,485,489,503,506],crystallin:[6,112,293,372,469,506],crystallis:334,crystallogr:[128,175],crystallograph:[372,503],crystallographi:[128,175,372],cs1:175,cs_chunk:6,cs_im:[41,485],cs_re:[41,485],csanyi:[150,446,456],cscl:434,csequ:6,csh:[11,12,397],cshrc:[11,12],csic:[409,466,468,470,473],csinfo:6,csisi:[409,466,468,470,473],csld:[],cst:408,cstherm:6,cstyle:482,csvr:[],ctcm:[385,408],ctemp_cor:234,cterm:316,ctr:9,ctype:11,cu1:175,cu2:175,cu3au:434,cube:[6,42,174,179,224,234,348,372,506],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:390,cummul:[3,6,222,225,226,227,229,240,245,251,253,327,330,331,332,333,335,342,416,503],cumul:[6,214,216,219,220,221,235,243,251,265,267,272,281,311,312,379],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,61,63,65,75,77,86,94,111,112,118,126,127,140,151,156,164,166,172,174,177,180,199,200,201,202,203,204,205,208,209,213,216,220,221,222,224,225,226,227,228,229,230,231,235,236,241,243,245,248,249,251,257,264,267,268,273,274,275,281,286,287,288,290,296,297,302,303,305,308,309,310,311,314,315,316,317,318,319,320,321,323,325,326,327,330,331,332,338,339,342,343,344,345,346,347,349,350,352,367,368,369,370,373,374,376,377,378,379,384,390,397,399,403,408,410,411,414,417,418,421,431,432,434,435,436,439,445,447,448,451,452,453,454,457,468,470,471,474,480,481,482,483,485,486,487,488,489,491,492,493,495,497,499,500,502,503,507,512,513,514,515,516],curv:[6,176,243,293],curvatur:[413,449,477],custom:[],cut0:483,cut1:494,cut2:494,cut:[],cuthi:[292,304],cutinn:[392,431,432],cutlo:[292,304],cutmax:445,cutoff1:[396,403,422,426,430,433,442,450],cutoff2:[391,393,394,396,402,403,422,426,430,433,442,450,471],cutoff:[3,6,8,10,16,18,40,46,47,55,56,63,74,76,77,81,94,99,116,118,125,126,150,174,177,179,180,226,227,232,239,292,301,302,304,306,308,311,315,327,340,344,348,350,367,369,370,377,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,398,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,450,455,456,457,458,459,460,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,483,487,490,494,506,512],cutoff_glob:[],cutoff_inn:[],cutoffa:409,cutoffc:409,cuu3:408,cval:175,cvd:334,cvel:316,cvff:[],cwiggl:[3,264,344,347,349,512],cyan:[2,203,204],cycl:[3,243,265,267,268,272],cyclic:[3,196],cygwin:12,cylind:[3,4,75,203,216,249,297,345,348,488],cylindr:[6,249,324,345],cypress:384,cyrot:390,cyrstal:293,d3q15:254,d3q19:254,d_double_doubl:15,d_e:339,d_flag2:300,d_flag:300,d_name:[123,200,300,329,495],d_single_doubl:15,d_single_singl:15,d_sx:300,d_sy:300,d_sz:300,daan:337,dai:12,daili:12,daivi:288,damag:[],dammak:306,damp:[3,6,207,212,251,252,253,258,267,268,272,298,301,302,306,311,330,331,343,345,346,376,377,379,391,393,395,400,403,410,414,422,430,442,450,465,471,499,506],damp_com:252,damp_drud:252,dampen:[311,506],dampflag:[345,414],dan:17,danger:[3,12,243,350,404,503],dangl:179,daniel:9,darden:[370,403],darkblu:204,darkcyan:204,darken:203,darkgoldenrod:204,darkgrai:204,darkgreen:204,darkkhaki:204,darkmagenta:204,darkolivegreen:204,darkorang:204,darkorchid:204,darkr:204,darksalmon:204,darkseagreen:204,darkslateblu:204,darkslategrai:204,darkturquois:204,darkviolet:204,dasgupta:302,dash:[414,502],dat:[6,98,196,213,481],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,312],dataset:312,datatyp:3,date:[0,4,6,12,13,199,447,448,512],datom1:125,datom2:125,datom3:125,datom4:125,datum:[3,6,43,68,71,73,84,101,118,125,200,217],davenport:433,davi:344,david:[9,19,369,370,468,470],daw:[408,445],dbg:14,dcd:[3,6,7,200,202,203,204,205,294,486,490],ddim:199,deactiv:430,dealt:250,debug:[6,7,11,12,13,14,17,128,132,175,176,294,299,367,369,384,418,439,474,483,484,492,495,502,512],deby:[],decai:[99,400,477],decid:[3,6,12,16,75,264,300,311,340,500,507],decipher:372,declar:202,declin:327,decod:203,decompos:[94,456],decomposit:[3,5,7,18,64,213,294,315],decoupl:[6,506],decreas:[3,200,201,210,211,218,227,230,236,241,243,251,338,369],decrement:316,deepli:366,deeppink:204,deepskyblu:204,def:[12,13,483],defaul:63,defect:[6,74,174,437],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,182,183,184,185,186,187,188,190,191,193,194,195,196,197,198,199,200,201,202,203,204,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,224,225,226,227,228,230,231,234,235,236,238,241,242,243,246,249,250,251,252,253,254,262,264,266,267,268,269,270,271,272,273,274,275,277,278,279,282,284,285,286,287,288,289,290,292,293,294,296,297,298,300,302,304,309,311,312,313,314,317,321,325,327,329,330,331,332,333,335,336,337,339,341,342,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,362,363,364,365,367,369,370,372,374,376,377,378,379,380,381,382,383,384,386,387,388,389,391,392,393,394,395,396,397,398,400,401,403,404,405,406,407,409,410,412,413,414,415,416,417,418,420,422,423,424,425,426,427,428,429,430,431,432,433,437,438,439,440,441,442,444,445,447,448,449,450,451,452,453,454,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,485,486,488,489,490,491,494,495,496,497,499,500,502,503,506,508,509,510,511,512,513],definit:[2,3,6,8,12,13,82,85,126,150,204,216,217,218,219,220,221,222,230,238,249,272,312,329,341,344,347,349,351,363,367,378,387,390,398,405,406,410,420,445,452,454,456,472,483,485,487,494,496,511,512],defint:503,deform:[],deg2theta:175,deg:506,degener:[3,296],degrad:[8,18,293,370,494],degre:[3,6,8,20,21,24,28,29,32,35,36,38,68,84,99,101,103,105,106,108,110,111,116,122,153,154,155,156,157,158,159,160,161,162,163,164,165,166,168,169,175,176,182,183,186,187,194,196,199,203,216,227,234,243,245,246,251,252,257,267,268,272,273,274,275,286,287,288,290,294,296,310,311,314,330,331,332,337,353,355,359,362,364,377,403,408,416,495,503,506,513],degress:[156,216],del:499,delai:[3,6,12,380,407,503],deleg:417,delet:[2,3,7,8,12,55,59,62,65,174,179,180,207,216,217,219,220,221,222,225,227,240,243,267,312,330,331,350,352,368,378,380,383,439,464,485,486,487,488,496,497,502,507,508,510,512,513],delete_atom:[],delete_bond:[],delete_el:213,deli:199,delimit:[483,512],deloc:[268,410,455],delr:434,delt_lo:499,delta:[],delta_1:390,delta_3:390,delta_7:390,delta_conf:3,delta_ij:[434,445],delta_mu:[],delta_pi:390,delta_r:445,delta_sigma:390,delta_ua:[],delx:199,delz:199,dem:[],demand:306,demo:11,demon:291,demonstr:[301,434],den:297,dendrim:416,denniston:[9,254,256,257,258,293],denomin:[7,181],denot:[128,234,252,293,304,306,400,415,417,448,452,454],dens:[75,227,410],densiti:[3,6,7,9,18,41,42,61,109,126,136,150,162,174,176,208,209,213,216,220,221,224,230,241,254,257,260,261,293,297,298,302,339,344,372,374,378,385,386,390,408,434,435,436,445,449,455,459,461,462,463,485,494,495,503,511],density_continu:454,density_summ:454,depart:[0,7],departur:[265,301],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,68,71,73,74,75,84,99,101,112,118,119,122,123,124,125,129,150,152,153,159,163,164,170,176,177,182,183,184,185,186,187,188,190,191,193,194,195,196,199,200,201,203,204,207,208,209,210,211,214,216,218,219,220,222,223,224,226,228,230,236,237,242,245,246,247,249,251,252,254,256,257,264,267,269,270,271,272,273,274,275,276,277,284,286,287,288,290,292,303,306,308,311,313,314,315,321,327,330,331,332,334,336,338,339,341,343,344,347,348,349,350,352,353,354,355,356,358,359,362,364,370,372,377,378,380,381,382,384,385,386,388,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,408,409,410,411,412,413,414,415,416,417,422,423,424,425,426,427,428,429,430,431,434,435,437,438,440,441,442,444,445,447,448,449,450,455,456,457,465,466,467,468,469,470,471,473,475,476,477,480,482,485,487,488,491,495,497,499,502,503,505,512,513],dependend:6,depflag:12,dephas:[480,499],depos:231,deposit:[],deprec:[3,302,447],depth:[52,154,203,339,413,449],dequidt:9,der:[94,117,398,399,430,447,448,476,506],deriv:[6,7,8,9,38,57,65,94,150,170,196,217,228,230,243,251,264,267,269,270,271,272,273,274,275,292,298,302,306,336,337,339,344,345,348,376,378,386,390,398,403,410,411,415,424,428,429,434,437,447,448,465,467,476,506],derjagin:476,derlet:292,descend:204,descent:[7,376],descib:[41,203,302],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,71,74,75,77,95,120,123,126,128,140,150,151,154,155,156,160,161,164,167,169,170,174,175,176,178,179,188,193,196,200,201,202,207,208,209,216,217,218,219,220,221,222,224,227,228,229,230,231,233,234,239,244,245,248,249,250,251,252,253,254,256,257,258,262,266,267,268,272,280,289,292,294,299,300,301,302,303,304,311,316,324,327,328,329,330,331,332,333,334,335,336,337,342,344,345,347,352,369,370,372,375,376,377,378,379,383,386,387,389,391,392,393,395,396,397,398,399,400,403,408,410,411,413,414,415,417,420,422,423,424,425,426,427,428,429,430,431,432,433,434,437,438,444,445,446,447,448,449,450,455,456,457,464,465,466,467,468,469,470,471,473,475,476,477,478,480,482,483,485,486,487,488,489,495,498,499,502,507,512,513,514],descript:[],descriptor:[150,200,418],deserno:370,design:[0,3,6,7,8,11,13,14,15,17,128,158,161,175,213,227,233,234,267,268,292,293,312,334,339,387,388,389,392,395,400,402,410,430,431,432,435,436,445,448,467],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,61,75,95,98,122,127,151,158,176,189,199,216,222,228,230,241,243,244,251,252,253,257,267,288,296,297,298,299,302,306,311,314,327,330,331,332,333,338,345,360,366,369,370,372,375,377,378,379,404,408,416,431,432,466,468,470,481,482,483,485,489,494,499,500,502,503,512,513,514],desk:7,desktop:[4,6,7,10,12,203],despit:506,destabil:390,destre:362,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,69,70,71,75,79,82,97,98,102,111,113,115,117,119,121,122,124,127,129,150,151,153,154,155,156,159,169,170,171,173,176,177,180,181,184,195,199,200,201,203,204,207,208,209,213,216,217,218,219,220,222,224,226,227,228,229,230,231,241,243,244,245,246,248,249,251,253,254,258,264,265,266,267,268,269,270,271,272,273,274,275,279,281,286,287,288,289,290,293,296,297,298,300,301,303,304,305,311,314,315,327,330,331,332,333,334,335,337,338,339,340,341,342,343,350,352,354,363,369,370,373,377,378,380,381,384,385,386,387,389,390,392,394,395,396,397,398,399,400,403,404,410,411,413,414,415,416,417,422,423,424,425,426,427,428,429,430,431,432,433,434,438,439,444,447,448,449,455,456,457,465,472,475,476,478,483,485,486,487,488,490,491,494,495,497,500,503,504,507,512,513,516],detect:[2,3,12,43,63,65,93,99,242,297,338,379,399,416,421,480,482,485,496,499,512],determ:384,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,71,75,94,111,117,119,122,128,129,137,151,164,165,174,175,176,199,200,201,203,204,205,206,210,211,212,215,216,217,218,219,220,221,222,223,224,228,230,231,234,236,243,246,247,249,251,252,257,262,264,265,267,273,274,275,286,287,288,290,292,294,297,298,301,308,309,310,311,312,313,317,319,321,327,330,331,332,334,340,341,344,345,346,347,348,349,350,363,369,370,372,378,380,381,384,386,387,394,399,403,407,408,412,414,417,418,426,434,437,439,448,449,455,464,467,471,476,482,485,486,488,490,492,495,499,501,502,504,511,512,513],determinist:315,detil:118,devan:[9,450],devanathan:470,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,248,272,296,301,302,305,386,390,410,436,437,455,473,487],devemi:9,deviat:[265,272,292,412],deviator:9,devic:[1,3,12,15,17,248,384],device_typ:384,devin:[303,399],devis:436,dfactor:203,dff:506,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,370],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,305,437],dhi:[61,199,230,297],dhug:[265,301],dhugoniot:[265,301],dia:434,diagnost:[],diagon:[3,6,90,150,151,152,228,267,298,311,342,452,454],diagonalstyl:456,diagram:[42,128,175,195,224,294],diallo:416,diam:[203,204,297,378],diamet:[3,6,41,43,123,176,200,201,203,204,208,209,251,297,311,327,329,343,345,378,398,413,414,424,449,472,476,485,486,495],diamond:[372,410,434],diamter:[41,297],dick:6,dicsuss:264,dictat:[214,265],did:[3,12,377,404,407,408,414,439,468,470,493],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,172,341,369],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,63,66,71,74,75,94,99,103,105,106,130,150,152,153,154,155,156,157,159,162,163,164,165,166,168,169,170,176,177,179,184,195,196,199,200,203,204,207,209,212,214,216,219,224,225,226,227,228,229,230,234,239,242,243,244,245,246,247,248,251,252,254,264,267,268,269,270,271,273,274,275,277,279,282,284,285,286,287,290,292,294,296,298,301,302,303,306,309,311,314,316,324,325,327,330,331,332,335,336,337,339,342,343,344,345,348,352,353,363,366,368,369,370,372,373,375,376,378,379,381,382,383,384,385,386,390,394,395,397,398,399,404,405,406,408,410,413,414,415,417,420,422,423,425,426,433,434,435,436,438,439,441,445,447,448,449,450,451,452,454,455,456,457,465,466,467,468,470,472,473,476,479,480,482,483,485,487,488,489,490,493,494,495,497,499,500,502,503,504,506,511,512,513,514],differenti:[1,3,6,29,196,369,400,445,469],difficult:[228,294,384,416,494],difficulti:[99,116,314,447],diffract:[],diffus:[],digit:[2,3,204,352,437,512],dih_table1:196,dih_table2:196,dihder:[],dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:226,dihydrid:410,dij:314,dilat:[],dim1:3,dim2:3,dim:[3,61,75,153,157,158,159,162,163,164,165,166,168,176,199,220,230,249,345,372,434,488,511,512,513],dimdim:512,dimems:293,dimens:[],dimensinon:75,dimension:[3,40,99,122,128,150,153,156,157,158,159,162,163,164,165,166,168,175,198,216,220,266,293,339,372,375,379,445,485,495],dimensionless:[114,131,132,134,137,139,141,146,150,339,370,456,476],diment:3,dimentionless:145,dimer:[6,311,434],dimgrai:204,dimstr:[42,224],dinola:[298,330],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,41,200,201,329,506],dir1:496,dir2:496,dir:[1,3,4,8,10,11,12,265,292,301,326,445,447,448,483,496,512],dirac:150,direc:445,direct:[],directli:[3,6,8,9,11,12,94,123,150,152,200,201,202,203,210,236,245,249,254,293,312,331,343,345,346,347,348,372,376,384,385,386,391,393,394,400,403,408,410,422,426,439,442,450,464,483,495,496,497,503,512],directoi:14,directori:[],disabl:[3,12,16,339,421,483,498,512],disadvantag:[6,224],disallow:[200,230,267],disappear:487,discard:[2,3,42,75,218,220,224,340,348,482,487,488],discontinu:[196,377,428],discourag:434,discov:[13,340],discret:[6,8,41,43,203,204,251,254],discuss:[],disk:[6,91,92,99,169,198,231,243,297,483],disloc:[74,437],disord:[40,74,437],disp:[],dispar:449,disperion:[403,426],dispers:[3,6,7,9,174,293,369,370,394,403,426,431,439,448,467,473],displac:[],displace_atom:[],displace_box:61,displacemet:488,displai:[11,13,22,37,45,56,184,195,200,203,354,363,397,465],dispters:3,disregard:437,dissip:[6,9,41,87,88,238,244,251,293,315,336,337,392,404,405,406,414,431,432,465],dissolut:225,dist:[6,73,98,118,127,200,294,310,407,464,480,513],distanc:[],distinct:[6,234,308,369,449],distinguish:[6,93,150,257,410,484,512],distort:[174,385],distrbut:385,distribut:[],distro:[121,397,444,445],ditto:[8,12,14,15,16,17,18,43,125,226,477,483],div:8,divd:127,diverg:[3,12,40,311,337,386,487,506,514],divid:[3,6,16,42,98,122,127,136,138,151,173,174,184,195,204,216,217,219,224,230,292,335,342,347,369,377,379,411,448,455,473,494,502,512],divis:[6,254,390,420,430,482,503,512],dl_poli:[6,7],dlambda:170,dlammps_async_imd:248,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,203],dlammps_gzip:[3,12,200,203,338,485,486,490],dlammps_jpeg:[3,12,203],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,203],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,200],dlen:495,dlmp_intel_offload:[9,12,16],dlo:[61,199,230,297],dlopen:6,dlvo:[7,398,476],dm_lb:254,dmax:[327,375],dmpvtk:201,dmpvtp:201,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,59,61,65,69,71,79,94,97,102,111,113,114,115,117,119,121,122,124,127,129,151,154,155,156,169,171,173,176,177,178,184,195,199,200,201,202,203,204,205,207,208,209,214,215,216,217,218,219,220,221,222,231,243,251,252,262,267,268,273,274,275,279,286,287,288,289,290,297,300,311,324,327,330,331,332,341,345,348,350,352,354,363,368,377,378,379,384,385,386,389,397,399,400,408,409,411,416,417,419,420,434,435,436,439,441,444,445,446,456,465,466,468,470,472,473,483,485,486,487,488,490,493,494,495,502,503,507,512,513,514,515],docuement:449,dodd:43,dodgerblu:204,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,61,64,65,70,74,75,76,94,95,98,113,117,120,126,127,128,152,154,156,158,159,164,166,170,175,176,177,178,180,182,184,189,195,196,199,200,201,202,203,204,207,213,214,216,220,223,224,226,227,228,230,234,236,239,240,243,244,247,249,251,252,254,257,263,267,268,269,270,271,273,274,275,286,287,288,289,290,298,299,300,304,306,309,311,327,330,332,334,335,339,342,343,344,347,348,349,350,355,356,357,359,360,362,368,369,370,371,372,378,379,380,385,386,387,388,389,390,392,394,395,396,398,399,400,401,403,404,407,408,409,410,412,413,414,415,417,418,419,420,421,424,425,427,428,429,431,432,434,435,436,437,439,445,446,447,448,449,451,452,453,454,455,456,457,458,459,460,461,462,463,464,466,467,468,469,470,471,472,473,475,476,477,478,480,481,482,483,485,486,487,488,489,492,493,495,496,497,498,499,502,503,506,507,512,516],doegenomestolif:7,doesn:[3,7,8,12,176,200,201,214,220,221,324,378,380,384,386,399,409,419,447,448,466,468,469,470,473,485,487],dof:[3,8,122,154,155,156,169,216,311,513],dof_per_atom:[156,216],dof_per_chunk:[156,216],doff:[378,485],doi:[6,229],domain:[3,6,7,12,13,18,40,42,43,60,63,64,75,128,165,175,178,199,202,203,204,207,214,224,228,230,231,247,250,254,267,268,294,306,311,315,339,344,345,369,370,379,384,407,439,480,482,485,489,502],domin:[1,410,499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12,13,29,95,152,174,339,385,408,411,430,434,435,436,445,465,474,483],embt:183,emi:[7,9],emil:9,emol:[447,448,503],emphas:414,empir:[9,213,331,386,410],emploi:[293,302,306,469],empti:[3,59,75,174,178,311,369,380,421,485,496,497,512],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,40,41,44,46,47,48,49,50,51,52,54,55,56,57,62,63,64,66,70,82,85,90,94,95,105,106,107,108,109,110,114,117,119,121,122,128,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,152,153,154,155,158,160,162,163,167,168,170,174,175,182,183,185,186,187,188,189,190,191,193,194,195,196,200,201,202,204,205,207,208,209,210,211,212,214,218,221,223,225,226,227,229,230,231,236,237,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,260,261,263,265,267,268,269,270,271,272,273,274,275,276,277,278,279,280,282,284,285,286,287,288,289,290,292,293,294,296,297,301,302,303,304,305,306,307,308,310,311,313,314,316,317,318,319,320,321,323,324,326,327,330,332,333,334,335,336,337,339,340,342,343,344,345,346,347,348,351,353,355,356,358,359,360,362,363,364,370,377,379,383,384,385,386,388,389,390,391,392,393,394,395,396,398,399,400,401,402,403,404,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,435,436,437,439,440,441,442,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,483,486,487,488,492,494,504,512,516],enclos:[2,6,12,178,200,299,352,434,455,481,483,493,512],encod:[13,40,43,200,203,204,300,417],encompass:[3,6,41,43,59,61,126,177,323,341,465,488],encount:[3,8,12,61,116,219,383,490,512],encourag:[7,8,305,325],end12i:123,end12x:123,end12z:123,end1i:123,end1x:123,end1z:123,end2i:123,end2x:123,end2z:123,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,41,42,43,59,61,75,123,179,180,183,199,200,201,203,204,205,208,209,217,219,221,222,227,230,244,249,251,253,266,267,268,281,298,310,311,316,327,330,331,332,333,335,338,339,342,346,349,350,368,369,378,379,383,384,404,408,413,420,433,437,449,452,454,456,457,474,480,483,485,486,487,488,490,492,493,497,501,503,506,512,516],end_of_step:8,endbondtors:[3,183,189,485],endif:8,energet:[227,386,448],energi:[],energy_compon:455,energy_update_freq:448,enforc:[6,9,59,60,113,199,200,201,202,203,205,207,214,227,230,267,291,293,303,311,314,352,369,422,482,512,513],enforce2d:[],eng:[11,68,73,118,200,241,350,352,399,436],eng_previ:352,engil:9,engilitycorp:9,engin:[213,230,296,316,336,408,435],engr:[],enhanc:[209,213,480],enlarg:[61,203],enough:[3,41,63,93,176,177,179,180,224,252,297,301,306,311,340,344,345,348,380,384,400,443,485,489,490],enpub:408,enrti:[],ensembl:[],ensight:6,ensur:[3,6,150,200,201,214,218,228,243,244,267,317,338,370,390,407,430,466,473],enter:[59,166,411,437,473,499],enthalpi:[133,269,270,271,408,502,503,512],entir:[0,2,3,6,11,14,15,42,43,65,87,88,95,119,120,122,126,128,151,156,175,176,204,207,208,209,216,220,221,224,227,229,240,243,244,247,251,252,263,267,269,270,271,272,273,274,275,292,294,296,309,311,325,339,341,352,384,403,426,439,467,485,493,494],entireti:472,entiti:[6,8,41,43,200,311],entri:[3,8,12,38,43,57,68,73,84,101,118,125,128,137,140,141,142,143,144,146,147,148,174,196,201,204,208,219,220,221,229,239,301,350,378,390,409,434,441,448,456,466,467,468,469,470,473,512],entropi:499,entry1:[38,57,204,397,467],entry2:204,entryn:204,enumer:[177,200,478],enumuer:6,env:384,environ:[1,3,6,11,12,16,17,18,203,245,250,292,384,385,390,397,399,409,410,445,468,482,496,512],epair:[117,204,412,416,447,448,503],epen:[447,448],epfl:[245,250],epp:403,epq:403,eps0:476,eps14:430,epsilon0:470,epsilon:[3,6,36,46,47,51,54,55,94,182,208,209,243,311,327,344,348,375,377,389,395,396,398,400,401,402,403,413,415,416,417,420,421,422,423,424,425,426,427,428,429,430,433,438,442,449,450,460,466,471,472,475,476,494,506,511],epsilon_0:477,epsilon_14:395,epsilon_:449,epsilon_d:401,epsilon_i:[413,439,449],epsilon_i_:449,epsilon_i_a:[413,449],epsilon_i_b:[413,449],epsilon_i_c:[413,449],epsilon_ij:439,epsilon_j:[413,439,449],epsilon_j_:449,epsilon_j_a:[413,449],epsilon_j_b:[413,449],epsilon_j_c:[413,449],epsilon_lj:449,epton:444,eqch:171,eqeq:[447,448],eqp:403,eqq:403,equal:[2,3,6,8,11,12,17,40,42,55,65,68,71,73,75,80,84,93,94,98,101,118,120,125,127,129,151,154,170,172,174,176,199,203,204,207,208,209,210,211,214,217,218,219,222,223,224,228,230,231,236,243,244,246,247,249,251,252,254,257,258,264,265,272,283,292,294,297,299,301,302,303,306,308,310,311,313,316,321,323,330,331,332,335,336,337,339,341,342,344,347,349,350,352,368,372,377,379,380,381,383,384,399,404,406,412,413,416,420,431,437,438,445,447,448,449,451,452,453,455,456,457,467,472,473,477,481,482,483,485,487,488,492,493,496,499,501,503,512,513],equat:[3,6,7,8,9,98,116,122,128,175,184,195,207,228,234,235,238,239,245,251,252,254,257,265,266,267,268,272,288,292,294,301,302,306,314,315,327,335,339,342,344,345,347,349,362,369,370,398,403,404,406,410,411,414,419,431,432,434,439,449,452,454,459,460,462,463,477,506],equi:268,equidist:266,equil:[3,302,373,492,516],equilater:495,equilibr:[3,4,5,6,7,9,61,98,176,207,214,217,227,228,243,265,267,268,288,289,301,302,303,304,335,336,337,342,399,400,447,448,481,495],equilibria:342,equilibribum:[225,226],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,61,159,160,183,185,228,230,243,244,245,252,254,267,272,288,301,302,306,310,314,316,324,327,334,335,337,342,353,355,359,362,399,434,441,455,506],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:213,equival:[6,12,13,29,61,63,134,135,143,148,174,178,204,219,222,228,230,243,251,267,288,298,310,311,347,386,404,410,455,468,470,471,485,488,493,494,503,506],equlibrium:6,equliibr:[302,304],er3:175,eradiu:[41,123,201,410,485],eras:[313,336],erat:[230,432],erc:400,erfc:[400,422,439],erforc:[123,201],erg:511,erhart:[214,408,468,470],ermscal:387,ernst:9,eror:3,eros:434,erose_form:434,erot:[],errata:[468,470],erratum:344,erron:3,error:[],erta:414,ervel:[123,201,485],escap:[231,506],especi:[8,16,164,176,207,214,224,243,301,306,309,310,384,482],espresso:[9,305],essenti:[8,11,12,27,95,138,157,158,159,162,163,164,165,166,168,185,217,272,293,343,370,386,400,422,470,490,503],essex:29,establish:[94,247],estim:[1,3,6,10,12,38,42,57,98,151,213,224,235,265,327,334,369,370,375,439,448,467,499,503],esu:511,esub:434,eta:[6,254,267,301,302,304,343,409,411,413,445,469,473,511],eta_dot:267,eta_ij:445,eta_ji:411,etag:[41,485],etail:503,etap:267,etap_dot:267,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,71,96,97,98,103,119,120,123,125,151,153,156,157,158,159,160,162,163,164,165,166,168,170,176,178,179,180,189,200,201,203,204,207,208,213,214,215,216,219,220,221,222,225,226,230,231,241,243,244,251,267,297,308,312,339,340,348,352,368,369,377,378,379,380,382,408,409,417,430,432,437,443,447,448,466,468,470,473,480,483,485,486,487,492,494,495,499,500,501,502,503,504,506,511,512,514,516],ethernet:18,etol:[377,379,480,499],etot0:301,etot:[6,103,105,106,120,151,162,204,234,252,265,301,502,503],eu2:175,eu3:175,euler:[377,379],eulerian:213,euqat:458,europhi:254,ev_tal:8,evalu:[2,3,9,11,12,38,57,75,94,95,98,117,127,129,150,152,156,166,174,176,199,200,201,203,204,208,209,210,211,213,215,216,217,218,219,220,221,222,223,230,236,244,246,247,249,250,251,252,293,299,302,313,317,321,330,331,332,341,344,347,349,350,352,369,370,375,377,384,437,439,445,451,453,455,467,480,481,483,487,488,490,492,493,494,495,499,501,503,512,513],evalut:[352,483],evan:[164,288],evanseck:[6,20,182,395,497],evapor:[],evaul:[8,377],evdwl:[117,152,447,448,503],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,74,75,95,117,129,174,177,178,192,196,200,201,204,207,208,209,214,215,216,219,220,221,222,224,225,226,228,230,231,234,249,252,265,267,268,293,297,306,308,311,312,323,327,335,339,342,344,348,350,361,369,375,377,379,384,389,410,411,414,417,420,439,449,473,474,478,485,486,488,490,491,492,494,495,497,500,502,503,504,506,516],evenli:[3,42,151,196,224,254,420,474],event:[],eventu:[3,6,12,15,178,302,499],ever:[9,55,57,250,327],evera:[398,413,449,465],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,75,76,98,123,129,138,164,179,200,201,202,203,204,205,207,208,209,210,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,240,241,243,245,247,248,249,254,255,263,267,268,272,291,292,293,297,298,299,300,301,302,303,304,306,308,309,311,312,314,316,327,329,330,331,332,333,334,335,338,339,340,341,342,350,352,368,370,379,380,381,384,404,407,417,430,447,448,455,461,479,480,481,485,487,489,490,492,493,494,499,500,501,503,507,512,516],everyth:[8,117,507],everywher:[126,424],eviri:410,evolut:[245,254,294,480],evolv:[254,294,340],ewald:[2,3,5,6,7,8,9,12,95,120,128,151,340,369,370,377,391,393,394,400,403,410,422,426,442,450,465,467,471],ewald_disp:403,ewalddisp:3,exact:[22,42,45,75,132,170,179,184,224,227,244,245,251,252,253,297,306,307,327,339,354,369,397,487,492,499,512,514,516],exactli:[3,6,12,14,17,38,42,43,57,61,75,76,98,126,154,160,167,176,196,208,209,219,224,230,235,239,244,251,252,253,268,280,281,289,293,301,327,332,333,346,384,397,404,408,414,417,431,439,467,487,488,495,499,512],exager:506,examin:[6,8,17,227,293],examp:[483,512],exampl:[],exce:[3,6,16,17,18,42,60,75,178,215,216,219,220,221,222,224,228,230,235,240,267,293,308,312,318,319,327,377,384,485,512],exceed:[3,42,61,224,230,267,327,493],excel:410,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,75,96,97,118,119,122,127,151,153,154,155,156,157,158,159,160,162,163,164,165,166,167,168,169,176,180,182,183,184,185,186,187,188,190,191,193,194,195,196,199,200,201,204,207,210,216,217,219,223,224,228,230,237,242,243,246,249,251,253,267,268,269,270,271,272,273,274,275,276,277,280,281,284,286,287,288,289,290,294,303,304,311,313,314,324,327,330,332,333,339,343,347,350,351,352,353,354,355,356,358,359,362,363,364,369,370,372,374,378,379,380,382,383,384,385,386,388,391,392,393,394,395,396,397,398,399,400,402,403,404,408,409,410,411,412,413,414,415,416,417,422,423,424,425,426,427,428,429,430,431,432,435,440,441,442,444,447,448,449,450,457,465,466,467,468,469,470,471,473,475,476,477,480,482,483,485,487,488,490,493,494,495,496,497,499,503,506,511,512,513,515],excess:[218,410],exchang:[2,3,6,8,63,64,207,213,214,243,251,303,311,335,339,342,369,384,410,500],exchange:369,excit:410,exclud:[3,6,9,12,16,17,65,75,122,150,156,163,164,180,200,216,220,225,226,255,263,296,309,311,334,345,350,377,378,380,392,414,417,420,431,432,439,464,497],exclus:[1,3,12,16,94,384,399,437,439,494,504],excurs:[267,480],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,62,177,203,248,305,352,368,371,383,481,483,493,496,499,512],exempl:455,exemplari:244,exemplifi:410,exert:[6,249,252,306,346,347,348,370],exhaust:[213,383,512],exhibit:[99,267,376,410,494],exist:[3,6,7,8,11,12,13,16,37,56,61,71,74,132,176,177,195,202,203,204,207,212,223,226,228,231,243,296,297,299,350,351,353,355,356,357,359,363,373,378,384,405,406,417,447,464,474,481,483,485,486,487,496,497,498,507,512,513,514],exit:[2,3,11,12,42,59,200,224,239,368,383,483,484,493,502,512],exlanatori:3,exp:[],expand:[],expans:[12,150,200,496,512],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,75,111,157,168,174,196,224,236,243,245,264,292,298,300,301,306,311,350,370,380,397,434,437,439,480,483,485,487,490,494,499,512],expens:[6,75,204,292,296,311,339,350,369,370,380,384,483],experi:[6,13,15,17,223,231,248,257,266,298,310,311,375,379,404,439,494,499],experienc:[6,12,256,257],experiment:[243,369,384,499],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,61,65,68,71,73,75,76,77,80,81,84,93,101,156,164,196,200,201,203,204,207,216,217,222,224,226,228,230,267,292,300,311,324,350,352,368,369,372,378,379,383,389,408,420,455,457,472,483,486,487,490,492,495,506,507,512,516],explan:[3,6,61,123,150,200,201,216,266,292,417,479,482,483,485,494],explanatori:[3,8,127,200,201,215,216,219,220,221,311,378,482,512],explantori:[3,307],explic:438,explicit:[6,9,11,22,45,81,94,123,126,170,184,208,209,230,318,319,354,374,386,387,390,395,397,408,410,421,431,471,479,482,486,489,507],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,75,119,122,153,163,166,174,176,182,183,185,186,187,188,190,191,193,194,196,200,201,204,210,220,223,230,237,242,244,246,251,267,269,270,271,272,273,274,275,276,277,284,286,287,288,290,300,301,303,311,313,314,330,332,333,339,343,347,353,355,356,358,359,362,364,378,384,385,386,388,391,392,393,394,395,396,397,398,399,400,401,403,404,407,408,409,411,412,413,414,415,416,417,421,422,423,424,425,426,427,428,429,430,431,435,437,439,440,441,442,444,449,450,457,458,459,460,461,462,463,465,466,467,468,469,470,471,473,475,476,477,485,487,488,494,495,497,498,504,506,507],explictli:[16,498],exploit:[15,17,294],explor:[128,175],expon:[3,302,304,408,413,416,430,438,450],exponenti:[94,445,466,473,477,499,512],expos:11,exposit:[213,404,407],express:[6,150,162,176,208,209,228,264,292,302,339,345,352,390,408,410,424,434,455,456,465,512],expressiont:390,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,67,72,83,89,90,91,94,95,98,100,103,106,107,117,119,127,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,201,207,210,211,214,222,223,229,232,236,241,242,243,245,246,247,249,251,253,265,267,272,281,292,293,309,310,311,313,316,321,324,326,330,331,332,333,334,336,337,339,341,344,348,349,413,434,437,448,449,456,502,503,511],extent:[1,3,42,43,46,59,75,174,178,200,212,220,224,249,346,349,369,372,386,451,453,467,482,485,488],exterior:[3,6,174,348],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,75,111,119,120,122,128,151,153,154,155,157,159,162,163,164,165,166,168,169,175,176,177,178,182,204,219,224,226,267,299,300,301,311,327,377,378,381,382,403,414,417,420,434,439,482,483,485,488,497,506,512],extract:[3,6,11,13,36,65,67,72,83,94,100,117,125,127,129,208,209,304,379,400,411,434,456,483,490,502],extract_atom:11,extract_comput:[11,483],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,203,218,228,230,267,337,410,469,506],extrema:430,extrins:213,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[172,341],f_a:[468,469,470],f_ave:127,f_c:469,f_f:470,f_fix_id:301,f_foo:512,f_harm:337,f_i:[29,445],f_id:[6,75,127,129,200,201,207,215,216,217,218,219,220,221,222,262,329,341,503,512],f_ij:445,f_indent:222,f_int:336,f_j:29,f_jj:98,f_k:445,f_langevin:339,f_max:[301,306],f_msst:265,f_r:[252,468,469,470],f_sigma:390,f_solid:337,f_ss:6,f_temp:[],face:[3,6,59,61,75,164,174,178,212,220,221,344,346,347,348,349,372,413,434,449,485,488],face_threshold:174,facet:174,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,245,297,327,337,414,447,455,497],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,76,94,98,111,118,125,126,128,150,170,175,178,182,193,199,200,203,204,208,209,217,224,228,230,231,243,248,251,253,254,265,267,268,272,294,298,302,310,314,317,319,327,331,335,342,343,344,348,359,370,372,378,384,386,387,390,391,393,395,400,401,402,404,405,406,410,414,417,421,422,434,437,439,441,442,448,450,457,466,471,482,485,488,489,494,497,499,500,503,506,511,512],factori:[3,483],factoriz:369,fail:[3,9,11,12,61,180,228,231,369,377,379,402,448,483],failur:[131,452,484,512],fairli:[11,439,494,499,507],faken:77,falcon:248,fall:[3,6,204,219,297,483,512],fals:[93,350,352,455,512],fame:8,famili:[473,482],familiar:[0,11,507],fan:445,far:[3,6,12,17,59,61,63,93,200,201,204,205,224,225,226,228,231,267,292,310,311,327,344,355,359,375,379,380,472,483,485,490,503],farago:251,farrel:[468,470],farther:200,fashion:[6,8,42,75,176,204,207,208,209,214,220,224,226,231,243,245,249,264,265,267,269,270,271,272,273,274,275,283,286,287,288,289,290,300,301,303,311,316,320,326,329,337,339,343,344,345,347,349,379,417,431,488,497,512,515],fasolino:419,fast:[6,7,9,12,13,17,40,200,201,278,301,340,369,370,392,431,432,437,465,467,487,492,494,503,513,516],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,114,119,122,153,163,182,183,185,186,187,188,190,191,193,194,196,200,201,204,210,223,224,230,237,242,246,250,251,267,269,270,271,272,273,274,275,276,277,284,286,287,288,290,298,302,303,311,313,314,327,330,332,334,336,339,343,347,353,355,356,358,359,362,364,369,370,381,382,384,385,386,388,390,391,392,393,394,395,396,397,398,399,400,403,404,408,409,411,412,413,414,415,416,417,422,423,424,425,426,427,428,429,430,431,435,440,441,442,444,449,450,457,465,466,467,468,469,470,471,473,475,476,477,480,488,494,498,506],fastest:[1,6,14,17,164,220,339,340,384,482],fatal:[3,502],fault:[74,448],faulti:12,fava:413,favor:227,favorit:7,fbmc:334,fcc:[],fcm:[283,512],fdirect:234,fdotr:418,fdt:[],fdti:94,fe2:175,fe3:175,fe_md_boundari:213,featu:8,featur:[],fecr:408,feedback:[7,248],feel:[7,248,249,257,292,348,350,379,439],felling:436,felt:348,femtosecond:511,fene:[],fennel:[400,422],fep:[],ferguson:[6,182,497],fermi:[1,9,10,12,15,162,384,470],fermion:410,fernando:433,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,65,205,215,216,217,219,220,221,222,252,267,297,300,302,314,341,369,377,378,379,386,455,482,485,490,494,496,504,514],fewer:[1,3,11,15,16,63,257,494],fewest:3,fextern:241,feynman:294,fff:483,ffield:[399,411,447,448,455],ffmpeg:[3,12,203],ffplai:203,fft:[1,3,7,9,11,12,14,15,95,119,120,151,293,369,370,494],fft_inc:[12,370],fft_lib:12,fft_path:12,fftbench:[369,504],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:464,fictiti:[6,210,211,236,241,245,294,310,400,422,426,464],field1:[486,490],field2:486,field:[],fifth:[324,441],figur:[1,3,8,12,301,482,483,507],fij:403,file0:292,file1:[11,13,292,338,352,378,490,492,496],file2:[11,13,338,352,378,490,492,496],file:[],file_from:202,filen:378,filenam:[3,12,13,38,42,57,196,200,201,203,204,205,213,216,217,218,219,220,221,222,224,229,239,292,296,299,302,303,304,307,308,311,312,338,339,366,367,368,378,379,385,386,390,400,408,409,411,419,434,435,436,441,445,446,447,448,455,456,466,467,468,469,470,473,481,482,483,486,487,492,496,503,512,514,515,516],filennam:492,filep:[3,200,201,204,487,492,516],filepo:308,fill:[7,9,176,203,297,339,372,380,390,437,448,488,507],filter:[204,213],final_integr:8,final_integrate_respa:8,finchham:[6,158,402],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,63,75,77,94,127,179,196,205,214,227,228,239,240,243,266,292,297,298,306,310,375,377,379,380,400,417,422,426,434,455,465,467,506,507,512],find_custom:8,fine:[16,17,180,210,236,337,380,384,507,512],finer:[150,176,512],finest:369,finger:[176,199,264,488],finish:[6,11,42,224,352,366,368,369,381,383,384,472,490,512,513],finit:[],finni:[7,408,465],finvers:234,fiorin:[9,229],fire:[],firebrick:204,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,75,86,95,98,112,113,114,116,122,126,127,137,140,143,144,148,151,161,164,170,172,174,175,177,178,179,183,196,200,201,202,203,204,205,207,208,216,217,219,220,221,222,224,227,230,239,243,244,249,254,264,265,266,267,292,294,299,300,301,303,308,311,314,316,324,325,327,328,329,336,337,338,339,341,345,350,352,353,360,372,377,378,379,380,383,384,385,386,389,390,391,393,395,397,399,400,408,410,411,414,415,417,418,419,420,421,422,426,431,432,434,436,437,439,441,445,447,448,455,456,464,466,467,468,469,470,473,477,480,481,482,483,485,486,487,490,492,494,497,498,499,502,503,506,507,512,513,514,516],fischer:[6,9,19,20,182,395,497],fit:[3,6,9,12,38,57,196,239,310,327,386,390,419,434,439,460,467,469,493,507,512],five:[77,162,301,378,390,435,485,499],fix:[],fix_adapt:[170,209,430],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,214,297],fix_eo:9,fix_evapor:214,fix_flux:213,fix_gcmc:[214,378],fix_gl:245,fix_gld:245,fix_grav:297,fix_id:[3,228,265,267,269,270,271,272,273,274,275,298,301],fix_manifoldforc:507,fix_modifi:[],fix_mov:[199,345],fix_nh:8,fix_npt:245,fix_nv:507,fix_nvt:[214,243],fix_poem:[3,6,9],fix_pour:[3,231],fix_qbmsst:9,fix_qeq:[3,399],fix_rattl:314,fix_reax_bond:447,fix_rigid:[257,389],fix_saed_vtk:312,fix_setforc:8,fix_shak:314,fix_shardlow:9,fix_srd:3,fix_styl:272,fix_temp_rescal:333,fixedpoint:[228,267],fixextern:241,fixid:213,fji:403,flag1:[233,382],flag2:[233,382],flag:[3,8,9,11,12,14,15,16,17,41,69,78,79,86,93,96,97,102,112,113,115,128,171,175,179,200,201,203,204,205,222,227,229,233,248,251,255,257,263,264,293,300,311,324,326,327,334,338,347,350,367,370,378,382,383,384,386,416,421,434,437,464,480,482,483,485,486,487,489,490,491,495,507,512],flag_buck:394,flag_coul:[394,403,426],flag_lj:[403,426],flagfld:[392,431,432],flaghi:[3,392,431,432],flaglog:[392,431,432],flagn:233,flagvf:[392,431,432],flat:[6,339,344,345,349],flavor:[2,7,12],fld:[],flen:387,flex_press:387,flexibl:[3,6,8,177,203,216,220,229,245,268,335,342,410,469,503],flip:[3,6,230,267,346,347],floor:512,flop:12,floralwhit:204,flow:[],fluctuat:[6,66,94,228,243,244,251,254,267,272,292,293,315,337,339,362,406],fluid:[],fluid_veloc:258,flush:[3,204,502],flux:[],flv:203,fly:[7,9,12,42,203,207,213,218,231,234,311,314,340,390,437,503,506],fmackai:9,fmag:232,fmass:294,fmax:[377,503],fmomentum:234,fmsec:[2,204,251,252,264,267,298,311,330,331,494,505,511,513],fname:368,fno:[9,12,16],fnorm:[377,503],fnpt:234,fnvt:234,foce:417,fock:387,focu:314,fogarti:[9,304,448],foil:[150,292,456],fold:[325,494],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,74,75,77,87,98,99,105,106,116,123,126,127,129,150,151,154,155,156,162,164,169,172,174,176,177,182,185,186,187,188,190,191,193,194,196,200,202,203,204,207,213,214,215,216,217,218,219,220,221,222,224,229,230,231,234,235,238,239,241,243,244,245,248,250,251,252,254,257,265,267,272,273,274,275,286,287,288,290,293,294,296,299,300,301,302,304,306,308,310,311,312,314,329,330,331,332,335,336,337,338,339,341,342,350,351,355,356,357,358,359,362,364,367,372,374,377,378,379,384,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,401,402,403,404,405,406,407,408,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,439,440,441,442,444,445,446,447,448,449,450,452,454,455,456,457,458,459,460,461,462,463,464,466,467,468,469,470,471,472,473,475,476,477,478,480,482,483,485,486,488,490,492,493,494,497,499,500,501,506,507,512,513,515],foo:[4,8,11,12,200,203,241,483,496,512],foot:6,footprint:[12,384],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:257,forcefield:[310,416],forcegroup:254,forcezero:375,ford:403,forestgreen:204,forev:75,forget:[252,506],forgiv:267,fork:[],form:[2,3,6,8,12,19,22,45,55,65,69,78,79,81,86,94,96,97,99,102,112,113,115,126,150,151,170,171,180,184,204,207,208,209,226,244,245,251,253,257,264,288,293,304,306,310,311,339,344,348,353,354,357,362,374,376,378,379,386,387,390,397,405,406,408,410,412,416,417,421,433,434,436,437,441,442,445,447,448,449,455,456,457,465,467,468,469,470,476,479,482,483,485,490,495,502,506,512],formal:[6,82,85,98,244,245,251,267,294,327,335,455],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,71,81,184,196,200,201,202,203,204,205,216,219,220,221,222,224,226,239,293,296,300,302,304,307,311,312,323,338,339,350,351,354,374,378,379,385,386,390,397,408,411,421,434,436,446,447,448,450,456,467,473,474,482,483,485,486,487,490,501,502,503,512,514],former:[6,12,16,40,42,204,224,339,343,390,392,491,497,512],formerli:[7,13],formul:[1,9,41,66,151,210,236,251,267,288,302,304,310,314,338,369,386,390,408,410,413,434,444],formula:[2,3,6,7,13,21,22,37,45,55,56,74,77,94,96,97,98,103,105,106,115,122,128,129,151,153,154,155,156,157,158,159,160,162,163,164,165,166,167,168,169,175,176,181,183,184,195,199,200,208,209,210,211,216,217,218,219,222,223,230,236,246,247,249,251,252,264,292,293,299,308,313,321,325,327,330,331,332,341,344,347,349,350,352,353,354,356,363,372,378,386,387,389,390,395,396,397,398,403,404,408,409,413,414,415,416,418,421,422,424,425,426,428,429,431,432,434,438,439,440,449,450,457,465,466,467,468,469,470,473,475,476,481,485,488,495,502,503,511,512,513],forth:[1,6,11,12,13,14,15,383,483,488,492],fortran:[3,6,9,11,12,13,241,408,417,434,447,448],fortun:8,forward:[3,8,94,368,379,384],foster:[390,444,445],foul:179,found:[3,6,9,12,77,170,200,227,229,243,248,254,293,334,340,352,368,380,397,400,403,480,486,487,502],four:[6,11,55,86,112,113,150,172,265,339,362,378,379,437,480],fourier:[],fourth:[6,114,310,324,334,395,441,455],fox:[6,128,182,463,497],fphi:[38,57,467],fpic:12,fplo:[38,57,467],fprime:467,fqdn:250,fqq:403,frac:[],fraction:[1,3,6,8,12,16,40,42,85,119,151,179,199,203,204,214,225,226,227,228,265,297,301,308,309,327,332,333,372,379,384,390,392,414,431,432,490,495],fragment:[43,248,308],fraig:43,frame:[90,150,204,213,265,301,346,413],framer:[203,204],framework:[5,245,385,456],franc:9,fraunhof:9,free:[5,6,7,9,13,29,62,65,74,94,170,208,209,292,327,336,337,338,339,376,379,387,410,430,437,445,476,482],freedom:[3,6,8,103,105,106,108,110,111,122,153,154,155,156,157,158,159,160,161,162,163,164,165,166,168,169,216,227,234,243,245,251,252,257,267,268,272,273,274,275,286,287,288,290,294,296,311,314,330,3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ran:[],grand:[3,9,207,214,243],granflow:5,granular:[],graph:11,graphen:489,graphic:11,grasp:5,gravit:246,graviti:[],grdient:213,great:[3,13,301,507],greater:[1,3,10,63,75,93,174,204,228,244,267,292,332,346,384,389,391,393,394,420,439,480,482,485,488,494,499,512,513],greathous:13,greatli:[128,499],green:[2,6,98,140,141,203,204,293,294,335,390,507],green_kubo:6,greenyellow:204,greffet:306,greg:[7,9],grest:[46,47,227,327,370,394,414,426,497],grew:75,grid:[3,12,42,64,128,164,175,178,201,224,254,306,327,339,340,367,369,370,479,482,485,487,489,494],grigera:6,grime:41,grmask:[3,512],gromac:[],gronbech:[251,369],groot:404,ground:[6,87,88,238,315,410],group1:[158,179,380],group2:[95,152,158,177,179,380],group2ndx:[],group:[],group_id:11,groupbig:327,groupid1:[257,311],groupid2:[257,311],groupid:485,groupnam:380,grouptyp:243,grow:[3,6,8,212,230,231,249,251,267,292,341,414,485,497],grow_arrai:8,grow_reset:8,growth:[6,334],grueneisen:9,gsmooth_factor:434,gstyle:[3,482],gtl:7,gtx285:14,gtx450:14,gtx460:14,gtx470:14,gtx560:14,gtx580:14,guarante:[68,73,84,101,118,125,176,179,200,235,302,368,372,495],guess:[3,200,298,486,507],gui:[7,11,507],guid:[1,17,41,82,85,108,109,110,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,207,260,261,317,318,319,320,323,340,444,452,454,458,459,460,461,462,463,495],guidelin:[1,8,14,15,16,17,18,19,369,467],guidlin:17,gullet:434,gulp:6,gumbsch:376,gunnel:437,gunsteren:[298,330,430],gunzenmul:7,gunzip:12,guo:[6,20,182,188,395,497],gwald:3,gyrat:[],gzip:[3,12,200,201,203,204,338,379,485,486,490],h12:413,h2o:[41,378],h5cc:202,h5md1:202,haak:[298,330],had:[3,6,11,13,61,65,200,201,204,205,219,222,227,228,244,245,247,251,252,253,265,267,269,270,271,272,273,274,275,286,287,288,290,297,298,327,330,331,332,339,404,407,414,464,487,491,494,500,503],hafskjold:6,half:[1,3,6,8,9,16,17,40,42,60,61,178,203,215,224,230,251,267,339,344,348,380,384,387,390,398,410,437,451,453,485,487,488,495,506],halfwai:[42,203,204,420,507],halperin:99,halsei:414,halt:[42,204,224,247,352,502],halv:203,ham:[38,57],hamak:[344,348,398,449],hamilton:74,hamiltonian:[207,245,267,268,331,410,494],hammond:[369,370],han:408,hand:[3,6,9,19,55,152,176,194,199,203,254,264,372,400,410,485,488,495,498],handl:[3,16,203,229,304,384,387,410,431,448,473,483,499],hang:[3,12,482,483],happen:[3,6,8,12,15,18,63,126,180,204,214,217,380,384,483,486,493],happi:8,haptic:248,hara:469,hard:[1,257,304,310,311,407,447,455,488],harden:[9,457],harder:[344,348,506],hardi:[213,252,369,370,506],hardwar:[1,9,10,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,119,122,153,163,182,183,185,186,187,188,190,191,193,194,196,210,223,230,237,242,246,251,267,269,270,271,272,273,274,275,276,277,284,286,287,288,290,303,311,313,314,330,332,343,347,353,355,356,358,359,362,364,369,370,384,385,386,388,391,392,393,394,395,396,398,399,400,403,404,408,409,411,412,413,414,415,416,417,422,423,424,425,426,427,428,429,430,431,435,440,441,442,444,449,450,457,466,467,468,469,470,471,473,475,476,477,488,498],hardwir:[3,17,345],hardy2:370,harm:387,harmon:[],harmonic_fix_wal:432,harpertown:18,harrison:386,hart:327,hartre:[387,408,410,437,511],hasan:9,hash:[40,485],hassl:310,hat:[6,266],have:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,46,47,48,49,50,52,54,55,57,59,61,65,66,68,69,70,73,74,75,76,77,79,81,86,93,97,98,99,102,112,113,114,115,116,119,122,123,124,125,126,140,150,151,152,153,154,155,156,157,159,163,165,168,169,171,172,173,174,176,177,178,179,180,182,183,185,186,187,188,190,191,193,194,196,199,200,201,202,203,204,205,210,212,214,215,216,217,220,221,222,223,224,225,226,227,228,230,231,236,237,240,242,243,244,245,246,247,248,249,251,252,253,254,257,262,264,265,267,269,270,271,272,273,274,275,276,277,281,284,286,287,288,289,290,292,294,296,297,298,300,301,302,303,306,309,311,313,314,321,323,327,328,330,331,332,333,334,338,339,340,341,343,344,345,346,347,348,349,350,351,352,353,355,356,358,359,360,362,364,369,370,372,375,376,377,378,379,380,381,384,385,386,387,388,390,391,392,393,394,395,396,398,399,400,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,422,423,424,425,426,427,428,429,430,431,432,434,435,436,437,439,440,441,442,444,445,447,448,449,450,454,455,457,466,467,468,469,470,471,472,473,475,476,477,479,480,482,483,485,486,487,488,489,490,491,492,493,494,495,497,499,500,502,503,504,506,507,511,512,513,514,515,516],haven:483,hayoun:306,hayr:251,hbcut:447,hbnewflag:447,hbond:[],hbond_cutoff:448,hcp:[66,70,77,372,434],hdf5:[9,202],he1:175,head:[6,21,183,353,412,416,447,448,500,507],header:[3,6,7,8,12,177,200,203,204,205,216,217,219,220,221,222,265,301,308,312,339,378,385,390,408,464,482,485,495,502],heal:494,heat:[],heatconduct:[],heavi:327,heavili:[42,224],heavisid:339,hecht:327,heenen:9,height:[203,231,297,379,412],heisenberg:[],held:[6,75,327,379,414],helic:188,helium:388,helix:[],hello:483,help:[3,8,12,14,15,16,17,18,19,200,228,230,26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resid:13,residu:248,residue1:380,resist:[6,248],resolut:[218,455,467],resolv:[228,294,327,432,507],resort:3,resourc:[7,385,408],respa:[3,16,235,248,267,382,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,401,403,404,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,431,432,433,434,435,436,437,438,440,442,444,446,447,448,449,450,455,456,457,458,459,460,461,462,463,464,466,467,468,469,470,472,473,475,476,477,478,493,494,505,512],respecifi:437,respect:[1,6,9,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,46,47,48,49,50,52,54,55,57,61,74,75,94,96,105,106,119,122,128,132,152,153,158,161,163,170,174,175,182,183,185,186,187,188,190,191,193,194,196,201,203,204,219,220,221,226,227,228,230,246,249,251,252,254,267,269,270,271,272,273,274,275,276,277,284,286,287,288,290,302,303,311,312,316,324,326,339,344,347,353,355,356,358,359,362,364,367,369,370,374,377,378,383,384,385,386,388,390,391,392,393,394,395,396,398,399,400,403,404,408,409,411,412,413,414,415,416,417,422,423,424,425,426,427,428,429,430,431,434,435,437,439,440,441,442,444,449,450,454,455,456,457,466,467,468,469,470,471,473,475,476,477,482,486,495,498,506,512,514,516],respon:9,respond:[6,7,159,230,410,444],respons:[6,7,265,335,342],resquar:[],rest:[6,8,12,300,304,310,390,432,434,502,503,506],restart1:294,restart2:294,restart2data:[],restart:[],restartfil:[12,13],restor:[3,8,62,63,112,176,208,209,300,316,324,329,351,502,503],restore_bia:8,restore_bias_al:8,restrain:[],restraint:[9,229,265,310,326,421],restratin:310,restrict:[],result:[1,2,3,6,7,9,10,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,46,47,48,49,50,52,54,55,57,65,66,69,70,75,79,94,97,98,102,112,113,115,119,120,122,124,125,126,127,128,129,151,153,156,159,163,170,171,173,175,176,179,182,183,185,186,187,188,190,191,193,194,196,199,200,201,203,204,207,210,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,234,237,239,242,243,244,246,251,252,254,258,265,267,269,270,271,272,273,274,275,276,277,284,286,287,288,289,290,293,294,302,303,308,309,311,313,314,327,330,332,335,336,337,339,340,341,343,344,345,347,349,352,353,355,356,358,359,362,364,369,370,379,382,384,385,386,388,391,392,393,394,395,396,398,399,400,403,404,408,409,410,411,412,413,414,415,416,417,422,423,424,425,426,427,428,429,430,431,432,434,435,437,439,440,441,442,444,448,449,450,457,466,467,468,469,470,471,473,475,476,477,480,482,485,487,488,489,490,494,495,496,497,499,511,512,513],resum:512,retain:[2,225,226,386,390,437,482],retart:[33,51,189,360],retir:[3,447],retreiv:8,retriev:[6,8,241,435,436,512],reus:[3,497],rev:[6,13,66,74,99,116,120,150,151,164,214,245,251,253,265,267,268,272,288,293,303,306,311,316,327,331,334,336,337,342,376,390,398,399,400,403,408,409,410,413,414,419,424,431,432,433,434,436,445,449,456,466,468,469,470,473,480],revers:[2,6,8,94,187,227,249,267,291,292,302,320,335,336,342,379,430,494,506],review:[150,302,316,334,437,446,456,480,499,506,507],rewind:368,rewrap:200,rewrit:[5,12],rewritten:19,rezwanur:444,rfac0:[150,456],rfactor:327,rfile:311,rg0:325,rgb:204,rh3:175,rh4:175,rhaphson:3,rheolog:6,rhi:467,rho0:[434,452,454,462,463],rho0_meam:434,rho:[],rho_0:[462,463],rho_alpha_beta:408,rho_bkgd:434,rho_colloid:344,rho_e:339,rho_fin:338,rho_i:[435,436],rho_initi:338,rho_ref_meam:434,rho_wal:344,rhodo:[9,10],rhodopsin:[1,10],rhohi:297,rholo:297,rhosum:[],ribier:376,richard:9,richardson:311,richi:[9,19],rick:[302,303,399,455],rick_and_stuart:303,ridg:[9,19],right:[3,6,11,12,42,152,176,194,195,199,201,224,227,249,254,264,291,352,372,400,485,488,495,507,512],rightmost:[42,224],rigid:[],rigidifi:311,rii:[96,97],rij:[99,116,225,226,292,404,405,406,464],rin:[416,427,428],ring:[],rino:[77,473],rinv:369,rirj:[345,414],rise:[],risi:[150,456],risk:[8,310,494],rix:[96,97],rjk:[225,226],rjone:[7,9,13],rlo:467,rmask:[3,512],rmass:3,rmax:[75,177,225],rmdir:496,rmin0:[150,456],rmin:[75,177,226,424],rmsd:338,rnemd:6,robert:9,robin:204,robust:[375,376,377],rock:434,rockett:445,rod:311,rodata:12,rodnei:306,roi:7,role:334,roll:12,ronchetti:116,room:[59,61],root:[11,94,96,97,202,334,338,384,408,492],rosati:40,rose:434,ross:434,rosski:294,rosybrown:204,rot:[6,98,294,310,334,513],rotat:[],rotation:116,rotaton:488,rough:[6,176,203,349],roughli:[7,10,12,42,159,203,218,243,251,252,266,267,281,298,311,327,330,331,334,370,379,384,451,453,487,494],round:[],rous:244,rout:[94,416,430],routin:[5,6,8,11,15,16,38,40,57,95,180,182,254,437,446,467,498],roux:[6,234,252,471,506],row:[6,68,69,71,73,79,84,97,101,102,113,115,118,124,125,126,129,156,164,171,173,174,175,216,217,219,220,221,222,257,311,339,341,349,410],royalblu:204,rozero:434,rperp:[264,320],rpi:296,rpm:12,rrespa:[1,3,5,7,8,16,208,209,264,267,380,385,386,387,388,389,391,392,393,394,395,396,398,399,400,401,403,404,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,431,432,433,434,435,436,438,440,442,444,446,447,448,449,450,451,452,453,454,455,456,457,458,459,46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:511,statcoulomb:511,state:[],statement:[3,483,484,507],stationari:[],statist:[3,6,12,34,40,42,53,66,192,218,225,226,227,244,245,251,252,253,296,297,301,306,311,314,327,338,339,340,361,377,379,386,404,407,414,431,476,480,487,493,495,499,502,503],statu:[3,12,55,62,131,180,229,234,252,399,484,499],statvolt:511,std:12,stdin:[3,12,368],steadi:[6,265,272,301],steelblu:204,steep:467,steepest:[7,376],steer:[7,9,229,232,316],stegailov:339,steinhardt:[65,116],steinhaus:506,stencil:[3,254,369],step:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,19,40,75,98,105,106,120,126,127,138,151,162,172,174,200,202,203,204,205,207,208,209,213,214,216,217,218,219,220,221,222,224,225,226,227,228,230,231,234,235,240,241,243,245,248,249,252,265,281,292,293,297,299,300,301,302,303,304,312,314,315,316,317,327,329,332,333,334,335,336,337,338,339,340,341,342,349,350,352,368,369,375,377,379,380,404,412,416,434,437,447,448,455,480,482,483,487,489,490,492,493,494,499,500,502,503,506,512,516],stepani:316,stepwis:94,stesman:334,steve:[0,5,7,13],steven:227,stiff:[6,41,52,225,226,293,294,377,444,506],stile:401,still:[1,3,6,9,11,12,13,14,17,38,39,42,58,63,75,99,118,126,174,180,196,197,198,200,201,204,208,209,224,247,251,281,302,306,327,339,352,365,369,370,375,396,408,413,414,417,421,431,443,447,449,457,465,485,487,493,507],stilling:[3,5,7,9,15,95,152,409,436,445,465,466,473,497],stipul:248,stl:[9,75,320,323],stl_surf:323,stochast:[4,7,9,207,245,315,327,334,349,406,407],stockmay:41,stoddard:403,stoichiometri:455,stoke:[254,343],stokesian:9,stoll:[251,253],stone:[9,19,370,403],stop:[],stopstep:512,stopthresh:[42,224],storag:[3,12,15,341,384,497],store:[],store_st:328,storm:12,stouch:7,str:512,straatsma:6,straddl:[3,61,63,166,249,311,324,350,485,489,495],straight:311,straightforward:[4,13,410,506],strain:[],strang:[196,203,512],strategi:[],stratford:254,strcmp:352,stream:[3,6,122,151,156,159,160,203,213,230,244,245,251,252,288,297,306,327,513],streamlin:[12,493],streitz:[],streiz:400,strength:[3,9,150,170,181,203,310,344,348,417,448,449,497],stress:[],stretch:[3,55,61,127,225,316],strict:456,strictli:[6,42,196,224,265,301,334,485],stride2:512,stride:[204,245,492,501,512],strietz:400,strike:231,string:[2,3,6,11,12,42,176,200,201,202,204,216,217,218,219,220,221,222,224,243,299,312,352,371,383,434,445,446,447,456,481,483,485,495,496,502,503,512],strip:512,strong:[10,302,386],stronger:6,strongest:[431,432],strongli:[1,6,13,231,311,314,339,437,506],structrur:3,structur:[],structured_point:312,strucur:77,stuart:[302,303,386,399,455,465],stub:12,stuck:228,student:296,studi:[6,114,424,455],studio:[],stukowski:[214,408],style1:[33,51,189,360,417,485],style2:[33,51,189,360,417,485],style:[],style_nam:[267,268],stylecomput:455,stylist:8,sub1:496,sub:[1,3,4,6,7,8,9,11,12,13,18,33,37,40,41,42,43,51,56,60,63,65,67,71,72,83,94,98,100,117,150,170,178,189,195,202,203,204,208,209,224,228,230,267,268,272,293,301,306,311,314,315,339,340,348,350,360,363,372,374,384,389,399,407,413,414,416,417,420,439,447,448,449,455,471,472,477,482,485,488,494,502],sub_styl:[67,72,83,100],subbox:[127,203,204],subcutoff:420,subdirectori:[],subdivis:254,subdomain:254,subequ:11,subgroup:[200,515],subinterv:202,subject:[6,42,179,224,471],submit:[],subramaniyan:13,subroutin:384,subscript:[11,339,353,411,473,512],subsequ:[3,6,11,12,42,61,112,177,204,218,224,228,243,334,339,340,341,372,383,408,465,483,485,486,492,495,496,505,512,516],subset:[6,11,12,16,42,85,150,200,201,204,224,263,267,269,270,271,272,273,274,275,297,298,302,311,379,384,386,390,417,439,479,482,485,487,490,494,512],substanti:[6,16,466,494],substep:267,substitut:[1,2,3,12,200,250,379,383,410,439,483,496,512],substract:400,substrat:[178,228,267,269,270,271,273,274,275,298,311,485],substyl:[430,494],subsystem:339,subtl:[103,105,106,245],subtleti:162,subtract:[3,6,55,65,75,98,103,106,111,112,114,122,151,153,154,155,156,157,158,159,160,162,163,164,165,166,168,169,200,201,207,216,243,244,247,251,252,253,255,259,263,288,295,311,350,380,429,485,495,503,512,513],succe:12,succeed:[217,218],succes:218,succesfulli:3,success:[2,6,11,12,14,15,126,200,204,214,217,228,231,243,281,297,311,327,334,352,377,379,483,484,492,493,500],successfulli:[3,11,200,231,483,496],successulli:11,successv:490,sucessfulli:3,sudden:36,suddenli:348,sudo:[11,12],sufac:43,suffer:[16,17,18,342,348,384],suffici:[2,3,7,17,18,42,63,75,202,220,224,265,267,293,327,334,341,344,352,421,439,485,506],suffix2:12,suffix:[],suggest:[0,6,7,12,265,301,483,506],suit:[7,13,209,254,410],suitabl:[4,12,13,17,55,94,200,227,300,331,390,397,414,430,434,447,448,480,499],sukumaran:218,sum:[3,6,8,12,41,74,75,80,85,90,95,96,97,99,103,107,112,114,116,119,120,122,126,127,133,149,150,151,153,156,157,158,159,162,163,164,165,166,168,170,172,173,174,216,217,219,220,221,222,231,241,244,251,252,257,292,293,297,301,306,311,312,316,326,337,339,341,344,348,350,369,370,377,389,400,404,410,411,420,422,425,434,447,448,456,472,483,503,506,511,512,513],summar:[6,411,455],summari:[],summat:[6,9,43,74,95,116,369,370,39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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","&lt;no title&gt;","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[37,40,41,56,59,60,61,63,64,75,94,95,99,111,112,114,116,117,128,132,133,150,156,164,165,169,175,176,179,181,195,198,199,200,201,203,204,205,206,208,209,210,212,213,214,216,220,221,222,225,226,228,229,230,231,235,240,243,244,249,251,252,253,254,255,257,262,265,267,268,272,288,289,293,294,297,298,299,300,301,303,306,308,309,311,312,327,329,334,335,336,337,340,342,344,346,350,363,367,369,370,372,373,375,376,378,380,381,382,384,387,390,392,410,431,432,437,439,447,448,464,465,480,481,482,485,486,488,490,492,493,494,497,499,501,502,503,504,505,511,513,514,515],"function":512,"long":[218,391,393,394,395,396,400,402,403,422,426,430,442,450,471],"new":8,"static":12,acceler:1,account:507,ackland:66,acknowledg:7,adapt:[208,209],addforc:210,addit:[12,13,507],addtorqu:211,adiabat:6,adjust_dt:317,adp:385,after:507,airebo:386,alloi:408,amber2lmp:13,amber:6,angl:[8,67,68],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:69,append:212,arrai:6,aspher:[6,9,89,154,269,273,277,278,286],atc:[9,213],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,86,88,92,99,104,105,108,109,110,116,120,121,123,150,151,174,212,214,215,300,512],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:223,awpmd:[9,387],balanc:[42,224],barostat:6,basal:70,beck:388,berendsen:[298,330],between:6,binary2txt:13,bodi:[6,8,9,43,71,155,270,274,279,287,389],bond:[8,13,72,73,225,226,227,307],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:390,born:[391,402],boundari:[7,59],box:[6,60,228],branch:507,brownian:392,buck:[393,394,402,433],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,chang:507,change_box:61,charmm:[6,20,182,395,430],chunk:[6,69,75,79,97,102,113,115,124,156,171,173,216],citat:7,class2:[9,21,44,183,353,396],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,344,398,476],colvar:[9,13,229],com:[78,79,157],comb3:399,comb:[303,399],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,508,509,510,511,512,513,514,515,516],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,512],compute_modifi:111,condit:7,conduct:[6,335],conserv:405,constant:[6,512],constraint:7,contact:[80,130],contact_radiu:[],coord:81,core:6,coreshel:9,correl:[217,218],cosin:[23,24,25,26,27,28,185],cossq:355,coul:[391,393,394,395,396,400,401,402,415,422,426,430,442,450],coupl:6,creat:226,create_atom:176,create_bond:177,create_box:178,createatom:13,creation:7,csld:331,csvr:331,cubic:424,cuda:[9,14,119,122,153,163,210,223,237,242,246,267,276,313,314,330,332,343,391,393,395,396,408,414,415,422,423,425,428,440,466,468],custom:[8,200,201],cut:[50,387,393,396,400,403,410,412,422,423,430,438,442,471],cvff:356,damag:[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pt:[311,507],adp:[],adri:[9,308,448,449],adust:171,advanc:[3,249,391,481,492],advantag:[1,6,8,11,14,18,40,41,42,225,385,410,495,500],advect:[3,6,328],advertis:8,advis:[380,447],afer:3,affect:[1,6,10,14,15,16,17,41,63,64,76,96,128,152,161,175,181,204,205,210,217,218,220,221,222,223,226,227,228,229,231,232,242,248,250,252,258,265,269,270,271,272,274,275,276,282,287,288,289,291,312,313,326,340,350,363,370,376,377,378,380,381,382,385,411,432,433,440,483,484,486,488,489,491,494,496],affin:[16,17,18,231,385,400],afil:246,aforement:18,afresh:[300,494,513],afshar:405,after:[],afterrun:494,afterward:3,afterword:42,ag1:176,ag2:176,again:[6,11,12,16,17,65,151,157,163,171,201,205,231,248,298,354,369,380,432,433,481,483,484,486,488,493,500,502,513,515],against:[11,12,13,67,232,380,448,449],aggreg:[6,12,69,72,74,85,102,119,126,248,264,310,312,326,481,514],aggress:[248,500],agilio:[9,13],agre:[3,8,197,378,387,420,449],agreement:[5,7],ahd:417,ahead:347,aidan:[0,5,7,9,13,373],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:204,akohlmei:[7,9,13,206,249],aktulga:[7,9,305,449],al2o3:456,al2o3_001:[129,313],al3:176,ala:[255,456],alain:9,alat:[293,435],alb:[446,469,471],albeit:311,albert:9,alchem:[95,171],alcohol:343,alcu:[386,391],alcu_eam:446,alderton:404,alejandr:[268,269],alessandro:13,algebra:438,algorithm:[0,1,6,7,8,9,42,64,205,214,225,228,231,255,257,258,282,295,303,312,315,316,335,336,340,343,348,376,377,378,382,385,407,411,433,438,453,455,481,483,500],alia:[9,12,16],alias:[1,371],aliceblu:205,align:[6,9,12,29,42,76,179,197,221,225,250,373,486,489,507],alkali:411,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,60,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,170,171,172,173,174,175,176,177,178,179,180,181,183,185,190,196,197,198,201,202,203,204,205,206,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,239,240,241,242,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,261,263,264,266,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,285,286,287,288,289,290,291,292,293,294,295,297,298,299,300,301,302,303,304,305,307,308,309,310,311,312,313,314,315,316,317,318,319,320,324,325,327,328,329,330,331,332,335,336,337,338,339,340,341,342,343,345,346,347,348,349,350,351,352,353,354,355,359,364,366,368,369,370,371,372,373,375,378,379,380,381,382,384,385,386,387,388,390,391,392,394,395,396,397,398,400,401,404,405,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,431,432,433,434,435,436,437,438,439,440,441,442,443,445,446,447,448,449,450,451,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,483,484,485,486,487,488,489,490,491,493,494,495,496,497,498,499,500,501,503,504,505,507,508,512,513,514,515,516,517],allen:[29,95,404,414],allentildeslei:95,allign:3,allindex:352,alloc:[3,5,6,8,9,11,12,63,242,342,379,381,385,444,449,486,494],allocat:3,alloi:[],allosw:76,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,58,60,61,62,64,65,66,82,100,117,119,153,155,156,157,170,175,176,177,179,185,196,197,201,202,204,205,206,208,209,211,213,214,215,217,218,219,220,221,222,223,225,227,228,229,230,231,232,236,237,242,244,245,246,247,249,252,255,258,259,263,265,268,269,293,297,298,299,300,301,302,306,312,313,315,317,319,320,324,328,335,336,337,338,340,341,342,343,344,345,351,353,355,364,370,371,373,378,379,380,381,384,385,387,388,391,392,393,394,395,396,401,409,411,415,416,417,418,423,427,432,433,438,440,446,449,450,453,455,456,465,472,475,477,481,484,486,488,489,490,491,492,493,496,498,499,500,503,504,508,513,514],almost:[2,3,12,63,250,302,340,371,382,385,465],alo:401,alon:[6,7,228,308,448,449,484],alond:13,along:[6,8,12,29,41,76,95,129,175,176,177,200,201,204,217,228,250,255,256,260,265,267,302,312,315,317,321,325,326,335,339,340,346,349,351,373,376,377,378,380,401,404,415,418,421,423,427,435,448,449,468,486,489,496,497,513],alonso:[436,437],alpha:[6,12,52,209,255,294,302,303,307,378,386,389,392,401,405,407,409,410,412,417,422,423,435,441,445,470,472,504,507],alpha_:[],alpha_c:431,alpha_i:457,alpha_ialpha_j:[],alpha_lj:431,alphabet:[2,3,22,37,45,56,66,185,196,208,355,364,379,398,466,486],alphanumer:[3,66,208,301,309,353,379,513],alreadi:[3,7,8,9,12,16,17,18,43,58,177,178,180,203,213,217,221,222,225,227,231,259,300,302,328,351,352,379,380,405,416,418,425,433,465,475,478,482,486,487,491,496,512,513],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,61,62,64,66,70,76,77,78,80,82,87,95,97,98,100,103,113,114,115,116,117,118,123,125,127,128,130,151,152,153,154,155,156,157,158,159,160,161,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eth:[448,449],chenoweth_2008:[448,449],chi:[102,166,200,293,303,305,366,412,414,514],chiefli:447,child:8,chip:[7,9,12,17,18,385,499],chipot:230,chiral:363,chmod:[11,12],cho:435,chocol:[7,205],choic:[3,6,9,12,15,16,18,41,42,55,95,152,155,156,170,181,197,217,221,222,225,228,231,232,246,252,255,266,268,295,303,312,335,364,371,376,377,380,382,385,418,431,440,444,486,495,496,499,500,506,507,512],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,95,128,167,168,204,226,227,228,229,232,241,252,255,266,268,270,271,272,273,274,275,276,298,299,316,328,332,346,370,371,377,475,481,483,495,501],chose:[469,471],chosen:[2,3,6,12,17,151,177,180,189,197,204,210,215,229,232,241,244,245,253,255,266,268,273,295,298,309,328,332,335,336,341,343,344,350,371,372,377,385,406,407,411,415,422,425,451,469,481,495,500,501,507],chri:175,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,98,103,114,116,125,157,172,174,217],chute:[4,9,10,247],ciccotti:315,cieplak:[6,183,498],cii:218,cij:218,ciko:2,circl:[43,76,324],circular:[3,6,155,199],circumst:18,circumv:[100,117,307],citat:[],cite:[3,7,8,12,252,456],civ:9,ckio:2,cko:2,cl1:176,clarendon:[29,404],clarifi:[7,469,471],clariti:353,clark:443,class2:[],classic:[0,3,5,6,7,8,9,242,295,302,307,340,365,411],classifi:[466,474],claus:484,clean:[6,12,14,15,17,494],cleanli:[485,516],clear:[],clearli:7,clebsch:151,clermont:[9,13],clever:490,click:[2,11,22,37,45,56,177,185,196,204,249,355,364,380,398,466,508],client:[249,251],climb:[267,380,500],clinic:[7,13],clo:[166,200,514],clock:[12,481,500],clockwis:346,clone:508,close:[3,6,11,12,13,40,42,71,76,152,180,201,227,228,229,246,253,255,268,289,312,315,346,349,369,371,374,376,377,380,385,387,391,401,402,421,435,440,448,452,454,468,471,490,496,507,508,510],closer:[3,10,42,127,175,200,201,225,229,233,337,380],closest:[227,293,312,343,414,450,465,475],cloud:[456,507],clovertown:18,clsuter:77,clump1:[297,312],clump2:[297,312],clump3:[297,312],clump:312,cluster:[],clutter:3,cmap:486,cmatrix:246,cmax:435,cmd:[11,12,295,497],cmdarg:11,cmin:435,cmm:[],cmoput:144,cn1:218,cn2:218,cna:[],cnn:218,cnr:[9,13],cnt:[418,490],co2:[41,176,315,379],coars:[7,9,10,29,36,41,55,189,297,312,328,416,451,495,498],coarser:[371,513],coarsest:151,code:[],coeff:[3,7,8,12,21,22,33,45,51,183,184,185,190,354,355,361,398,418,422,440,453,455,458,486],coeffcient:486,coeffici:[],coefficienct:405,coefficient0:409,coefficient1:409,coeffieci:[6,389,421],coeffincientn:409,coexist:[244,411],cohes:[6,412,435],coincid:[133,349,396,432,433,481],colberg:203,cold:[6,162,244,248,381,507],coldest:336,coleman8:9,coleman:[9,129,176,313],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,91,98,103,108,114,116,125,157,165,172,174,177,201,202,205,217,230,258,264,297,307,310,312,351,370,379,381,399,486,493,499,505,517],collid:[236,328,350],colliex:176,collinear:[3,297],collis:[3,255,328,346,350,408,415,478],colllis:328,colloid:[],colombo:40,colon:[206,351,487],color1:205,color2:205,color:[3,9,42,201,204,205,225,245,302,307],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,130,151,152,157,165,172,174,175,176,197,201,202,205,208,216,217,218,220,221,222,223,258,265,266,302,312,329,330,340,350,413,417,448,449,487,501,503,513],columnar:175,colvar:[],colvarmodul:12,com:[],comamnd:231,comand:228,comannd:385,comb3:[],comb:[],comb_1:304,comb_2:304,combiant:402,combin:[3,6,7,9,11,13,36,41,66,69,74,85,95,102,113,119,126,155,156,170,201,204,214,220,249,258,268,295,301,316,332,341,349,352,354,370,371,373,377,385,399,401,402,407,411,412,418,430,431,457,467,469,471,472,474,477,489,494,499,507,513],come:[],comfort:[12,13],comit:508,comm:[0,3,11,12,64,78,203,249,251,252,371,380,385,405,440,445,468,488],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,183,197,201,240,253,312,340,379,380,386,409,410,412,422,435,442,449,456,457,467,468,469,470,471,474,483,484,486,507,508,513],commerci:7,commit:[9,508],commmand:[3,6,12,62,118,290,421,480,481,483,500,516],common:[],commonli:[3,6,9,12,17,25,60,62,115,117,179,201,204,206,365,416,425,457,469,471,486,489,498],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,175,180,181,204,205,225,226,227,229,230,231,249,251,255,257,258,259,268,294,301,303,304,305,312,316,328,340,351,368,370,381,382,383,385,407,408,444,479,483,484,495,496,513,515,517],communc:370,comp:[7,203,251,252,315,371,380,411,440,445,450,464,468,470],compact:[66,208,398,466],compani:[5,7],compar:[1,3,4,6,8,12,17,40,94,121,129,160,176,185,196,205,235,303,351,353,370,371,378,380,435,456,481,500,501,507,512],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,184,185,196,354,355,364,397,466],compat:[3,5,7,8,9,11,12,13,17,18,42,76,128,130,188,201,206,210,216,217,218,220,221,222,223,225,294,306,332,335,342,345,348,370,385,419,438,440,468,483,484,513],compens:[6,226,227,310,381,411],compet:339,competit:371,compil:[3,7,8,9,12,13,14,15,16,17,18,19,175,201,203,204,206,249,339,371,385,438,486,487,491,513],compl:17,complain:[11,12,17],complement:435,complementari:[7,401,423],complet:[3,6,9,11,12,15,42,62,76,205,221,225,230,258,295,298,301,328,339,341,352,353,369,380,385,412,453,455,473,481,486,491,494,498,500,503,507,513],complex:[4,6,8,11,12,13,25,41,43,65,100,117,151,153,165,177,178,255,324,349,368,380,411,438,468,484,486,489,513],compli:[335,339],complic:[6,7,9,12,13,215,244,484],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,96,97,98,99,100,103,104,107,114,115,116,117,118,119,120,121,123,124,128,138,141,142,143,144,147,148,149,151,152,154,155,156,157,158,159,160,161,162,163,164,165,166,167,169,170,172,173,174,200,201,202,204,205,211,212,216,217,218,219,220,221,222,223,224,228,229,231,232,237,242,247,251,252,255,258,260,264,265,267,268,269,273,274,275,276,287,288,289,291,292,294,295,296,299,310,312,314,315,317,321,322,325,328,331,332,333,335,342,343,348,349,350,370,373,377,378,379,380,385,405,411,415,432,433,453,455,456,457,486,487,496,504,513,514],componenet:6,composit:[6,215,255,409],compound:[400,411,412,474],compres:[76,125,217],compress:[],compris:[41,349,450,473],compton:[129,176],comptu:3,compuat:371,comput:[],computation:[3,6,226,227,340,391],computational:507,compute_arrai:8,compute_fep:[210,431],compute_group_group:244,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[129,313],compute_scalar:8,compute_temp:8,compute_ti:210,compute_vector:8,compute_xrd:176,concaten:[2,3,516],concav:349,concentr:[76,409],concept:[6,157,167,217,495],conceptu:[3,6,76,165,229,231,380,401,418,435,491],concern:[6,78,95,203,245],concetr:76,concis:[11,339],conclud:12,concret:8,concurr:[16,371,513],conden:[340,469,471],condens:[6,159,340,387,403,409,423,474],condit:[],conducit:6,conduct:[],cone:489,confer:438,confid:[3,500],config:[12,201,483],configfil:230,configur:[1,2,6,12,15,17,38,62,133,179,197,200,201,204,208,229,230,231,232,236,244,251,252,282,295,303,339,368,378,380,387,391,410,435,438,467,469,471,474,481,486,488,489,500,508],confin:[486,500],conflict:[3,12,41,202,440,484,508],conform:[3,6,13,62,228,229,267,311,317,339,363,380,411,498],confus:[3,474],conjuct:[9,405],conjug:[7,8,252,377,411,448,449],conjunct:[6,7,76,94,95,125,160,165,171,177,181,205,209,210,252,255,259,282,298,299,303,304,305,307,312,316,328,336,343,348,370,371,380,392,394,398,401,405,411,417,423,440,443,451,472,486,489,493,507,517],connect:[3,6,9,95,162,180,228,249,297,312,315,325,380,402,415,448,449,465,471,483,484,486,490,507],conner:387,connor:387,conput:3,consecut:[3,11,12,40,76,177,205,209,210,232,249,250,401,423,427,481,487,489],consequ:[1,6,215,340,422,500],conserv:[],consid:[6,75,76,83,95,126,159,162,163,180,201,202,205,209,210,216,218,221,225,227,228,232,256,269,294,312,335,336,339,340,343,371,398,411,418,449,450,456,465,481,482,484,487,488,489,491,494,496,504,507,513],consider:[6,8,252,253,331,332,333,385,495],consist:[3,6,8,9,11,12,41,43,69,74,85,102,114,119,122,123,126,157,160,162,177,189,200,206,211,212,217,231,232,235,237,242,245,252,253,254,265,268,270,271,272,273,274,275,276,277,278,280,281,282,283,285,286,287,288,289,290,291,299,302,307,309,311,312,331,332,333,334,344,370,371,373,379,380,385,387,391,393,399,401,411,414,418,421,432,433,435,438,440,450,453,455,456,468,475,484,486,487,488,489,490,491,498,507,513],consistent_fe_initi:214,consit:312,constant:[],constitu:[3,6,258,312,345,349,399,450],constitut:[453,455],constrain:[3,6,8,154,155,156,157,158,160,163,164,165,166,167,169,170,208,217,232,244,245,250,258,262,297,298,310,312,315,326,336,343,378,379,411,491,498,507],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,100,117,129,151,176,229,268,294,311,349,381,385,404,438,440,465,467,468,489,490,505,513],constructor:[8,11],consult:449,consum:[1,307,444,513],consumpt:368,contact:[],contact_stiff:[452,454],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,95,99,127,129,151,153,157,165,175,176,177,179,183,185,196,197,201,202,204,205,206,208,209,210,214,216,217,218,220,221,222,223,225,230,232,237,240,246,250,251,252,255,266,282,293,294,297,298,300,302,305,309,312,313,318,328,335,339,340,349,350,353,369,371,379,380,383,384,386,387,388,391,400,401,404,409,410,411,418,419,435,438,442,446,447,448,449,457,467,468,469,470,471,472,474,481,482,483,484,486,487,488,489,491,493,495,498,500,501,503,504,507,508,513,515,517],content:[4,8,9,12,18,449,502,504],context:[3,6,8,12,17,127,128,205,226,227,232,297,309,344,377,477,486,493,502,512,513,514],contibut:75,contigu:483,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,87,113,114,173,205,208,209,210,215,217,218,219,220,221,222,223,225,228,229,230,231,232,244,245,246,248,249,250,252,253,254,260,265,266,268,270,271,272,273,274,275,276,287,288,289,290,291,296,298,301,302,312,313,317,327,328,330,337,338,340,346,349,353,369,384,385,391,405,408,425,428,448,449,450,453,455,470,481,484,486,488,489,494,500,501,503,504,513,515],continuum:[6,7,9,214,340,453,455],contour_integr:214,contract:[62,229,231,268,299,312],contradictori:3,contrain:315,contraint:282,contrari:[246,253],contrast:[1,6,43,56,67,159,162,202,231,351,453,455,477,516],contrib:340,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,210,215,216,217,218,220,221,222,223,229,244,252,255,258,259,263,269,289,290,297,298,306,309,312,313,315,342,370,378,380,388,405,408,409,411,418,432,433,438,440,448,449,456,498,504,507,508],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,95,99,133,151,186,201,202,204,208,214,215,225,229,230,231,248,249,252,253,268,270,271,272,273,274,275,276,299,304,312,319,320,331,332,333,340,344,368,370,382,411,414,438,448,449,452,454,467,471,481,483,495,501,502],control_typ:214,controlfil:449,convect:99,conveni:[6,12,29,201,206,223,313,373,457,472,508,513],convent:[3,8,29,188,195,196,202,205,311,325,352,409,411,513],converg:[3,6,42,96,201,202,204,206,211,225,228,229,237,242,273,302,304,307,311,315,376,377,378,380,400,401,423,456,481,493,500],convers:[3,8,151,204,205,215,218,299,370,401,402,403,411,423,427,431,443,484,500,512],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,99,177,184,201,204,205,218,223,266,298,351,354,356,360,363,373,380,386,409,438,469,471,478,484,486,487,488,493,503,507,512,513,515,517],convex:[43,349],convinc:[7,12],cook:9,cooki:7,cool:[7,167,248,310],cooordin:[201,202],cooper:[5,7],coord123:125,coord1:[3,125,217,221,222],coord2:[3,125,217,221,222],coord3:[3,125,217,221,222],coord:[],coordb:456,coordbb:456,coordiat:378,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,95,97,98,103,113,114,116,124,125,127,145,151,160,166,172,174,175,177,181,200,201,202,203,204,205,206,208,211,216,217,220,221,222,225,226,227,228,229,230,231,232,235,237,238,242,244,247,248,249,250,251,252,253,265,267,268,270,271,272,274,275,276,289,292,293,294,297,298,299,309,310,312,314,315,317,322,325,326,327,328,330,338,339,340,347,348,350,351,373,378,379,380,385,386,387,390,410,456,481,486,487,488,489,491,494,496,500,507,513,514],coordn:[125,217],coorind:[],copi:[0,3,4,8,9,11,12,15,17,41,130,204,340,380,398,448,484,508],copper:478,coproccesor:16,coprocessor:[1,7,9,16,17,385,499],coproprocessor:17,copy_arrai:8,copyright:[7,8,297],coral:205,core:[],core_shel:159,coreshel:[],cornel:[6,183,498],corner123i:124,corner123x:124,corner123z:124,corner1i:124,corner1x:124,corner1z:124,corner2i:124,corner2x:124,corner2z:124,corner3i:124,corner3x:124,corner3z:124,corner:[3,6,41,124,204,349,350,373,473,486,508],cornflowerblu:205,cornsilk:205,corp:9,corpor:16,corr:400,correct:[3,6,9,11,12,16,17,62,95,96,112,113,118,121,127,159,164,171,202,204,231,244,246,252,268,269,289,297,299,302,339,345,349,370,380,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,403,404,405,408,409,410,411,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,478,479,486,501,504,507,508],correction_max_iter:214,correctli:[3,8,11,17,76,87,112,113,114,154,155,156,158,160,162,163,164,165,166,169,170,173,201,205,211,232,237,242,253,262,268,269,305,312,315,325,327,346,349,380,381,385,403,433,438,483,484,486,496,508,512,514],correl:[],correpond:240,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,95,106,107,120,123,124,125,126,129,130,138,141,142,143,144,145,147,148,149,151,154,155,164,171,175,176,183,184,185,186,187,188,189,191,192,194,195,197,200,201,202,204,205,209,210,211,217,219,220,221,222,224,227,229,231,238,242,243,247,252,255,256,264,265,266,268,270,271,272,273,274,275,276,277,278,282,285,287,288,289,291,294,295,299,304,312,314,315,331,333,335,344,345,346,348,349,350,352,354,355,356,357,359,360,363,365,371,375,377,379,380,386,387,389,392,393,394,395,396,397,398,399,400,401,404,405,409,410,411,412,413,414,415,416,417,418,421,423,424,425,426,427,428,429,430,431,432,435,436,438,440,441,442,443,445,446,448,449,450,451,456,457,458,467,468,469,470,471,472,474,476,477,478,481,483,484,486,487,489,499,500,501,503,504,507,513],correspondingli:[432,433,495],corrupt:3,cosin:[],cosineshift:27,cosmo:[246,251],cossq:[],cost:[1,6,10,11,12,17,40,42,76,120,129,152,176,204,205,217,221,222,225,226,227,241,268,304,340,370,371,383,401,423,427,438,440,467,483,495],costheta0:[467,469,471,474],costheta:446,costli:[11,96,246,381],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,95,98,103,114,116,120,123,125,157,167,172,174,190,201,202,204,205,209,210,217,218,221,225,231,242,251,301,302,303,307,310,312,314,328,329,335,339,340,341,345,349,351,353,361,367,369,376,378,381,385,388,413,417,418,421,448,449,482,483,484,486,488,490,493,494,501,502,507,513,514],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,96,118,119,127,152,178,182,303,305,341,370,371,378,385,392,394,395,396,397,400,401,402,403,404,411,415,416,418,423,427,431,434,440,443,448,449,451,456,466,471,472,474,477,491,498,504,507,512],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,99,125,127,128,165,175,181,211,212,215,217,220,221,222,224,225,232,237,241,244,250,268,282,298,315,331,332,349,371,378,379,380,382,385,413,417,440,504,513],counter:[3,346,481,492,494,500],counteract:244,counterbal:248,counterbalanc:29,counterpart:[201,312,481],counterproduct:18,coupl:[],courant:318,cours:[3,8,137,139,171,201,209,210,245,311,325,339,345,347,348,350,351,371,432,458,483,486,499,507,513,515],courtesi:373,cov:456,coval:[6,9,29,411,435,456,507],covari:246,cover:[6,76,197,205,214,255,411,473],coverag:[76,221],cpc:251,cpp:[1,3,6,8,9,11,12,13,95,201,209,210,242,315],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,205,219,235,253,341,368,371,385,398,466,481,499,500,503,504,505,513],cpuremain:504,cr2:176,cr3:176,crack:[4,381],crada:[5,7],crai:[5,7,13,18,201],crash:[3,12,381,507],craympi:385,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:214,create_faceset:214,create_group:203,create_nodeset:214,createatom:[],creation:[],crimson:205,critchlei:297,criteria:[3,127,178,204,205,226,227,228,263,378,445,473,488,491,513],criterion:[12,42,132,177,180,215,225,228,244,282,304,318,346,351,378,380,400,411,415,456,491,500,501],criterioni:500,critic:[6,49,50,266,335,340,378],crmax:76,crmin:76,cross:[3,12,22,76,97,155,175,185,201,202,204,216,221,227,231,265,267,289,312,321,325,327,336,343,355,373,380,396,405,408,409,416,417,418,423,425,427,446,451,453,455,469,471,478,486,490,496,515],crossov:1,crossterm:486,crozier:[0,7,13],crucial:302,crystal:[3,4,6,13,78,117,293,294,338,373,381,486,490,504,507],crystallin:[6,113,294,373,470,507],crystallis:335,crystallogr:[129,176],crystallograph:[373,504],crystallographi:[129,176,373],cs1:176,cs_chunk:6,cs_im:[41,486],cs_re:[41,486],csanyi:[151,447,457],cscl:435,csequ:6,csh:[11,12,398],cshrc:[11,12],csic:[410,467,469,471,474],csinfo:6,csisi:[410,467,469,471,474],csld:[],cst:409,cstherm:6,cstyle:483,csvr:[],ctcm:[386,409],ctemp_cor:235,cterm:317,ctr:9,ctype:11,cu1:176,cu2:176,cu3au:435,cube:[6,42,175,180,225,235,349,373,507],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:391,cummul:[3,6,223,226,227,228,230,241,246,252,254,328,331,332,333,334,336,343,417,504],cumul:[6,215,217,220,221,222,236,244,252,266,268,273,282,312,313,380],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,87,95,112,113,119,127,128,141,152,157,165,167,173,175,178,181,200,201,202,203,204,205,206,209,210,214,217,221,222,223,225,226,227,228,229,230,231,232,236,237,242,244,246,249,250,252,258,265,268,269,274,275,276,282,287,288,289,291,297,298,303,304,306,309,310,311,312,315,316,317,318,319,320,321,322,324,326,327,328,331,332,333,339,340,343,344,345,346,347,348,350,351,353,368,369,370,371,374,375,377,378,379,380,385,391,398,400,404,409,411,412,415,418,419,422,432,433,435,436,437,440,446,448,449,452,453,454,455,458,469,471,472,475,481,482,483,484,486,487,488,489,490,492,493,494,496,498,500,501,503,504,508,513,514,515,516,517],curv:[6,177,244,294],curvatur:[414,450,478],custom:[],cut0:484,cut1:495,cut2:495,cut:[],cuthi:[293,305],cutinn:[393,432,433],cutlo:[293,305],cutmax:446,cutoff1:[397,404,423,427,431,434,443,451],cutoff2:[392,394,395,397,403,404,423,427,431,434,443,451,472],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,95,100,117,119,126,127,151,175,178,180,181,227,228,233,240,293,302,303,305,307,309,312,316,328,341,345,349,351,368,370,371,378,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,399,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450,451,456,457,458,459,460,461,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,484,488,491,495,507,513],cutoff_glob:[],cutoff_inn:[],cutoffa:410,cutoffc:410,cuu3:409,cval:176,cvd:335,cvel:317,cvff:[],cwiggl:[3,265,345,348,350,513],cyan:[2,204,205],cycl:[3,244,266,268,269,273],cyclic:[3,197],cygwin:12,cylind:[3,4,76,204,217,250,298,346,349,489],cylindr:[6,250,325,346],cypress:385,cyrot:391,cyrstal:294,d3q15:255,d3q19:255,d_double_doubl:15,d_e:340,d_flag2:301,d_flag:301,d_name:[124,201,301,330,496],d_single_doubl:15,d_single_singl:15,d_sx:301,d_sy:301,d_sz:301,daan:338,dai:12,daili:12,daivi:289,damag:[],dammak:307,damp:[3,6,208,213,252,253,254,259,268,269,273,299,302,303,307,312,331,332,344,346,347,377,378,380,392,394,396,401,404,411,415,423,431,443,451,466,472,500,507],damp_com:253,damp_drud:253,dampen:[312,507],dampflag:[346,415],dan:17,danger:[3,12,244,351,405,504],dangl:180,daniel:9,darden:[371,404],darkblu:205,darkcyan:205,darken:204,darkgoldenrod:205,darkgrai:205,darkgreen:205,darkkhaki:205,darkmagenta:205,darkolivegreen:205,darkorang:205,darkorchid:205,darkr:205,darksalmon:205,darkseagreen:205,darkslateblu:205,darkslategrai:205,darkturquois:205,darkviolet:205,dasgupta:303,dash:[415,503],dat:[6,99,197,214,482],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,313],dataset:313,datatyp:3,date:[0,4,6,12,13,200,448,449,513],datom1:126,datom2:126,datom3:126,datom4:126,datum:[3,6,43,69,72,74,85,102,119,126,201,218],davenport:434,davi:345,david:[9,19,370,371,469,471],daw:[409,446],dbg:14,dcd:[3,6,7,201,203,204,205,206,295,487,491],ddim:200,deactiv:431,dealt:251,debug:[6,7,11,12,13,14,17,58,129,133,176,177,295,300,368,370,385,419,440,475,484,485,493,496,503,513],deby:[],decai:[100,401,478],decid:[3,6,12,16,76,265,301,312,341,501,508],decipher:373,declar:203,declin:328,decod:204,decompos:[95,457],decomposit:[3,5,7,18,65,214,295,316],decoupl:[6,507],decreas:[3,201,202,211,212,219,228,231,237,242,244,252,339,370],decrement:317,deepli:367,deeppink:205,deepskyblu:205,def:[12,13,484],defaul:64,defect:[6,75,175,438],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,183,184,185,186,187,188,189,191,192,194,195,196,197,198,199,200,201,202,203,204,205,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,227,228,229,231,232,235,236,237,239,242,243,244,247,250,251,252,253,254,255,263,265,267,268,269,270,271,272,273,274,275,276,278,279,280,283,285,286,287,288,289,290,291,293,294,295,297,298,299,301,303,305,310,312,313,314,315,318,322,326,328,330,331,332,333,334,336,337,338,340,342,343,345,346,347,348,349,350,351,353,354,355,356,357,358,359,360,363,364,365,366,368,370,371,373,375,377,378,379,380,381,382,383,384,385,387,388,389,390,392,393,394,395,396,397,398,399,401,402,404,405,406,407,408,410,411,413,414,415,416,417,418,419,421,423,424,425,426,427,428,429,430,431,432,433,434,438,439,440,441,442,443,445,446,448,449,450,451,452,453,454,455,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,483,484,486,487,489,490,491,492,495,496,497,498,500,501,503,504,507,509,510,511,512,513,514],definit:[2,3,6,8,12,13,83,86,127,151,205,217,218,219,220,221,222,223,231,239,250,273,313,330,342,345,348,350,352,364,368,379,388,391,399,406,407,411,421,446,453,455,457,473,484,486,488,495,497,512,513],defint:504,deform:[],deg2theta:176,deg:507,degener:[3,297],degrad:[8,18,294,371,495],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,100,102,104,106,107,109,111,112,117,123,154,155,156,157,158,159,160,161,162,163,164,165,166,167,169,170,176,177,183,184,187,188,195,197,200,204,217,228,235,244,246,247,252,253,258,268,269,273,274,275,276,287,288,289,291,295,297,311,312,315,331,332,333,338,354,356,360,363,365,378,404,409,417,496,504,507,514],degress:[157,217],del:500,delai:[3,6,12,381,408,504],deleg:418,delet:[2,3,7,8,12,55,60,63,66,175,180,181,208,217,218,220,221,222,223,226,228,241,244,268,313,331,332,351,353,369,379,381,384,440,465,486,487,488,489,497,498,503,508,509,511,513,514],delete_atom:[],delete_bond:[],delete_el:214,deli:200,delimit:[484,513],deloc:[269,411,456],delr:435,delt_lo:500,delta:[],delta_1:391,delta_3:391,delta_7:391,delta_conf:3,delta_ij:[435,446],delta_mu:[],delta_pi:391,delta_r:446,delta_sigma:391,delta_ua:[],delx:200,delz:200,dem:[],demand:307,demo:11,demon:292,demonstr:[302,435],den:298,dendrim:417,denniston:[9,255,257,258,259,294],denomin:[7,182],denot:[129,235,253,294,305,307,401,416,418,449,453,455],dens:[76,228,411],densiti:[3,6,7,9,18,41,42,62,110,127,137,151,163,175,177,209,210,214,217,221,222,225,231,242,255,258,261,262,294,298,299,303,340,345,373,375,379,386,387,391,409,435,436,437,446,450,456,460,462,463,464,486,495,496,504,512],density_continu:455,density_summ:455,depart:[0,7],departur:[266,302],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,100,102,113,119,120,123,124,125,126,130,151,153,154,160,164,165,171,177,178,183,184,185,186,187,188,189,191,192,194,195,196,197,200,201,202,204,205,208,209,210,211,212,215,217,219,220,221,223,224,225,227,229,231,237,238,243,246,247,248,250,252,253,255,257,258,265,268,270,271,272,273,274,275,276,277,278,285,287,288,289,291,293,304,307,309,312,314,315,316,322,328,331,332,333,335,337,339,340,342,344,345,348,349,350,351,353,354,355,356,357,359,360,363,365,371,373,378,379,381,382,383,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,404,405,409,410,411,412,413,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,435,436,438,439,441,442,443,445,446,448,449,450,451,456,457,458,466,467,468,469,470,471,472,474,476,477,478,481,483,486,488,489,492,496,498,500,503,504,506,513,514],dependend:6,depflag:12,dephas:[481,500],depos:232,deposit:[],deprec:[3,303,448],depth:[52,155,204,340,414,450],dequidt:9,der:[95,118,399,400,431,448,449,477,507],deriv:[6,7,8,9,38,57,66,95,151,171,197,218,229,231,244,252,265,268,270,271,272,273,274,275,276,293,299,303,307,337,338,340,345,346,349,377,379,387,391,399,404,411,412,416,425,429,430,435,438,448,449,466,468,477,507],derjagin:477,derlet:293,descend:205,descent:[7,377],descib:[41,204,303],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,96,121,124,127,129,141,151,152,155,156,157,161,162,165,168,170,171,175,176,177,179,180,189,194,197,201,202,203,208,209,210,217,218,219,220,221,222,223,225,228,229,230,231,232,234,235,240,245,246,249,250,251,252,253,254,255,257,258,259,263,267,268,269,273,281,290,293,295,300,301,302,303,304,305,312,317,325,328,329,330,331,332,333,334,335,336,337,338,343,345,346,348,353,370,371,373,376,377,378,379,380,384,387,388,390,392,393,394,396,397,398,399,400,401,404,409,411,412,414,415,416,418,421,423,424,425,426,427,428,429,430,431,432,433,434,435,438,439,445,446,447,448,449,450,451,456,457,458,465,466,467,468,469,470,471,472,474,476,477,478,479,481,483,484,486,487,488,489,490,496,499,500,503,508,513,514,515],descript:[],descriptor:[151,201,419],deserno:371,design:[0,3,6,7,8,11,13,14,15,17,129,159,162,176,214,228,234,235,268,269,293,294,313,335,340,388,389,390,393,396,401,403,411,431,432,433,436,437,446,449,468],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,96,99,123,128,152,159,177,190,200,217,223,229,231,242,244,245,252,253,254,258,268,289,297,298,299,300,303,307,312,315,328,331,332,333,334,339,346,361,367,370,371,373,376,378,379,380,405,409,417,432,433,467,469,471,482,483,484,486,490,495,500,501,503,504,513,514,515],desk:7,desktop:[4,6,7,10,12,204],despit:507,destabil:391,destre:363,destroi:[9,11,40,226,227],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,98,99,103,112,114,116,118,120,122,123,125,128,130,151,152,154,155,156,157,160,170,171,172,174,177,178,181,182,185,196,200,201,202,204,205,208,209,210,214,217,218,219,220,221,223,225,227,228,229,230,231,232,242,244,245,246,247,249,250,252,254,255,259,265,266,267,268,269,270,271,272,273,274,275,276,280,282,287,288,289,290,291,294,297,298,299,301,302,304,305,306,312,315,316,328,331,332,333,334,335,336,338,339,340,341,342,343,344,351,353,355,364,370,371,374,378,379,381,382,385,386,387,388,390,391,393,395,396,397,398,399,400,401,404,405,411,412,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,433,434,435,439,440,445,448,449,450,456,457,458,466,473,476,477,479,484,486,487,488,489,491,492,495,496,498,501,504,505,508,513,514,517],detect:[2,3,12,43,64,66,94,100,243,298,339,380,400,417,422,481,483,486,497,500,513],determ:385,determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,95,112,118,120,123,129,130,138,152,165,166,175,176,177,200,201,202,204,205,206,207,211,212,213,216,217,218,219,220,221,222,223,224,225,229,231,232,235,237,244,247,248,250,252,253,258,263,265,266,268,274,275,276,287,288,289,291,293,295,298,299,302,309,310,311,312,313,314,318,320,322,328,331,332,333,335,341,342,345,346,347,348,349,350,351,364,370,371,373,379,381,382,385,387,388,395,400,404,408,409,413,415,418,419,427,435,438,440,449,450,456,465,468,472,477,483,486,487,489,491,493,496,500,502,503,505,512,513,514],determinist:316,detil:119,devan:[9,451],devanathan:471,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,249,273,297,302,303,306,387,391,411,437,438,456,474,488],devemi:9,deviat:[266,273,293,413],deviator:9,devic:[1,3,12,15,17,249,385],device_typ:385,devin:[304,400],devis:437,dfactor:204,dff:507,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,371],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,306,438],dhi:[62,200,231,298],dhug:[266,302],dhugoniot:[266,302],dia:435,diagnost:[],diagon:[3,6,91,151,152,153,229,268,299,312,343,453,455],diagonalstyl:457,diagram:[42,129,176,196,225,295],diallo:417,diam:[204,205,298,379],diamet:[3,6,41,43,124,177,201,202,204,205,209,210,252,298,312,328,330,344,346,379,399,414,415,425,450,473,477,486,487,496],diamond:[373,411,435],diamter:[41,298],dick:6,dicsuss:265,dictat:[215,266],did:[3,12,378,405,408,409,415,440,469,471,494],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,173,342,370],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,95,100,104,106,107,131,151,153,154,155,156,157,158,160,163,164,165,166,167,169,170,171,177,178,180,185,196,197,200,201,204,205,208,210,213,215,217,220,225,226,227,228,229,230,231,235,240,243,244,245,246,247,248,249,252,253,255,265,268,269,270,271,272,274,275,276,278,280,283,285,286,287,288,291,293,295,297,299,302,303,304,307,310,312,315,317,325,326,328,331,332,333,336,337,338,340,343,344,345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t:435,emac:[],email:[0,3,5,7,8,9,11,412],emb:[3,9,349],emb_lin_neg:435,embed:[3,4,5,7,9,11,12,13,29,96,153,175,340,386,409,412,431,435,436,437,446,466,475,484],embt:184,emi:[7,9],emil:9,emol:[448,449,504],emphas:415,empir:[9,214,332,387,411],emploi:[294,303,307,470],empti:[3,60,76,175,179,312,370,381,422,486,497,498,513],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,40,41,44,46,47,48,49,50,51,52,54,55,56,57,63,64,65,67,71,83,86,91,95,96,106,107,108,109,110,111,115,118,120,122,123,129,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,154,155,156,159,161,163,164,168,169,171,175,176,183,184,186,187,188,189,190,191,192,194,195,196,197,201,202,203,205,206,208,209,210,211,212,213,215,219,222,224,226,227,228,230,231,232,237,238,241,242,243,244,245,246,247,249,250,251,252,253,254,255,256,257,258,259,261,262,264,266,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,285,286,287,288,289,290,291,293,294,295,297,298,302,303,304,305,306,307,308,309,311,312,314,315,317,318,319,320,321,322,324,325,327,328,331,333,334,335,336,337,338,340,341,343,344,345,346,347,348,349,352,354,356,357,359,360,361,363,364,365,371,378,380,384,385,386,387,389,390,391,392,393,394,395,396,397,399,400,401,402,403,404,405,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,440,441,442,443,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,476,477,478,484,487,488,489,493,495,505,513,517],enclos:[2,6,12,179,201,300,353,435,456,482,484,494,513],encod:[13,40,43,201,204,205,301,418],encompass:[3,6,41,43,60,62,127,178,324,342,466,489],encount:[3,8,12,62,117,220,384,491,513],encourag:[7,8,306,326],end12i:124,end12x:124,end12z:124,end1i:124,end1x:124,end1z:124,end2i:124,end2x:124,end2z:124,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,41,42,43,58,60,62,76,124,180,181,184,200,201,202,204,205,206,209,210,218,220,222,223,228,231,245,250,252,254,267,268,269,282,299,311,312,317,328,331,332,333,334,336,339,340,343,347,350,351,369,370,379,380,384,385,405,409,414,421,434,438,450,453,455,457,458,475,481,484,486,487,488,489,491,493,494,498,502,504,507,513,517],end_of_step:8,endbondtors:[3,184,190,486],endif:8,energet:[228,387,449],energi:[],energy_compon:456,energy_update_freq:449,enforc:[6,9,60,61,114,200,201,202,203,204,206,208,215,228,231,268,292,294,304,312,315,353,370,423,483,513,514],enforce2d:[],eng:[11,69,74,119,201,242,351,353,400,437],eng_previ:353,engil:9,engilitycorp:9,engin:[214,231,297,317,337,409,436],engr:[],enhanc:[210,214,481],enlarg:[62,204],enough:[3,41,64,94,177,178,180,181,225,253,298,302,307,312,341,345,346,349,381,385,401,444,486,490,491],enpub:409,enrti:[],ensembl:[],ensight:6,ensur:[3,6,151,201,202,215,219,229,244,245,268,318,339,371,391,408,431,467,474],enter:[60,167,412,438,474,500],enthalpi:[134,270,271,272,409,503,504,513],entir:[0,2,3,6,11,14,15,42,43,66,88,89,96,120,121,123,127,129,152,157,176,177,205,208,209,210,217,221,222,225,228,230,241,244,245,248,252,253,264,268,270,271,272,273,274,275,276,293,295,297,310,312,326,340,342,353,385,404,427,440,468,486,494,495],entireti:473,entiti:[6,8,41,43,201,312],entri:[3,8,12,38,43,57,69,74,85,102,119,126,129,138,141,142,143,144,145,147,148,149,175,197,202,205,209,220,221,222,230,240,302,351,379,391,410,435,442,449,457,467,468,469,470,471,474,513],entropi:500,entry1:[38,57,205,398,468],entry2:205,entryn:205,enumer:[178,201,479],enumuer:6,env:385,environ:[1,3,6,11,12,16,17,18,204,246,251,293,385,386,391,398,400,410,411,446,469,483,497,513],epair:[118,205,413,417,448,449,504],epen:[448,449],epfl:[246,251],epp:404,epq:404,eps0:477,eps14:431,epsilon0:471,epsilon:[3,6,36,46,47,51,54,55,95,183,209,210,244,312,328,345,349,376,378,390,396,397,399,401,402,403,404,414,416,417,418,421,422,423,424,425,426,427,428,429,430,431,434,439,443,450,451,461,467,472,473,476,477,495,507,512],epsilon_0:478,epsilon_14:396,epsilon_:450,epsilon_d:402,epsilon_i:[414,440,450],epsilon_i_:450,epsilon_i_a:[414,450],epsilon_i_b:[414,450],epsilon_i_c:[414,450],epsilon_ij:440,epsilon_j:[414,440,450],epsilon_j_:450,epsilon_j_a:[414,450],epsilon_j_b:[414,450],epsilon_j_c:[414,450],epsilon_lj:450,epton:445,eqch:172,eqeq:[448,449],eqp:404,eqq:404,equal:[2,3,6,8,11,12,17,40,42,55,66,69,72,74,76,81,85,94,95,99,102,119,121,126,128,130,152,155,171,173,175,177,200,204,205,208,209,210,211,212,215,218,219,220,223,224,225,229,231,232,237,244,245,247,248,250,252,253,255,258,259,265,266,273,284,293,295,298,300,302,303,304,307,309,311,312,314,317,322,324,331,332,333,336,337,338,340,342,343,345,348,350,351,353,369,373,378,380,381,382,384,385,400,405,407,413,414,417,421,432,438,439,446,448,449,450,452,453,454,456,457,458,468,473,474,478,482,483,484,486,488,489,493,494,497,500,502,504,513,514],equat:[3,6,7,8,9,99,117,123,129,176,185,196,208,229,235,236,239,240,246,252,253,255,258,266,267,268,269,273,289,293,295,302,303,307,315,316,328,336,340,343,345,346,348,350,363,370,371,399,404,405,407,411,412,415,420,432,433,435,440,450,453,455,460,461,463,464,478,507],equi:269,equidist:267,equil:[3,303,374,493,517],equilater:496,equilibr:[3,4,5,6,7,9,62,99,177,208,215,218,228,229,244,266,268,269,289,290,302,303,304,305,336,337,338,343,400,401,448,449,482,496],equilibria:343,equilibribum:[226,227],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,62,160,161,184,186,229,231,244,245,246,253,255,268,273,289,302,303,307,311,315,317,325,328,335,336,338,343,354,356,360,363,400,435,442,456,507],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:214,equival:[6,12,13,29,62,64,135,136,144,149,175,179,205,220,223,229,231,244,252,268,289,299,311,312,348,387,405,411,456,469,471,472,486,489,494,495,504,507],equlibrium:6,equliibr:[303,305],er3:176,eradiu:[41,124,202,411,486],eras:[314,337],erat:[231,433],erc:401,erfc:[401,423,440],erforc:[124,202],erg:512,erhart:[215,409,469,471],ermscal:388,ernst:9,eror:3,eros:435,erose_form:435,erot:[],errata:[469,471],erratum:345,erron:3,error:[],erta:415,ervel:[124,202,486],escap:[232,507],especi:[8,16,165,177,208,215,225,244,302,307,310,311,385,483],espresso:[9,306],essenti:[8,11,12,27,96,139,158,159,160,163,164,165,166,167,169,186,218,273,294,344,371,387,401,423,471,491,504],essex:29,establish:[95,248],estim:[1,3,6,10,12,38,42,57,99,152,214,225,236,266,328,335,370,371,376,440,449,468,500,504],esu:512,esub:435,eta:[6,255,268,302,303,305,344,410,412,414,446,470,474,512],eta_dot:268,eta_ij:446,eta_ji:412,etag:[41,486],etail:504,etap:268,etap_dot:268,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,97,98,99,104,120,121,124,126,152,154,157,158,159,160,161,163,164,165,166,167,169,171,177,179,180,181,190,201,202,204,205,208,209,214,215,216,217,220,221,222,223,226,227,231,232,242,244,245,252,268,298,309,313,340,341,349,353,369,370,378,379,380,381,383,409,410,418,431,433,438,444,448,449,467,469,471,474,481,484,486,487,488,493,495,496,500,501,502,503,504,505,507,512,513,515,517],ethernet:18,etol:[378,380,481,500],etot0:302,etot:[6,104,106,107,121,152,163,205,235,253,266,302,503,504],eu2:176,eu3:176,euler:[378,380],eulerian:214,euqat:459,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,95,96,99,118,128,130,151,153,157,167,175,177,200,201,202,204,205,209,210,211,212,214,216,217,218,219,220,221,222,223,224,231,237,245,247,248,250,251,252,253,294,300,303,314,318,322,331,332,333,342,345,348,350,351,353,370,371,376,378,385,438,440,446,452,454,456,468,481,482,484,488,489,491,493,494,495,496,500,502,504,513,514],evalut:[353,484],evan:[165,289],evanseck:[6,20,183,396,498],evapor:[],evaul:[8,378],evdwl:[118,153,448,449,504],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,96,118,130,175,178,179,193,197,201,202,205,208,209,210,215,216,217,220,221,222,223,225,226,227,229,231,232,235,250,253,266,268,269,294,298,307,309,312,313,324,328,336,340,343,345,349,351,362,370,376,378,380,385,390,411,412,415,418,421,440,450,474,475,479,486,487,489,491,492,493,495,496,498,501,503,504,505,507,517],evenli:[3,42,58,152,197,225,255,421,475],event:[],eventu:[3,6,12,15,179,303,500],ever:[9,55,57,251,328],evera:[399,414,450,466],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,99,124,130,139,165,180,201,202,203,204,205,206,208,209,210,211,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,236,241,242,244,246,248,249,250,255,256,264,268,269,273,292,293,294,298,299,300,301,302,303,304,305,307,309,310,312,313,315,317,328,330,331,332,333,334,335,336,339,340,341,342,343,351,353,369,371,380,381,382,385,405,408,418,431,448,449,456,462,480,481,482,486,488,490,491,493,494,495,500,501,502,504,508,513,517],everyth:[8,118,508],everywher:[127,425],eviri:411,evolut:[246,255,295,481],evolv:[255,295,341],ewald:[2,3,5,6,7,8,9,12,96,121,129,152,341,370,371,378,392,394,395,401,404,411,423,427,443,451,466,468,472],ewald_disp:404,ewalddisp:3,exact:[22,42,45,76,133,171,180,185,225,228,245,246,252,253,254,298,307,308,328,340,355,370,398,488,493,500,513,515,517],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,99,127,155,161,168,177,197,209,210,220,225,231,236,240,245,252,253,254,269,281,282,290,294,302,328,333,334,347,385,398,405,409,415,418,432,440,468,488,489,496,500,513],exager:507,examin:[6,8,17,228,294],examp:[484,513],exampl:[],exce:[3,6,16,17,18,42,61,76,179,216,217,220,221,222,223,225,229,231,236,241,268,294,309,313,319,320,328,378,385,486,513],exceed:[3,42,62,225,231,268,328,494],excel:411,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,97,98,119,120,123,128,152,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,177,181,183,184,185,186,187,188,189,191,192,194,195,196,197,200,201,202,205,208,211,217,218,220,224,225,229,231,238,243,244,247,250,252,254,268,269,270,271,272,273,274,275,276,277,278,281,282,285,287,288,289,290,291,295,304,305,312,314,315,325,328,331,333,334,340,344,348,351,352,353,354,355,356,357,359,360,363,364,365,370,371,373,375,379,380,381,383,384,385,386,387,389,392,393,394,395,396,397,398,399,400,401,403,404,405,409,410,411,412,413,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,433,436,441,442,443,445,448,449,450,451,458,466,467,468,469,470,471,472,474,476,477,478,481,483,484,486,488,489,491,494,495,496,497,498,500,504,507,512,513,514,516],excess:[219,411],exchang:[2,3,6,8,64,65,208,214,215,244,252,304,312,336,340,343,370,385,411,501],exchange:370,excit:411,exclud:[3,6,9,12,16,17,66,76,123,151,157,164,165,181,201,217,221,226,227,256,264,297,310,312,335,346,351,378,379,381,393,415,418,421,432,433,440,465,498],exclus:[1,3,12,16,95,385,400,438,440,495,505],excurs:[268,481],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,178,204,249,306,353,369,372,384,482,484,494,497,500,513],exempl:456,exemplari:245,exemplifi:411,exert:[6,250,253,307,347,348,349,371],exhaust:[214,384,513],exhibit:[100,268,377,411,495],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,133,177,178,196,203,204,205,208,213,224,227,229,232,244,297,298,300,351,352,354,356,357,358,360,364,374,379,385,406,407,418,448,465,475,482,484,486,487,488,497,498,499,508,513,514,515],exit:[2,3,11,12,42,60,201,225,240,369,384,484,485,494,503,513],exlanatori:3,exp:[],expand:[],expans:[12,151,201,497,513],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,112,158,169,175,197,225,237,244,246,265,293,299,301,302,307,312,351,371,381,398,435,438,440,481,484,486,488,491,495,500,513],expens:[6,76,205,293,297,312,340,351,370,371,381,385,484],experi:[6,13,15,17,224,232,249,258,267,299,311,312,376,380,405,440,495,500],experienc:[6,12,257,258],experiment:[244,370,385,500],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,94,102,157,165,197,201,202,204,205,208,217,218,223,225,227,229,231,268,293,301,312,325,351,353,369,370,373,379,380,384,390,409,421,456,458,473,484,487,488,491,493,496,507,508,513,517],explan:[3,6,62,124,151,201,202,217,267,293,418,480,483,484,486,495],explanatori:[3,8,128,201,202,216,217,220,221,222,312,379,483,513],explantori:[3,308],explic:439,explicit:[6,9,11,22,45,82,95,124,127,171,185,209,210,231,319,320,355,375,387,388,391,396,398,409,411,422,432,472,480,483,487,490,508],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,120,123,154,164,167,175,177,183,184,186,187,188,189,191,192,194,195,197,201,202,205,211,221,224,231,238,243,245,247,252,268,270,271,272,273,274,275,276,277,278,285,287,288,289,291,301,302,304,312,314,315,331,333,334,340,344,348,354,356,357,359,360,363,365,379,385,386,387,389,392,393,394,395,396,397,398,399,400,401,402,404,405,408,409,410,412,413,414,415,416,417,418,422,423,424,425,426,427,428,429,430,431,432,436,438,440,441,442,443,445,450,451,458,459,460,461,462,463,464,466,467,468,469,470,471,472,474,476,477,478,486,488,489,495,496,498,499,505,507,508],explictli:[16,499],exploit:[15,17,295],explor:[129,176],expon:[3,303,305,409,414,417,431,439,451],exponenti:[95,446,467,474,478,500,513],expos:11,exposit:[214,405,408],express:[6,151,163,177,209,210,229,265,293,303,340,346,353,391,409,411,425,435,456,457,466,513],expressiont:391,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,90,91,92,95,96,99,101,104,107,108,118,120,128,130,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,202,208,211,212,215,223,224,230,233,237,242,243,244,246,247,248,250,252,254,266,268,273,282,293,294,310,311,312,314,317,322,325,327,331,332,333,334,335,337,338,340,342,345,349,350,414,435,438,449,450,457,503,504,512],extent:[1,3,42,43,46,60,76,175,179,201,213,221,225,250,347,350,370,373,387,452,454,468,483,486,489],exterior:[3,6,175,349],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,112,120,121,123,129,152,154,155,156,158,160,163,164,165,166,167,169,170,176,177,178,179,183,205,220,225,227,268,300,301,302,312,328,378,379,382,383,404,415,418,421,435,440,483,484,486,489,498,507,513],extract:[3,6,11,13,36,66,68,73,84,95,101,118,126,128,130,209,210,305,380,401,412,435,457,484,491,503],extract_atom:11,extract_comput:[11,484],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,61,204,219,229,231,268,338,411,470,507],extrema:431,extrins:214,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[173,342],f_a:[469,470,471],f_ave:128,f_c:470,f_f:471,f_fix_id:302,f_foo:513,f_harm:338,f_i:[29,446],f_id:[6,76,128,130,201,202,208,216,217,218,219,220,221,222,223,263,330,342,504,513],f_ij:446,f_indent:223,f_int:337,f_j:29,f_jj:99,f_k:446,f_langevin:340,f_max:[302,307],f_msst:266,f_r:[253,469,470,471],f_sigma:391,f_solid:338,f_ss:6,f_temp:[],face:[3,6,60,62,76,165,175,179,213,221,222,345,347,348,349,350,373,414,435,450,486,489],face_threshold:175,facet:175,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,246,298,328,338,415,448,456,498],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,95,99,112,119,126,127,129,151,171,176,179,183,194,200,201,204,205,209,210,218,225,229,231,232,244,249,252,254,255,266,268,269,273,295,299,303,311,315,318,320,328,332,336,343,344,345,349,360,371,373,379,385,387,388,391,392,394,396,401,402,403,405,406,407,411,415,418,422,423,435,438,440,442,443,449,451,458,467,472,483,486,489,490,495,498,500,501,504,507,512,513],factori:[3,484],factoriz:370,fail:[3,9,11,12,62,181,229,232,370,378,380,403,449,484],failur:[132,453,485,513],fairli:[11,440,495,500,508],faken:78,falcon:249,fall:[3,6,205,220,298,484,513],fals:[94,351,353,456,513],fame:8,famili:[474,483],familiar:[0,11,508],fan:446,far:[3,6,12,17,60,62,64,94,201,202,205,206,225,226,227,229,232,268,293,311,312,328,345,356,360,376,380,381,473,484,486,491,504],farago:252,farrel:[469,471],farther:201,fashion:[6,8,42,76,177,205,208,209,210,215,221,225,227,232,244,246,250,265,266,268,270,271,272,273,274,275,276,284,287,288,289,290,291,301,302,304,312,317,321,327,330,338,340,344,345,346,348,350,380,418,432,489,498,513,516],fasolino:420,fast:[6,7,9,12,13,17,40,201,202,279,302,341,370,371,393,432,433,438,466,468,488,493,495,504,514,517],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,115,120,123,154,164,183,184,186,187,188,189,191,192,194,195,197,201,202,205,211,224,225,231,238,243,247,251,252,268,270,271,272,273,274,275,276,277,278,285,287,288,289,291,299,303,304,312,314,315,328,331,333,335,337,340,344,348,354,356,357,359,360,363,365,370,371,382,383,385,386,387,389,391,392,393,394,395,396,397,398,399,400,401,404,405,409,410,412,413,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,436,441,442,443,445,450,451,458,466,467,468,469,470,471,472,474,476,477,478,481,489,495,499,507],fastest:[1,6,14,17,165,221,340,341,385,483],fatal:[3,503],fault:[75,449],faulti:12,fava:414,favor:228,favorit:7,fbmc:335,fcc:[],fcm:[284,513],fdirect:235,fdotr:419,fdt:[],fdti:95,fe2:176,fe3:176,fe_md_boundari:214,featu:8,featur:[],fecr:409,feedback:[7,249],feel:[7,249,250,258,293,349,351,380,440],felling:437,felt:349,femtosecond:512,fene:[],fennel:[401,423],fep:[],ferguson:[6,183,498],fermi:[1,9,10,12,15,163,385,471],fermion:411,fernando:434,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,206,216,217,218,220,221,222,223,253,268,298,301,303,315,342,370,378,379,380,387,456,483,486,491,495,497,505,515],fewer:[1,3,11,15,16,64,258,495],fewest:3,fextern:242,feynman:295,fff:484,ffield:[400,412,448,449,456],ffmpeg:[3,12,204],ffplai:204,fft:[1,3,7,9,11,12,14,15,96,120,121,152,294,370,371,495],fft_inc:[12,371],fft_lib:12,fft_path:12,fftbench:[370,505],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:465,fictiti:[6,211,212,237,242,246,295,311,401,423,427,465],field1:[487,491],field2:487,field:[],fifth:[325,442],figur:[1,3,8,12,302,483,484,508],fij:404,file0:293,file1:[11,13,293,339,353,379,491,493,497],file2:[11,13,339,353,379,491,493,497],file:[],file_from:203,filen:379,filenam:[3,12,13,38,42,57,197,201,202,204,205,206,214,217,218,219,220,221,222,223,225,230,240,293,297,300,303,304,305,308,309,312,313,339,340,367,368,369,379,380,386,387,391,401,409,410,412,420,435,436,437,442,446,447,448,449,456,457,467,468,469,470,471,474,482,483,484,487,488,493,497,504,513,515,516,517],filennam:493,filep:[3,201,202,205,488,493,517],filepo:309,fill:[7,9,177,204,298,340,373,381,391,438,449,489,508],filter:[205,214],final_integr:8,final_integrate_respa:8,finchham:[6,159,403],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,95,128,180,197,206,215,228,229,240,241,244,267,293,298,299,307,311,376,378,380,381,401,418,423,427,435,456,466,468,507,508,513],find_custom:8,fine:[16,17,181,211,237,338,381,385,508,513],finer:[151,177,513],finest:370,finger:[177,200,265,489],finish:[6,11,42,225,353,367,369,370,382,384,385,473,491,513,514],finit:[],finni:[7,409,466],finvers:235,fiorin:[9,230],fire:[],firebrick:205,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,87,96,99,113,114,115,117,123,127,128,138,141,144,145,149,152,162,165,171,173,175,176,178,179,180,184,197,201,202,203,204,205,206,208,209,217,218,220,221,222,223,225,228,231,240,244,245,250,255,265,266,267,268,293,295,300,301,302,304,309,312,315,317,325,326,328,329,330,337,338,339,340,342,346,351,353,354,361,373,378,379,380,381,384,385,386,387,390,391,392,394,396,398,400,401,409,411,412,415,416,418,419,420,421,422,423,427,432,433,435,437,438,440,442,446,448,449,456,457,465,467,468,469,470,471,474,478,481,482,483,484,486,487,488,491,493,495,498,499,500,503,504,507,508,513,514,515,517],fischer:[6,9,19,20,183,396,498],fit:[3,6,9,12,38,57,197,240,311,328,387,391,420,435,440,461,468,470,494,508,513],five:[78,163,302,379,391,436,486,500],fix:[],fix_adapt:[171,210,431],fix_atom_swap:[],fix_bal:65,fix_deposit:[3,215,298],fix_eo:9,fix_evapor:215,fix_flux:214,fix_gcmc:[215,379],fix_gl:246,fix_gld:246,fix_grav:298,fix_id:[3,229,266,268,270,271,272,273,274,275,276,299,302],fix_manifoldforc:508,fix_modifi:[],fix_mov:[200,346],fix_nh:8,fix_npt:246,fix_nv:508,fix_nvt:[215,244],fix_poem:[3,6,9],fix_pour:[3,232],fix_qbmsst:9,fix_qeq:[3,400],fix_rattl:315,fix_reax_bo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initialt:340,inlclud:11,inlcud:[],inlin:484,inner2:[396,416],inner:[3,8,16,58,201,250,353,369,376,377,378,380,384,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,404,405,408,409,410,411,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,445,447,448,449,450,451,456,457,458,459,460,461,462,463,464,465,467,468,469,470,471,473,474,475,476,477,478,479,495,500,513],inner_distance_cutoff:417,innergroup:258,innermost:[38,57,76,383,468,495],innernod:258,innner:429,inordin:341,inorgan:[6,474],inp:[230,353,457,474],input1:[69,72,74,85,102,119,124,125,126,128,130,330],input2:[69,72,74,85,102,119,124,125,126,128,130,330],input:[],input_doubl:3,inquir:318,insensit:12,insert:[3,5,7,8,9,12,62,177,208,232,244,250,298,370,457,465,484,490,507],insid:[2,3,6,8,11,76,140,146,177,201,202,205,216,221,222,232,233,241,244,250,255,258,298,312,328,345,347,348,349,350,351,368,373,425,484,485,486,488,489,496,500,513],insight:[6,13],instabl:[255,404,455],instal:[],instanc:[6,9,11,209,230,246,347,413,418,440,446,484,507],instantan:[6,66,228,229,245,246,268,273,294,299,302,307,309,312,335,492,504],instanti:[6,11,12,214,418,483],instead:[1,3,6,8,11,12,13,17,18,41,42,62,64,66,75,76,98,113,128,155,159,181,197,201,202,210,217,220,221,222,223,225,229,230,244,252,255,258,259,294,300,310,312,330,348,368,370,371,374,381,385,394,395,409,422,424,431,435,438,466,472,481,489,493,500,502,507,513],institut:[9,249,297],instruct:[],insuffici:[3,6,12],insult:268,insur:[3,6,11,12,17,40,41,64,78,112,114,177,178,197,201,202,204,205,211,226,227,232,237,238,241,242,244,247,252,264,300,301,310,312,328,340,345,349,350,351,353,369,379,381,385,399,414,418,444,450,468,479,483,484,486,487,491,494,495,503,504,513,514],int_max:3,inteatom:10,integ:[3,6,8,11,12,40,41,43,67,72,75,76,117,124,126,128,130,151,175,177,180,181,183,187,188,192,197,200,201,204,205,215,217,221,222,226,227,228,232,234,242,244,245,246,249,252,253,254,255,294,297,298,301,302,307,312,328,330,332,335,339,340,359,370,373,393,405,407,408,421,435,448,449,453,455,457,481,483,484,485,486,494,495,496,500,503,513,514],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,219,245,447,486],intens:[1,3,6,9,66,70,79,80,94,97,98,99,103,113,114,115,116,123,125,127,128,129,130,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,172,173,174,176,208,217,218,220,221,222,223,225,226,227,228,236,241,248,258,266,268,273,309,312,313,328,336,340,342,343,503,504,512],intepol:513,inter:[14,18,43,64,65,157,180,181,201,228,252,254,267,304,312,370,380,391,496,507,513,515,517],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,34,37,40,41,43,45,51,53,55,56,58,60,64,66,69,74,77,82,85,95,96,100,102,117,118,119,121,123,126,127,133,134,135,136,138,139,140,141,142,143,144,146,147,148,149,151,152,153,155,156,170,171,175,178,179,180,181,182,183,185,189,190,193,196,201,202,208,209,210,226,227,228,243,244,249,250,252,254,258,282,293,295,297,298,303,305,311,312,319,320,328,329,335,340,344,345,346,349,350,355,356,357,358,360,362,364,370,371,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,449,450,451,453,455,456,457,458,465,466,467,468,469,470,471,472,473,474,475,476,477,478,481,484,486,488,490,491,495,496,498,503,504,507,515],interatom:[3,4,7,9,10,177,201,267,337,338,386,391,409,411,419,435,438,456,470,513],intercept:129,interchang:6,interconnect:18,interconvert:411,intereract:40,interesect:349,interest:[1,5,7,8,9,11,13,76,176,295,335,338,371,410,433,448,449,484,513],interf:[385,508],interfac:[],interfer:[12,268,387],interg:[6,507],intergr:[495,499],interi:433,interior:[3,6,42,349,489],interlac:435,interleav:[6,177,494],intermedi:[6,12,62,204,267,293,363,380,484,485,494,498],intermix:481,intermolecular:[153,387],intern:[],internal_element_set:214,internal_quadratur:214,internet:251,interpenetr:435,interpentr:[460,461,463],interpol:[6,15,38,57,110,197,204,205,214,240,255,293,370,371,380,391,440,449,462,468,469],interpret:[2,6,11,204,220,415,458,481,484,500,513],interrupt:302,intersect:[3,6,129,205,349,351,489],intersert:349,interspers:378,interstiti:[175,438],intertia:[3,103],interv:[3,6,99,203,218,252,268,302,307,308,320,456,462,481,500,513],intestieti:129,intial:[6,385,387],intiial:[42,491],intiti:[3,327],intra:312,intra_energi:244,intramolecular:[29,153,244],introduc:[6,9,100,117,204,268,302,307,312,363,370,386,401,411,423,427,431,467,500,513],introduct:[],intsal:[],intuit:373,inv:[129,176,313],invalid:[3,12,76,97,180,282,380,432,433,488],invari:[117,144,149,151],invent:315,invers:[],invert:[1,6,181,294],invis:349,invoc:[175,228,385,453,455,484],invok:[1,3,6,7,8,9,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,58,62,66,70,76,79,80,8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39,255,259,316,438,481,500],resembl:[307,508],resepct:6,reserv:[12,249,507],reservoir:[99,244,248,252,340],reset:[],reset_atomic_reference_posit:214,reset_dt:8,reset_target:8,reset_tim:214,reset_timestep:[],resid:13,residu:249,residue1:381,resist:[6,249],resolut:[219,456,468],resolv:[229,295,328,433,508],resort:3,resourc:[7,386,409],respa:[3,16,236,249,268,383,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,404,405,408,409,410,411,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,432,433,434,435,436,437,438,439,441,443,445,447,448,449,450,451,456,457,458,459,460,461,462,463,464,465,467,468,469,470,471,473,474,476,477,478,479,494,495,506,513],respecifi:438,respect:[1,6,9,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,46,47,48,49,50,52,54,55,57,62,75,76,95,97,106,107,120,123,129,133,153,154,159,162,164,171,175,176,183,184,186,187,188,189,191,192,194,195,197,202,204,205,220,221,222,227,228,229,231,247,250,252,253,255,268,270,271,272,273,274,275,276,277,278,285,287,288,289,291,303,304,312,313,317,325,327,340,345,348,354,356,357,359,360,363,365,368,370,371,375,378,379,384,385,386,387,389,391,392,393,394,395,396,397,399,400,401,404,405,409,410,412,413,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,435,436,438,440,441,442,443,445,450,451,455,456,457,458,467,468,469,470,471,472,474,476,477,478,483,487,496,499,507,513,515,517],respon:9,respond:[6,7,160,231,411,445],respons:[6,7,266,336,343],resquar:[],rest:[6,8,12,301,305,311,391,433,435,503,504,507],restart1:295,restart2:295,restart2data:[],restart:[],restartfil:[12,13],restor:[3,8,63,64,113,177,209,210,301,317,325,330,352,503,504],restore_bia:8,restore_bias_al:8,restrain:[],restraint:[9,230,266,311,327,422],restratin:311,restrict:[],result:[1,2,3,6,7,9,10,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,46,47,48,49,50,52,54,55,57,66,67,70,71,76,80,95,98,99,103,113,114,116,120,121,123,125,126,127,128,129,130,152,154,157,160,164,171,172,174,176,177,180,183,184,186,187,188,189,191,192,194,195,197,200,201,202,204,205,208,211,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,235,238,240,243,244,245,247,252,253,255,259,266,268,270,271,272,273,274,275,276,277,278,285,287,288,289,290,291,294,295,303,304,309,310,312,314,315,328,331,333,336,337,338,340,341,342,344,345,346,348,350,353,354,356,357,359,360,363,365,370,371,380,383,385,386,387,389,392,393,394,395,396,397,399,400,401,404,405,409,410,411,412,413,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,433,435,436,438,440,441,442,443,445,449,450,451,458,467,468,469,470,471,472,474,476,477,478,481,483,486,488,489,490,491,495,496,497,498,500,512,513,514],resum:513,retain:[2,226,227,387,391,438,483],retart:[33,51,190,361],retir:[3,448],retreiv:8,retriev:[6,8,242,436,437,513],reus:[3,498],rev:[6,13,67,75,100,117,121,151,152,165,215,246,252,254,266,268,269,273,289,294,304,307,312,317,328,332,335,337,338,343,377,391,399,400,401,404,409,410,411,414,415,420,425,432,433,434,435,437,446,450,457,467,469,470,471,474,481],revers:[2,6,8,95,188,228,250,268,292,293,303,321,336,337,343,380,431,495,507],review:[151,303,317,335,438,447,457,481,500,507,508],rewind:369,rewrap:201,rewrit:[5,12],rewritten:19,rezwanur:445,rfac0:[151,457],rfactor:328,rfile:312,rg0:326,rgb:205,rh3:176,rh4:176,rhaphson:3,rheolog:6,rhi:468,rho0:[435,453,455,463,464],rho0_meam:435,rho:[],rho_0:[463,464],rho_alpha_beta:409,rho_bkgd:435,rho_colloid:345,rho_e:340,rho_fin:339,rho_i:[436,437],rho_initi:339,rho_ref_meam:435,rho_wal:345,rhodo:[9,10],rhodopsin:[1,10],rhohi:298,rholo:298,rhosum:[],ribier:377,richard:9,richardson:312,richi:[9,19],rick:[303,304,400,456],rick_and_stuart:304,ridg:[9,19],right:[3,6,11,12,42,153,177,195,196,200,202,225,228,250,255,265,292,353,373,401,486,489,496,508,513],rightmost:[42,225],rigid:[],rigidifi:312,rii:[97,98],rij:[100,117,226,227,293,405,406,407,465],rin:[417,428,429],ring:[],rino:[78,474],rinv:370,rirj:[346,415],rise:[],risi:[151,457],risk:[8,311,495],rix:[97,98],rjk:[226,227],rjone:[7,9,13],rlo:468,rmask:[3,513],rmass:3,rmax:[76,178,226],rmdir:497,rmin0:[151,457],rmin:[76,178,227,425],rmsd:339,rnemd:6,robert:9,robin:205,robust:[376,377,378],rock:435,rockett:446,rod:312,rodata:12,rodnei:307,roi:7,role:335,roll:12,ronchetti:117,room:[60,62],root:[11,95,97,98,203,335,339,385,409,493],rosati:40,rose:435,ross:435,rosski:295,rosybrown:205,rot:[6,99,295,311,335,514],rotat:[],rotation:117,rotaton:489,rough:[6,177,204,350],roughli:[7,10,12,42,160,204,219,244,252,253,267,268,282,299,312,328,331,332,335,371,380,385,452,454,488,495],round:[],rous:245,rout:[95,417,431],routin:[5,6,8,11,15,16,38,40,57,96,181,183,255,438,447,468,499],roux:[6,235,253,472,507],row:[6,69,70,72,74,80,85,98,102,103,114,116,119,125,126,127,130,157,165,172,174,175,176,217,218,220,221,222,223,258,312,340,342,350,411],royalblu:205,rozero:435,rperp:[265,321],rpi:297,rpm:12,rrespa:[1,3,5,7,8,16,209,210,265,268,381,386,387,388,389,390,392,393,394,395,396,397,3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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","&lt;no title&gt;","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":226,"default":[37,40,41,56,60,61,62,64,65,76,95,96,100,112,113,115,117,118,129,133,134,151,157,165,166,170,176,177,180,182,196,199,200,201,202,204,205,206,207,209,210,211,213,214,215,217,221,222,223,226,227,229,230,231,232,236,241,244,245,250,252,253,254,255,256,258,263,266,268,269,273,289,290,294,295,298,299,300,301,302,304,307,309,310,312,313,328,330,335,336,337,338,341,343,345,347,351,364,368,370,371,373,374,376,377,379,381,382,383,385,388,391,393,411,432,433,438,440,448,449,465,466,481,482,483,486,487,489,491,493,494,495,498,500,502,503,504,505,506,512,514,515,516],"function":513,"long":[219,392,394,395,396,397,401,403,404,423,427,431,443,451,472],"new":8,"static":12,acceler:1,account:508,ackland:67,acknowledg:7,adapt:[209,210],addforc:211,addit:[12,13,508],addtorqu:212,adiabat:6,adjust_dt:318,adp:386,after:508,airebo:387,alloi:409,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:213,arrai:6,aspher:[6,9,90,155,270,274,278,279,287],atc:[9,214],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,87,89,93,100,105,106,109,110,111,117,121,122,124,151,152,175,213,215,216,301,513],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:224,awpmd:[9,388],balanc:[42,225],barostat:6,basal:71,beck:389,berendsen:[299,331],between:6,binary2txt:13,bodi:[6,8,9,43,72,156,271,275,280,288,390],bond:[8,13,73,74,226,227,228,308],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:391,born:[392,403],boundari:[7,60],box:[6,61,229],branch:508,brownian:393,buck:[394,395,403,434],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:508,change_box:62,charmm:[6,20,183,396,431],chunk:[6,70,76,80,98,103,114,116,125,157,172,174,217],citat:7,class2:[9,21,44,184,354,397],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,345,399,477],colvar:[9,13,230],com:[79,80,158],comb3:400,comb:[304,400],come:5,comm_modifi:64,comm_styl:65,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,509,510,511,512,513,514,515,516,517],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,513],compute_modifi:112,condit:7,conduct:[6,336],conserv:406,constant:[6,513],constraint:7,contact:[81,131],contact_radiu:[],coord:82,core:6,coreshel:9,correl:[218,219],cosin:[23,24,25,26,27,28,186],cossq:356,coul:[392,394,395,396,397,401,402,403,416,423,427,431,443,451],coupl:6,creat:227,create_atom:177,create_bond:178,create_box:179,createatom:13,creation:7,csld:332,csvr:332,cubic:425,cuda:[9,14,120,123,154,164,211,224,238,243,247,268,277,314,315,331,333,344,392,394,396,397,409,415,416,423,424,426,429,441,467,469],custom:[8,201,202],cut:[50,388,394,397,401,404,411,413,423,424,431,439,443,4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33,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,509,510,511,512,513,514,515,516,517],system:6,tabl:[0,6,38,57,197,240,468,469],tad:500,taitwat:[463,464],talli:[9,153],temp:[154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,331,332,333,334],temper:501,temperatur:6,tersoff:[469,470,471],test:11,tfmc:335,thermal:[6,336],thermo:[6,502,513],thermo_modifi:503,thermo_styl:504,thermodynam:[6,8],thermostat:6,thole:472,time:[6,223],timer:505,timestep:506,tip3p:6,tip4p:[6,401,423,427,431],tip:12,tlsph:[138,139,140,141,142,143,144,453],tlsph_defgrad:[],tlsph_dt:[],tlsph_num_neigh:[],tlsph_shape:[],tlsph_strain:[],tlsph_strain_rat:[],tlsph_stress:[],tmd:339,tool:[12,13],torqu:172,transform:235,tri:[286,473],tri_surfac:454,triangl:145,triangle_mesh_vertic:[],triclin:6,tstat:405,ttm:340,tune:341,tutori:508,type:7,ulsph:[146,147,148,149,455],ulsph_num_neigh:[],ulsph_strain:[],ulsph_strain_r:[],ulsph_stress:[],umbrella:365,uncomput:509,undump:510,unfix:511,unit:512,uppercas:4,user:[9,12,14,16,18],vacf:173,valu:[6,513],variabl:[6,8,513],variou:1,vashishta:474,vcm:174,vector:[6,342,513],veloc:514,version:[0,5,12],vertic:145,via:12,vim:13,viscos:[6,343],viscou:[259,344],visual:6,vol:150,voronoi:[9,175],vtk:[9,201,202,313],wall:[6,345,346,347,348,349,350],wall_surfac:324,warn:3,water:6,weight:220,what:[7,12],wolf:[392,401],wrapper:11,write:6,write_data:515,write_dump:516,write_restart:517,written:508,xmgrace:13,xmovi:13,xrd:176,xtc:9,your:508,yukawa:[476,477],zbl:[471,478],zero:[39,59,198,366,479]}})
\ No newline at end of file
diff --git a/doc/temper.html b/doc/temper.html
index 4cd3098b97..4719db1d4c 100644
--- a/doc/temper.html
+++ b/doc/temper.html
@@ -162,9 +162,9 @@ two processors.  You will simply not get the performance speed-up you
 would see with one or more physical processors per replica.  See <a class="reference internal" href="Section_howto.html#howto-5"><span>this section</span></a> of the manual for further
 discussion.</p>
 <p>Each replica&#8217;s temperature is controlled at a different value by a fix
-with <em>fix-ID</em> that controls temperature.  Possible fix styles are
-<a class="reference internal" href="fix_nh.html"><em>nvt</em></a>, <a class="reference internal" href="fix_nh.html"><em>temp/berendsen</em></a>,
-<a class="reference internal" href="fix_langevin.html"><em>langevin</em></a> and <a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale</em></a>.
+with <em>fix-ID</em> that controls temperature. Most thermostat fix styles
+(with and without included time integration) are supported. The command
+will print an error message and abort, if the chosen fix is unsupported.
 The desired temperature is specified by <em>temp</em>, which is typically a
 variable previously set in the input script, so that each partition is
 assigned a different temperature.  See the <a class="reference internal" href="variable.html"><em>variable</em></a>
diff --git a/doc/temper.txt b/doc/temper.txt
index 85cc105d84..ef09bbab53 100644
--- a/doc/temper.txt
+++ b/doc/temper.txt
@@ -42,9 +42,9 @@ section"_Section_howto.html#howto_5 of the manual for further
 discussion.
 
 Each replica's temperature is controlled at a different value by a fix
-with {fix-ID} that controls temperature.  Possible fix styles are
-"nvt"_fix_nh.html, "temp/berendsen"_fix_nh.html,
-"langevin"_fix_langevin.html and "temp/rescale"_fix_temp_rescale.html.
+with {fix-ID} that controls temperature. Most thermostat fix styles
+(with and without included time integration) are supported. The command
+will print an error message and abort, if the chosen fix is unsupported.
 The desired temperature is specified by {temp}, which is typically a
 variable previously set in the input script, so that each partition is
 assigned a different temperature.  See the "variable"_variable.html

From 5dceda8b15a01de9075de0ab4eb272f7165c4ae7 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 7 Apr 2016 21:14:57 +0000
Subject: [PATCH 07/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@14811
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/_sources/bond_write.txt | 74 +++++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)
 create mode 100644 doc/_sources/bond_write.txt

diff --git a/doc/_sources/bond_write.txt b/doc/_sources/bond_write.txt
new file mode 100644
index 0000000000..66cf5884bc
--- /dev/null
+++ b/doc/_sources/bond_write.txt
@@ -0,0 +1,74 @@
+.. index:: bond_write
+
+bond_write command
+==================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   bond_write btype N inner outer file keyword itype jtype
+
+* btype = bond types
+* N = # of values
+* inner,outer = inner and outer bond length (distance units)
+* file = name of file to write values to
+* keyword = section name in file for this set of tabulated values
+* itype,jtype = 2 atom types (optional)
+* 
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   bond_write 1 500 0.5 3.5 table.txt Harmonic_1
+   bond_write 3 1000 0.1 6.0 table.txt Morse
+
+Description
+"""""""""""
+
+Write energy and force values to a file as a function of distance for
+the currently defined bond potential.  This is useful for plotting the
+potential function or otherwise debugging its values.  If the file
+already exists, the table of values is appended to the end of the file
+to allow multiple tables of energy and force to be included in one
+file.
+
+The energy and force values are computed at distances from inner to
+outer for 2 interacting atoms forming a bond of type btype, using the
+appropriate :doc:`bond_coeff <bond_coeff>` coefficients. N evenly spaced
+distances are used.
+
+For example, for N = 7, inner = 1.0, and outer = 4.0,
+values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.
+
+The file is written in the format used as input for the
+:doc:`bond_style <bond_style>` *table* option with *keyword* as the
+section name.  Each line written to the file lists an index number
+(1-N), a distance (in distance units), an energy (in energy units),
+and a force (in force units).
+
+Restrictions
+""""""""""""
+
+
+All force field coefficients for bond and other kinds of interactions
+must be set before this command can be invoked.
+
+Due to how the bond force is computed, an inner value > 0.0 must
+be specified even if the potential has a finite value at r = 0.0.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond_style table <bond_table>`,
+:doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm

From 6a1e85d32ae03991549f8e4f8f5a3ee87dfee9fe Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 7 Apr 2016 21:16:06 +0000
Subject: [PATCH 08/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@14812
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Section_commands.html         | 60 ++++++++++++++--------------
 doc/Section_commands.txt          |  1 +
 doc/_sources/Section_commands.txt | 66 +++++++++++++++----------------
 3 files changed, 64 insertions(+), 63 deletions(-)

diff --git a/doc/Section_commands.html b/doc/Section_commands.html
index a0b5680239..a980738ee7 100644
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -463,8 +463,8 @@ in the command&#8217;s documentation.</p>
 <table border="1" class="docutils">
 <colgroup>
 <col width="17%" />
-<col width="15%" />
 <col width="17%" />
+<col width="15%" />
 <col width="17%" />
 <col width="17%" />
 <col width="17%" />
@@ -478,109 +478,109 @@ in the command&#8217;s documentation.</p>
 <td><a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a></td>
 </tr>
 <tr class="row-even"><td><a class="reference internal" href="bond_style.html"><em>bond_style</em></a></td>
+<td><a class="reference internal" href="bond_write.html"><em>bond_write</em></a></td>
 <td><a class="reference internal" href="boundary.html"><em>boundary</em></a></td>
 <td><a class="reference internal" href="box.html"><em>box</em></a></td>
 <td><a class="reference internal" href="change_box.html"><em>change_box</em></a></td>
 <td><a class="reference internal" href="clear.html"><em>clear</em></a></td>
-<td><a class="reference internal" href="comm_modify.html"><em>comm_modify</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="comm_style.html"><em>comm_style</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="comm_modify.html"><em>comm_modify</em></a></td>
+<td><a class="reference internal" href="comm_style.html"><em>comm_style</em></a></td>
 <td><a class="reference internal" href="compute.html"><em>compute</em></a></td>
 <td><a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a></td>
 <td><a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a></td>
 <td><a class="reference internal" href="create_bonds.html"><em>create_bonds</em></a></td>
-<td><a class="reference internal" href="create_box.html"><em>create_box</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="create_box.html"><em>create_box</em></a></td>
+<td><a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a></td>
 <td><a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></td>
 <td><a class="reference internal" href="dielectric.html"><em>dielectric</em></a></td>
 <td><a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a></td>
 <td><a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a></td>
-<td><a class="reference internal" href="dimension.html"><em>dimension</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="dimension.html"><em>dimension</em></a></td>
+<td><a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a></td>
 <td><a class="reference internal" href="dump.html"><em>dump</em></a></td>
 <td><a class="reference internal" href="dump_image.html"><em>dump image</em></a></td>
 <td><a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a></td>
 <td><a class="reference internal" href="dump_image.html"><em>dump movie</em></a></td>
-<td><a class="reference internal" href="echo.html"><em>echo</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix.html"><em>fix</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="echo.html"><em>echo</em></a></td>
+<td><a class="reference internal" href="fix.html"><em>fix</em></a></td>
 <td><a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a></td>
 <td><a class="reference internal" href="group.html"><em>group</em></a></td>
 <td><a class="reference internal" href="if.html"><em>if</em></a></td>
 <td><a class="reference internal" href="info.html"><em>info</em></a></td>
-<td><a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="improper_style.html"><em>improper_style</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a></td>
+<td><a class="reference internal" href="improper_style.html"><em>improper_style</em></a></td>
 <td><a class="reference internal" href="include.html"><em>include</em></a></td>
 <td><a class="reference internal" href="jump.html"><em>jump</em></a></td>
 <td><a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a></td>
 <td><a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a></td>
-<td><a class="reference internal" href="label.html"><em>label</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="lattice.html"><em>lattice</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="label.html"><em>label</em></a></td>
+<td><a class="reference internal" href="lattice.html"><em>lattice</em></a></td>
 <td><a class="reference internal" href="log.html"><em>log</em></a></td>
 <td><a class="reference internal" href="mass.html"><em>mass</em></a></td>
 <td><a class="reference internal" href="minimize.html"><em>minimize</em></a></td>
 <td><a class="reference internal" href="min_modify.html"><em>min_modify</em></a></td>
-<td><a class="reference internal" href="min_style.html"><em>min_style</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="molecule.html"><em>molecule</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="min_style.html"><em>min_style</em></a></td>
+<td><a class="reference internal" href="molecule.html"><em>molecule</em></a></td>
 <td><a class="reference internal" href="neb.html"><em>neb</em></a></td>
 <td><a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a></td>
 <td><a class="reference internal" href="neighbor.html"><em>neighbor</em></a></td>
 <td><a class="reference internal" href="newton.html"><em>newton</em></a></td>
-<td><a class="reference internal" href="next.html"><em>next</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="package.html"><em>package</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="next.html"><em>next</em></a></td>
+<td><a class="reference internal" href="package.html"><em>package</em></a></td>
 <td><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></td>
 <td><a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a></td>
 <td><a class="reference internal" href="pair_style.html"><em>pair_style</em></a></td>
 <td><a class="reference internal" href="pair_write.html"><em>pair_write</em></a></td>
-<td><a class="reference internal" href="partition.html"><em>partition</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="prd.html"><em>prd</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="partition.html"><em>partition</em></a></td>
+<td><a class="reference internal" href="prd.html"><em>prd</em></a></td>
 <td><a class="reference internal" href="print.html"><em>print</em></a></td>
 <td><a class="reference internal" href="processors.html"><em>processors</em></a></td>
 <td><a class="reference internal" href="python.html"><em>python</em></a></td>
 <td><a class="reference internal" href="quit.html"><em>quit</em></a></td>
-<td><a class="reference internal" href="read_data.html"><em>read_data</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="read_dump.html"><em>read_dump</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="read_data.html"><em>read_data</em></a></td>
+<td><a class="reference internal" href="read_dump.html"><em>read_dump</em></a></td>
 <td><a class="reference internal" href="read_restart.html"><em>read_restart</em></a></td>
 <td><a class="reference internal" href="region.html"><em>region</em></a></td>
 <td><a class="reference internal" href="replicate.html"><em>replicate</em></a></td>
 <td><a class="reference internal" href="rerun.html"><em>rerun</em></a></td>
-<td><a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="restart.html"><em>restart</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a></td>
+<td><a class="reference internal" href="restart.html"><em>restart</em></a></td>
 <td><a class="reference internal" href="run.html"><em>run</em></a></td>
 <td><a class="reference internal" href="run_style.html"><em>run_style</em></a></td>
 <td><a class="reference internal" href="set.html"><em>set</em></a></td>
 <td><a class="reference internal" href="shell.html"><em>shell</em></a></td>
-<td><a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="suffix.html"><em>suffix</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a></td>
+<td><a class="reference internal" href="suffix.html"><em>suffix</em></a></td>
 <td><a class="reference internal" href="tad.html"><em>tad</em></a></td>
 <td><a class="reference internal" href="temper.html"><em>temper</em></a></td>
 <td><a class="reference internal" href="thermo.html"><em>thermo</em></a></td>
 <td><a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a></td>
-<td><a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="timer.html"><em>timer</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a></td>
+<td><a class="reference internal" href="timer.html"><em>timer</em></a></td>
 <td><a class="reference internal" href="timestep.html"><em>timestep</em></a></td>
 <td><a class="reference internal" href="uncompute.html"><em>uncompute</em></a></td>
 <td><a class="reference internal" href="undump.html"><em>undump</em></a></td>
 <td><a class="reference internal" href="unfix.html"><em>unfix</em></a></td>
-<td><a class="reference internal" href="units.html"><em>units</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="variable.html"><em>variable</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="units.html"><em>units</em></a></td>
+<td><a class="reference internal" href="variable.html"><em>variable</em></a></td>
 <td><a class="reference internal" href="velocity.html"><em>velocity</em></a></td>
 <td><a class="reference internal" href="write_data.html"><em>write_data</em></a></td>
 <td><a class="reference internal" href="write_dump.html"><em>write_dump</em></a></td>
 <td><a class="reference internal" href="write_restart.html"><em>write_restart</em></a></td>
-<td>&nbsp;</td>
 </tr>
 </tbody>
 </table>
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index d0f5e34bad..72a9907dd9 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -375,6 +375,7 @@ in the command's documentation.
 "balance"_balance.html,
 "bond_coeff"_bond_coeff.html,
 "bond_style"_bond_style.html,
+"bond_write"_bond_write.html,
 "boundary"_boundary.html,
 "box"_box.html,
 "change_box"_change_box.html,
diff --git a/doc/_sources/Section_commands.txt b/doc/_sources/Section_commands.txt
index 8c872a653f..d32bf8f28f 100644
--- a/doc/_sources/Section_commands.txt
+++ b/doc/_sources/Section_commands.txt
@@ -400,39 +400,39 @@ included when LAMMPS was built.  Not all packages are included in a
 default LAMMPS build.  These dependencies are listed as Restrictions
 in the command's documentation.
 
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`angle_coeff <angle_coeff>`       | :doc:`angle_style <angle_style>`   | :doc:`atom_modify <atom_modify>`       | :doc:`atom_style <atom_style>`         | :doc:`balance <balance>`               | :doc:`bond_coeff <bond_coeff>`         |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`bond_style <bond_style>`         | :doc:`boundary <boundary>`         | :doc:`box <box>`                       | :doc:`change_box <change_box>`         | :doc:`clear <clear>`                   | :doc:`comm_modify <comm_modify>`       |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`comm_style <comm_style>`         | :doc:`compute <compute>`           | :doc:`compute_modify <compute_modify>` | :doc:`create_atoms <create_atoms>`     | :doc:`create_bonds <create_bonds>`     | :doc:`create_box <create_box>`         |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`delete_atoms <delete_atoms>`     | :doc:`delete_bonds <delete_bonds>` | :doc:`dielectric <dielectric>`         | :doc:`dihedral_coeff <dihedral_coeff>` | :doc:`dihedral_style <dihedral_style>` | :doc:`dimension <dimension>`           |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`displace_atoms <displace_atoms>` | :doc:`dump <dump>`                 | :doc:`dump image <dump_image>`         | :doc:`dump_modify <dump_modify>`       | :doc:`dump movie <dump_image>`         | :doc:`echo <echo>`                     |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`fix <fix>`                       | :doc:`fix_modify <fix_modify>`     | :doc:`group <group>`                   | :doc:`if <if>`                         | :doc:`info <info>`                     | :doc:`improper_coeff <improper_coeff>` |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`improper_style <improper_style>` | :doc:`include <include>`           | :doc:`jump <jump>`                     | :doc:`kspace_modify <kspace_modify>`   | :doc:`kspace_style <kspace_style>`     | :doc:`label <label>`                   |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`lattice <lattice>`               | :doc:`log <log>`                   | :doc:`mass <mass>`                     | :doc:`minimize <minimize>`             | :doc:`min_modify <min_modify>`         | :doc:`min_style <min_style>`           |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`molecule <molecule>`             | :doc:`neb <neb>`                   | :doc:`neigh_modify <neigh_modify>`     | :doc:`neighbor <neighbor>`             | :doc:`newton <newton>`                 | :doc:`next <next>`                     |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`package <package>`               | :doc:`pair_coeff <pair_coeff>`     | :doc:`pair_modify <pair_modify>`       | :doc:`pair_style <pair_style>`         | :doc:`pair_write <pair_write>`         | :doc:`partition <partition>`           |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`prd <prd>`                       | :doc:`print <print>`               | :doc:`processors <processors>`         | :doc:`python <python>`                 | :doc:`quit <quit>`                     | :doc:`read_data <read_data>`           |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`read_dump <read_dump>`           | :doc:`read_restart <read_restart>` | :doc:`region <region>`                 | :doc:`replicate <replicate>`           | :doc:`rerun <rerun>`                   | :doc:`reset_timestep <reset_timestep>` |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`restart <restart>`               | :doc:`run <run>`                   | :doc:`run_style <run_style>`           | :doc:`set <set>`                       | :doc:`shell <shell>`                   | :doc:`special_bonds <special_bonds>`   |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`suffix <suffix>`                 | :doc:`tad <tad>`                   | :doc:`temper <temper>`                 | :doc:`thermo <thermo>`                 | :doc:`thermo_modify <thermo_modify>`   | :doc:`thermo_style <thermo_style>`     |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`timer <timer>`                   | :doc:`timestep <timestep>`         | :doc:`uncompute <uncompute>`           | :doc:`undump <undump>`                 | :doc:`unfix <unfix>`                   | :doc:`units <units>`                   |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
-| :doc:`variable <variable>`             | :doc:`velocity <velocity>`         | :doc:`write_data <write_data>`         | :doc:`write_dump <write_dump>`         | :doc:`write_restart <write_restart>`   |                                        |
-+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`angle_coeff <angle_coeff>`       | :doc:`angle_style <angle_style>`       | :doc:`atom_modify <atom_modify>`   | :doc:`atom_style <atom_style>`         | :doc:`balance <balance>`               | :doc:`bond_coeff <bond_coeff>`         |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`bond_style <bond_style>`         | :doc:`bond_write <bond_write>`         | :doc:`boundary <boundary>`         | :doc:`box <box>`                       | :doc:`change_box <change_box>`         | :doc:`clear <clear>`                   |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`comm_modify <comm_modify>`       | :doc:`comm_style <comm_style>`         | :doc:`compute <compute>`           | :doc:`compute_modify <compute_modify>` | :doc:`create_atoms <create_atoms>`     | :doc:`create_bonds <create_bonds>`     |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`create_box <create_box>`         | :doc:`delete_atoms <delete_atoms>`     | :doc:`delete_bonds <delete_bonds>` | :doc:`dielectric <dielectric>`         | :doc:`dihedral_coeff <dihedral_coeff>` | :doc:`dihedral_style <dihedral_style>` |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`dimension <dimension>`           | :doc:`displace_atoms <displace_atoms>` | :doc:`dump <dump>`                 | :doc:`dump image <dump_image>`         | :doc:`dump_modify <dump_modify>`       | :doc:`dump movie <dump_image>`         |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`echo <echo>`                     | :doc:`fix <fix>`                       | :doc:`fix_modify <fix_modify>`     | :doc:`group <group>`                   | :doc:`if <if>`                         | :doc:`info <info>`                     |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`improper_coeff <improper_coeff>` | :doc:`improper_style <improper_style>` | :doc:`include <include>`           | :doc:`jump <jump>`                     | :doc:`kspace_modify <kspace_modify>`   | :doc:`kspace_style <kspace_style>`     |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`label <label>`                   | :doc:`lattice <lattice>`               | :doc:`log <log>`                   | :doc:`mass <mass>`                     | :doc:`minimize <minimize>`             | :doc:`min_modify <min_modify>`         |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`min_style <min_style>`           | :doc:`molecule <molecule>`             | :doc:`neb <neb>`                   | :doc:`neigh_modify <neigh_modify>`     | :doc:`neighbor <neighbor>`             | :doc:`newton <newton>`                 |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`next <next>`                     | :doc:`package <package>`               | :doc:`pair_coeff <pair_coeff>`     | :doc:`pair_modify <pair_modify>`       | :doc:`pair_style <pair_style>`         | :doc:`pair_write <pair_write>`         |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`partition <partition>`           | :doc:`prd <prd>`                       | :doc:`print <print>`               | :doc:`processors <processors>`         | :doc:`python <python>`                 | :doc:`quit <quit>`                     |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`read_data <read_data>`           | :doc:`read_dump <read_dump>`           | :doc:`read_restart <read_restart>` | :doc:`region <region>`                 | :doc:`replicate <replicate>`           | :doc:`rerun <rerun>`                   |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`reset_timestep <reset_timestep>` | :doc:`restart <restart>`               | :doc:`run <run>`                   | :doc:`run_style <run_style>`           | :doc:`set <set>`                       | :doc:`shell <shell>`                   |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`special_bonds <special_bonds>`   | :doc:`suffix <suffix>`                 | :doc:`tad <tad>`                   | :doc:`temper <temper>`                 | :doc:`thermo <thermo>`                 | :doc:`thermo_modify <thermo_modify>`   |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`thermo_style <thermo_style>`     | :doc:`timer <timer>`                   | :doc:`timestep <timestep>`         | :doc:`uncompute <uncompute>`           | :doc:`undump <undump>`                 | :doc:`unfix <unfix>`                   |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
+| :doc:`units <units>`                   | :doc:`variable <variable>`             | :doc:`velocity <velocity>`         | :doc:`write_data <write_data>`         | :doc:`write_dump <write_dump>`         | :doc:`write_restart <write_restart>`   |
++----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
 
 These are additional commands in USER packages, which can be used if
 :ref:`LAMMPS is built with the appropriate package <start_3>`.

From 9c1857fa629764251d38d4899c1a8d4c1fc41a28 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 7 Apr 2016 22:22:19 +0000
Subject: [PATCH 09/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@14813
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/USER-INTEL/TEST/README                 | 143 ++++++++++++---------
 src/USER-INTEL/TEST/in.intel.lc            |  66 ++++------
 src/USER-INTEL/TEST/in.intel.lj            |  43 +++++++
 src/USER-INTEL/TEST/in.intel.rhodo         |  34 +++--
 src/USER-INTEL/TEST/in.intel.sw            |  23 +++-
 src/USER-INTEL/TEST/in.intel.tersoff       |  23 +++-
 src/USER-INTEL/TEST/in.intel.water         |  59 ++++-----
 src/USER-INTEL/TEST/in.lc_generate_restart |  57 ++++++++
 8 files changed, 291 insertions(+), 157 deletions(-)
 create mode 100644 src/USER-INTEL/TEST/in.intel.lj
 create mode 100644 src/USER-INTEL/TEST/in.lc_generate_restart

diff --git a/src/USER-INTEL/TEST/README b/src/USER-INTEL/TEST/README
index 62b8a58188..ed06c4b4b8 100644
--- a/src/USER-INTEL/TEST/README
+++ b/src/USER-INTEL/TEST/README
@@ -1,67 +1,88 @@
-If you run in another directory, please edit the read_data line to point to
-the data.rhodo file. This is included in the LAMMPS distribution in the
-'bench' directory.
+#############################################################################
+# Benchmarks
+#
+# in.intel.lj -		Atomic fluid (LJ Benchmark)
+# in.intel.rhodo -	Protein (Rhodopsin Benchmark)
+# in.intel.lc -	 	Liquid Crystal w/ Gay-Berne potential
+# in.intel.sw -		Silicon benchmark with Stillinger-Weber
+# in.intel.tersoff -	Silicon benchmark with Tersoff
+# in.intel.water - 	Coarse-grain water benchmark using Stillinger-Weber
+#
+#############################################################################
 
-++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-Expected times are the expected LOOP times based on runs using dual-socket
-Intel Xeon processor E5-2697 V2 with Intel Xeon Phi coprocessor 7120P.
-++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+#############################################################################
+# Expected Timesteps/second on E5-2697v3 with turbo on and HT enabled
+#
+# in.intel.lj -		131.943
+# in.intel.rhodo -	8.661
+# in.intel.lc -	 	14.015
+# in.intel.sw -		103.53
+# in.intel.tersoff -	55.525
+# in.intel.water - 	44.079
+#
+#############################################################################
+
+#############################################################################
+# For Haswell and Broadwell architectures, depending on the compiler version, 
+# it may give better performance to compile for an AVX target (with -xAVX 
+# compiler option) instead of -xHost or -xCORE-AVX2 for some of the 
+# workloads due to inefficient code generation for gathers. Aside from
+# Tersoff, this will not significantly impact performance because FMA 
+# sensitive routines will still use AVX2 (MKL and SVML detect the processor 
+# at runtime)
+#############################################################################
+
+#############################################################################
+# The default benchmark timesteps will run between 30s and 1 minute with
+# the Intel package. You can specify a multiplier for all of the benchmarks
+# to increase or decrease the runtime. Example commandline arguments:
+#
+# -v m 2		# Run for twice as long
+# -v m 0.5		# Run for half as long
+#############################################################################
+
+#	Example for running benchmarks:
+
+# 	Number of physical cores per node not including hyperthreads
+export LMP_CORES=28
+
+#      If hyperthreading is enabled, number of hyperthreads to use per core
+#      (2 for Xeon; 2 or 4 for Xeon Phi)
+export OMP_NUM_THREADS=2
+                        
+#      Name of the LAMMPS binary
+export LMP_BIN=../../lmp_intel_cpu
+
+#      LAMMPS root directory
+export LMP_ROOT=../../../
+               
+source /opt/intel/parallel_studio_xe_2016.2.062/psxevars.sh
+export I_MPI_PIN_DOMAIN=core
+export I_MPI_FABRICS=shm		# For single node
+
+#      Generate the restart file for use with liquid crystal benchmark
+mpirun -np $LMP_CORES $LMP_BIN -in in.lc_generate_restart -log none
+
+#      Benchmark to run
+export bench=in.intel.lj
 
 
-TO RUN WITHOUT A PACKAGE:
------------------------------------------------------------------------------
-mpirun -np 48 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s off
-mpirun -np 48 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0 -v s off
+#############################################################################
+# To run without a optimization package
+#############################################################################
+mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none
 
+#############################################################################
+# To run with USER-OMP package
+#############################################################################
+mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk omp 0
 
-TO RUN WITH OMP PACKAGE
------------------------------------------------------------------------------
-env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s omp
-+++++++++++++++++++++++
-+ EXPECTED TIME: 20.33s
-+++++++++++++++++++++++
-
-env OMP_NUM_THREADS=1 mpirun -np 48 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0 -v s omp
-+++++++++++++++++++++++
-+ EXPECTED TIME: 19.92s
-+++++++++++++++++++++++
-
-
-TO RUN WITH INTEL+OMP PACKAGE WITHOUT OFFLOAD:
------------------------------------------------------------------------------
-env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s intel
-+++++++++++++++++++++++
-+ EXPECTED TIME: 16.94s
-+++++++++++++++++++++++
-
-env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0 -v s intel
-+++++++++++++++++++++++
-+ EXPECTED TIME: 5.80s
-+++++++++++++++++++++++
-
-
-TO RUN WITH INTEL+OMP PACKAGE WITH OFFLOAD TO XEON PHI (AUTO-BALANCED):
------------------------------------------------------------------------------
-env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b -1 -v s intel
-+++++++++++++++++++++++
-+ EXPECTED TIME: 12.31s
-+++++++++++++++++++++++
-
-env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b -1 -v s intel
-+++++++++++++++++++++++
-+ EXPECTED TIME: 4.00s
-+++++++++++++++++++++++
-
-
-TO RUN WITH INTEL+OMP PACKAGE WITH OFFLOAD TO XEON PHI (FIXED BALANCE):
------------------------------------------------------------------------------
-env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0.68 -v s intel
-+++++++++++++++++++++++
-+ EXPECTED TIME: 11.40s
-+++++++++++++++++++++++
-
-env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0.53 -v s intel
-+++++++++++++++++++++++
-+ EXPECTED TIME: 3.93s
-+++++++++++++++++++++++
+#############################################################################
+# To run with USER-INTEL package and no coprocessor
+#############################################################################
+mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk intel 0
 
+#############################################################################
+# To run with USER-INTEL and automatic load balancing to 1 coprocessor
+#############################################################################
+mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk intel 1
diff --git a/src/USER-INTEL/TEST/in.intel.lc b/src/USER-INTEL/TEST/in.intel.lc
index feabfdc2e6..0172ba3b4d 100644
--- a/src/USER-INTEL/TEST/in.intel.lc
+++ b/src/USER-INTEL/TEST/in.intel.lc
@@ -2,60 +2,44 @@
 # biaxial ellipsoid mesogens in isotropic phase
 # shape: 2 1.5 1
 # cutoff 4.0 with skin 0.8
-# NPT, T=2.4, P=8.0
 
-package intel 1 mode mixed balance $b
-package omp 0
-suffix $s
-# processors * * * grid numa
+variable        w index 10	# Warmup Timesteps
+variable        t index 840	# Main Run Timesteps
+variable        m index 1	# Main Run Timestep Multiplier
+variable        n index 0	# Use NUMA Mapping for Multi-Node
+variable	p index 0	# Use Power Measurement
 
 variable        x index 4
 variable        y index 2
 variable        z index 2
 
-variable i equal $x*32
-variable j equal $y*32
-variable k equal $z*32
+variable        rr equal floor($t*$m)
 
-units	      lj
-atom_style    ellipsoid
+if "$n > 0"	then "processors * * * grid numa"
 
-# creation
-lattice	      sc 0.22
-region	      box block 0 $i 0 $j 0 $k
-create_box    1 box
-create_atoms  1 box
+units		lj
+atom_style	ellipsoid
+pair_style	gayberne 1.0 3.0 1.0 4.0
+read_restart	restart.lc
+replicate       $x $y $z
 
-# read_data     data.gb
+compute		rot all temp/asphere
+group		spheroid type 1
+variable	dof equal count(spheroid)+3
+compute_modify	rot extra ${dof}
 
-set type 1 mass 1.5
-set type 1 shape 1 1.5 2
-set	      group all quat/random 982381
+pair_style	gayberne 1.0 3.0 1.0 4.0
+pair_coeff	1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
 
-compute	      rot all temp/asphere
-group	      spheroid type 1
-variable      dof equal count(spheroid)+3
-compute_modify rot extra ${dof}
+neighbor	0.8 bin
 
-velocity      all create 2.4 41787 loop geom
+timestep	0.002
 
-pair_style    gayberne 1.0 3.0 1.0 4.0
-pair_coeff    1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
+thermo		100
 
-neighbor      0.8 bin
+fix		1 all nve/asphere
 
-timestep      0.002
-thermo	      300
-
-# equilibration run
-fix	      1 all npt/asphere temp 2.4 2.4 0.1 iso 5.0 8.0 0.1
-compute_modify 1_temp extra ${dof}
-run	      210
-thermo        100
-
-reset_timestep 0
-unfix 1
-fix         1 all nve/asphere
-run 10
-run	      50
+if "$p > 0"	then "run_style verlet/power"
 
+if "$w > 0"	then "run $w"
+run             ${rr}
diff --git a/src/USER-INTEL/TEST/in.intel.lj b/src/USER-INTEL/TEST/in.intel.lj
new file mode 100644
index 0000000000..8931ca24bc
--- /dev/null
+++ b/src/USER-INTEL/TEST/in.intel.lj
@@ -0,0 +1,43 @@
+# 3d Lennard-Jones melt
+
+variable	w index 10	# Warmup Timesteps
+variable	t index 7900	# Main Run Timesteps
+variable	m index 1	# Main Run Timestep Multiplier
+variable	n index 0	# Use NUMA Mapping for Multi-Node
+variable	p index 0	# Use Power Measurement
+
+variable	x index 4
+variable	y index 2
+variable	z index 2
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+variable	rr equal floor($t*$m)
+
+if "$n > 0"	then "processors * * * grid numa"
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+thermo		1000
+
+if "$p > 0"	then "run_style verlet/power"
+
+if "$w > 0"	then "run $w"
+run		${rr}
diff --git a/src/USER-INTEL/TEST/in.intel.rhodo b/src/USER-INTEL/TEST/in.intel.rhodo
index 4b227b3d1e..37b0d65d7d 100644
--- a/src/USER-INTEL/TEST/in.intel.rhodo
+++ b/src/USER-INTEL/TEST/in.intel.rhodo
@@ -1,27 +1,39 @@
 # Rhodopsin model
 
-package intel 1 mode mixed balance $b
-package omp 0
-suffix $s
+variable	w index 10	# Warmup Timesteps
+variable	t index 520	# Main Run Timesteps
+variable	m index 1	# Main Run Timestep Multiplier
+variable	n index 0	# Use NUMA Mapping for Multi-Node
+variable        b index 3       # Neighbor binsize
+variable	p index 0	# Use Power Measurement
+variable	c index 0	# 1 to use collectives for PPPM
+variable        d index 0       # 1 to use 'diff ad' for PPPM
 
 variable	x index 4
 variable	y index 2
 variable	z index 2
 
+variable	rr equal floor($t*$m)
+variable        root getenv LMP_ROOT
+
+if "$n > 0"	then "processors * * * grid numa"
+
 units           real  
-neigh_modify    delay 5 every 1   
+neigh_modify    delay 5 every 1 binsize $b
 
 atom_style      full  
-atom_modify	map hash
 bond_style      harmonic 
 angle_style     charmm 
 dihedral_style  charmm 
 improper_style  harmonic 
 pair_style      lj/charmm/coul/long 8.0 10.0 
 pair_modify     mix arithmetic 
-kspace_style    pppm 1e-4 
+kspace_style    pppm 1e-4
 
-read_data       ../../../bench/data.rhodo
+if "$c > 0"	then "kspace_modify collective yes"
+if "$d > 0"	then "kspace_modify diff ad"
+
+read_data       ${root}/bench/data.rhodo
 
 replicate	$x $y $z
 
@@ -31,9 +43,11 @@ fix             2 all npt temp 300.0 300.0 100.0 &
 
 special_bonds   charmm
  
-thermo          50
+thermo          100
 thermo_style    multi 
 timestep        2.0
 
-run 10
-run		100
+if "$p > 0"	then "run_style verlet/power"
+
+if "$w > 0"	then "run $w"
+run		${rr}
diff --git a/src/USER-INTEL/TEST/in.intel.sw b/src/USER-INTEL/TEST/in.intel.sw
index eceabcc254..077c9bb4fb 100644
--- a/src/USER-INTEL/TEST/in.intel.sw
+++ b/src/USER-INTEL/TEST/in.intel.sw
@@ -1,7 +1,10 @@
 # bulk Si via Stillinger-Weber
-package intel 1 mode mixed balance $b
-package omp 0
-suffix $s
+
+variable        w index 10      # Warmup Timesteps
+variable        t index 6200	# Main Run Timesteps
+variable        m index 1       # Main Run Timestep Multiplier
+variable        n index 0       # Use NUMA Mapping for Multi-Node
+variable        p index 0       # Use Power Measurement
 
 variable	x index 2
 variable	y index 2
@@ -10,6 +13,10 @@ variable	z index 4
 variable	xx equal 20*$x
 variable	yy equal 20*$y
 variable	zz equal 10*$z
+variable        rr equal floor($t*$m)
+variable        root getenv LMP_ROOT
+
+if "$n > 0"     then "processors * * * grid numa"
 
 units		metal
 atom_style	atomic
@@ -20,7 +27,7 @@ create_box	1 box
 create_atoms	1 box
 
 pair_style	sw
-pair_coeff	* * ../../../bench/POTENTIALS/Si.sw Si
+pair_coeff	* * ${root}/bench/POTENTIALS/Si.sw Si
 mass            1 28.06
 
 velocity	all create 1000.0 376847 loop geom
@@ -29,8 +36,10 @@ neighbor	1.0 bin
 neigh_modify    delay 5 every 1
 
 fix		1 all nve
-
+thermo		1000
 timestep	0.001
 
-run             10
-run		100
+if "$p > 0"     then "run_style verlet/power"
+
+if "$w > 0"     then "run $w"
+run             ${rr}
diff --git a/src/USER-INTEL/TEST/in.intel.tersoff b/src/USER-INTEL/TEST/in.intel.tersoff
index b6fab53b7e..f0c6a88f75 100644
--- a/src/USER-INTEL/TEST/in.intel.tersoff
+++ b/src/USER-INTEL/TEST/in.intel.tersoff
@@ -1,7 +1,10 @@
 # bulk Si via Tersoff
-package intel 1 mode mixed balance $b
-package omp 0
-suffix $s
+
+variable        w index 10      # Warmup Timesteps
+variable        t index 2420	# Main Run Timesteps
+variable        m index 1       # Main Run Timestep Multiplier
+variable        n index 0       # Use NUMA Mapping for Multi-Node
+variable        p index 0       # Use Power Measurement
 
 variable        x index 2
 variable        y index 2
@@ -10,6 +13,10 @@ variable        z index 4
 variable        xx equal 20*$x
 variable        yy equal 20*$y
 variable        zz equal 10*$z
+variable        rr equal floor($t*$m)
+variable        root getenv LMP_ROOT
+
+if "$n > 0"     then "processors * * * grid numa"
 
 units		metal
 atom_style	atomic
@@ -20,7 +27,7 @@ create_box	1 box
 create_atoms	1 box
 
 pair_style	tersoff
-pair_coeff	* * ../../../bench/POTENTIALS/Si.tersoff Si
+pair_coeff	* * ${root}/bench/POTENTIALS/Si.tersoff Si
 mass            1 28.06
 
 velocity	all create 1000.0 376847 loop geom
@@ -29,8 +36,10 @@ neighbor	1.0 bin
 neigh_modify    delay 5 every 1
 
 fix		1 all nve
-
+thermo		1000
 timestep	0.001
 
-run 10
-run		100
+if "$p > 0"     then "run_style verlet/power"
+
+if "$w > 0"     then "run $w"
+run             ${rr}
diff --git a/src/USER-INTEL/TEST/in.intel.water b/src/USER-INTEL/TEST/in.intel.water
index 41e28cdc3b..1c1fca311f 100644
--- a/src/USER-INTEL/TEST/in.intel.water
+++ b/src/USER-INTEL/TEST/in.intel.water
@@ -1,48 +1,45 @@
-package intel 1 mode mixed balance $b
-package omp 0
-suffix $s
+# Coarse-grain water simulation using Stillinger-Weber
 
-# processors * * * grid numa
+variable        w index 10      # Warmup Timesteps
+variable        t index 2600	# Main Run Timesteps
+variable        m index 1       # Main Run Timestep Multiplier
+variable        n index 0       # Use NUMA Mapping for Multi-Node
+variable        p index 0       # Use Power Measurement
 
 variable	x index 4
 variable	y index 2
 variable	z index 2
+variable        rr equal floor($t*$m)
 
-units        real
-atom_style   atomic
+if "$n > 0"     then "processors * * * grid numa"
 
-boundary     p p p
-lattice	     fcc 4.8
-#region	     waterbox block -10 10 -10 10 -10 10
-#create_box   1 waterbox
-#create_atoms 1 region waterbox
+units		real
+atom_style	atomic
 
-read_data mW_32k_cube.data
-reset_timestep 0
-replicate $x $y $z
+read_data	mW_32k_cube.data
+reset_timestep	0
+replicate	$x $y $z
 
-pair_style   sw
-pair_coeff   * * mW.sw mW
+pair_style	sw
+pair_coeff	* * mW.sw mW
 
-mass	     1 18.015 #g/mol
-group	     mW type 1
+mass		1 18.015 #g/mol
+group		mW type 1
 
-neighbor     1 bin #Angstroms
-neigh_modify every 2 delay 2 check yes
+neighbor	2 bin #Angstroms
+neigh_modify	every 1 delay 4
 
-fix 	     1 all nvt temp 300.0 300.0 1000.0
+fix		1 all nvt temp 300.0 300.0 1000.0
 
-#velocity     all create 300.0 2323 dist gaussian #Kelvin
-velocity     all zero linear
+velocity	all zero linear
 
-timestep     10 #femtoseconds
+timestep	10 #femtoseconds
 
-#variable     Density equal "mass(mW)/vol/0.602214179"
-#thermo_style custom step temp press pe spcpu
-thermo_modify norm yes
+thermo_modify	norm yes
 
-#restart	      100 mW_32k_cube.res mW_32k_cube.res
-thermo	      100
+thermo		1000
 
-run	      10 #actual runs
-run	      100
+if "$p > 0"     then "run_style verlet/power"
+
+if "$w > 0"     then "run $w"
+run		${rr}
diff --git a/src/USER-INTEL/TEST/in.lc_generate_restart b/src/USER-INTEL/TEST/in.lc_generate_restart
new file mode 100644
index 0000000000..8ae53c5c8e
--- /dev/null
+++ b/src/USER-INTEL/TEST/in.lc_generate_restart
@@ -0,0 +1,57 @@
+# Gay-Berne benchmark
+# biaxial ellipsoid mesogens in isotropic phase
+# shape: 2 1.5 1
+# cutoff 4.0 with skin 0.8
+# NPT, T=2.4, P=8.0
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	i equal $x*32
+variable	j equal $y*32
+variable	k equal $z*32
+
+units		lj
+atom_style	ellipsoid
+
+lattice		sc 0.22
+region		box block 0 $i 0 $j 0 $k
+create_box	1 box
+create_atoms	1 box
+
+set		type 1 mass 1.5
+set		type 1 shape 1 1.5 2
+set		group all quat/random 982381
+
+compute		rot all temp/asphere
+group		spheroid type 1
+variable	dof equal count(spheroid)+3
+compute_modify	rot extra ${dof}
+
+velocity	all create 2.4 41787 loop geom
+
+pair_style	gayberne 1.0 3.0 1.0 4.0
+pair_coeff	1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
+
+neighbor	0.8 bin
+
+timestep	0.002
+thermo		300
+
+# equilibration run
+fix		1 all npt/asphere temp 2.4 2.4 0.1 iso 5.0 8.0 0.1
+compute_modify	1_temp extra ${dof}
+run		2000
+
+unfix 1
+fix		1 all npt/asphere temp 2.4 2.4 0.1 iso 8.0 8.0 0.1
+compute_modify	1_temp extra ${dof}
+run		2000
+
+unfix 1
+fix		1 all nve/asphere
+run		2000
+reset_timestep	0
+run 0
+write_restart	restart.lc

From 9aa7608bd0d7fb918ae0f8516c3718bb213e85e8 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 7 Apr 2016 22:22:25 +0000
Subject: [PATCH 10/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@14814
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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

diff --git a/src/USER-INTEL/neigh_half_bin_intel.cpp b/src/USER-INTEL/neigh_half_bin_intel.cpp
index 8759da987a..fbb2be3db0 100644
--- a/src/USER-INTEL/neigh_half_bin_intel.cpp
+++ b/src/USER-INTEL/neigh_half_bin_intel.cpp
@@ -342,7 +342,7 @@ void Neighbor::hbnni(const int offload, NeighList *list, void *buffers_in,
     in(ilist:length(0) alloc_if(0) free_if(0)) \
     in(atombin:length(aend) alloc_if(0) free_if(0)) \
     in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
-    in(maxnbors,nthreads,maxspecial,nstencil,pad_width,offload)  \
+    in(maxnbors,nthreads,maxspecial,nstencil,pad_width,offload,nall)  \
     in(separate_buffers, astart, aend, nlocal, molecular, ntypes) \
     in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
     out(overflow:length(5) alloc_if(0) free_if(0)) \

From dd562698ef4daa6e289a7b0c7c1f5c73c6a687c1 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 7 Apr 2016 22:25:40 +0000
Subject: [PATCH 11/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@14816
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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

diff --git a/src/version.h b/src/version.h
index d6d3155048..503f2be8c4 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "28 Mar20 2016"
+#define LAMMPS_VERSION "7 Apr 2016"

From e9085c47c15c08732c57893e1de69ddba4b57881 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 7 Apr 2016 22:26:34 +0000
Subject: [PATCH 12/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@14817
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Manual.html | 4 ++--
 doc/Manual.txt  | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/Manual.html b/doc/Manual.html
index f3367b055b..61056b5c25 100644
--- a/doc/Manual.html
+++ b/doc/Manual.html
@@ -134,8 +134,8 @@
             
   <H1></H1><div class="section" id="lammps-documentation">
 <h1>LAMMPS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="mar20-2016-version">
-<h2>28 Mar20 2016 version<a class="headerlink" href="#mar20-2016-version" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="apr-2016-version">
+<h2>7 Apr 2016 version<a class="headerlink" href="#apr-2016-version" title="Permalink to this headline">¶</a></h2>
 </div>
 <div class="section" id="version-info">
 <h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline">¶</a></h2>
diff --git a/doc/Manual.txt b/doc/Manual.txt
index 04d31246e5..2fb5fe9685 100644
--- a/doc/Manual.txt
+++ b/doc/Manual.txt
@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="28 Mar20 2016 version">
+<META NAME="docnumber" CONTENT="7 Apr 2016 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 <H1></H1>
 
 LAMMPS Documentation :c,h3
-28 Mar20 2016 version :c,h4
+7 Apr 2016 version :c,h4
 
 Version info: :h4