git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1502 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/COLLOID/pair_colloid.cpp

@@ -53,6 +53,7 @@ PairColloid::~PairColloid()
     memory->destroy_2d_double_array(d2);
     memory->destroy_2d_double_array(a1);
     memory->destroy_2d_double_array(a2);
+    memory->destroy_2d_double_array(diameter);
     memory->destroy_2d_double_array(cut);		
     memory->destroy_2d_double_array(offset);
     memory->destroy_2d_double_array(sigma3);
@@ -229,6 +230,7 @@ void PairColloid::allocate()
   d2 = memory->create_2d_double_array(n+1,n+1,"pair:d2");
   a1 = memory->create_2d_double_array(n+1,n+1,"pair:a1");
   a2 = memory->create_2d_double_array(n+1,n+1,"pair:a2");
+  diameter = memory->create_2d_double_array(n+1,n+1,"pair:diameter");
   cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");
   offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
   sigma3 = memory->create_2d_double_array(n+1,n+1,"pair:sigma3");
@@ -292,6 +294,7 @@ void PairColloid::coeff(int narg, char **arg)
 	error->all("Invalid d1 or d2 value for pair colloid coeff");
       d1[i][j] = d1_one;
       d2[i][j] = d2_one;
+      diameter[i][j] = 0.5*(d1_one+d2_one);
       cut[i][j] = cut_one;
       setflag[i][j] = 1;
       count++;
@@ -312,6 +315,7 @@ double PairColloid::init_one(int i, int j)
     sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
     d1[i][j] = mix_distance(d1[i][i],d1[j][j]);
     d2[i][j] = mix_distance(d2[i][i],d2[j][j]);
+    diameter[i][j] = 0.5 * (d1[i][j] + d2[i][j]);
     cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
   }
 
@@ -340,6 +344,7 @@ double PairColloid::init_one(int i, int j)
   sigma[j][i] = sigma[i][j];
   sigma3[j][i] = sigma3[i][j];
   sigma6[j][i] = sigma6[i][j];
+  diameter[j][i] = diameter[i][j];
   cut[j][i] = cut[i][j];
   cutsq[j][i] = cutsq[i][j] = cut[i][j] * cut[i][j];
 
@@ -516,3 +521,11 @@ double PairColloid::single(int i, int j, int itype, int jtype, double rsq,
 
   return factor_lj*phi;
 }
+
+/* ---------------------------------------------------------------------- */
+
+void *PairColloid::extract(char *str)
+{
+  if (strcmp(str,"diameter") == 0) return (void *) diameter;
+  return NULL;
+}

src/COLLOID/pair_colloid.h

@@ -31,11 +31,12 @@ class PairColloid : public Pair {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
   double single(int, int, int, int, double, double, double, double &);
+  void *extract(char *);
 
  private:
   double cut_global;
   double **cut;
-  double **a12,**d1,**d2,**a1,**a2,**offset;
+  double **a12,**d1,**d2,**diameter,**a1,**a2,**offset;
   double **sigma,**sigma3,**sigma6;
   double **lj1,**lj2,**lj3,**lj4;
   int **form;

src/COLLOID/pair_lubricate.cpp

@@ -352,8 +352,6 @@ void PairLubricate::init_style()
 {
   if (!atom->torque_flag || atom->shape == NULL)
     error->all("Pair lubricate requires atom attributes torque, shape");
-  if (domain->dimension != 3)
-    error->all("Pair lubricate only available for 3d");
 
   // insure all particle shapes are spherical
 

src/comm.cpp

@@ -29,6 +29,7 @@
 #include "neighbor.h"
 #include "modify.h"
 #include "fix.h"
+#include "group.h"
 #include "compute.h"
 #include "error.h"
 #include "memory.h"
@@ -57,6 +58,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
   user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0;
   grid2proc = NULL;
 
+  igroup = 0;
   style = SINGLE;
   multilo = multihi = NULL;
   cutghostmulti = NULL;
@@ -170,6 +172,7 @@ void Comm::init()
 {
   triclinic = domain->triclinic;
   map_style = atom->map_style;
+  groupbit = group->bitmask[igroup];
 
   // comm_only = 1 if only x,f are exchanged in forward/reverse comm
 
@@ -605,7 +608,7 @@ void Comm::borders()
 {
   int i,n,itype,iswap,dim,ineed,maxneed,nsend,nrecv,nfirst,nlast,smax,rmax;
   double lo,hi;
-  int *type;
+  int *type,*mask;
   double **x;
   double *buf,*mlo,*mhi;
   MPI_Request request;
@@ -648,6 +651,30 @@ void Comm::borders()
       }
 
       nsend = 0;
+
+      // SINGLE vs MULTI, all atoms versus only atoms in group
+
+      if (igroup) {
+	mask = atom->mask;
+	if (style == SINGLE) {
+	  for (i = nfirst; i < nlast; i++)
+	    if (mask[i] & groupbit) {
+	      if (x[i][dim] >= lo && x[i][dim] <= hi) {
+		if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
+		sendlist[iswap][nsend++] = i;
+	      }
+	    }
+	} else {
+	  for (i = nfirst; i < nlast; i++)
+	    if (mask[i] & groupbit) {
+	      itype = type[i];
+	      if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
+		if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
+		sendlist[iswap][nsend++] = i;
+	      }
+	    }
+	}
+      } else {
 	if (style == SINGLE) {
 	  for (i = nfirst; i < nlast; i++)
 	    if (x[i][dim] >= lo && x[i][dim] <= hi) {
@@ -663,6 +690,7 @@ void Comm::borders()
 	    }
 	  }
 	}
+      }
 
       // pack up list of border atoms
 
@@ -1466,11 +1494,22 @@ void Comm::free_multi()
 
 void Comm::set(int narg, char **arg)
 {
-  if (narg != 1) error->all("Illegal communicate command");
+  if (narg < 1) error->all("Illegal communicate command");
 
   if (strcmp(arg[0],"single") == 0) style = SINGLE;
   else if (strcmp(arg[0],"multi") == 0) style = MULTI;
   else error->all("Illegal communicate command");
+
+  int iarg = 1;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"group") == 0) {
+      if (iarg+2 > narg) error->all("Illegal communicate command");
+      igroup = group->find(arg[iarg+1]);
+      if (igroup < 0)
+	error->all("Invalid group ID in communicate command");
+      iarg += 2;
+    } else error->all("Illegal communicate command");
+  }
 }
 
 /* ----------------------------------------------------------------------

src/comm.h

@@ -71,6 +71,7 @@ class Comm : protected Pointers {
   int comm_x_only,comm_f_only;      // 1 if only exchange x,f in for/rev comm
   int map_style;                    // non-0 if global->local mapping is done
   int ***grid2proc;                 // which proc owns i,j,k loc in 3d grid
+  int igroup,groupbit;              // only communicate this group
 
   int *firstrecv;                   // where to put 1st recv atom in each swap
   int **sendlist;                   // list of atoms to send in each swap

src/neigh_derive.cpp

@@ -67,10 +67,9 @@ void Neighbor::half_from_full_no_newton(NeighList *list)
       if (j > i) neighptr[n++] = j;
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -145,10 +144,9 @@ void Neighbor::half_from_full_newton(NeighList *list)
       neighptr[n++] = joriginal;
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -217,10 +215,9 @@ void Neighbor::skip_from(NeighList *list)
       neighptr[n++] = joriginal;
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -311,12 +308,11 @@ void Neighbor::skip_from_granular(NeighList *list)
       shearptr[nn++] = shearptr_skip[3*jj+2];
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     firsttouch[i] = touchptr;
     firstshear[i] = shearptr;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -454,10 +450,9 @@ void Neighbor::skip_from_respa(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");

src/neigh_full.cpp

@@ -47,6 +47,7 @@ void Neighbor::full_nsq(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -83,10 +84,9 @@ void Neighbor::full_nsq(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -132,6 +132,7 @@ void Neighbor::full_bin(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -173,10 +174,9 @@ void Neighbor::full_bin(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -225,6 +225,7 @@ void Neighbor::full_multi(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -271,10 +272,9 @@ void Neighbor::full_multi(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");

src/neigh_gran.cpp

@@ -74,6 +74,7 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -142,15 +143,13 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
       }
     }	       
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     if (fix_history) {
       firsttouch[i] = touchptr;
       firstshear[i] = shearptr;
     }
-
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -194,6 +193,7 @@ void Neighbor::granular_nsq_newton(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -239,10 +239,9 @@ void Neighbor::granular_nsq_newton(NeighList *list)
       if (rsq <= cutsq) neighptr[n++] = j;
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -314,6 +313,7 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -389,15 +389,13 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     if (fix_history) {
       firsttouch[i] = touchptr;
       firstshear[i] = shearptr;
     }
-
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -446,6 +444,7 @@ void Neighbor::granular_bin_newton(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -501,10 +500,9 @@ void Neighbor::granular_bin_newton(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -553,6 +551,7 @@ void Neighbor::granular_bin_newton_tri(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -592,10 +591,9 @@ void Neighbor::granular_bin_newton_tri(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");

src/neigh_half_bin.cpp

@@ -57,6 +57,7 @@ void Neighbor::half_bin_no_newton(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -100,10 +101,9 @@ void Neighbor::half_bin_no_newton(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -150,6 +150,7 @@ void Neighbor::half_bin_newton(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -214,10 +215,9 @@ void Neighbor::half_bin_newton(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -264,6 +264,7 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -308,10 +309,9 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");

src/neigh_half_multi.cpp

@@ -60,6 +60,7 @@ void Neighbor::half_multi_no_newton(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -108,10 +109,9 @@ void Neighbor::half_multi_no_newton(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -161,6 +161,7 @@ void Neighbor::half_multi_newton(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -232,10 +233,9 @@ void Neighbor::half_multi_newton(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -285,6 +285,7 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -334,10 +335,9 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");

src/neigh_half_nsq.cpp

@@ -48,6 +48,7 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -82,10 +83,9 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -125,6 +125,7 @@ void Neighbor::half_nsq_newton(NeighList *list)
   int npnt = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -175,10 +176,9 @@ void Neighbor::half_nsq_newton(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");

src/neigh_respa.cpp

@@ -68,6 +68,7 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
   int npnt_middle = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -131,10 +132,9 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -209,6 +209,7 @@ void Neighbor::respa_nsq_newton(NeighList *list)
   int npnt_middle = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -288,10 +289,9 @@ void Neighbor::respa_nsq_newton(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -373,6 +373,7 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
   int npnt_middle = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -445,10 +446,9 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -529,6 +529,7 @@ void Neighbor::respa_bin_newton(NeighList *list)
   int npnt_middle = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -634,10 +635,9 @@ void Neighbor::respa_bin_newton(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -718,6 +718,7 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
   int npnt_middle = 0;
 
   for (i = 0; i < nlocal; i++) {
+    if (include_group && !(mask[i] & include_groupbit)) continue;
 
     if (pgsize - npnt < oneatom) {
       npnt = 0;
@@ -792,10 +793,9 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
       }
     }
 
-    ilist[inum] = i;
+    ilist[inum++] = i;
     firstneigh[i] = neighptr;
     numneigh[i] = n;
-    inum++;
     npnt += n;
     if (npnt >= pgsize)
       error->one("Neighbor list overflow, boost neigh_modify one or page");

src/neighbor.cpp

@@ -90,6 +90,8 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
 
   // pair exclusion list info
 
+  include_group = 0;
+
   nex_type = maxex_type = 0;
   ex1_type = ex2_type = NULL;
   ex_type = NULL;
@@ -338,6 +340,8 @@ void Neighbor::init()
 
   n = atom->ntypes;
 
+  include_groupbit = group->bitmask[include_group];
+
   if (nex_type == 0 && nex_group == 0 && nex_mol == 0) exclude = 0;
   else exclude = 1;
 
@@ -920,9 +924,21 @@ int Neighbor::check_distance()
 {
   double delx,dely,delz,rsq;
 
-  int nlocal = atom->nlocal;
   double **x = atom->x;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
   int flag = 0;
+
+  if (include_group) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & include_groupbit) {
+	delx = x[i][0] - xhold[i][0];
+	dely = x[i][1] - xhold[i][1];
+	delz = x[i][2] - xhold[i][2];
+	rsq = delx*delx + dely*dely + delz*delz;
+	if (rsq > triggersq) flag = 1;
+      }
+  } else {
     for (int i = 0; i < nlocal; i++) {
       delx = x[i][0] - xhold[i][0];
       dely = x[i][1] - xhold[i][1];
@@ -930,6 +946,7 @@ int Neighbor::check_distance()
       rsq = delx*delx + dely*dely + delz*delz;
       if (rsq > triggersq) flag = 1;
     }
+  }
 
   int flagall;
   MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
@@ -1288,6 +1305,12 @@ void Neighbor::modify_params(int narg, char **arg)
       if (binsize_user <= 0.0) binsizeflag = 0;
       else binsizeflag = 1;
       iarg += 2;
+    } else if (strcmp(arg[iarg],"include") == 0) {
+      if (iarg+2 > narg) error->all("Illegal neigh_modify command");
+      include_group = group->find(arg[iarg+1]);
+      if (include_group == -1)
+	error->all("Invalid group ID in neigh_modify command");
+      iarg += 2;
     } else if (strcmp(arg[iarg],"exclude") == 0) {
       if (iarg+2 > narg) error->all("Illegal neigh_modify command");
 
@@ -1395,35 +1418,30 @@ int Neighbor::find_special(int i, int j)
 void Neighbor::bin_atoms()
 {
   int i,ibin,nall;
-  double **x;
-
-  nall = atom->nlocal + atom->nghost;
-  x = atom->x;
 
   for (i = 0; i < mbins; i++) binhead[i] = -1;
 
   // bin in reverse order so linked list will be in forward order
   // also puts ghost atoms at end of list, which is necessary
 
+  double **x = atom->x;
+  int *mask = atom->mask;
+  nall = atom->nlocal + atom->nghost;
+
+  if (include_group) {
+    for (i = nall-1; i >= 0; i--)
+      if (mask[i] & include_groupbit) {
+	ibin = coord2bin(x[i]);
+	bins[i] = binhead[ibin];
+	binhead[ibin] = i;
+      }
+  } else {
     for (i = nall-1; i >= 0; i--) {
       ibin = coord2bin(x[i]);
       bins[i] = binhead[ibin];
       binhead[ibin] = i;
     }
-
-  /*
-  for (i = nlocal; i < nall; i++) {
-    ibin = coord2bin(x[i]);
-    bins[i] = binhead[ibin];
-    binhead[ibin] = i;
   }
-
-  for (i = 0; i < nlocal; i++) {
-    ibin = coord2bin(x[i]);
-    bins[i] = binhead[ibin];
-    binhead[ibin] = i;
-  }
-  */
 }
 
 /* ----------------------------------------------------------------------

src/neighbor.h

@@ -123,6 +123,9 @@ class Neighbor : protected Pointers {
 
   int special_flag[4];             // flags for 1-2, 1-3, 1-4 neighbors
 
+  int include_group;               // only form neighbor lists on this group
+  int include_groupbit;
+
   int exclude;                     // 0 if no type/group exclusions, 1 if yes
 
   int nex_type;                    // # of entries in type exclusion list

src/pair_lj_cut.cpp

@@ -717,6 +717,6 @@ double PairLJCut::single(int i, int j, int itype, int jtype, double rsq,
 
 void *PairLJCut::extract(char *str)
 {
-  if (strcmp(str,"sigma") == 0) return (void *) sigma;
+  if (strcmp(str,"diameter") == 0) return (void *) sigma;
   return NULL;
 }