git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4355 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/MANYBODY/pair_eam.cpp

@@ -667,14 +667,19 @@ void PairEAM::file2array()
   // set of z2r arrays only fill lower triangular Nelement matrix
   // value = n = sum over rows of lower-triangular matrix until reach irow,icol
   // swap indices when irow < icol to stay lower triangular
-  // OK if map = -1 (non-EAM atom in pair hybrid) b/c type2z2r not used
+  // if map = -1 (non-EAM atom in pair hybrid):
+  //   type2z2r is not used by non-opt
+  //   but set type2z2r to 0 since accessed by opt
 
   int irow,icol;
   for (i = 1; i <= ntypes; i++) {
     for (j = 1; j <= ntypes; j++) {
       irow = map[i];
       icol = map[j];
-      if (irow == -1 || icol == -1) continue;
+      if (irow == -1 || icol == -1) {
+	type2z2r[i][j] = 0;
+	continue;
+      }
       if (irow < icol) {
 	irow = map[j];
 	icol = map[i];

src/MANYBODY/pair_eam_alloy.cpp

@@ -298,14 +298,19 @@ void PairEAMAlloy::file2array()
   // set of z2r arrays only fill lower triangular Nelement matrix
   // value = n = sum over rows of lower-triangular matrix until reach irow,icol
   // swap indices when irow < icol to stay lower triangular
-  // OK if map = -1 (non-EAM atom in pair hybrid) b/c type2z2r not used
+  // if map = -1 (non-EAM atom in pair hybrid):
+  //   type2z2r is not used by non-opt
+  //   but set type2z2r to 0 since accessed by opt
 
   int irow,icol;
   for (i = 1; i <= ntypes; i++) {
     for (j = 1; j <= ntypes; j++) {
       irow = map[i];
       icol = map[j];
-      if (irow == -1 || icol == -1) continue;
+      if (irow == -1 || icol == -1) {
+	type2z2r[i][j] = 0;
+	continue;
+      }
       if (irow < icol) {
 	irow = map[j];
 	icol = map[i];

src/MANYBODY/pair_eam_fs.cpp

@@ -305,14 +305,19 @@ void PairEAMFS::file2array()
   // set of z2r arrays only fill lower triangular Nelement matrix
   // value = n = sum over rows of lower-triangular matrix until reach irow,icol
   // swap indices when irow < icol to stay lower triangular
-  // OK if map = -1 (non-EAM atom in pair hybrid) b/c type2z2r not used
+  // if map = -1 (non-EAM atom in pair hybrid):
+  //   type2z2r is not used by non-opt
+  //   but set type2z2r to 0 since accessed by opt
 
   int irow,icol;
   for (i = 1; i <= ntypes; i++) {
     for (j = 1; j <= ntypes; j++) {
       irow = map[i];
       icol = map[j];
-      if (irow == -1 || icol == -1) continue;
+      if (irow == -1 || icol == -1) {
+	type2z2r[i][j] = 0;
+	continue;
+      }
       if (irow < icol) {
 	irow = map[j];
 	icol = map[i];

src/finish.cpp

@@ -414,8 +414,9 @@ void Finish::end(int flag)
       int inum = neighbor->lists[m]->inum;
       int *ilist = neighbor->lists[m]->ilist;
       int *numneigh = neighbor->lists[m]->numneigh;
-      for (int ii = 0; ii < inum; ii++)
-	nneigh += numneigh[ilist[ii]];
+      if (numneigh)
+	for (i = 0; i < inum; i++)
+	  nneigh += numneigh[ilist[i]];
     }
     
     tmp = nneigh;
@@ -443,9 +444,13 @@ void Finish::end(int flag)
     
     if (m < neighbor->old_nrequest) {
       nneigh = 0;
-      for (i = 0; i < atom->nlocal; i++)
-	nneigh += neighbor->lists[m]->numneigh[i];
-      
+      int inum = neighbor->lists[m]->inum;
+      int *ilist = neighbor->lists[m]->ilist;
+      int *numneigh = neighbor->lists[m]->numneigh;
+      if (numneigh)
+	for (i = 0; i < inum; i++)
+	  nneigh += numneigh[ilist[i]];
+
       tmp = nneigh;
       stats(1,&tmp,&ave,&max,&min,10,histo);
       if (me == 0) {

src/neigh_list.cpp

@@ -32,6 +32,7 @@ NeighList::NeighList(LAMMPS *lmp, int size) : Pointers(lmp)
   maxlocal = 0;
   pgsize = size;
 
+  inum = 0;
   ilist = NULL;
   numneigh = NULL;
   firstneigh = NULL;