From d71b0884578855238e8ab97e23c44cccb8cb710e Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Mon, 28 Jun 2010 22:06:53 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4355
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/MANYBODY/pair_eam.cpp | 9 +++++++--
src/MANYBODY/pair_eam_alloy.cpp | 9 +++++++--
src/MANYBODY/pair_eam_fs.cpp | 9 +++++++--
src/finish.cpp | 15 ++++++++++-----
src/neigh_list.cpp | 1 +
5 files changed, 32 insertions(+), 11 deletions(-)
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index de2c10501e..2b29a38c25 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/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];
diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp
index a13468acff..202758091e 100644
--- a/src/MANYBODY/pair_eam_alloy.cpp
+++ b/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];
diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp
index d42bdce4c4..74cdd61f60 100644
--- a/src/MANYBODY/pair_eam_fs.cpp
+++ b/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];
diff --git a/src/finish.cpp b/src/finish.cpp
index 72acf8497c..05ecd4ec84 100644
--- a/src/finish.cpp
+++ b/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) {
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index 0aca03a382..9426c3df68 100644
--- a/src/neigh_list.cpp
+++ b/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;
--
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