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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1515 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2008-02-15 19:06:53 +00:00
parent 9fa38a6e94
commit 9864ead231
27 changed files with 243 additions and 110 deletions
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50
src/neighbor.cpp
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@ -340,8 +340,6 @@ 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;
@ -925,27 +923,16 @@ int Neighbor::check_distance()
double delx,dely,delz,rsq;
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int flag = 0;
if (include_group) nlocal = atom->nfirst;
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];
delz = x[i][2] - xhold[i][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq > triggersq) flag = 1;
}
int flag = 0;
for (int i = 0; i < nlocal; i++) {
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;
}
int flagall;
@ -1308,8 +1295,11 @@ void Neighbor::modify_params(int narg, char **arg)
} 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)
if (include_group < 0)
error->all("Invalid group ID in neigh_modify command");
if (include_group && (atom->firstgroupname == NULL ||
strcmp(arg[iarg+1],atom->firstgroupname) != 0))
error->all("Neigh_modify include group != atom_modify first group");
iarg += 2;
} else if (strcmp(arg[iarg],"exclude") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
@ -1417,7 +1407,7 @@ int Neighbor::find_special(int i, int j)
void Neighbor::bin_atoms()
{
int i,ibin,nall;
int i,ibin;
for (i = 0; i < mbins; i++) binhead[i] = -1;
@ -1426,15 +1416,23 @@ void Neighbor::bin_atoms()
double **x = atom->x;
int *mask = atom->mask;
nall = atom->nlocal + atom->nghost;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (include_group) {
for (i = nall-1; i >= 0; i--)
if (mask[i] & include_groupbit) {
int bitmask = group->bitmask[include_group];
for (i = nall-1; i >= nlocal; i--) {
if (mask[i] & bitmask) {
ibin = coord2bin(x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
}
for (i = atom->nfirst; i >= 0; i--) {
ibin = coord2bin(x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
} else {
for (i = nall-1; i >= 0; i--) {
ibin = coord2bin(x[i]);