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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@937 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-10-03 16:22:30 +00:00
parent 92ff097469
commit 9be7620ace
96 changed files with 3347 additions and 3735 deletions
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50
src/compute_centro_atom.cpp
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@ -17,6 +17,8 @@
#include "modify.h"
#include "update.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
@ -34,7 +36,6 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
peratom_flag = 1;
size_peratom = 0;
neigh_full_once = 1;
nmax = 0;
centro = NULL;
@ -61,15 +62,31 @@ void ComputeCentroAtom::init()
if (strcmp(modify->compute[i]->style,"centro/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning("More than one compute centro/atom");
// need an occasional full neighbor list
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
}
/* ---------------------------------------------------------------------- */
void ComputeCentroAtom::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeCentroAtom::compute_peratom()
{
int j,k,jj,kk,n,numneigh;
int i,j,k,ii,jj,kk,n,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,value;
int *neighs;
int *ilist,*jlist,*numneigh,**firstneigh;
double pairs[66];
// grow centro array if necessary
@ -82,9 +99,14 @@ void ComputeCentroAtom::compute_peratom()
scalar_atom = centro;
}
// if needed, build a full neighbor list
// invoke full neighbor list (will copy or build if necessary)
if (!neighbor->full_every) neighbor->build_full();
neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// compute centro-symmetry parameter for each atom in group
// use full neighbor list
@ -95,20 +117,21 @@ void ComputeCentroAtom::compute_peratom()
int nall = atom->nlocal + atom->nghost;
double cutsq = force->pair->cutforce * force->pair->cutforce;
for (int i = 0; i < nlocal; i++)
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
neighs = neighbor->firstneigh_full[i];
numneigh = neighbor->numneigh_full[i];
jlist = firstneigh[i];
jnum = numneigh[i];
// insure distsq and nearest arrays are long enough
if (numneigh > maxneigh) {
if (jnum > maxneigh) {
memory->sfree(distsq);
memory->sfree(nearest);
maxneigh = numneigh;
maxneigh = jnum;
distsq = (double *) memory->smalloc(maxneigh*sizeof(double),
"compute/centro/atom:distsq");
nearest = (int *) memory->smalloc(maxneigh*sizeof(int),
@ -120,8 +143,8 @@ void ComputeCentroAtom::compute_peratom()
// nearest[] = atom indices of neighbors
n = 0;
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j >= nall) j %= nall;
delx = xtmp - x[j][0];
@ -169,7 +192,8 @@ void ComputeCentroAtom::compute_peratom()
value = 0.0;
for (j = 0; j < 6; j++) value += pairs[j];
centro[i] = value;
}
} else centro[i] = 0.0;
}
}
/* ----------------------------------------------------------------------