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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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49
src/compute_coord_atom.cpp
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@ -17,6 +17,8 @@
#include "atom.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
@ -30,13 +32,12 @@ using namespace LAMMPS_NS;
ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all("Illegal compute centro/atom command");
if (narg != 4) error->all("Illegal compute coord/atom command");
cutoff = atof(arg[3]);
peratom_flag = 1;
size_peratom = 0;
neigh_full_once = 1;
nmax = 0;
coordination = NULL;
@ -56,6 +57,15 @@ void ComputeCoordAtom::init()
if (force->pair == NULL || cutoff > force->pair->cutforce)
error->all("Compute coord/atom cutoff is longer than pairwise cutoff");
// 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;
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"coord/atom") == 0) count++;
@ -65,11 +75,18 @@ void ComputeCoordAtom::init()
/* ---------------------------------------------------------------------- */
void ComputeCoordAtom::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeCoordAtom::compute_peratom()
{
int j,k,n,numneigh;
int i,j,ii,jj,inum,jnum,n;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighs;
int *ilist,*jlist,*numneigh,**firstneigh;
// grow coordination array if necessary
@ -81,9 +98,14 @@ void ComputeCoordAtom::compute_peratom()
scalar_atom = coordination;
}
// 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 coordination number for each atom in group
// use full neighbor list to count atoms less than cutoff
@ -94,17 +116,18 @@ void ComputeCoordAtom::compute_peratom()
int nall = atom->nlocal + atom->nghost;
double cutsq = cutoff*cutoff;
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];
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];
@ -115,8 +138,10 @@ void ComputeCoordAtom::compute_peratom()
}
coordination[i] = n;
}
} else coordination[i] = 0.0;
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */