ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

87
src/compute_stress_atom.cpp
View File

@ -15,6 +15,8 @@
#include "compute_stress_atom.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "modify.h"
#include "comm.h"
#include "update.h"
@ -40,7 +42,6 @@ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
peratom_flag = 1;
size_peratom = 6;
comm_reverse = 6;
neigh_half_once = 1;
// process args
@ -85,6 +86,14 @@ void ComputeStressAtom::init()
if (force->pair == NULL || force->pair->single_enable == 0)
error->all("Pair style does not support computing per-atom stress");
pairflag = 1;
// need an occasional half neighbor list
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
} else pairflag = 0;
if (bondrequest && force->bond) bondflag = 1;
@ -99,12 +108,19 @@ void ComputeStressAtom::init()
/* ---------------------------------------------------------------------- */
void ComputeStressAtom::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeStressAtom::compute_peratom()
{
int i,j,k,n,i1,i2,itype,jtype,numneigh,iflag;
int i,j,ii,jj,n,i1,i2,inum,jnum,itype,jtype,iflag,jflag;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,eng;
double factor_coul,factor_lj,fforce,rmass;
int *neighs;
int *ilist,*jlist,*numneigh,**firstneigh;
Pair::One one;
// grow stress array if necessary
@ -136,12 +152,18 @@ void ComputeStressAtom::compute_peratom()
// compute pairwise stress for atoms via pair->single()
// if neither atom is in compute group, skip that pair
// only add stress to atoms in group
if (pairflag) {
// if needed, build a half neighbor list
// invoke half neighbor list (will copy or build if necessary)
if (!neighbor->half_every) neighbor->build_half();
neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@ -153,18 +175,20 @@ void ComputeStressAtom::compute_peratom()
int *type = atom->type;
int nall = nlocal + atom->nghost;
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
iflag = mask[i] & groupbit;
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
if (iflag == 0 && (mask[j] & groupbit) == 0) continue;
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
jflag = mask[j] & groupbit;
if (iflag == 0 && jflag == 0) continue;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@ -183,13 +207,15 @@ void ComputeStressAtom::compute_peratom()
force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,0,one);
fforce = one.fforce;
stress[i][0] -= delx*delx*fforce;
stress[i][1] -= dely*dely*fforce;
stress[i][2] -= delz*delz*fforce;
stress[i][3] -= delx*dely*fforce;
stress[i][4] -= delx*delz*fforce;
stress[i][5] -= dely*delz*fforce;
if (newton_pair || j < nlocal) {
if (iflag) {
stress[i][0] -= delx*delx*fforce;
stress[i][1] -= dely*dely*fforce;
stress[i][2] -= delz*delz*fforce;
stress[i][3] -= delx*dely*fforce;
stress[i][4] -= delx*delz*fforce;
stress[i][5] -= dely*delz*fforce;
}
if (jflag && (newton_pair || j < nlocal)) {
stress[j][0] -= delx*delx*fforce;
stress[j][1] -= dely*dely*fforce;
stress[j][2] -= delz*delz*fforce;
@ -205,6 +231,7 @@ void ComputeStressAtom::compute_peratom()
// compute bond stress for atoms via bond->single()
// if neither atom is in compute group, skip that bond
// only add stress to atoms in group
if (bondflag) {
double **x = atom->x;
@ -218,7 +245,9 @@ void ComputeStressAtom::compute_peratom()
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
if ((mask[i1] & groupbit) == 0 && (mask[i2] & groupbit) == 0) continue;
iflag = mask[i1] & groupbit;
jflag = mask[i2] & groupbit;
if (iflag == 0 && jflag == 0) continue;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
@ -228,14 +257,16 @@ void ComputeStressAtom::compute_peratom()
rsq = delx*delx + dely*dely + delz*delz;
force->bond->single(type,rsq,i1,i2,0,fforce,eng);
stress[i1][0] -= delx*delx*fforce;
stress[i1][1] -= dely*dely*fforce;
stress[i1][2] -= delz*delz*fforce;
stress[i1][3] -= delx*dely*fforce;
stress[i1][4] -= delx*delz*fforce;
stress[i1][5] -= dely*delz*fforce;
if (newton_bond || i2 < nlocal) {
if (iflag) {
stress[i1][0] -= delx*delx*fforce;
stress[i1][1] -= dely*dely*fforce;
stress[i1][2] -= delz*delz*fforce;
stress[i1][3] -= delx*dely*fforce;
stress[i1][4] -= delx*delz*fforce;
stress[i1][5] -= dely*delz*fforce;
}
if (jflag && (newton_bond || i2 < nlocal)) {
stress[i2][0] -= delx*delx*fforce;
stress[i2][1] -= dely*dely*fforce;
stress[i2][2] -= delz*delz*fforce;