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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1193 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-11-30 21:54:30 +00:00
parent d9df67ded2
commit 8fb52958ce
124 changed files with 4220 additions and 3618 deletions
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355
src/compute_stress_atom.cpp
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@ -11,60 +11,54 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#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"
#include "force.h"
#include "bond.h"
#include "pair.h"
#include "domain.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 3) error->all("Illegal compute stress/atom command");
peratom_flag = 1;
size_peratom = 6;
pressatomflag = 1;
timeflag = 1;
comm_reverse = 6;
// process args
kerequest = pairrequest = bondrequest = 1;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"ke") == 0) {
if (iarg+2 > narg) error->all("Illegal compute ebond/atom command");
if (strcmp(arg[iarg+1],"yes") == 0) kerequest = 1;
else if (strcmp(arg[iarg+1],"no") == 0) kerequest = 0;
iarg += 2;
} else if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+2 > narg) error->all("Illegal compute ebond/atom command");
if (strcmp(arg[iarg+1],"yes") == 0) pairrequest = 1;
else if (strcmp(arg[iarg+1],"no") == 0) pairrequest = 0;
iarg += 2;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+2 > narg) error->all("Illegal compute ebond/atom command");
if (strcmp(arg[iarg+1],"yes") == 0) bondrequest = 1;
else if (strcmp(arg[iarg+1],"no") == 0) bondrequest = 0;
iarg += 2;
} else error->all("Illegal compute ebond/atom command");
if (narg == 3) {
keflag = 1;
pairflag = 1;
bondflag = angleflag = dihedralflag = improperflag = 1;
} else {
keflag = 0;
pairflag = 0;
bondflag = angleflag = dihedralflag = improperflag = 0;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"ke") == 0) keflag = 1;
else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1;
else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1;
else error->all("Illegal compute stress/atom command");
iarg++;
}
}
nmax = 0;
@ -80,50 +74,13 @@ ComputeStressAtom::~ComputeStressAtom()
/* ---------------------------------------------------------------------- */
void ComputeStressAtom::init()
{
if (pairrequest) {
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;
else bondflag = 0;
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"stress/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning("More than one compute stress/atom");
}
/* ---------------------------------------------------------------------- */
void ComputeStressAtom::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeStressAtom::compute_peratom()
{
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 *ilist,*jlist,*numneigh,**firstneigh;
Pair::One one;
int i,j;
// grow stress array if necessary
invoked = 1;
// grow local stress array if necessary
if (atom->nmax > nmax) {
memory->destroy_2d_double_array(stress);
@ -133,199 +90,115 @@ void ComputeStressAtom::compute_peratom()
vector_atom = stress;
}
// clear stress array
// n includes ghosts only if newton flag is set
// npair includes ghosts if either newton flag is set
// b/c some bonds/dihedrals call pair::ev_tally with pairwise info
// nbond includes ghosts if newton_bond is set
// ntotal includes ghosts if either newton flag is set
int nlocal = atom->nlocal;
int npair = nlocal;
int nbond = nlocal;
int ntotal = nlocal;
if (force->newton) npair += atom->nghost;
if (force->newton_bond) nbond += atom->nghost;
if (force->newton) ntotal += atom->nghost;
if (force->newton) n = nlocal + atom->nghost;
else n = nlocal;
// clear local stress array
for (i = 0; i < n; i++) {
stress[i][0] = 0.0;
stress[i][1] = 0.0;
stress[i][2] = 0.0;
stress[i][3] = 0.0;
stress[i][4] = 0.0;
stress[i][5] = 0.0;
for (i = 0; i < ntotal; i++)
for (j = 0; j < 6; j++)
stress[i][j] = 0.0;
// add in per-atom contributions from each force
if (pairflag && force->pair) {
double **vatom = force->pair->vatom;
for (i = 0; i < npair; i++)
for (j = 0; j < 6; j++)
stress[i][j] += vatom[i][j];
}
// 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) {
// invoke half neighbor list (will copy or build if necessary)
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;
double **cutsq = force->pair->cutsq;
int newton_pair = force->newton_pair;
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int nall = nlocal + atom->nghost;
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;
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 {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,0,one);
fforce = one.fforce;
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;
stress[j][3] -= delx*dely*fforce;
stress[j][4] -= delx*delz*fforce;
stress[j][5] -= dely*delz*fforce;
}
}
}
}
if (bondflag && force->bond) {
double **vatom = force->bond->vatom;
for (i = 0; i < nbond; i++)
for (j = 0; j < 6; j++)
stress[i][j] += vatom[i][j];
}
// 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;
int *mask = atom->mask;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int newton_bond = force->newton_bond;
int type;
for (n = 0; n < nbondlist; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
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];
delz = x[i1][2] - x[i2][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
force->bond->single(type,rsq,i1,i2,0,fforce,eng);
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;
stress[i2][3] -= delx*dely*fforce;
stress[i2][4] -= delx*delz*fforce;
stress[i2][5] -= dely*delz*fforce;
}
}
if (angleflag && force->angle) {
double **vatom = force->angle->vatom;
for (i = 0; i < nbond; i++)
for (j = 0; j < 6; j++)
stress[i][j] += vatom[i][j];
}
// communicate stress between neighbor procs
if (dihedralflag && force->dihedral) {
double **vatom = force->dihedral->vatom;
for (i = 0; i < nbond; i++)
for (j = 0; j < 6; j++)
stress[i][j] += vatom[i][j];
}
if (improperflag && force->improper) {
double **vatom = force->improper->vatom;
for (i = 0; i < nbond; i++)
for (j = 0; j < 6; j++)
stress[i][j] += vatom[i][j];
}
// communicate ghost energy between neighbor procs
if (force->newton) comm->reverse_comm_compute(this);
// remove double counting
// zero virial of atoms not in group
// only do this after comm since ghost contributions must be included
for (i = 0; i < nlocal; i++) {
stress[i][0] *= 0.5;
stress[i][1] *= 0.5;
stress[i][2] *= 0.5;
stress[i][3] *= 0.5;
stress[i][4] *= 0.5;
stress[i][5] *= 0.5;
}
int *mask = atom->mask;
for (i = 0; i < nlocal; i++)
if (!(mask[i] & groupbit)) {
stress[i][0] = 0.0;
stress[i][1] = 0.0;
stress[i][2] = 0.0;
stress[i][3] = 0.0;
stress[i][4] = 0.0;
stress[i][5] = 0.0;
}
// include kinetic energy term for each atom in group
// mvv2e converts mv^2 to energy
if (kerequest) {
if (keflag) {
double **v = atom->v;
double *mass = atom->mass;
int *mask = atom->mask;
int *type = atom->type;
double mvv2e = force->mvv2e;
for (i = 0; i < nlocal; i++) {
double rmass;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
rmass = mvv2e * mass[type[i]];
stress[i][0] -= rmass*v[i][0]*v[i][0];
stress[i][1] -= rmass*v[i][1]*v[i][1];
stress[i][2] -= rmass*v[i][2]*v[i][2];
stress[i][3] -= rmass*v[i][0]*v[i][1];
stress[i][4] -= rmass*v[i][0]*v[i][2];
stress[i][5] -= rmass*v[i][1]*v[i][2];
stress[i][0] += rmass*v[i][0]*v[i][0];
stress[i][1] += rmass*v[i][1]*v[i][1];
stress[i][2] += rmass*v[i][2]*v[i][2];
stress[i][3] += rmass*v[i][0]*v[i][1];
stress[i][4] += rmass*v[i][0]*v[i][2];
stress[i][5] += rmass*v[i][1]*v[i][2];
}
}
// convert to pressure units (actually stress/volume = -pressure)
double nktv2p = -force->nktv2p;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
stress[i][0] *= nktv2p;
stress[i][1] *= nktv2p;
stress[i][2] *= nktv2p;
stress[i][3] *= nktv2p;
stress[i][4] *= nktv2p;
stress[i][5] *= nktv2p;
}
}
// convert to pressure units (actually stress/volume = pressure)
double nktv2p = force->nktv2p;
for (i = 0; i < nlocal; i++) {
stress[i][0] *= nktv2p;
stress[i][1] *= nktv2p;
stress[i][2] *= nktv2p;
stress[i][3] *= nktv2p;
stress[i][4] *= nktv2p;
stress[i][5] *= nktv2p;
}
}
/* ---------------------------------------------------------------------- */