forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@711 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
03c056ccca
commit
c2515c1083
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@ -72,10 +72,11 @@ void ComputeEpairAtom::init()
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void ComputeEpairAtom::compute_peratom()
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{
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int i,j,k,n,itype,jtype,numneigh;
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int i,j,k,n,itype,jtype,numneigh,iflag;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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double factor_coul,factor_lj,e;
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double factor_coul,factor_lj,eng;
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int *neighs;
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Pair::One one;
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// grow energy array if necessary
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@ -90,8 +91,11 @@ void ComputeEpairAtom::compute_peratom()
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// clear energy array
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// n includes ghosts only if newton_pair flag is set
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if (force->newton_pair) n = atom->nlocal + atom->nghost;
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else n = atom->nlocal;
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int nlocal = atom->nlocal;
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int newton_pair = force->newton_pair;
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if (newton_pair) n = nlocal + atom->nghost;
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else n = nlocal;
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for (i = 0; i < n; i++) energy[i] = 0.0;
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@ -99,30 +103,30 @@ void ComputeEpairAtom::compute_peratom()
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if (!neighbor->half_every) neighbor->build_half();
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// compute pairwise energy for all atoms via pair->single()
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// ignore compute group, since using half neighbor list
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// compute pairwise energy for atoms via pair->single()
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// if neither atom is in compute group, skip that pair
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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double **cutsq = force->pair->cutsq;
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double **x = atom->x;
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int *mask = atom->mask;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int nall = atom->nlocal + atom->nghost;
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Pair::One one;
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int nall = nlocal + atom->nghost;
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for (i = 0; i < nlocal; i++) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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iflag = mask[i] & groupbit;
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neighs = neighbor->firstneigh[i];
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numneigh = neighbor->numneigh[i];
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for (k = 0; k < numneigh; k++) {
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j = neighs[k];
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if (iflag == 0 && (mask[j] & groupbit) == 0) continue;
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if (j < nall) factor_coul = factor_lj = 1.0;
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else {
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@ -139,30 +143,30 @@ void ComputeEpairAtom::compute_peratom()
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if (rsq < cutsq[itype][jtype]) {
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force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,1,one);
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e = one.eng_coul + one.eng_vdwl;
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energy[i] += e;
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energy[j] += e;
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eng = one.eng_coul + one.eng_vdwl;
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energy[i] += eng;
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if (newton_pair || j < nlocal) energy[j] += eng;
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}
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}
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}
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// communicate energy between neigchbor procs
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if (force->newton_pair) comm->reverse_comm_compute(this);
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if (newton_pair) comm->reverse_comm_compute(this);
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// remove double counting of per-atom energy
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for (i = 0; i < nlocal; i++) energy[i] *= 0.5;
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// for EAM, include embedding function contribution to energy
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// only for atoms in compute group
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if (eamstyle) {
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int *type = atom->type;
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double etmp = 0.0;
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for (i = 0; i < nlocal; i++) {
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force->pair->single_embed(i,type[i],etmp);
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energy[i] += etmp;
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if (mask[i] & groupbit) {
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force->pair->single_embed(i,type[i],eng);
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energy[i] += eng;
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}
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}
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}
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}
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@ -19,7 +19,9 @@
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#include "comm.h"
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#include "update.h"
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#include "force.h"
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#include "bond.h"
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#include "pair.h"
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#include "domain.h"
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#include "memory.h"
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#include "error.h"
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@ -33,13 +35,37 @@ using namespace LAMMPS_NS;
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ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg != 3) error->all("Illegal compute stress/atom command");
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if (narg < 3) error->all("Illegal compute stress/atom command");
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peratom_flag = 1;
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size_peratom = 6;
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comm_reverse = 6;
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neigh_half_once = 1;
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// process args
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kerequest = pairrequest = bondrequest = 1;
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"ke") == 0) {
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if (iarg+2 > narg) error->all("Illegal compute ebond/atom command");
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if (strcmp(arg[iarg+1],"yes") == 0) kerequest = 1;
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else if (strcmp(arg[iarg+1],"no") == 0) kerequest = 0;
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iarg += 2;
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} else if (strcmp(arg[iarg],"pair") == 0) {
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if (iarg+2 > narg) error->all("Illegal compute ebond/atom command");
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if (strcmp(arg[iarg+1],"yes") == 0) pairrequest = 1;
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else if (strcmp(arg[iarg+1],"no") == 0) pairrequest = 0;
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iarg += 2;
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} else if (strcmp(arg[iarg],"bond") == 0) {
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if (iarg+2 > narg) error->all("Illegal compute ebond/atom command");
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if (strcmp(arg[iarg+1],"yes") == 0) bondrequest = 1;
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else if (strcmp(arg[iarg+1],"no") == 0) bondrequest = 0;
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iarg += 2;
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} else error->all("Illegal compute ebond/atom command");
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}
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nmax = 0;
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stress = NULL;
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}
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@ -55,8 +81,14 @@ ComputeStressAtom::~ComputeStressAtom()
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void ComputeStressAtom::init()
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{
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if (force->pair == NULL || force->pair->single_enable == 0)
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error->all("Pair style does not support computing per-atom stress");
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if (pairrequest) {
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if (force->pair == NULL || force->pair->single_enable == 0)
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error->all("Pair style does not support computing per-atom stress");
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pairflag = 1;
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} else pairflag = 0;
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if (bondrequest && force->bond) bondflag = 1;
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else bondflag = 0;
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int count = 0;
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for (int i = 0; i < modify->ncompute; i++)
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@ -69,8 +101,8 @@ void ComputeStressAtom::init()
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void ComputeStressAtom::compute_peratom()
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{
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int i,j,k,n,itype,jtype,numneigh;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int i,j,k,n,i1,i2,itype,jtype,numneigh,iflag;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq,eng;
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double factor_coul,factor_lj,fforce,rmass;
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int *neighs;
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Pair::One one;
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@ -86,10 +118,12 @@ void ComputeStressAtom::compute_peratom()
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}
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// clear stress array
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// n includes ghosts only if newton_pair flag is set
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// n includes ghosts only if newton flag is set
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if (force->newton_pair) n = atom->nlocal + atom->nghost;
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else n = atom->nlocal;
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int nlocal = atom->nlocal;
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if (force->newton) n = nlocal + atom->nghost;
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else n = nlocal;
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for (i = 0; i < n; i++) {
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stress[i][0] = 0.0;
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@ -100,73 +134,123 @@ void ComputeStressAtom::compute_peratom()
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stress[i][5] = 0.0;
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}
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// if needed, build a half neighbor list
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// compute pairwise stress for atoms via pair->single()
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// if neither atom is in compute group, skip that pair
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if (!neighbor->half_every) neighbor->build_half();
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if (pairflag) {
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// compute pairwise stress for all atoms via pair->single()
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// use half neighbor list
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// if needed, build a half neighbor list
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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double **cutsq = force->pair->cutsq;
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if (!neighbor->half_every) neighbor->build_half();
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double **x = atom->x;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int nall = atom->nlocal + atom->nghost;
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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double **cutsq = force->pair->cutsq;
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int newton_pair = force->newton_pair;
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for (i = 0; i < nlocal; i++) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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neighs = neighbor->firstneigh[i];
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numneigh = neighbor->numneigh[i];
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for (k = 0; k < numneigh; k++) {
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j = neighs[k];
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double **x = atom->x;
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int *mask = atom->mask;
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int *type = atom->type;
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int nall = nlocal + atom->nghost;
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if (j < nall) factor_coul = factor_lj = 1.0;
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else {
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factor_coul = special_coul[j/nall];
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factor_lj = special_lj[j/nall];
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j %= nall;
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}
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for (i = 0; i < nlocal; i++) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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iflag = mask[i] & groupbit;
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neighs = neighbor->firstneigh[i];
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numneigh = neighbor->numneigh[i];
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for (k = 0; k < numneigh; k++) {
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j = neighs[k];
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if (iflag == 0 && (mask[j] & groupbit) == 0) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,0,one);
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fforce = one.fforce;
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stress[i][0] -= delx*delx*fforce;
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stress[i][1] -= dely*dely*fforce;
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stress[i][2] -= delz*delz*fforce;
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stress[i][3] -= delx*dely*fforce;
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stress[i][4] -= delx*delz*fforce;
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stress[i][5] -= dely*delz*fforce;
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if (force->newton_pair || j < nlocal) {
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stress[j][0] -= delx*delx*fforce;
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stress[j][1] -= dely*dely*fforce;
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stress[j][2] -= delz*delz*fforce;
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stress[j][3] -= delx*dely*fforce;
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stress[j][4] -= delx*delz*fforce;
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stress[j][5] -= dely*delz*fforce;
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if (j < nall) factor_coul = factor_lj = 1.0;
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else {
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factor_coul = special_coul[j/nall];
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factor_lj = special_lj[j/nall];
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j %= nall;
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}
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,0,one);
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fforce = one.fforce;
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stress[i][0] -= delx*delx*fforce;
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stress[i][1] -= dely*dely*fforce;
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stress[i][2] -= delz*delz*fforce;
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stress[i][3] -= delx*dely*fforce;
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stress[i][4] -= delx*delz*fforce;
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stress[i][5] -= dely*delz*fforce;
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if (newton_pair || j < nlocal) {
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stress[j][0] -= delx*delx*fforce;
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stress[j][1] -= dely*dely*fforce;
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stress[j][2] -= delz*delz*fforce;
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stress[j][3] -= delx*dely*fforce;
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stress[j][4] -= delx*delz*fforce;
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stress[j][5] -= dely*delz*fforce;
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}
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}
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}
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}
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}
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// compute bond stress for atoms via bond->single()
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// if neither atom is in compute group, skip that bond
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if (bondflag) {
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double **x = atom->x;
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int *mask = atom->mask;
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int **bondlist = neighbor->bondlist;
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int nbondlist = neighbor->nbondlist;
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int newton_bond = force->newton_bond;
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int type;
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for (n = 0; n < nbondlist; n++) {
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i1 = bondlist[n][0];
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i2 = bondlist[n][1];
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type = bondlist[n][2];
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if ((mask[i1] & groupbit) == 0 && (mask[i2] & groupbit) == 0) continue;
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delx = x[i1][0] - x[i2][0];
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dely = x[i1][1] - x[i2][1];
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delz = x[i1][2] - x[i2][2];
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domain->minimum_image(delx,dely,delz);
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rsq = delx*delx + dely*dely + delz*delz;
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force->bond->single(type,rsq,i1,i2,0,fforce,eng);
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stress[i1][0] -= delx*delx*fforce;
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stress[i1][1] -= dely*dely*fforce;
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stress[i1][2] -= delz*delz*fforce;
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stress[i1][3] -= delx*dely*fforce;
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stress[i1][4] -= delx*delz*fforce;
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stress[i1][5] -= dely*delz*fforce;
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if (newton_bond || i2 < nlocal) {
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stress[i2][0] -= delx*delx*fforce;
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stress[i2][1] -= dely*dely*fforce;
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stress[i2][2] -= delz*delz*fforce;
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stress[i2][3] -= delx*dely*fforce;
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stress[i2][4] -= delx*delz*fforce;
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stress[i2][5] -= dely*delz*fforce;
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}
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}
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}
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// communicate stress between neighbor procs
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if (force->newton_pair) comm->reverse_comm_compute(this);
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if (force->newton) comm->reverse_comm_compute(this);
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// remove double counting of per-atom stress
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// remove double counting
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for (i = 0; i < nlocal; i++) {
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stress[i][0] *= 0.5;
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@ -177,21 +261,27 @@ void ComputeStressAtom::compute_peratom()
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stress[i][5] *= 0.5;
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}
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// include kinetic energy term for each atom
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// include kinetic energy term for each atom in group
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// mvv2e converts mv^2 to energy
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double **v = atom->v;
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double *mass = atom->mass;
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double mvv2e = force->mvv2e;
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for (i = 0; i < nlocal; i++) {
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rmass = mvv2e * mass[type[i]];
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stress[i][0] -= rmass*v[i][0]*v[i][0];
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stress[i][1] -= rmass*v[i][1]*v[i][1];
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stress[i][2] -= rmass*v[i][2]*v[i][2];
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stress[i][3] -= rmass*v[i][0]*v[i][1];
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stress[i][4] -= rmass*v[i][0]*v[i][2];
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stress[i][5] -= rmass*v[i][1]*v[i][2];
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if (kerequest) {
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double **v = atom->v;
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double *mass = atom->mass;
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int *mask = atom->mask;
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int *type = atom->type;
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double mvv2e = force->mvv2e;
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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rmass = mvv2e * mass[type[i]];
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stress[i][0] -= rmass*v[i][0]*v[i][0];
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stress[i][1] -= rmass*v[i][1]*v[i][1];
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stress[i][2] -= rmass*v[i][2]*v[i][2];
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stress[i][3] -= rmass*v[i][0]*v[i][1];
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stress[i][4] -= rmass*v[i][0]*v[i][2];
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stress[i][5] -= rmass*v[i][1]*v[i][2];
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}
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}
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}
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// convert to pressure units (actually stress/volume = pressure)
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@ -30,7 +30,10 @@ class ComputeStressAtom : public Compute {
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int memory_usage();
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private:
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int pairrequest,bondrequest,kerequest;
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int pairflag,bondflag;
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int nmax;
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double **stress;
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};
|
||||
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ enum{TAG,MOL,TYPE,X,Y,Z,XS,YS,ZS,XU,YU,ZU,IX,IY,IZ,
|
|||
VX,VY,VZ,FX,FY,FZ,
|
||||
Q,MUX,MUY,MUZ,
|
||||
QUATW,QUATI,QUATJ,QUATK,TQX,TQY,TQZ,
|
||||
EPAIR,KE,ETOTAL,CENTRO,SXX,SYY,SZZ,SXY,SXZ,SYZ,
|
||||
EPAIR,EBOND,KE,ETOTAL,CENTRO,SXX,SYY,SZZ,SXY,SXZ,SYZ,
|
||||
COMPUTE};
|
||||
enum{LT,LE,GT,GE,EQ,NEQ};
|
||||
enum{INT,DOUBLE};
|
||||
|
|
@ -57,9 +57,11 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
|
|||
|
||||
// flags, IDs, and memory for compute objects dump may create
|
||||
|
||||
index_epair = index_ke = index_etotal = index_centro = index_stress = -1;
|
||||
index_epair = index_ebond = index_ke =
|
||||
index_etotal = index_centro = index_stress = -1;
|
||||
|
||||
style_epair = "epair/atom";
|
||||
style_ebond = "ebond/atom";
|
||||
style_ke = "ke/atom";
|
||||
style_etotal = "etotal/atom";
|
||||
style_centro = "centro/atom";
|
||||
|
|
@ -79,6 +81,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
|
|||
// create the requested Computes
|
||||
|
||||
if (index_epair >= 0) create_compute(style_epair,NULL);
|
||||
if (index_ebond >= 0) create_compute(style_ebond,NULL);
|
||||
if (index_ke >= 0) create_compute(style_ke,NULL);
|
||||
if (index_etotal >= 0) create_compute(style_etotal,style_epair);
|
||||
if (index_centro >= 0) create_compute(style_centro,NULL);
|
||||
|
|
@ -122,6 +125,7 @@ DumpCustom::~DumpCustom()
|
|||
// delete Compute classes if dump custom created them
|
||||
|
||||
if (index_epair >= 0) modify->delete_compute(id_compute[index_epair]);
|
||||
if (index_ebond >= 0) modify->delete_compute(id_compute[index_ebond]);
|
||||
if (index_ke >= 0) modify->delete_compute(id_compute[index_ke]);
|
||||
if (index_etotal >= 0) modify->delete_compute(id_compute[index_etotal]);
|
||||
if (index_centro >= 0) modify->delete_compute(id_compute[index_centro]);
|
||||
|
|
@ -430,6 +434,9 @@ int DumpCustom::count()
|
|||
} else if (thresh_array[ithresh] == EPAIR) {
|
||||
ptr = compute[index_epair]->scalar_atom;
|
||||
nstride = 1;
|
||||
} else if (thresh_array[ithresh] == EBOND) {
|
||||
ptr = compute[index_ebond]->scalar_atom;
|
||||
nstride = 1;
|
||||
} else if (thresh_array[ithresh] == KE) {
|
||||
ptr = compute[index_ke]->scalar_atom;
|
||||
nstride = 1;
|
||||
|
|
@ -701,6 +708,10 @@ void DumpCustom::parse_fields(int narg, char **arg)
|
|||
pack_choice[i] = &DumpCustom::pack_epair;
|
||||
vtype[i] = DOUBLE;
|
||||
index_epair = add_compute(style_epair,1);
|
||||
} else if (strcmp(arg[iarg],"ebond") == 0) {
|
||||
pack_choice[i] = &DumpCustom::pack_ebond;
|
||||
vtype[i] = DOUBLE;
|
||||
index_ebond = add_compute(style_ebond,1);
|
||||
} else if (strcmp(arg[iarg],"ke") == 0) {
|
||||
pack_choice[i] = &DumpCustom::pack_ke;
|
||||
vtype[i] = DOUBLE;
|
||||
|
|
@ -943,6 +954,12 @@ int DumpCustom::modify_param(int narg, char **arg)
|
|||
index_epair = add_compute(style_epair,1);
|
||||
create_compute(style_epair,NULL);
|
||||
}
|
||||
} else if (strcmp(arg[1],"ebond") == 0) {
|
||||
thresh_array[nthresh] = EBOND;
|
||||
if (index_ebond < 0) {
|
||||
index_ebond = add_compute(style_ebond,1);
|
||||
create_compute(style_ebond,NULL);
|
||||
}
|
||||
} else if (strcmp(arg[1],"ke") == 0) {
|
||||
thresh_array[nthresh] = KE;
|
||||
if (index_ke < 0) {
|
||||
|
|
@ -1591,6 +1608,20 @@ void DumpCustom::pack_epair(int n)
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustom::pack_ebond(int n)
|
||||
{
|
||||
double *ebond = compute[index_ebond]->scalar_atom;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (choose[i]) {
|
||||
buf[n] = ebond[i];
|
||||
n += size_one;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustom::pack_ke(int n)
|
||||
{
|
||||
double *ke = compute[index_ke]->scalar_atom;
|
||||
|
|
|
|||
|
|
@ -50,8 +50,9 @@ class DumpCustom : public Dump {
|
|||
|
||||
// index = where keyword's Compute is in list
|
||||
// style = style of Compute object
|
||||
int index_epair,index_ke,index_etotal,index_centro,index_stress;
|
||||
char *style_epair,*style_ke,*style_etotal,*style_centro,*style_stress;
|
||||
int index_epair,index_ebond,index_ke,index_etotal,index_centro,index_stress;
|
||||
char *style_epair,*style_ebond,*style_ke,*style_etotal;
|
||||
char *style_centro,*style_stress;
|
||||
|
||||
// private methods
|
||||
|
||||
|
|
@ -117,6 +118,7 @@ class DumpCustom : public Dump {
|
|||
void pack_etotal(int);
|
||||
void pack_ke(int);
|
||||
void pack_epair(int);
|
||||
void pack_ebond(int);
|
||||
void pack_centro(int);
|
||||
void pack_sxx(int);
|
||||
void pack_syy(int);
|
||||
|
|
|
|||
Loading…
Reference in New Issue