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fix_peri_neigh.cpp
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Sun, Jun 2, 15:01

fix_peri_neigh.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA)
------------------------------------------------------------------------- */
#include <math.h>
#include "fix_peri_neigh.h"
#include "pair_peri_pmb.h"
#include "pair_peri_lps.h"
#include "pair_peri_ves.h"
#include "pair_peri_eps.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "comm.h"
#include "update.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "pair.h"
#include "lattice.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
Fix(lmp, narg, arg)
{
isPMB = isLPS = isVES = isEPS = 0;
if (force->pair_match("peri/pmb",1)) isPMB = 1;
if (force->pair_match("peri/lps",1)) isLPS = 1;
if (force->pair_match("peri/ves",1)) isVES = 1;
if (force->pair_match("peri/eps",1)) isEPS = 1;
restart_global = 1;
restart_peratom = 1;
first = 1;
// perform initial allocation of atom-based arrays
// register with atom class
// set maxpartner = 1 as placeholder
maxpartner = 1;
npartner = NULL;
partner = NULL;
deviatorextention = NULL;
deviatorBackextention = NULL;
deviatorPlasticextension = NULL;
lambdaValue = NULL;
r0 = NULL;
vinter = NULL;
wvolume = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
// initialize npartner to 0 so atom migration is OK the 1st time
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) npartner[i] = 0;
// set comm sizes needed by this fix
comm_forward = 1;
}
/* ---------------------------------------------------------------------- */
FixPeriNeigh::~FixPeriNeigh()
{
// unregister this fix so atom class doesn't invoke it any more
atom->delete_callback(id,0);
atom->delete_callback(id,1);
// delete locally stored arrays
memory->destroy(npartner);
memory->destroy(partner);
memory->destroy(deviatorextention);
memory->destroy(deviatorBackextention);
memory->destroy(deviatorPlasticextension);
memory->destroy(lambdaValue);
memory->destroy(r0);
memory->destroy(vinter);
memory->destroy(wvolume);
}
/* ---------------------------------------------------------------------- */
int FixPeriNeigh::setmask()
{
int mask = 0;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixPeriNeigh::init()
{
if (!first) return;
// need a full neighbor list once
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
// compute PD scale factor, stored in Atom class, used by DumpCFG
int nlocal = atom->nlocal;
double vone = 0.0;
for (int i = 0; i < nlocal; i++) vone += atom->vfrac[i];
double vave;
MPI_Allreduce(&vone,&vave,1,MPI_DOUBLE,MPI_SUM,world);
if (atom->natoms) vave /= atom->natoms;
if (vave > 0.0) atom->pdscale = 1.44 / pow(vave,1.0/3.0);
else atom->pdscale = 1.0;
}
/* ---------------------------------------------------------------------- */
void FixPeriNeigh::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ----------------------------------------------------------------------
For minimization: setup as with dynamics
------------------------------------------------------------------------- */
void FixPeriNeigh::min_setup(int vflag)
{
setup(vflag);
}
/* ----------------------------------------------------------------------
create initial list of neighbor partners via call to neighbor->build()
must be done in setup (not init) since fix init comes before neigh init
------------------------------------------------------------------------- */
void FixPeriNeigh::setup(int vflag)
{
int i,j,ii,jj,itype,jtype,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh;
int **firstneigh;
double **x = atom->x;
double *vfrac = atom->vfrac;
int *type = atom->type;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
// only build list of bonds on very first run
if (!first) return;
first = 0;
// build full neighbor list, will copy or build as necessary
neighbor->build_one(list);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// scan neighbor list to set maxpartner
Pair *anypair = force->pair_match("peri",0);
double **cutsq = anypair->cutsq;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
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]) npartner[i]++;
}
}
maxpartner = 0;
for (i = 0; i < nlocal; i++) maxpartner = MAX(maxpartner,npartner[i]);
int maxall;
MPI_Allreduce(&maxpartner,&maxall,1,MPI_INT,MPI_MAX,world);
maxpartner = maxall;
// realloc arrays with correct value for maxpartner
memory->destroy(partner);
memory->destroy(deviatorextention);
memory->destroy(deviatorBackextention);
memory->destroy(deviatorPlasticextension);
memory->destroy(lambdaValue);
memory->destroy(r0);
memory->destroy(npartner);
npartner = NULL;
partner = NULL;
deviatorextention = NULL;
deviatorBackextention = NULL;
deviatorPlasticextension = NULL;
lambdaValue = NULL;
r0 = NULL;
grow_arrays(atom->nmax);
// create partner list and r0 values from neighbor list
// compute vinter for each atom
for (i = 0; i < nlocal; i++) {
npartner[i] = 0;
vinter[i] = 0.0;
wvolume[i] = 0.0;
if (isEPS) lambdaValue[i] = 0.0;
}
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
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]) {
partner[i][npartner[i]] = tag[j];
if (isVES)
deviatorextention[i][npartner[i]] =
deviatorBackextention[i][npartner[i]] = 0.0;
if (isEPS)
deviatorPlasticextension[i][npartner[i]] = 0.0;
r0[i][npartner[i]] = sqrt(rsq);
npartner[i]++;
vinter[i] += vfrac[j];
}
}
}
// sanity check: does any atom appear twice in any neigborlist?
// should only be possible if using pbc and domain < 2*delta
if (domain->xperiodic || domain->yperiodic || domain->zperiodic) {
for (i = 0; i < nlocal; i++) {
jnum = npartner[i];
for (jj = 0; jj < jnum; jj++) {
for (int kk = jj+1; kk < jnum; kk++) {
if (partner[i][jj] == partner[i][kk])
error->one(FLERR,"Duplicate particle in PeriDynamic bond - "
"simulation box is too small");
}
}
}
}
// compute wvolume for each atom
double **x0 = atom->x0;
double half_lc = 0.5*(domain->lattice->xlattice);
double vfrac_scale;
PairPeriLPS *pairlps = NULL;
PairPeriVES *pairves = NULL;
PairPeriEPS *paireps = NULL;
if (isLPS)
pairlps = static_cast<PairPeriLPS*>(anypair);
else if (isVES)
pairves = static_cast<PairPeriVES*>(anypair);
else if (isEPS)
paireps = static_cast<PairPeriEPS*>(anypair);
for (i = 0; i < nlocal; i++) {
double xtmp0 = x0[i][0];
double ytmp0 = x0[i][1];
double ztmp0 = x0[i][2];
jnum = npartner[i];
itype = type[i];
// loop over partners of particle i
for (jj = 0; jj < jnum; jj++) {
// if bond already broken, skip this partner
if (partner[i][jj] == 0) continue;
// lookup local index of partner particle
j = atom->map(partner[i][jj]);
// skip if particle is "lost"
if (j < 0) continue;
double delx0 = xtmp0 - x0[j][0];
double dely0 = ytmp0 - x0[j][1];
double delz0 = ztmp0 - x0[j][2];
double rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
double delta = sqrt(cutsq[itype][jtype]);
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
// for PMB, influence = 1.0, otherwise invoke influence function
if (isPMB)
wvolume[i] += 1.0 * rsq0 * vfrac[j] * vfrac_scale;
else if (isLPS)
wvolume[i] += pairlps->influence_function(delx0,dely0,delz0) *
rsq0 * vfrac[j] * vfrac_scale;
else if (isVES)
wvolume[i] += pairves->influence_function(delx0,dely0,delz0) *
rsq0 * vfrac[j] * vfrac_scale;
else if (isEPS)
wvolume[i] += paireps->influence_function(delx0,dely0,delz0) *
rsq0 * vfrac[j] * vfrac_scale;
}
}
// communicate wvolume to ghosts
comm->forward_comm_fix(this);
// bond statistics
int n = 0;
for (i = 0; i < nlocal; i++) n += npartner[i];
int nall;
MPI_Allreduce(&n,&nall,1,MPI_INT,MPI_SUM,world);
if (comm->me == 0) {
if (screen) {
fprintf(screen,"Peridynamic bonds:\n");
fprintf(screen," total # of bonds = %d\n",nall);
fprintf(screen," bonds/atom = %g\n",(double)nall/atom->natoms);
}
if (logfile) {
fprintf(logfile,"Peridynamic bonds:\n");
fprintf(logfile," total # of bonds = %d\n",nall);
fprintf(logfile," bonds/atom = %g\n",(double)nall/atom->natoms);
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixPeriNeigh::memory_usage()
{
int nmax = atom->nmax;
int bytes = nmax * sizeof(int);
bytes += nmax*maxpartner * sizeof(tagint);
bytes += nmax*maxpartner * sizeof(double);
if (isVES) {
bytes += nmax*maxpartner * sizeof(double);
bytes += nmax*maxpartner * sizeof(double);
}
if (isEPS) {
bytes += nmax*maxpartner * sizeof(double);
bytes += nmax * sizeof(double);
}
bytes += nmax * sizeof(double);
bytes += nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixPeriNeigh::grow_arrays(int nmax)
{
memory->grow(npartner,nmax,"peri_neigh:npartner");
memory->grow(partner,nmax,maxpartner,"peri_neigh:partner");
if (isVES) {
memory->grow(deviatorextention,nmax,maxpartner,
"peri_neigh:deviatorextention");
memory->grow(deviatorBackextention,nmax,maxpartner,
"peri_neigh:deviatorBackextention");
}
if (isEPS) memory->grow(deviatorPlasticextension,nmax,maxpartner,
"peri_neigh:deviatorPlasticextension");
memory->grow(r0,nmax,maxpartner,"peri_neigh:r0");
if (isEPS) memory->grow(lambdaValue,nmax,"peri_neigh:lambdaValue");
memory->grow(vinter,nmax,"peri_neigh:vinter");
memory->grow(wvolume,nmax,"peri_neigh:wvolume");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixPeriNeigh::copy_arrays(int i, int j, int delflag)
{
npartner[j] = npartner[i];
for (int m = 0; m < npartner[j]; m++) {
partner[j][m] = partner[i][m];
if (isVES) {
deviatorextention[j][m] = deviatorextention[i][m];
deviatorBackextention[j][m] = deviatorBackextention[i][m];
}
if (isEPS)
deviatorPlasticextension[j][m] = deviatorPlasticextension[i][m];
r0[j][m] = r0[i][m];
}
if (isEPS) lambdaValue[j] = lambdaValue[i];
vinter[j] = vinter[i];
wvolume[j] = wvolume[i];
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixPeriNeigh::pack_exchange(int i, double *buf)
{
// compact list by eliminating partner = 0 entries
// set buf[0] after compaction
int m = 1;
for (int n = 0; n < npartner[i]; n++) {
if (partner[i][n] == 0) continue;
buf[m++] = partner[i][n];
if (isVES) {
buf[m++] = deviatorextention[i][n];
buf[m++] = deviatorBackextention[i][n];
}
if (isEPS) buf[m++] = deviatorPlasticextension[i][n];
buf[m++] = r0[i][n];
}
if (isVES) buf[0] = m/4;
else if (isEPS) buf[0] = m/3;
else buf[0] = m/2;
if (isEPS) buf[m++] = lambdaValue[i];
buf[m++] = vinter[i];
buf[m++] = wvolume[i];
return m;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixPeriNeigh::unpack_exchange(int nlocal, double *buf)
{
int m = 0;
npartner[nlocal] = static_cast<int> (buf[m++]);
for (int n = 0; n < npartner[nlocal]; n++) {
partner[nlocal][n] = static_cast<tagint> (buf[m++]);
if (isVES) {
deviatorextention[nlocal][n] = buf[m++];
deviatorBackextention[nlocal][n] = buf[m++];
}
if (isEPS) deviatorPlasticextension[nlocal][n] = buf[m++];
r0[nlocal][n] = buf[m++];
}
if (isEPS) lambdaValue[nlocal] = buf[m++];
vinter[nlocal] = buf[m++];
wvolume[nlocal] = buf[m++];
return m;
}
/* ---------------------------------------------------------------------- */
int FixPeriNeigh::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = wvolume[j];
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixPeriNeigh::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++)
wvolume[i] = buf[m++];
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixPeriNeigh::write_restart(FILE *fp)
{
int n = 0;
double list[2];
list[n++] = first;
list[n++] = maxpartner;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixPeriNeigh::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
first = static_cast<int> (list[n++]);
maxpartner = static_cast<int> (list[n++]);
// grow 2D arrays now, cannot change size of 2nd array index later
grow_arrays(atom->nmax);
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixPeriNeigh::pack_restart(int i, double *buf)
{
int m = 0;
if (isVES) buf[m++] = 4*npartner[i] + 4;
else if (isEPS) buf[m++] = 3*npartner[i] + 5;
else buf[m++] = 2*npartner[i] + 4;
buf[m++] = npartner[i];
for (int n = 0; n < npartner[i]; n++) {
buf[m++] = partner[i][n];
if (isVES) {
buf[m++] = deviatorextention[i][n];
buf[m++] = deviatorBackextention[i][n];
}
if (isEPS) buf[m++] = deviatorPlasticextension[i][n];
buf[m++] = r0[i][n];
}
if (isEPS) buf[m++] = lambdaValue[i];
buf[m++] = vinter[i];
buf[m++] = wvolume[i];
return m;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixPeriNeigh::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
npartner[nlocal] = static_cast<int> (extra[nlocal][m++]);
for (int n = 0; n < npartner[nlocal]; n++) {
partner[nlocal][n] = static_cast<tagint> (extra[nlocal][m++]);
if (isVES) {
deviatorextention[nlocal][n] = extra[nlocal][m++];
deviatorBackextention[nlocal][n] = extra[nlocal][m++];
}
if (isEPS) deviatorPlasticextension[nlocal][n] = extra[nlocal][m++];
r0[nlocal][n] = extra[nlocal][m++];
}
if (isEPS) lambdaValue[nlocal] = extra[nlocal][m++];
vinter[nlocal] = extra[nlocal][m++];
wvolume[nlocal] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixPeriNeigh::maxsize_restart()
{
if (isVES) return 4*maxpartner + 4;
if (isEPS) return 3*maxpartner + 5;
return 2*maxpartner + 4;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixPeriNeigh::size_restart(int nlocal)
{
if (isVES) return 4*npartner[nlocal] + 4;
if (isEPS) return 3*npartner[nlocal] + 5;
return 2*npartner[nlocal] + 4;
}

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