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fix_shear_history.cpp
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Sun, Jul 13, 11:46

fix_shear_history.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.
------------------------------------------------------------------------- */
#include "string.h"
#include "stdio.h"
#include "fix_shear_history.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "force.h"
#include "pair.h"
#include "update.h"
#include "modify.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXTOUCH 15
/* ---------------------------------------------------------------------- */
FixShearHistory::FixShearHistory(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
restart_peratom = 1;
// perform initial allocation of atom-based arrays
// register with atom class
npartner = NULL;
partner = NULL;
shearpartner = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
// initialize npartner to 0 so neighbor list creation is OK the 1st time
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) npartner[i] = 0;
}
/* ---------------------------------------------------------------------- */
FixShearHistory::~FixShearHistory()
{
// 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->sfree(npartner);
memory->destroy_2d_int_array(partner);
memory->destroy_3d_double_array(shearpartner);
}
/* ---------------------------------------------------------------------- */
int FixShearHistory::setmask()
{
int mask = 0;
mask |= PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixShearHistory::init()
{
if (atom->tag_enable == 0)
error->all("Pair style granular with history requires atoms have IDs");
}
/* ----------------------------------------------------------------------
copy shear partner info from neighbor lists to atom arrays
so can be exchanged with atoms
------------------------------------------------------------------------- */
void FixShearHistory::pre_exchange()
{
int i,j,ii,jj,m,inum,jnum;
int *ilist,*jlist,*numneigh,**firstneigh;
int *touch,**firsttouch;
double *shear,*allshear,**firstshear;
// zero npartners for all current atoms
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) npartner[i] = 0;
// copy shear info from neighbor list atoms to atom arrays
int *tag = atom->tag;
NeighList *list = pair->list;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
firsttouch = list->listgranhistory->firstneigh;
firstshear = list->listgranhistory->firstdouble;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
jlist = firstneigh[i];
allshear = firstshear[i];
jnum = numneigh[i];
touch = firsttouch[i];
for (jj = 0; jj < jnum; jj++) {
if (touch[jj]) {
shear = &allshear[3*jj];
j = jlist[jj];
if (npartner[i] < MAXTOUCH) {
m = npartner[i];
partner[i][m] = tag[j];
shearpartner[i][m][0] = shear[0];
shearpartner[i][m][1] = shear[1];
shearpartner[i][m][2] = shear[2];
}
npartner[i]++;
if (j < nlocal) {
if (npartner[j] < MAXTOUCH) {
m = npartner[j];
partner[j][m] = tag[i];
shearpartner[j][m][0] = -shear[0];
shearpartner[j][m][1] = -shear[1];
shearpartner[j][m][2] = -shear[2];
}
npartner[j]++;
}
}
}
}
// test for too many touching neighbors
int flag = 0;
for (i = 0; i < nlocal; i++)
if (npartner[i] >= MAXTOUCH) flag = 1;
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all("Too many touching neighbors - boost MAXTOUCH");
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixShearHistory::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax * sizeof(int);
bytes += nmax*MAXTOUCH * sizeof(int);
bytes += nmax*MAXTOUCH*3 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixShearHistory::grow_arrays(int nmax)
{
npartner = (int *) memory->srealloc(npartner,nmax*sizeof(int),
"shear_history:npartner");
partner = memory->grow_2d_int_array(partner,nmax,MAXTOUCH,
"shear_history:partner");
shearpartner =
memory->grow_3d_double_array(shearpartner,nmax,MAXTOUCH,3,
"shear_history:shearpartner");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixShearHistory::copy_arrays(int i, int j)
{
npartner[j] = npartner[i];
for (int m = 0; m < npartner[j]; m++) {
partner[j][m] = partner[i][m];
shearpartner[j][m][0] = shearpartner[i][m][0];
shearpartner[j][m][1] = shearpartner[i][m][1];
shearpartner[j][m][2] = shearpartner[i][m][2];
}
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixShearHistory::pack_exchange(int i, double *buf)
{
int m = 0;
buf[m++] = npartner[i];
for (int n = 0; n < npartner[i]; n++) {
buf[m++] = partner[i][n];
buf[m++] = shearpartner[i][n][0];
buf[m++] = shearpartner[i][n][1];
buf[m++] = shearpartner[i][n][2];
}
return m;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixShearHistory::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<int> (buf[m++]);
shearpartner[nlocal][n][0] = buf[m++];
shearpartner[nlocal][n][1] = buf[m++];
shearpartner[nlocal][n][2] = buf[m++];
}
return m;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixShearHistory::pack_restart(int i, double *buf)
{
int m = 0;
buf[m++] = 4*npartner[i] + 2;
buf[m++] = npartner[i];
for (int n = 0; n < npartner[i]; n++) {
buf[m++] = partner[i][n];
buf[m++] = shearpartner[i][n][0];
buf[m++] = shearpartner[i][n][1];
buf[m++] = shearpartner[i][n][2];
}
return m;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixShearHistory::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<int> (extra[nlocal][m++]);
shearpartner[nlocal][n][0] = extra[nlocal][m++];
shearpartner[nlocal][n][1] = extra[nlocal][m++];
shearpartner[nlocal][n][2] = extra[nlocal][m++];
}
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixShearHistory::maxsize_restart()
{
return 4*MAXTOUCH + 2;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixShearHistory::size_restart(int nlocal)
{
return 4*npartner[nlocal] + 2;
}

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