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lammps/src/fix_store.cpp
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fix_store.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 <stdlib.h>
#include <string.h>
#include "fix_store.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{UNKNOWN,GLOBAL,PERATOM};
/* ---------------------------------------------------------------------- */
FixStore::FixStore(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
if (narg != 6) error->all(FLERR,"Illegal fix store command");
// 4th arg determines GLOBAL vs PERATOM values
// syntax: id group style global nrow ncol
// Nrow by Ncol array of global values
// Ncol = 1 is vector, Ncol > 1 is array
// syntax: id group style peratom 0/1 nvalues
// 0/1 flag = not-store or store peratom values in restart file
// nvalues = # of peratom values, N = 1 is vector, N > 1 is array
nvalues = vecflag = 0;
flavor = UNKNOWN;
if (strcmp(arg[3],"global") == 0) flavor = GLOBAL;
else if (strcmp(arg[3],"peratom") == 0) flavor = PERATOM;
else error->all(FLERR,"Illegal fix store command");
// GLOBAL values are always written to restart file
// PERATOM restart_peratom is set by caller
if (flavor == GLOBAL) {
restart_global = 1;
nrow = force->inumeric(FLERR,arg[4]);
ncol = force->inumeric(FLERR,arg[5]);
if (nrow <= 0 || ncol <= 0)
error->all(FLERR,"Illegal fix store command");
vecflag = 0;
if (ncol == 1) vecflag = 1;
}
if (flavor == PERATOM) {
restart_peratom = force->inumeric(FLERR,arg[4]);
nvalues = force->inumeric(FLERR,arg[5]);
if (restart_peratom < 0 or restart_peratom > 1 || nvalues <= 0)
error->all(FLERR,"Illegal fix store command");
vecflag = 0;
if (nvalues == 1) vecflag = 1;
}
vstore = NULL;
astore = NULL;
// allocate vector or array and restart buffer rbuf
// for PERATOM, register with Atom class
if (flavor == GLOBAL) {
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
else memory->create(astore,nrow,ncol,"fix/store:astore");
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
}
if (flavor == PERATOM) {
grow_arrays(atom->nmax);
atom->add_callback(0);
if (restart_peratom) atom->add_callback(1);
rbuf = NULL;
}
// zero the storage
// PERATOM may be comm->exchanged before filled by caller
if (flavor == GLOBAL) {
if (vecflag)
for (int i = 0; i < nrow; i++) vstore[i] = 0.0;
else
for (int i = 0; i < nrow; i++)
for (int j = 0; j < ncol; j++)
astore[i][j] = 0.0;
}
if (flavor == PERATOM) {
int nlocal = atom->nlocal;
if (vecflag)
for (int i = 0; i < nlocal; i++) vstore[i] = 0.0;
else
for (int i = 0; i < nlocal; i++)
for (int j = 0; j < nvalues; j++)
astore[i][j] = 0.0;
}
}
/* ---------------------------------------------------------------------- */
FixStore::~FixStore()
{
// unregister callbacks to this fix from Atom class
if (flavor == PERATOM) {
atom->delete_callback(id,0);
if (restart_peratom) atom->delete_callback(id,1);
}
memory->destroy(vstore);
memory->destroy(astore);
memory->destroy(rbuf);
}
/* ---------------------------------------------------------------------- */
int FixStore::setmask()
{
int mask = 0;
return mask;
}
/* ----------------------------------------------------------------------
reset size of global vector/array
invoked by caller if size is unknown at time this fix is instantiated
caller will do subsequent initialization
------------------------------------------------------------------------- */
void FixStore::reset_global(int nrow_caller, int ncol_caller)
{
memory->destroy(vstore);
memory->destroy(astore);
memory->destroy(rbuf);
vstore = NULL;
astore = NULL;
vecflag = 0;
if (ncol_caller == 1) vecflag = 1;
nrow = nrow_caller;
ncol = ncol_caller;
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
else memory->create(astore,nrow,ncol,"fix/store:astore");
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
}
/* ----------------------------------------------------------------------
write global array to restart file
------------------------------------------------------------------------- */
void FixStore::write_restart(FILE *fp)
{
// fill rbuf with size and vec/array values
rbuf[0] = nrow;
rbuf[1] = ncol;
if (vecflag) memcpy(&rbuf[2],vstore,nrow*sizeof(double));
else memcpy(&rbuf[2],&astore[0][0],nrow*ncol*sizeof(double));
int n = nrow*ncol + 2;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(rbuf,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use global array from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixStore::restart(char *buf)
{
// first 2 values in buf are vec/array sizes
double *dbuf = (double *) buf;
int nrow_restart = dbuf[0];
int ncol_restart = dbuf[1];
// if size of vec/array has changed,
// means the restart file is setting size of vec or array and doing init
// because caller did not know size at time this fix was instantiated
// reallocate vstore or astore accordingly
if (nrow != nrow_restart || ncol != ncol_restart) {
memory->destroy(vstore);
memory->destroy(astore);
memory->destroy(rbuf);
vstore = NULL;
astore = NULL;
vecflag = 0;
if (ncol_restart == 1) vecflag = 1;
nrow = nrow_restart;
ncol = ncol_restart;
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
else memory->create(astore,nrow,ncol,"fix/store:astore");
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
}
int n = nrow*ncol;
if (vecflag) memcpy(vstore,&dbuf[2],n*sizeof(double));
else memcpy(&astore[0][0],&dbuf[2],n*sizeof(double));
}
/* ----------------------------------------------------------------------
allocate atom-based array
------------------------------------------------------------------------- */
void FixStore::grow_arrays(int nmax)
{
if (vecflag) memory->grow(vstore,nmax,"store:vstore");
else memory->grow(astore,nmax,nvalues,"store:astore");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixStore::copy_arrays(int i, int j, int delflag)
{
if (vecflag) vstore[j] = vstore[i];
else
for (int m = 0; m < nvalues; m++)
astore[j][m] = astore[i][m];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixStore::pack_exchange(int i, double *buf)
{
if (vecflag) buf[0] = vstore[i];
else
for (int m = 0; m < nvalues; m++)
buf[m] = astore[i][m];
return nvalues;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixStore::unpack_exchange(int nlocal, double *buf)
{
if (vecflag) vstore[nlocal] = buf[0];
else
for (int m = 0; m < nvalues; m++)
astore[nlocal][m] = buf[m];
return nvalues;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixStore::pack_restart(int i, double *buf)
{
buf[0] = nvalues+1;
if (vecflag) buf[1] = vstore[i];
else
for (int m = 0; m < nvalues; m++)
buf[m+1] = astore[i][m];
return nvalues+1;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixStore::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++;
if (vecflag) vstore[nlocal] = extra[nlocal][m];
else
for (int i = 0; i < nvalues; i++)
astore[nlocal][i] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixStore::maxsize_restart()
{
return nvalues+1;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixStore::size_restart(int nlocal)
{
return nvalues+1;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double FixStore::memory_usage()
{
double bytes = 0.0;
if (flavor == GLOBAL) bytes += nrow*ncol * sizeof(double);
if (flavor == PERATOM) bytes += atom->nmax*nvalues * sizeof(double);
return bytes;
}
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