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dump_cfg_gz.cpp
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Mon, Jun 17, 19:55

dump_cfg_gz.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 "dump_cfg_gz.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "update.h"
#include <string.h>
using namespace LAMMPS_NS;
#define UNWRAPEXPAND 10.0
DumpCFGGZ::DumpCFGGZ(LAMMPS *lmp, int narg, char **arg) :
DumpCFG(lmp, narg, arg)
{
gzFp = NULL;
if (!compressed)
error->all(FLERR,"Dump cfg/gz only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpCFGGZ::~DumpCFGGZ()
{
if (gzFp) gzclose(gzFp);
gzFp = NULL;
fp = NULL;
}
/* ----------------------------------------------------------------------
generic opening of a dump file
ASCII or binary or gzipped
some derived classes override this function
------------------------------------------------------------------------- */
void DumpCFGGZ::openfile()
{
// single file, already opened, so just return
if (singlefile_opened) return;
if (multifile == 0) singlefile_opened = 1;
// if one file per timestep, replace '*' with current timestep
char *filecurrent = filename;
if (multiproc) filecurrent = multiname;
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
}
// each proc with filewriter = 1 opens a file
if (filewriter) {
if (append_flag) {
gzFp = gzopen(filecurrent,"ab9");
} else {
gzFp = gzopen(filecurrent,"wb9");
}
if (gzFp == NULL) error->one(FLERR,"Cannot open dump file");
} else gzFp = NULL;
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
}
/* ---------------------------------------------------------------------- */
void DumpCFGGZ::write_header(bigint n)
{
// set scale factor used by AtomEye for CFG viz
// default = 1.0
// for peridynamics, set to pre-computed PD scale factor
// so PD particles mimic C atoms
// for unwrapped coords, set to UNWRAPEXPAND (10.0)
// so molecules are not split across periodic box boundaries
double scale = 1.0;
if (atom->peri_flag) scale = atom->pdscale;
else if (unwrapflag == 1) scale = UNWRAPEXPAND;
char str[64];
sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT);
gzprintf(gzFp,str,n);
gzprintf(gzFp,"A = %g Angstrom (basic length-scale)\n",scale);
gzprintf(gzFp,"H0(1,1) = %g A\n",domain->xprd);
gzprintf(gzFp,"H0(1,2) = 0 A \n");
gzprintf(gzFp,"H0(1,3) = 0 A \n");
gzprintf(gzFp,"H0(2,1) = %g A \n",domain->xy);
gzprintf(gzFp,"H0(2,2) = %g A\n",domain->yprd);
gzprintf(gzFp,"H0(2,3) = 0 A \n");
gzprintf(gzFp,"H0(3,1) = %g A \n",domain->xz);
gzprintf(gzFp,"H0(3,2) = %g A \n",domain->yz);
gzprintf(gzFp,"H0(3,3) = %g A\n",domain->zprd);
gzprintf(gzFp,".NO_VELOCITY.\n");
gzprintf(gzFp,"entry_count = %d\n",nfield-2);
for (int i = 0; i < nfield-5; i++)
gzprintf(gzFp,"auxiliary[%d] = %s\n",i,auxname[i]);
}
/* ---------------------------------------------------------------------- */
void DumpCFGGZ::write_data(int n, double *mybuf)
{
gzwrite(gzFp,mybuf,sizeof(char)*n);
}
/* ---------------------------------------------------------------------- */
void DumpCFGGZ::write()
{
DumpCFG::write();
if (filewriter) {
if (multifile) {
gzclose(gzFp);
gzFp = NULL;
} else {
if (flush_flag)
gzflush(gzFp,Z_SYNC_FLUSH);
}
}
}

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