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dump_xyz.cpp
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Fri, Aug 16, 20:18

dump_xyz.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 "dump_xyz.h"
#include "atom.h"
#include "group.h"
#include "error.h"
#include "memory.h"
#include "update.h"
using namespace LAMMPS_NS;
#define ONELINE 128
#define DELTA 1048576
/* ---------------------------------------------------------------------- */
DumpXYZ::DumpXYZ(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg),
typenames(NULL)
{
if (narg != 5) error->all(FLERR,"Illegal dump xyz command");
if (binary || multiproc) error->all(FLERR,"Invalid dump xyz filename");
size_one = 5;
buffer_allow = 1;
buffer_flag = 1;
sort_flag = 1;
sortcol = 0;
if (format_default) delete [] format_default;
char *str = (char *) "%s %g %g %g";
int n = strlen(str) + 1;
format_default = new char[n];
strcpy(format_default,str);
ntypes = atom->ntypes;
typenames = NULL;
}
/* ---------------------------------------------------------------------- */
DumpXYZ::~DumpXYZ()
{
delete[] format_default;
format_default = NULL;
if (typenames) {
for (int i = 1; i <= ntypes; i++)
delete [] typenames[i];
delete [] typenames;
typenames = NULL;
}
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::init_style()
{
// format = copy of default or user-specified line format
delete [] format;
char *str;
if (format_line_user) str = format_line_user;
else str = format_default;
int n = strlen(str) + 2;
format = new char[n];
strcpy(format,str);
strcat(format,"\n");
// initialize typenames array to be backward compatible by default
// a 32-bit int can be maximally 10 digits plus sign
if (typenames == NULL) {
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
typenames[itype] = new char[12];
sprintf(typenames[itype],"%d",itype);
}
}
// setup function ptr
if (buffer_flag == 1) write_choice = &DumpXYZ::write_string;
else write_choice = &DumpXYZ::write_lines;
// open single file, one time only
if (multifile == 0) openfile();
}
/* ---------------------------------------------------------------------- */
int DumpXYZ::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"element") == 0) {
if (narg < ntypes+1)
error->all(FLERR, "Dump modify element names do not match atom types");
if (typenames) {
for (int i = 1; i <= ntypes; i++)
delete [] typenames[i];
delete [] typenames;
typenames = NULL;
}
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
int n = strlen(arg[itype]) + 1;
typenames[itype] = new char[n];
strcpy(typenames[itype],arg[itype]);
}
return ntypes+1;
}
return 0;
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::write_header(bigint n)
{
if (me == 0) {
fprintf(fp,BIGINT_FORMAT "\n",n);
fprintf(fp,"Atoms. Timestep: " BIGINT_FORMAT "\n",update->ntimestep);
}
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::pack(tagint *ids)
{
int m,n;
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
m = n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
if (ids) ids[n++] = tag[i];
}
}
/* ----------------------------------------------------------------------
convert mybuf of doubles to one big formatted string in sbuf
return -1 if strlen exceeds an int, since used as arg in MPI calls in Dump
------------------------------------------------------------------------- */
int DumpXYZ::convert_string(int n, double *mybuf)
{
int offset = 0;
int m = 0;
for (int i = 0; i < n; i++) {
if (offset + ONELINE > maxsbuf) {
if ((bigint) maxsbuf + DELTA > MAXSMALLINT) return -1;
maxsbuf += DELTA;
memory->grow(sbuf,maxsbuf,"dump:sbuf");
}
offset += sprintf(&sbuf[offset],format,
typenames[static_cast<int> (mybuf[m+1])],
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
}
return offset;
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::write_data(int n, double *mybuf)
{
(this->*write_choice)(n,mybuf);
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::write_string(int n, double *mybuf)
{
fwrite(mybuf,sizeof(char),n,fp);
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::write_lines(int n, double *mybuf)
{
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
typenames[static_cast<int> (mybuf[m+1])],
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
}
}

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