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dump_xyz.cpp
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Wed, Oct 2, 10:32

dump_xyz.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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"
/* ---------------------------------------------------------------------- */
DumpXYZ::DumpXYZ(int narg, char **arg) : Dump(narg, arg)
{
if (narg != 5) error->all("Illegal dump xyz command");
if (binary || multiproc) error->all("Invalid dump xyz filename");
size_one = 5;
char *str = "%d %g %g %g";
int n = strlen(str) + 1;
format_default = new char[n];
strcpy(format_default,str);
// allocate global array for atom coords if group is all
if (igroup == 0) {
natoms = static_cast<int> (atom->natoms);
if (natoms <= 0) error->all("Invalid natoms for dump xyz");
if (atom->tag_consecutive() == 0)
error->all("Atom IDs must be consecutive for dump xyz");
types = (int *) memory->smalloc(natoms*sizeof(int),"dump:types");
coords = (float *) memory->smalloc(3*natoms*sizeof(float),"dump:coords");
}
// one-time file open
if (multifile == 0) openfile();
ntotal = 0;
}
/* ---------------------------------------------------------------------- */
DumpXYZ::~DumpXYZ()
{
if (igroup == 0) {
memory->sfree(types);
memory->sfree(coords);
}
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::init()
{
delete [] format;
char *str;
if (format_user) str = format_user;
else str = format_default;
int n = strlen(str) + 2;
format = new char[n];
strcpy(format,str);
strcat(format,"\n");
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory in buf and global coords array
------------------------------------------------------------------------- */
int DumpXYZ::memory_usage()
{
int bytes = maxbuf * sizeof(double);
if (igroup == 0) {
bytes += natoms * sizeof(int);
bytes += 3*natoms * sizeof(float);
}
return bytes;
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::write_header(int n)
{
// realloc types & coords if necessary
if (igroup == 0 && n != natoms) {
memory->sfree(types);
memory->sfree(coords);
if (atom->tag_consecutive() == 0)
error->all("Atom IDs must be consecutive for dump xyz");
natoms = n;
types = (int *) memory->smalloc(natoms*sizeof(int),"dump:types");
coords = (float *) memory->smalloc(3*natoms*sizeof(float),"dump:coords");
}
fprintf(fp,"%d\n",n);
fprintf(fp,"Atoms\n");
}
/* ---------------------------------------------------------------------- */
int DumpXYZ::count()
{
if (igroup == 0) return atom->nlocal;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) m++;
return m;
}
/* ---------------------------------------------------------------------- */
int DumpXYZ::pack()
{
int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
int m = 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];
}
return m;
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::write_data(int n, double *buf)
{
// for group = all, spread buf atom coords into global arrays
// if last chunk of atoms in this snapshot, write global arrays to file
if (igroup == 0) {
int j,tag;
int m = 0;
for (int i = 0; i < n; i++) {
tag = static_cast<int> (buf[m]) - 1;
types[tag] = static_cast<int> (buf[m+1]);
j = 3*tag;
coords[j++] = buf[m+2];
coords[j++] = buf[m+3];
coords[j] = buf[m+4];
m += size_one;
}
ntotal += n;
if (ntotal == natoms) {
write_frame();
ntotal = 0;
}
// for group != all, write unsorted type,x,y,z to file
} else {
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
static_cast<int> (buf[m+1]),buf[m+2],buf[m+3],buf[m+4]);
m += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::write_frame()
{
int m = 0;
for (int i = 0; i < natoms; i++) {
fprintf(fp,format,types[i],coords[m],coords[m+1],coords[m+2]);
m += 3;
}
}

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