2006-09-28 03:51:49 +08:00
|
|
|
/* -----------------------------------------------------------------------
|
|
|
|
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.
|
|
|
|
------------------------------------------------------------------------ */
|
|
|
|
|
|
|
|
// Convert one or more LAMMPS binary dump files to ASCII text files
|
|
|
|
//
|
|
|
|
// this serial code must be compiled on a platform that can read the binary
|
|
|
|
// dump files since binary formats are not compatible across all platforms
|
|
|
|
//
|
|
|
|
// Syntax: binary2txt file1 file2 ...
|
|
|
|
// Creates: file1.txt file2.txt ...
|
|
|
|
|
2017-03-21 04:57:32 +08:00
|
|
|
#include <stdio.h>
|
|
|
|
#include <string.h>
|
2006-09-28 03:51:49 +08:00
|
|
|
|
2013-06-28 05:36:57 +08:00
|
|
|
// these must match settings in src/lmptype.h which builds LAMMPS with
|
|
|
|
// -DLAMMPS_SMALLBIG (the default), -DLAMMPS_BIGBIG, or -DLAMMPS_SMALLSMALL
|
|
|
|
// you can edit the tools/Makefile to enforce the same setting
|
|
|
|
// for the build of binary2txt, e.g.
|
|
|
|
// g++ -g -DLAMMPS_BIGBIG binarytxt.o -o binary2txt
|
|
|
|
// again -DLAMMPS_SMALLBIG is the default
|
2011-01-08 05:57:45 +08:00
|
|
|
|
2012-01-31 08:36:58 +08:00
|
|
|
#include "stdint.h"
|
|
|
|
#define __STDC_FORMAT_MACROS
|
|
|
|
#include "inttypes.h"
|
|
|
|
|
2013-06-28 05:36:57 +08:00
|
|
|
#ifndef PRId64
|
|
|
|
#define PRId64 "ld"
|
|
|
|
#endif
|
|
|
|
|
|
|
|
#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
|
|
|
|
#define LAMMPS_SMALLBIG
|
|
|
|
#endif
|
|
|
|
|
|
|
|
#if defined(LAMMPS_SMALLBIG)
|
|
|
|
typedef int tagint;
|
|
|
|
typedef int64_t bigint;
|
|
|
|
#define BIGINT_FORMAT "%" PRId64
|
|
|
|
#elif defined(LAMMPS_SMALLSMALL)
|
2012-01-31 08:36:58 +08:00
|
|
|
typedef int tagint;
|
2013-06-28 05:36:57 +08:00
|
|
|
typedef int bigint;
|
|
|
|
#define BIGINT_FORMAT "%d"
|
|
|
|
#else /* LAMMPS_BIGBIG */
|
|
|
|
typedef int64_t tagint;
|
2011-01-08 05:57:45 +08:00
|
|
|
typedef int64_t bigint;
|
2012-01-31 08:36:58 +08:00
|
|
|
#define BIGINT_FORMAT "%" PRId64
|
2013-06-28 05:36:57 +08:00
|
|
|
#endif
|
2011-01-08 05:57:45 +08:00
|
|
|
|
2012-01-31 08:36:58 +08:00
|
|
|
int main(int narg, char **arg)
|
2006-09-28 03:51:49 +08:00
|
|
|
{
|
|
|
|
int i,j,k,m,n;
|
2011-01-08 05:57:45 +08:00
|
|
|
bigint ntimestep,natoms;
|
|
|
|
int size_one,nchunk,triclinic;
|
2009-03-17 06:48:14 +08:00
|
|
|
double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz;
|
2011-04-12 03:42:41 +08:00
|
|
|
int boundary[3][2];
|
|
|
|
char boundstr[9];
|
|
|
|
|
2006-09-28 03:51:49 +08:00
|
|
|
int maxbuf = 0;
|
|
|
|
double *buf = NULL;
|
|
|
|
|
|
|
|
if (narg == 1) {
|
|
|
|
printf("Syntax: binary2txt file1 file2 ...\n");
|
2012-01-31 08:36:58 +08:00
|
|
|
return 1;
|
2006-09-28 03:51:49 +08:00
|
|
|
}
|
|
|
|
|
|
|
|
// loop over files
|
|
|
|
|
|
|
|
for (int iarg = 1; iarg < narg; iarg++) {
|
|
|
|
printf("%s:",arg[iarg]);
|
|
|
|
fflush(stdout);
|
|
|
|
FILE *fp = fopen(arg[iarg],"rb");
|
|
|
|
if (!fp) {
|
|
|
|
printf("ERROR: Could not open %s\n",arg[iarg]);
|
2012-01-31 08:36:58 +08:00
|
|
|
return 1;
|
2006-09-28 03:51:49 +08:00
|
|
|
}
|
|
|
|
|
|
|
|
n = strlen(arg[iarg]) + 1 + 4;
|
|
|
|
char *filetxt = new char[n];
|
|
|
|
strcpy(filetxt,arg[iarg]);
|
|
|
|
strcat(filetxt,".txt");
|
|
|
|
FILE *fptxt = fopen(filetxt,"w");
|
|
|
|
delete [] filetxt;
|
|
|
|
|
|
|
|
// loop over snapshots in file
|
|
|
|
|
|
|
|
while (1) {
|
|
|
|
|
2011-01-08 05:57:45 +08:00
|
|
|
fread(&ntimestep,sizeof(bigint),1,fp);
|
2006-09-28 03:51:49 +08:00
|
|
|
|
|
|
|
// detect end-of-file
|
|
|
|
|
|
|
|
if (feof(fp)) {
|
2019-09-10 21:38:44 +08:00
|
|
|
fclose(fp);
|
|
|
|
fclose(fptxt);
|
|
|
|
break;
|
2006-09-28 03:51:49 +08:00
|
|
|
}
|
|
|
|
|
2011-01-08 05:57:45 +08:00
|
|
|
fread(&natoms,sizeof(bigint),1,fp);
|
2009-03-17 06:48:14 +08:00
|
|
|
fread(&triclinic,sizeof(int),1,fp);
|
2011-04-12 03:42:41 +08:00
|
|
|
fread(&boundary[0][0],6*sizeof(int),1,fp);
|
2006-09-28 03:51:49 +08:00
|
|
|
fread(&xlo,sizeof(double),1,fp);
|
|
|
|
fread(&xhi,sizeof(double),1,fp);
|
|
|
|
fread(&ylo,sizeof(double),1,fp);
|
|
|
|
fread(&yhi,sizeof(double),1,fp);
|
|
|
|
fread(&zlo,sizeof(double),1,fp);
|
|
|
|
fread(&zhi,sizeof(double),1,fp);
|
2009-03-17 06:48:14 +08:00
|
|
|
if (triclinic) {
|
2019-09-10 21:38:44 +08:00
|
|
|
fread(&xy,sizeof(double),1,fp);
|
|
|
|
fread(&xz,sizeof(double),1,fp);
|
|
|
|
fread(&yz,sizeof(double),1,fp);
|
2009-03-17 06:48:14 +08:00
|
|
|
}
|
2006-09-28 03:51:49 +08:00
|
|
|
fread(&size_one,sizeof(int),1,fp);
|
|
|
|
fread(&nchunk,sizeof(int),1,fp);
|
2019-09-10 21:38:44 +08:00
|
|
|
|
2012-01-31 08:36:58 +08:00
|
|
|
fprintf(fptxt,"ITEM: TIMESTEP\n");
|
|
|
|
fprintf(fptxt,BIGINT_FORMAT "\n",ntimestep);
|
|
|
|
fprintf(fptxt,"ITEM: NUMBER OF ATOMS\n");
|
|
|
|
fprintf(fptxt,BIGINT_FORMAT "\n",natoms);
|
2011-04-12 03:42:41 +08:00
|
|
|
|
|
|
|
m = 0;
|
|
|
|
for (int idim = 0; idim < 3; idim++) {
|
2019-09-10 21:38:44 +08:00
|
|
|
for (int iside = 0; iside < 2; iside++) {
|
|
|
|
if (boundary[idim][iside] == 0) boundstr[m++] = 'p';
|
|
|
|
else if (boundary[idim][iside] == 1) boundstr[m++] = 'f';
|
|
|
|
else if (boundary[idim][iside] == 2) boundstr[m++] = 's';
|
|
|
|
else if (boundary[idim][iside] == 3) boundstr[m++] = 'm';
|
|
|
|
}
|
|
|
|
boundstr[m++] = ' ';
|
2011-04-12 03:42:41 +08:00
|
|
|
}
|
|
|
|
boundstr[8] = '\0';
|
2019-09-10 21:38:44 +08:00
|
|
|
|
2009-03-17 06:48:14 +08:00
|
|
|
if (!triclinic) {
|
2019-09-10 21:38:44 +08:00
|
|
|
fprintf(fptxt,"ITEM: BOX BOUNDS %s\n",boundstr);
|
|
|
|
fprintf(fptxt,"%g %g\n",xlo,xhi);
|
|
|
|
fprintf(fptxt,"%g %g\n",ylo,yhi);
|
|
|
|
fprintf(fptxt,"%g %g\n",zlo,zhi);
|
2009-03-17 06:48:14 +08:00
|
|
|
} else {
|
2019-09-10 21:38:44 +08:00
|
|
|
fprintf(fptxt,"ITEM: BOX BOUNDS %s xy xz yz\n",boundstr);
|
|
|
|
fprintf(fptxt,"%g %g %g\n",xlo,xhi,xy);
|
|
|
|
fprintf(fptxt,"%g %g %g\n",ylo,yhi,xz);
|
|
|
|
fprintf(fptxt,"%g %g %g\n",zlo,zhi,yz);
|
2009-03-17 06:48:14 +08:00
|
|
|
}
|
2006-09-28 03:51:49 +08:00
|
|
|
fprintf(fptxt,"ITEM: ATOMS\n");
|
|
|
|
|
2011-04-12 03:42:41 +08:00
|
|
|
|
|
|
|
|
2006-09-28 03:51:49 +08:00
|
|
|
// loop over processor chunks in file
|
|
|
|
|
|
|
|
for (i = 0; i < nchunk; i++) {
|
2019-09-10 21:38:44 +08:00
|
|
|
fread(&n,sizeof(int),1,fp);
|
|
|
|
|
|
|
|
// extend buffer to fit chunk size
|
|
|
|
|
|
|
|
if (n > maxbuf) {
|
|
|
|
if (buf) delete [] buf;
|
|
|
|
buf = new double[n];
|
|
|
|
maxbuf = n;
|
|
|
|
}
|
|
|
|
|
|
|
|
// read chunk and write as size_one values per line
|
|
|
|
|
|
|
|
fread(buf,sizeof(double),n,fp);
|
|
|
|
n /= size_one;
|
|
|
|
m = 0;
|
|
|
|
for (j = 0; j < n; j++) {
|
|
|
|
for (k = 0; k < size_one; k++) fprintf(fptxt,"%g ",buf[m++]);
|
|
|
|
fprintf(fptxt,"\n");
|
|
|
|
}
|
2006-09-28 03:51:49 +08:00
|
|
|
}
|
|
|
|
|
2012-01-31 08:36:58 +08:00
|
|
|
printf(" " BIGINT_FORMAT,ntimestep);
|
2006-09-28 03:51:49 +08:00
|
|
|
fflush(stdout);
|
|
|
|
}
|
|
|
|
printf("\n");
|
|
|
|
}
|
|
|
|
|
|
|
|
if (buf) delete [] buf;
|
2012-01-31 08:36:58 +08:00
|
|
|
return 0;
|
2006-09-28 03:51:49 +08:00
|
|
|
}
|