2ad9e06bac
Modifies the binary dump atom format to include columns information. binary2txt showcases how to detect the new format by checking for negative ntimestep values. It increases the binary file size 16 bytes per timestep.
229 lines
6.3 KiB
C++
229 lines
6.3 KiB
C++
/* -----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------ */
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// Convert one or more LAMMPS binary dump files to ASCII text files
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//
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// this serial code must be compiled on a platform that can read the binary
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// dump files since binary formats are not compatible across all platforms
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//
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// Syntax: binary2txt file1 file2 ...
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// Creates: file1.txt file2.txt ...
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#include <stdio.h>
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#include <string.h>
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// these must match settings in src/lmptype.h which builds LAMMPS with
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// -DLAMMPS_SMALLBIG (the default), -DLAMMPS_BIGBIG, or -DLAMMPS_SMALLSMALL
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// you can edit the tools/Makefile to enforce the same setting
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// for the build of binary2txt, e.g.
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// g++ -g -DLAMMPS_BIGBIG binarytxt.o -o binary2txt
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// again -DLAMMPS_SMALLBIG is the default
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#include "stdint.h"
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#define __STDC_FORMAT_MACROS
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#include "inttypes.h"
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#ifndef PRId64
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#define PRId64 "ld"
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#endif
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#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
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#define LAMMPS_SMALLBIG
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#endif
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#if defined(LAMMPS_SMALLBIG)
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typedef int tagint;
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typedef int64_t bigint;
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#define BIGINT_FORMAT "%" PRId64
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#elif defined(LAMMPS_SMALLSMALL)
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typedef int tagint;
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typedef int bigint;
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#define BIGINT_FORMAT "%d"
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#else /* LAMMPS_BIGBIG */
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typedef int64_t tagint;
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typedef int64_t bigint;
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#define BIGINT_FORMAT "%" PRId64
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#endif
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int main(int narg, char **arg)
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{
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int i,j,k,m,n;
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bigint ntimestep,natoms;
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int size_one,nchunk,triclinic;
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double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz;
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int boundary[3][2];
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char boundstr[9];
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int maxbuf = 0;
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double *buf = NULL;
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if (narg == 1) {
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printf("Syntax: binary2txt file1 file2 ...\n");
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return 1;
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}
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// loop over files
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for (int iarg = 1; iarg < narg; iarg++) {
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printf("%s:",arg[iarg]);
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fflush(stdout);
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FILE *fp = fopen(arg[iarg],"rb");
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if (!fp) {
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printf("ERROR: Could not open %s\n",arg[iarg]);
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return 1;
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}
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n = strlen(arg[iarg]) + 1 + 4;
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char *filetxt = new char[n];
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strcpy(filetxt,arg[iarg]);
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strcat(filetxt,".txt");
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FILE *fptxt = fopen(filetxt,"w");
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delete [] filetxt;
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// detect newer format
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char * formatname = nullptr;
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char * columns = nullptr;
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// loop over snapshots in file
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while (1) {
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fread(&ntimestep,sizeof(bigint),1,fp);
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// detect end-of-file
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if (feof(fp)) {
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fclose(fp);
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fclose(fptxt);
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break;
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}
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// detect newer format
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if (ntimestep < 0) {
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// first bigint encodes negative format name length
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bigint formatlen = -ntimestep;
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delete [] formatname;
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formatname = new char[formatlen + 1];
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fread(formatname, sizeof(char), formatlen, fp);
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formatname[formatlen] = '\0';
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// read the real ntimestep
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fread(&ntimestep,sizeof(bigint),1,fp);
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}
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fread(&natoms,sizeof(bigint),1,fp);
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fread(&triclinic,sizeof(int),1,fp);
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fread(&boundary[0][0],6*sizeof(int),1,fp);
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fread(&xlo,sizeof(double),1,fp);
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fread(&xhi,sizeof(double),1,fp);
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fread(&ylo,sizeof(double),1,fp);
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fread(&yhi,sizeof(double),1,fp);
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fread(&zlo,sizeof(double),1,fp);
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fread(&zhi,sizeof(double),1,fp);
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if (triclinic) {
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fread(&xy,sizeof(double),1,fp);
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fread(&xz,sizeof(double),1,fp);
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fread(&yz,sizeof(double),1,fp);
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}
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fread(&size_one,sizeof(int),1,fp);
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if (formatname) {
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// newer format includes columns string
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int len = 0;
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fread(&len, sizeof(int), 1, fp);
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delete [] columns;
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columns = new char[len+1];
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fread(columns, sizeof(char), len, fp);
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columns[len+1] = '\0';
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}
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fread(&nchunk,sizeof(int),1,fp);
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fprintf(fptxt,"ITEM: TIMESTEP\n");
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fprintf(fptxt,BIGINT_FORMAT "\n",ntimestep);
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fprintf(fptxt,"ITEM: NUMBER OF ATOMS\n");
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fprintf(fptxt,BIGINT_FORMAT "\n",natoms);
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m = 0;
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for (int idim = 0; idim < 3; idim++) {
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for (int iside = 0; iside < 2; iside++) {
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if (boundary[idim][iside] == 0) boundstr[m++] = 'p';
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else if (boundary[idim][iside] == 1) boundstr[m++] = 'f';
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else if (boundary[idim][iside] == 2) boundstr[m++] = 's';
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else if (boundary[idim][iside] == 3) boundstr[m++] = 'm';
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}
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boundstr[m++] = ' ';
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}
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boundstr[8] = '\0';
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if (!triclinic) {
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fprintf(fptxt,"ITEM: BOX BOUNDS %s\n",boundstr);
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fprintf(fptxt,"%-1.16e %-1.16e\n",xlo,xhi);
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fprintf(fptxt,"%-1.16e %-1.16e\n",ylo,yhi);
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fprintf(fptxt,"%-1.16e %-1.16e\n",zlo,zhi);
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} else {
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fprintf(fptxt,"ITEM: BOX BOUNDS %s xy xz yz\n",boundstr);
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fprintf(fptxt,"%-1.16e %-1.16e %-1.16e\n",xlo,xhi,xy);
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fprintf(fptxt,"%-1.16e %-1.16e %-1.16e\n",ylo,yhi,xz);
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fprintf(fptxt,"%-1.16e %-1.16e %-1.16e\n",zlo,zhi,yz);
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}
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if (columns)
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fprintf(fptxt,"ITEM: ATOMS %s\n", columns);
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else
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fprintf(fptxt,"ITEM: ATOMS\n");
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// loop over processor chunks in file
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for (i = 0; i < nchunk; i++) {
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fread(&n,sizeof(int),1,fp);
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// extend buffer to fit chunk size
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if (n > maxbuf) {
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if (buf) delete [] buf;
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buf = new double[n];
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maxbuf = n;
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}
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// read chunk and write as size_one values per line
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fread(buf,sizeof(double),n,fp);
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n /= size_one;
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m = 0;
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for (j = 0; j < n; j++) {
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for (k = 0; k < size_one; k++) {
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if(k+1 < size_one) {
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fprintf(fptxt,"%g ",buf[m++]);
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} else {
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fprintf(fptxt,"%g",buf[m++]);
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}
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}
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fprintf(fptxt,"\n");
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}
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}
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printf(" " BIGINT_FORMAT,ntimestep);
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fflush(stdout);
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}
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printf("\n");
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delete [] columns;
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delete [] formatname;
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}
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if (buf) delete [] buf;
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return 0;
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}
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