forked from lijiext/lammps
263 lines
7.3 KiB
C++
263 lines
7.3 KiB
C++
/* -----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/
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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 * magic_string = nullptr;
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char * columns = nullptr;
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char * unit_style = nullptr;
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// loop over snapshots in file
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while (1) {
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int endian = 0x0001;
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int revision = 0x0001;
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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 magic_string_len = -ntimestep;
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delete [] magic_string;
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magic_string = new char[magic_string_len + 1];
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fread(magic_string, sizeof(char), magic_string_len, fp);
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magic_string[magic_string_len] = '\0';
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// read endian flag
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fread(&endian, sizeof(int), 1, fp);
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// read revision number
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fread(&revision, sizeof(int), 1, fp);
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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 (magic_string && revision > 0x0001) {
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// newer format includes units string, columns string
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// and time
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int len = 0;
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fread(&len, sizeof(int), 1, fp);
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if (len > 0) {
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// has units
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delete [] unit_style;
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unit_style = new char[len+1];
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fread(unit_style, sizeof(char), len, fp);
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unit_style[len] = '\0';
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fprintf(fptxt, "ITEM: UNITS\n");
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fprintf(fptxt, "%s\n", unit_style);
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}
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char flag = 0;
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fread(&flag, sizeof(char), 1, fp);
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if (flag) {
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double time;
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fread(&time, sizeof(double), 1, fp);
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fprintf(fptxt, "ITEM: TIME\n%.16g\n", time);
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}
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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] = '\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 xy xz yz %s\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 [] magic_string;
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delete [] unit_style;
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columns = nullptr;
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magic_string = nullptr;
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unit_style = nullptr;
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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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