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lammps/tools/lmp2arc/src/ProcessPosFile05.c
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ProcessPosFile05.c
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/****************************** ProcessDumpFile.c ***************************
*
* Created 8/98 by John Carpenter
* Based on routines ReadLMPDump and CreateArcFile written by
* Mike Peachey during summer 1997
*
* This function reads the output from LAMMPS dumpfile
* and then writes it back out to an ACCELRYS arcfile using
* info from ReadCarfile.
*
*/
#include "lmp2.h"
void ProcessPosFile05(int num_posfiles,char *posnames[],struct Sys *sysinfo,FILE *ArcFile)
{
struct Boundary cell;
struct NewAtomCoordinates *coord;
FILE *PosFile;
char line[MAX_LINE_LENGTH];
int i,iax,itag,itype;
int nxx,nyy,nzz,matoms;
int frame, mskip,timestep;
int ifile;
float xx,yy,zz;
/* Function prototype declarations */
extern void unwrap_molecules(struct NewAtomCoordinates *,struct Sys *);
extern void WriteArcFrame(FILE *,int,int,struct Sys *);
/* Begin execution */
coord = calloc(sysinfo->natoms, sizeof(struct NewAtomCoordinates));
if ( coord == NULL )
{
fprintf(stderr,"Memory Allocation Problem(coord), exiting program");
exit(3);
}
/* process data */
fprintf(stderr,"\n Processing Timesteps for LAMMPS 2005 dump file\n\n");
frame = 0;
mskip = 0;
for (ifile=0; ifile < num_posfiles; ifile++) {
if ( (PosFile = fopen(posnames[ifile],"r")) == NULL ) {
fprintf(stderr,"Cannot open %s\n",posnames[ifile]);
exit(2);
}
while (fgets(line,MAX_LINE_LENGTH, PosFile) != NULL) {
if (strstr(line,"NUMBER OF ATOMS")) {
fgets(line,MAX_LINE_LENGTH, PosFile);
matoms = atoi(line);
if (matoms != sysinfo->natoms) {
fprintf(stderr,"Number of atoms in car and dump files do not match\n");
exit(1);
}
}
else if (strstr(line,"BOX BOUNDS")) {
/*
fprintf(stderr,"HERE 1\n");
*/
for (iax=0; iax < 3; iax++) {
fgets(line, MAX_LINE_LENGTH, PosFile);
cell.low[iax] = atof(strtok(line, " "));
cell.hi[iax] = atof(strtok(NULL, " \0\n"));
cell.size[iax] = cell.hi[iax] - cell.low[iax];
sysinfo->celldim[iax] = cell.size[iax];
}
}
else if (strstr(line,"TIMESTEP")) {
fscanf(PosFile,"%d",&timestep);
}
else if (strstr(line,"ATOMS")) {
if (trueflag) {
for (i=0; i<matoms; i++) {
fgets(line, MAX_LINE_LENGTH, PosFile);
sscanf(line,"%d %d %f %f %f %d %d %d",&itag,&itype,
&xx,&yy,&zz,&nxx,&nyy,&nzz);
coord[itag-1].type = itype;
coord[itag-1].fract[0] = xx;
coord[itag-1].fract[1] = yy;
coord[itag-1].fract[2] = zz;
coord[itag-1].truef[0] = nxx;
coord[itag-1].truef[1] = nyy;
coord[itag-1].truef[2] = nzz;
}
if (move_molecules) unwrap_molecules(coord,sysinfo);
for (i=0; i<matoms; i++) {
for (iax=0; iax<3; iax++)
coord[i].fract[iax] += coord[i].truef[iax];
}
}
else {
for (i=0; i<matoms; i++) {
fgets(line, MAX_LINE_LENGTH, PosFile);
sscanf(line,"%d %d %f %f %f",&itag,&itype,&xx,&yy,&zz);
coord[itag-1].type = itype;
coord[itag-1].fract[0] = xx;
coord[itag-1].fract[1] = yy;
coord[itag-1].fract[2] = zz;
}
if (move_molecules) unwrap_molecules(coord,sysinfo);
} /* end if on trueflag */
for (i=0; i<matoms; i++) {
sysinfo->atoms[i].xyz[0] = cell.size[0]*coord[i].fract[0];
sysinfo->atoms[i].xyz[1] = cell.size[1]*coord[i].fract[1];
sysinfo->atoms[i].xyz[2] = cell.size[2]*coord[i].fract[2];
}
/* Ready to write arc file entry */
if ((mskip >= nskip) || (frame == 0)) {
WriteArcFrame(ArcFile,frame,timestep,sysinfo);
frame++;
mskip = 0;
if (frame%20 == 0) fprintf(stderr," %d",frame);
if (frame%400 == 0) fprintf(stderr,"\n");
}
else
mskip++;
} /* end if on ITEM */
} /* end while over LINES*/
close(PosFile);
} /* end for loop over POS FILES */
fprintf(stderr,"\n\n %d frames were written to the ArcFile\n",frame);
}
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