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lammps/tools/lmp2arc/src/ReadCarFile.c
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ReadCarFile.c
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/****************************** ReadCarFile.c ******************************
*
* This function opens the .car file and extracts coordinate information
* into the atoms Atom structure
*
* THIS FUNCTION HAS BEEN MODIFIED FROM Msi2LMP2 AND USES THE ATOM
* STRUCTURE MEMBERS DIFFERENTLY
*/
#include "lmp2.h"
void ReadCarFile(FILE *CarF,struct Sys *sysinfo)
{
char line[MAX_LINE_LENGTH]; /* Stores lines as they are read in */
int k,m,n; /* counters */
int skip; /* lines to skip at beginning of file */
/* Determine Number of molecules & atoms */
rewind(CarF);
sysinfo->no_molecules = -1; /* Set to -1 because counter will be
incremented an extra time at the end of the file */
fgets(line,MAX_LINE_LENGTH,CarF); /* Read header line */
/* Check for periodicity, set periodic and skip */
if( strncmp(fgets(line,MAX_LINE_LENGTH,CarF),"PBC=ON",6) == 0)
{
sysinfo->periodic = 1;
skip = 5; /* Data starts 5 lines from beginning of file */
}
else
{
sysinfo->periodic = 0;
skip = 4;
}
/* First pass through file -- Count molecules */
while( fgets(line,MAX_LINE_LENGTH,CarF) != NULL )
if( strncmp(line,"end",3) == 0 )
sysinfo->no_molecules++;
/* Allocate space to keep track of the number of atoms within a molecule */
sysinfo->molinfo =
(struct Mol *) calloc(sysinfo->no_molecules,sizeof(struct Mol));
if ( sysinfo->molinfo == NULL )
{
puts("Could not allocate memory for molinfo");
exit(2);
}
/* Second pass through file -- Count atoms */
rewind(CarF);
for(n=0; n < skip; n++) /* Skip beginning lines */
fgets(line,MAX_LINE_LENGTH,CarF);
sysinfo->molinfo[0].start = 0;
sysinfo->molinfo[0].end = 0;
for(n=0; n < sysinfo->no_molecules; n++)
{
if (n != 0) {
sysinfo->molinfo[n].start = sysinfo->molinfo[n-1].end;
sysinfo->molinfo[n].end = sysinfo->molinfo[n-1].end;
}
while( strncmp(fgets(line,MAX_LINE_LENGTH,CarF),"end",3) )
sysinfo->molinfo[n].end++;
}
n = sysinfo->no_molecules-1;
sysinfo->natoms = sysinfo->molinfo[n].end;
/* Allocate space for atoms Atom structures */
sysinfo->atoms = (struct Atom *) calloc(sysinfo->natoms,
sizeof(struct Atom));
if( sysinfo->atoms == NULL )
{
puts("Could not allocate memory for AtomList");
exit(2);
}
/* Third pass through file -- Read+Parse Car File */
rewind(CarF);
for(n=0; n < skip; n++)
fgets(line,MAX_LINE_LENGTH,CarF);
for(m=0; m < sysinfo->no_molecules; m++)
{ /* m loops through molecules */
for(n=sysinfo->molinfo[m].start; n < sysinfo->molinfo[m].end; n++)
{ /* n loops through atoms within a molecule */
sysinfo->atoms[n].molecule = m;
fscanf(CarF,"%s %lf %lf %lf %s %s %s %s %f",
sysinfo->atoms[n].name,
&(sysinfo->atoms[n].xyz[0]),
&(sysinfo->atoms[n].xyz[1]),
&(sysinfo->atoms[n].xyz[2]),
sysinfo->atoms[n].res_name,
sysinfo->atoms[n].res_num,
sysinfo->atoms[n].potential,
sysinfo->atoms[n].element,
&(sysinfo->atoms[n].q));
} /* End n (atoms) loop */
fgets(line,MAX_LINE_LENGTH,CarF);
fgets(line,MAX_LINE_LENGTH,CarF);
} /* End m (molecule) loop */
} /* End ReadCarFile() */
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