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lmp2arc.c
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Thu, Feb 20, 00:20

lmp2arc.c
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/****************************** Lmp2arc.c ******************************
This program converts a contiguous set of LAMMPS dump (position) files
to a MSI .arc file using a .car file as the template. This enables one to
visualize a LAMMPS trajectory using Insight II.
by Michael Peachey & John Carpenter (SGI/Cray)
currently maintained by Kelly L. Anderson (AFRL/ML)
Version 0.1: 8/14/97 MJP
Version 1.0: 7/27/98 JEC
Version 1.1: 10/22/98 JEC
Version 1.2: 11/04/98 JEC
Version 1.3: 4/10/05 KLA
1. To build the program
% cd src
% make
% cp lmp2arc.exe ../bin
The program is only a few files so should compile
quickly.
2. Testing the program
There are three test jobs in the test directory
that one can run
% ../bin/lmp2arc.exe -car water8.car <<EOF > water8.arc
> water8.pos
> EOF
% diff water8.arc correct/water8.arc
% ../bin/lmp2arc.exe -move_mol -car water8.car <<EOF > water8.arc
> water8.pos
> EOF
% diff water8.arc correct/water8.arc.unwrap
% ../bin/lmp2arc.exe -trueflags -move_mol -car water8.car \
<<EOF > water8.arc
> water8.pos
> EOF
% diff water8.arc correct/water8.arc.trueflags
The only differences you should see are date differences.
3. Usage
Usage: lmp2arc.exe [options] -car carfile < infile > outfile
options
-trueflags (optional)
trueflags are present in the LAMMPS position file.
-move_mol (optional)
Unwraps molecules. All atoms in the position file are in
the simulation cell. This means that molecules which
are sticking out of the cell will have some of its
atoms "wrapped" to the other side of the periodic cell.
This leads to very messy visualizations. Specification
of -move_mol will attempt to "unwrap" or straighten
molecules and yield a reasonable visualization. However,
molecules which oscillate around half in or out of the
box may appear to jump from one side of the box to
the other.
Two algorithms are used depending upon the presence of
trueflags. The algorithm that uses trueflags is the
most robust, but the other geometric based algorithm
should be adequate.
-car filename
the name of the .car file that corresponds to the
position information. This is required.
-skip n (default is 0)
Skip every n timesteps in the position file.
-npico n (default is 2000)
Number of timesteps in 1 picosecond of simulation.
-2001 (default is 2005)
Version of LAMMPS to convert from.
stdin
file containing one or more names of LAMMPS position files
stdout
the name of the new .arc file
Examples:
% lmp2arc.exe -2001 -trueflags -move_mol -skip 4 -car water.car <<EOF > water.arc
water1.pos
water2.pos
EOF
>>>> Program output <<<<<
lmp2arc v1.2 - LAMMPS MD trajectory to MSI .arc file conversion
Car file name is water.car
Number of Atoms = 24
Number of Molecules = 8
Position file names:
water1.pos
water2.pos
Processing Timesteps
20 40 60 80 100
102 frames were written to the ArcFile
Program Exiting Normally
4. Questions or comments?
Send them to Kelly L. Anderson (kelly.anderson@cantab.net)
*/
#define MAIN
#include "lmp2.h"
/* External function prototypes */
extern void ReadCarFile(FILE *,struct Sys *);
extern void ProcessPosFile01(int,char **,struct Sys *,FILE *);
extern void ProcessPosFile05(int,char **,struct Sys *,FILE *);
int main(int argc, char *argv[])
{
int got_car,ierr,i;
char *carfilename;
struct Sys *sysinfo;
int num_posfiles;
int outv;
char *posnames[MAX_POS_FILES];
char line[MAX_LINE_LENGTH];
FILE *CarFile,*ArcFile;
/* default input values */
trueflag = 0;
move_molecules = 0;
nskip = 0;
got_car = 0;
npico = 2000;
outv = 2005;
/* read input options from command line
should do more error checking for missing args */
for (i = 1; i < argc; i++) {
if (!strcmp(argv[i],"-car")) {
carfilename = (char *) malloc(strlen(argv[i+1]));
strcpy(carfilename,argv[i+1]);
i++;
got_car = 1;
}
else if (!strcmp(argv[i],"-trueflags"))
trueflag = 1;
else if (!strcmp(argv[i],"-move_mol"))
move_molecules = 1;
else if (!strcmp(argv[i],"-2001")) {
outv = 2001;
fprintf(stderr,"\n LAMMPS 2001 file used.\n");
}
else if (!strcmp(argv[i],"-skip")) {
sscanf(argv[i+1],"%d",&nskip);
i++;
}
else if (!strcmp(argv[i],"-npico")) {
sscanf(argv[i+1],"%d",&npico);
i++;
}
else {
fprintf(stderr,"\nSyntax error: lmp2arc.exe [-2001] [-trueflags] [-move_mol] [-skip n]\n");
fprintf(stderr," [-npico m] -car carfile\n");
fprintf(stderr," < posfile_list > ArcFile\n");
exit(1);
}
}
/* Check for option inconsistancies */
if (!got_car) {
fprintf(stderr,"Must specify car file\n");
exit(1);
}
fprintf(stderr,"\n lmp2arc v1.3 - LAMMPS MD trajectory to ACCELRYS .arc file conversion\n\n");
sysinfo = (struct Sys *) calloc(1,sizeof(struct Sys));
/* Open CarFile */
fprintf(stderr,"\n Car file name is %s\n",carfilename);
if( (CarFile = fopen(carfilename,"r")) == NULL )
{
fprintf(stderr,"Cannot open %s\n",carfilename);
exit(2);
}
ReadCarFile(CarFile, sysinfo);
fclose(CarFile);
free(carfilename);
fprintf(stderr,"\n Number of Atoms = %d\n",sysinfo->natoms);
fprintf(stderr," Number of Molecules = %d\n",sysinfo->no_molecules);
/* Get position file names */
num_posfiles = 0;
while (gets(line) != NULL) {
if (ferror(stdin) == 0) {
posnames[num_posfiles] = (char *)calloc(strlen(line),sizeof(char));
posnames[num_posfiles] = strcpy(posnames[num_posfiles],line);
num_posfiles++;
}
else
perror(strerror(ferror(stdin)));
}
fprintf(stderr,"\n Position file names:\n");
for (i=0;i < num_posfiles; i++) fprintf(stderr," %s\n",posnames[i]);
/* Assign ArcFile to stdout */
ArcFile = stdout;
if (outv == 2001) {
ProcessPosFile01(num_posfiles,posnames,sysinfo,ArcFile);
}
else if (outv == 2005) {
ProcessPosFile05(num_posfiles,posnames,sysinfo,ArcFile);
}
fclose(ArcFile);
free(sysinfo);
fprintf(stderr,"\n\n Program Exiting Normally\n\n");
}

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