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msi2lmp.c
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Sat, May 25, 22:50

msi2lmp.c
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/*
*
* msi2lmp.exe V3.6
*
* v3.6 KLA - Changes to output to either lammps 2001 (F90 version) or to
* lammps 2005 (C++ version)
*
* v3.4 JEC - a number of minor changes due to way newline and EOF are generated
* on Materials Studio generated .car and .mdf files as well as odd
* behavior out of newer Linux IO libraries. ReadMdfFile was restructured
* in the process.
*
* v3.1 JEC - changed IO interface to standard in/out, forcefield file
* location can be indicated by environmental variable; added
* printing options, consistency checks and forcefield
* parameter versions sensitivity (highest one used)
*
* v3.0 JEC - program substantially rewritten to reduce execution time
* and be 98 % dynamic in memory use (still fixed limits on
* number of parameter types for different internal coordinate
* sets)
*
* v2.0 MDP - got internal coordinate information from mdf file and
* forcefield parameters from frc file thus eliminating
* need for Discover
*
* V1.0 SL - original version. Used .car file and internal coordinate
* information from Discover to produce LAMMPS data file.
*
* This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
* program to produce a LAMMPS data file.
*
* The program is started by supplying information at the command prompt
* according to the usage described below.
*
* USAGE: msi2lmp3 ROOTNAME {-print #} {-class #} {-frc FRC_FILE} -2001
*
* -- msi2lmp3 is the name of the executable
* -- ROOTNAME is the base name of the .car and .mdf files
*
* -- -print
* # is the print level: 0 - silent except for errors
* 1 - minimal (default)
* 2 - more verbose
* -- -class
* # is the class of forcefield to use (I = Class I e.g., CVFF)
* (II = Class II e.g., CFFx )
* default is -class I
*
* -- -frc - specifies name of the forcefield file (e.g., cff91)
*
* If the name includes a hard wired directory (i.e., if the name
* starts with . or /), then the name is used alone. Otherwise,
* the program looks for the forcefield file in $BIOSYM_LIBRARY.
* If $BIOSYM_LIBRARY is not set, then the current directory is
* used.
*
* If the file name does not include a dot after the first
* character, then .frc is appended to the name.
*
* For example, -frc cvff (assumes cvff.frc is in $BIOSYM_LIBRARY
* or .)
*
* -frc cff/cff91 (assumes cff91.frc is in
* $BIOSYM_LIBRARY/cff or ./cff)
*
* -frc /usr/local/biosym/forcefields/cff95 (absolute
* location)
*
* By default, the program uses $BIOSYM_LIBRARY/cvff.frc
*
* -- -2001 will output a data file for the FORTRAN 90 version of LAMMPS (2001)
* By default, the program will output for the C++ version of LAMMPS.
*
* -- output is written to a file called ROOTNAME.lammps{01/05}
*
*
****************************************************************
*
* Msi2lmp3
*
* This is the third version of a program that generates a LAMMPS
* data file based on the information in a MSI car file (atom
* coordinates) and mdf file (molecular topology). A key part of
* the program looks up forcefield parameters from an MSI frc file.
*
* The first version was written by Steve Lustig at Dupont, but
* required using Discover to derive internal coordinates and
* forcefield parameters
*
* The second version was written by Michael Peachey while an
* in intern in the Cray Chemistry Applications Group managed
* by John Carpenter. This version derived internal coordinates
* from the mdf file and looked up parameters in the frc file
* thus eliminating the need for Discover.
*
* The third version was written by John Carpenter to optimize
* the performance of the program for large molecular systems
* (the original code for deriving atom numbers was quadratic in time)
* and to make the program fully dynamic. The second version used
* fixed dimension arrays for the internal coordinates.
*
* John Carpenter can be contacted by sending email to
* jec374@earthlink.net
*
* November 2000
*/
#define MAIN
#include "Msi2LMP2.h"
int main (int argc, char *argv[])
{
int n,i,found_dot; /* Counter */
int outv;
char *string;
char *frc_dir_name;
char *frc_file_name;
FILE *DatF;
/* Functions called from within main */
/* All code is located in .c file with function name */
extern void FrcMenu();
extern void ReadCarFile();
extern void ReadMdfFile();
extern void ReadFrcFile();
extern void MakeLists();
extern void GetParameters(int);
extern void CheckLists();
extern void WriteDataFile(FILE *,char *,int);
outv = 2005;
pflag = 1;
forcefield = 1; /* Variable that identifies forcefield to use */
frc_file_name = (char *) calloc(160,sizeof(char));
frc_dir_name = (char *) calloc(160,sizeof(char));
frc_dir_name = getenv("BIOSYM_LIBRARY");
if (frc_dir_name == NULL) {
frc_file_name = strcpy(frc_file_name,"./cvff.frc");
}
else {
for (i=0; i < strlen(frc_dir_name); i++)
frc_file_name[i] = frc_dir_name[i];
frc_file_name = strcat(frc_file_name,"/cvff.frc");
}
if (argc < 2) { /* If no rootname was supplied, prompt for it */
fprintf(stderr,"The rootname of the .car and .mdf files must be entered\n");
}
else /* rootname was supplied as first argument, copy to rootname */
sprintf(rootname,"%s",argv[1]);
n = 2;
while (n < argc) {
if (strcmp(argv[n],"-class") == 0) {
if (strcmp(argv[n+1],"I") == 0) {
forcefield = 1;
n++;
}
else if (strcmp(argv[n+1],"II") == 0) {
forcefield = 2;
n++;
}
else {
fprintf(stderr,"Unrecognized Forcefield class: %s\n",
argv[n+1]);
n++;
}
}
else if (strcmp(argv[n],"-2001") == 0) {
outv = 2001;
n++;
}
else if (strcmp(argv[n],"-frc") == 0) {
if ((frc_dir_name != NULL) && (argv[n+1][0] != '.')) {
for (i=0; i < strlen(frc_dir_name); i++) {
frc_file_name[i] = frc_dir_name[i];
}
frc_file_name[strlen(frc_dir_name)] = '\0';
frc_file_name = strcat(frc_file_name,"/");
frc_file_name = strcat(frc_file_name,argv[n+1]);
}
else {
frc_file_name = strcpy(frc_file_name,argv[n+1]);
}
found_dot = 0;
for (i=1; i < strlen(frc_file_name); i++) {
if (frc_file_name[i] == '.') found_dot = 1;
}
if (found_dot == 0)
frc_file_name = strcat(frc_file_name,".frc");
n++;
}
else if (strstr(argv[n],"-p") != NULL) {
pflag = atoi(argv[n+1]);
n++;
}
else {
fprintf(stderr,"Unrecognized option: %s\n",argv[n]);
}
n++;
}
for (i=0; i < strlen(frc_file_name); i++)
FrcFileName[i] = frc_file_name[i];
free(frc_file_name);
if (pflag > 0) {
fprintf(stderr,"\nRunning Msi2lmp.....\n\n");
fprintf(stderr," Forcefield file name: %s\n",FrcFileName);
fprintf(stderr," Forcefield class: %d\n\n",forcefield);
}
if (((forcefield == 1) && (strstr(FrcFileName,"cff") != NULL) ||
(forcefield == 2) && (strstr(FrcFileName,"cvff") != NULL))) {
fprintf(stderr," WARNING - forcefield name and class appear to\n");
fprintf(stderr," be inconsistent - Errors may result\n\n");
}
/* Read in .car file */
ReadCarFile();
/*Read in .mdf file */
ReadMdfFile();
/* Define bonds, angles, etc...*/
if (pflag > 0) fprintf(stderr,"\n Building internal coordinate lists \n");
MakeLists();
/* Read .frc file into memory */
if (pflag > 0) fprintf(stderr,"\n Reading forcefield file \n");
ReadFrcFile();
/* Get forcefield parameters */
if (pflag > 0) fprintf(stderr,"\n Get parameters for this molecular system\n");
GetParameters(forcefield);
/* Do internal check of internal coordinate lists */
if (pflag > 0) fprintf(stderr,"\n Check parameters for internal consistency\n");
CheckLists();
if (outv == 2001) { fprintf(stderr,"\n Writing LAMMPS 2001 data file\n");
WriteDataFile01(rootname,forcefield);
}
else if (outv == 2005) {fprintf(stderr,"\n Writing LAMMPS 2005 data file\n");
WriteDataFile05(rootname,forcefield);
}
if (pflag > 0) fprintf(stderr,"\nNormal program termination\n");
}
#include <ctype.h>
int blank_line(char *line)
{
int i,n;
for (i=0,n=0; i < strlen(line); i++) {
if (isalnum((unsigned char)line[i])) n++;
}
if (n > 0) {
return(0);
}
else {
return(1);
}
}

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