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msi2lmp.c
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Thu, May 9, 23:46

msi2lmp.c
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/*
*
* msi2lmp.exe
*
* v3.9.4 AK- Make force field style hints optional with a flag
*
* v3.9.3 AK- Bugfix for triclinic cells.
*
* v3.9.2 AK- Support for writing out force field style hints
*
* v3.9.1 AK- Bugfix for Class2. Free allocated memory. Print version number.
*
* v3.9 AK - Rudimentary support for OPLS-AA
*
* v3.8 AK - Some refactoring and cleanup of global variables
* - Bugfixes for argument parsing and improper definitions
* - improved handling of box dimensions and image flags
* - port to compiling on windows using MinGW
* - more consistent print level handling
* - more consistent handling of missing parameters
* - Added a regression test script with examples.
*
* V3.7 STM - Added support for triclinic cells
*
* 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} {-ignore} {-nocenter} {-oldstyle}
*
* -- msi2lmp3 is the name of the executable
* -- ROOTNAME is the base name of the .car and .mdf files
* -- all opther flags are optional and can be abbreviated (e.g. -p instead of -print)
*
* -- -print
* # is the print level: 0 - silent except for errors
* 1 - minimal (default)
* 2 - more verbose
* 3 - even more verbose
* -- -class
* # is the class of forcefield to use (I or 1 = Class I e.g., CVFF, clayff)
* (II or 2 = Class II e.g., CFFx, COMPASS)
* (O or 0 = OPLS-AA)
* default is -class I
*
* -- -ignore - tells msi2lmp to ignore warnings and errors and keep going
*
* -- -nocenter - tells msi2lmp to not center the box around the (geometrical)
* center of the atoms, but around the origin
*
* -- -oldstyle - tells msi2lmp to write out a data file without style hints
* (to be compatible with older LAMMPS versions)
*
* -- -shift - tells msi2lmp to shift the entire system (box and coordinates)
* by a vector (default: 0.0 0.0 0.0)
*
* -- -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 $MSI2LMP_LIBRARY.
* If $MSI2LMP_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 $MSI2LMP_LIBRARY
* or .)
*
* -frc cff/cff91 (assumes cff91.frc is in
* $MSI2LMP_LIBRARY/cff or ./cff)
*
* -frc /usr/local/forcefields/cff95 (absolute
* location)
*
* By default, the program uses $MSI2LMP_LIBRARY/cvff.frc
*
* -- output is written to a file called ROOTNAME.data
*
*
****************************************************************
*
* 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
*/
#include "msi2lmp.h"
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
/* global variables */
char *rootname;
double pbc[6];
double box[3][3];
double shift[3];
int periodic = 1;
int TriclinicFlag = 0;
int forcefield = 0;
int centerflag = 1;
int hintflag = 1;
int pflag;
int iflag;
int *no_atoms;
int no_molecules;
int replicate[3];
int total_no_atoms = 0;
int total_no_bonds = 0;
int total_no_angles = 0;
int total_no_dihedrals = 0;
int total_no_angle_angles = 0;
int total_no_oops = 0;
int no_atom_types = 0;
int no_bond_types = 0;
int no_angle_types = 0;
int no_dihedral_types = 0;
int no_oop_types = 0;
int no_angleangle_types = 0;
char *FrcFileName = NULL;
FILE *CarF = NULL;
FILE *FrcF = NULL;
FILE *PrmF = NULL;
FILE *MdfF = NULL;
FILE *RptF = NULL;
struct Atom *atoms = NULL;
struct MoleculeList *molecule = NULL;
struct BondList *bonds = NULL;
struct AngleList *angles = NULL;
struct DihedralList *dihedrals = NULL;
struct OOPList *oops = NULL;
struct AngleAngleList *angleangles = NULL;
struct AtomTypeList *atomtypes = NULL;
struct BondTypeList *bondtypes = NULL;
struct AngleTypeList *angletypes = NULL;
struct DihedralTypeList *dihedraltypes = NULL;
struct OOPTypeList *ooptypes = NULL;
struct AngleAngleTypeList *angleangletypes = NULL;
void condexit(int val)
{
if (iflag == 0) exit(val);
}
static int check_arg(char **arg, const char *flag, int num, int argc)
{
if (num >= argc) {
printf("Missing argument to \"%s\" flag\n",flag);
return 1;
}
if (arg[num][0] == '-') {
printf("Incorrect argument to \"%s\" flag: %s\n",flag,arg[num]);
return 1;
}
return 0;
}
int main (int argc, char *argv[])
{
int n,i,found_sep;
const char *frc_dir_name = NULL;
const char *frc_file_name = NULL;
pflag = 1;
iflag = 0;
forcefield = FF_TYPE_CLASS1 | FF_TYPE_COMMON;
shift[0] = shift[1] = shift[2] = 0.0;
frc_dir_name = getenv("MSI2LMP_LIBRARY");
if (argc < 2) {
printf("usage: %s <rootname> [-class <I|1|II|2>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle]\n",argv[0]);
return 1;
} else { /* rootname was supplied as first argument, copy to rootname */
int len = strlen(argv[1]) + 1;
rootname = (char *)malloc(len);
strcpy(rootname,argv[1]);
}
n = 2;
while (n < argc) {
if (strncmp(argv[n],"-c",2) == 0) {
n++;
if (check_arg(argv,"-class",n,argc))
return 2;
if ((strcmp(argv[n],"I") == 0) || (strcmp(argv[n],"1") == 0)) {
forcefield = FF_TYPE_CLASS1 | FF_TYPE_COMMON;
} else if ((strcmp(argv[n],"II") == 0) || (strcmp(argv[n],"2") == 0)) {
forcefield = FF_TYPE_CLASS2 | FF_TYPE_COMMON;
} else if ((strcmp(argv[n],"O") == 0) || (strcmp(argv[n],"0") == 0)) {
forcefield = FF_TYPE_OPLSAA | FF_TYPE_COMMON;
} else {
printf("Unrecognized Forcefield class: %s\n",argv[n]);
return 3;
}
} else if (strncmp(argv[n],"-f",2) == 0) {
n++;
if (check_arg(argv,"-frc",n,argc))
return 4;
frc_file_name = argv[n];
} else if (strncmp(argv[n],"-s",2) == 0) {
if (n+3 > argc) {
printf("Missing argument(s) to \"-shift\" flag\n");
return 1;
}
shift[0] = atof(argv[++n]);
shift[1] = atof(argv[++n]);
shift[2] = atof(argv[++n]);
} else if (strncmp(argv[n],"-i",2) == 0 ) {
iflag = 1;
} else if (strncmp(argv[n],"-n",4) == 0 ) {
centerflag = 0;
} else if (strncmp(argv[n],"-o",4) == 0 ) {
hintflag = 0;
} else if (strncmp(argv[n],"-p",2) == 0) {
n++;
if (check_arg(argv,"-print",n,argc))
return 5;
pflag = atoi(argv[n]);
} else {
printf("Unrecognized option: %s\n",argv[n]);
return 6;
}
n++;
}
/* set defaults, if nothing else was given */
if (frc_dir_name == NULL)
#if (_WIN32)
frc_dir_name = "..\\frc_files";
#else
frc_dir_name = "../frc_files";
#endif
if (frc_file_name == NULL)
frc_file_name = "cvff.frc";
found_sep=0;
#ifdef _WIN32
if (isalpha(frc_file_name[0]) && (frc_file_name[1] == ':'))
found_sep=1; /* windows drive letter => full path. */
#endif
n = strlen(frc_file_name);
for (i=0; i < n; ++i) {
#ifdef _WIN32
if ((frc_file_name[i] == '/') || (frc_file_name[i] == '\\'))
found_sep=1+i;
#else
if (frc_file_name[i] == '/')
found_sep=1+i;
#endif
}
/* full pathname given */
if (found_sep) {
i = 0;
/* need to append extension? */
if ((n < 5) || (strcmp(frc_file_name+n-4,".frc") !=0))
i=1;
FrcFileName = (char *)malloc(n+1+i*4);
strcpy(FrcFileName,frc_file_name);
if (i) strcat(FrcFileName,".frc");
} else {
i = 0;
/* need to append extension? */
if ((n < 5) || (strcmp(frc_file_name+n-4,".frc") !=0))
i=1;
FrcFileName = (char *)malloc(n+2+i*4+strlen(frc_dir_name));
strcpy(FrcFileName,frc_dir_name);
#ifdef _WIN32
strcat(FrcFileName,"\\");
#else
strcat(FrcFileName,"/");
#endif
strcat(FrcFileName,frc_file_name);
if (i) strcat(FrcFileName,".frc");
}
if (pflag > 0) {
puts("\nRunning msi2lmp " MSI2LMP_VERSION "\n");
if (forcefield & FF_TYPE_CLASS1) puts(" Forcefield: Class I");
if (forcefield & FF_TYPE_CLASS2) puts(" Forcefield: Class II");
if (forcefield & FF_TYPE_OPLSAA) puts(" Forcefield: OPLS-AA");
printf(" Forcefield file name: %s\n",FrcFileName);
if (centerflag) puts(" Output is recentered around geometrical center");
if (hintflag) puts(" Output contains style flag hints");
else puts(" Style flag hints disabled");
printf(" System translated by: %g %g %g\n",shift[0],shift[1],shift[2]);
}
n = 0;
if (forcefield & FF_TYPE_CLASS1) {
if (strstr(FrcFileName,"cvff") != NULL) ++n;
if (strstr(FrcFileName,"clayff") != NULL) ++n;
} else if (forcefield & FF_TYPE_OPLSAA) {
if (strstr(FrcFileName,"oplsaa") != NULL) ++n;
} else if (forcefield & FF_TYPE_CLASS2) {
if (strstr(FrcFileName,"pcff") != NULL) ++n;
if (strstr(FrcFileName,"cff91") != NULL) ++n;
if (strstr(FrcFileName,"compass") != NULL) ++n;
}
if (n == 0) {
if (iflag > 0) fputs(" WARNING",stderr);
else fputs(" Error ",stderr);
fputs("- forcefield name and class appear to be inconsistent\n\n",stderr);
if (iflag == 0) return 7;
}
/* Read in .car file */
ReadCarFile();
/*Read in .mdf file */
ReadMdfFile();
/* Define bonds, angles, etc...*/
if (pflag > 0)
printf("\n Building internal coordinate lists \n");
MakeLists();
/* Read .frc file into memory */
if (pflag > 0)
printf("\n Reading forcefield file \n");
ReadFrcFile();
/* Get forcefield parameters */
if (pflag > 0)
printf("\n Get force field parameters for this system\n");
GetParameters();
/* Do internal check of internal coordinate lists */
if (pflag > 0)
printf("\n Check parameters for internal consistency\n");
CheckLists();
/* Write out the final data */
WriteDataFile(rootname);
/* free up memory to detect possible memory corruption */
free(rootname);
free(FrcFileName);
ClearFrcData();
for (n=0; n < no_molecules; n++) {
free(molecule[n].residue);
}
free(no_atoms);
free(molecule);
free(atoms);
free(atomtypes);
if (bonds) free(bonds);
if (bondtypes) free(bondtypes);
if (angles) free(angles);
if (angletypes) free(angletypes);
if (dihedrals) free(dihedrals);
if (dihedraltypes) free(dihedraltypes);
if (oops) free(oops);
if (ooptypes) free(ooptypes);
if (angleangles) free(angleangles);
if (angleangletypes) free(angleangletypes);
if (pflag > 0)
printf("\nNormal program termination\n");
return 0;
}

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