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lammps/tools/msi2lmp/src/msi2lmp.h
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msi2lmp.h
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/********************************
*
* Header file for msi2lmp conversion program.
*
* This is the header file for the third version of a program
* that generates a LAMMPS data file based on the information
* in an 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
* 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 derving atom numbers was quadratic in time)
* and to make the program fully dynamic. The second version used
* fixed dimension arrays for the internal coordinates.
*
* The thrid version was revised in Fall 2011 by
* Stephanie Teich-McGoldrick to add support non-orthogonal cells.
*
* The next revision was done in Summer 2013 by
* Axel Kohlmeyer to improve portability to Windows compilers,
* clean up command line parsing and improve compatibility with
* the then current LAMMPS versions. This revision removes
* compatibility with the obsolete LAMMPS version written in Fortran 90.
*/
# include <stdio.h>
#define PI_180 0.01745329251994329576
#define MAX_LINE_LENGTH 256
#define MAX_CONNECTIONS 8
#define MAX_STRING 64
#define MAX_NAME 16
#define MAX_ATOM_TYPES 100
#define MAX_BOND_TYPES 200
#define MAX_ANGLE_TYPES 300
#define MAX_DIHEDRAL_TYPES 400
#define MAX_OOP_TYPES 400
#define MAX_ANGLEANGLE_TYPES 400
#define MAX_TYPES 12000
#define FF_TYPE_COMMON 1<<0
#define FF_TYPE_CLASS1 1<<1
#define FF_TYPE_CLASS2 1<<2
#define FF_TYPE_OPLSAA 1<<3
struct ResidueList {
int start;
int end;
char name[MAX_NAME];
};
struct MoleculeList {
int start;
int end;
int no_residues;
struct ResidueList *residue;
};
/* Internal coodinate Lists */
struct BondList {
int type;
int members[2];
};
struct AngleList {
int type;
int members[3];
};
struct DihedralList {
int type;
int members[4];
};
struct OOPList {
int type;
int members[4];
};
struct AngleAngleList {
int type;
int members[4];
};
/* Internal coodinate Types Lists */
struct AtomTypeList
{
char potential[5];
double mass;
double params[2];
int no_connect;
};
struct BondTypeList {
int types[2];
double params[4];
};
struct AngleTypeList {
int types[3];
double params[4];
double bondangle_cross_term[4];
double bondbond_cross_term[3];
};
struct DihedralTypeList {
int types[4];
double params[6];
double endbonddihedral_cross_term[8];
double midbonddihedral_cross_term[4];
double angledihedral_cross_term[8];
double angleangledihedral_cross_term[3];
double bond13_cross_term[3];
};
struct OOPTypeList {
int types[4];
double params[3];
double angleangle_params[6];
};
struct AngleAngleTypeList {
int types[4];
double params[6];
};
/* ---------------------------------------------- */
struct Atom {
int molecule; /* molecule id */
int no; /* atom id */
char name[MAX_NAME]; /* atom name */
double x[3]; /* position vector */
int image[3]; /* image flag */
char potential[6]; /* atom potential type */
char element[4]; /* atom element */
double q; /* charge */
char residue_string[MAX_NAME]; /* residue string */
int no_connect; /* number of connections to atom */
char connections[MAX_CONNECTIONS][MAX_STRING]; /* long form, connection name*/
double bond_order[MAX_CONNECTIONS];
int conn_no[MAX_CONNECTIONS]; /* Atom number to which atom is connected */
int type;
};
extern char *rootname;
extern char *FrcFileName;
extern double pbc[6]; /* A, B, C, alpha, beta, gamma */
extern double box[3][3]; /* hi/lo for x/y/z and xy, xz, yz for triclinic */
extern double shift[3]; /* shift vector for all coordinates and box positions */
extern int periodic; /* 0= nonperiodic 1= 3-D periodic */
extern int TriclinicFlag; /* 0= Orthogonal 1= Triclinic */
extern int forcefield; /* BitMask: the value FF_TYPE_COMMON is set for common components of the options below,
* FF_TYPE_CLASS1 = ClassI, FF_TYPE_CLASS2 = ClassII, FF_TYPE_OPLSAA = OPLS-AA*/
extern int centerflag; /* 1= center box 0= keep box */
extern int pflag; /* print level: 0, 1, 2, 3 */
extern int iflag; /* 0 stop at errors 1 = ignore errors */
extern int *no_atoms;
extern int no_molecules;
extern int replicate[3];
extern int total_no_atoms;
extern int total_no_bonds;
extern int total_no_angles;
extern int total_no_dihedrals;
extern int total_no_angle_angles;
extern int total_no_oops;
extern int no_atom_types;
extern int no_bond_types;
extern int no_angle_types;
extern int no_dihedral_types;
extern int no_oop_types;
extern int no_angleangle_types;
extern FILE *CarF;
extern FILE *FrcF;
extern FILE *PrmF;
extern FILE *MdfF;
extern FILE *RptF;
extern struct Atom *atoms;
extern struct MoleculeList *molecule;
extern struct BondList *bonds;
extern struct AngleList *angles;
extern struct DihedralList *dihedrals;
extern struct OOPList *oops;
extern struct AngleAngleList *angleangles;
extern struct AtomTypeList *atomtypes;
extern struct BondTypeList *bondtypes;
extern struct AngleTypeList *angletypes;
extern struct DihedralTypeList *dihedraltypes;
extern struct OOPTypeList *ooptypes;
extern struct AngleAngleTypeList *angleangletypes;
extern void FrcMenu();
extern void ReadCarFile();
extern void ReadMdfFile();
extern void ReadFrcFile();
extern void ClearFrcData();
extern void MakeLists();
extern void GetParameters();
extern void CheckLists();
extern void WriteDataFile(char *);
extern void set_box(double box[3][3], double *h, double *h_inv);
extern void lamda2x(double *lamda, double *x, double *h, double *boxlo);
extern void x2lamda(double *x, double *lamda, double *h_inv, double *boxlo);
extern void condexit(int);
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