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* This file is part of the GROMACS molecular simulation package.
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#ifndef GMX_TOPOLOGY_TOPOLOGY_H
#define GMX_TOPOLOGY_TOPOLOGY_H
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/symtab.h"
#ifdef __cplusplus
extern "C" {
#endif
enum {
egcTC, egcENER, egcACC, egcFREEZE,
egcUser1, egcUser2, egcVCM, egcCompressedX,
egcORFIT, egcQMMM,
egcNR
};
typedef struct gmx_moltype_t
{
char **name; /* Name of the molecule type */
t_atoms atoms; /* The atoms in this molecule */
t_ilist ilist[F_NRE]; /* Interaction list with local indices */
t_block cgs; /* The charge groups */
t_blocka excls; /* The exclusions */
} gmx_moltype_t;
typedef struct gmx_molblock_t
{
int type; /* The molcule type index in mtop.moltype */
int nmol; /* The number of molecules in this block */
int natoms_mol; /* The number of atoms in one molecule */
int nposres_xA; /* The number of posres coords for top A */
rvec *posres_xA; /* The posres coords for top A */
int nposres_xB; /* The number of posres coords for top B */
rvec *posres_xB; /* The posres coords for top B */
} gmx_molblock_t;
typedef struct gmx_groups_t
{
t_grps grps[egcNR]; /* Groups of things */
int ngrpname; /* Number of groupnames */
char ***grpname; /* Names of the groups */
int ngrpnr[egcNR];
unsigned char *grpnr[egcNR]; /* Group numbers or NULL */
} gmx_groups_t;
/* This macro gives the group number of group type egc for atom i.
* This macro is useful, since the grpnr pointers are NULL
* for group types that have all entries 0.
*/
#define ggrpnr(groups, egc, i) ((groups)->grpnr[egc] ? (groups)->grpnr[egc][i] : 0)
/* The global, complete system topology struct, based on molecule types.
This structure should contain no data that is O(natoms) in memory. */
typedef struct gmx_mtop_t
{
char **name; /* Name of the topology */
gmx_ffparams_t ffparams;
int nmoltype;
gmx_moltype_t *moltype;
int nmolblock;
gmx_molblock_t *molblock;
gmx_bool bIntermolecularInteractions; /* Are there intermolecular
* interactions? */
t_ilist *intermolecular_ilist; /* List of intermolecular interactions
* using system wide atom indices,
* either NULL or size F_NRE */
int natoms;
int maxres_renum; /* Parameter for residue numbering */
int maxresnr; /* The maximum residue number in moltype */
t_atomtypes atomtypes; /* Atomtype properties */
t_block mols; /* The molecules */
gmx_groups_t groups;
t_symtab symtab; /* The symbol table */
} gmx_mtop_t;
/* The mdrun node-local topology struct, completely written out */
typedef struct gmx_localtop_t
{
t_idef idef; /* The interaction function definition */
t_atomtypes atomtypes; /* Atomtype properties */
t_block cgs; /* The charge groups */
t_blocka excls; /* The exclusions */
} gmx_localtop_t;
/* The old topology struct, completely written out, used in analysis tools */
typedef struct t_topology
{
char **name; /* Name of the topology */
t_idef idef; /* The interaction function definition */
t_atoms atoms; /* The atoms */
t_atomtypes atomtypes; /* Atomtype properties */
t_block cgs; /* The charge groups */
t_block mols; /* The molecules */
gmx_bool bIntermolecularInteractions; /* Inter.mol. int. ? */
t_blocka excls; /* The exclusions */
t_symtab symtab; /* The symbol table */
} t_topology;
void init_mtop(gmx_mtop_t *mtop);
void init_top(t_topology *top);
void done_moltype(gmx_moltype_t *molt);
void done_molblock(gmx_molblock_t *molb);
void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab);
void done_top(t_topology *top);
t_atoms *mtop2atoms(gmx_mtop_t *mtop);
/* generate a t_atoms struct for the system from gmx_mtop_t */
#ifdef __cplusplus
}
#endif
#endif
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