libgromacs-dev 2016.1-2 / usr / include / gromacs / topology / topology.h

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2011,2014,2015, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */
#ifndef GMX_TOPOLOGY_TOPOLOGY_H
#define GMX_TOPOLOGY_TOPOLOGY_H

#include <cstdio>

#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
};
/* Names corresponding to groups */
extern const char *gtypes[egcNR+1];

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 */

void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
             gmx_bool bShowNumbers);
void pr_top(FILE *fp, int indent, const char *title, const t_topology *top, gmx_bool bShowNumbers);

#ifdef __cplusplus
}
#endif

#endif