include/types/topology.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
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  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * GRoups of Organic Molecules in ACtion for Science
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 enum {
  40   egcTC,    egcENER,   egcACC, egcFREEZE,
  41   egcUser1, egcUser2,  egcVCM, egcXTC,
  42   egcORFIT, egcQMMM,
  43   egcNR
  44 };
  45
  46 typedef struct {
  47   char          **name;         /* Name of the molecule type            */
  48   t_atoms       atoms;          /* The atoms                            */
  49   t_ilist       ilist[F_NRE];
  50   t_block       cgs;            /* The charge groups                    */
  51   t_blocka      excls;          /* The exclusions                       */
  52 } gmx_moltype_t;
  53
  54 typedef struct {
  55   int           type;           /* The molcule type index in mtop.moltype */
  56   int           nmol;           /* The number of molecules in this block  */
  57   int           natoms_mol;     /* The number of atoms in one molecule    */
  58   int           nposres_xA;     /* The number of posres coords for top A  */
  59   rvec          *posres_xA;     /* The posres coords for top A            */
  60   int           nposres_xB;     /* The number of posres coords for top B  */
  61   rvec          *posres_xB;     /* The posres coords for top B            */
  62 } gmx_molblock_t;
  63
  64 typedef struct {
  65   t_grps         grps[egcNR];   /* Groups of things                     */
  66   int            ngrpname;      /* Number of groupnames                 */
  67   char           ***grpname;    /* Names of the groups                  */
  68   int            ngrpnr[egcNR];
  69   unsigned char  *grpnr[egcNR]; /* Group numbers or NULL                */
  70 } gmx_groups_t;
  71
  72 /* This macro gives the group number of group type egc for atom i.
  73  * This macro is useful, since the grpnr pointers are NULL
  74  * for group types that have all entries 0.
  75  */
  76 #define ggrpnr(groups,egc,i) ((groups)->grpnr[egc] ? (groups)->grpnr[egc][i] : 0)
  77
  78 /* The global topology struct, based on molecule types */
  79 typedef struct {
  80   char           **name;        /* Name of the topology                 */
  81   gmx_ffparams_t ffparams;
  82   int            nmoltype;
  83   gmx_moltype_t  *moltype;
  84   int            nmolblock;
  85   gmx_molblock_t *molblock;
  86   int            natoms;
  87   t_atomtypes    atomtypes;     /* Atomtype properties                  */
  88   t_block        mols;          /* The molecules                        */
  89   gmx_groups_t   groups;
  90   t_symtab       symtab;        /* The symbol table                     */
  91   gmx_cmap_t     cmap_grid;
  92 } gmx_mtop_t;
  93
  94 /* The mdrun local topology struct, completely written out */
  95 typedef struct {
  96   t_idef        idef;           /* The interaction function definition  */
  97   t_atomtypes   atomtypes;      /* Atomtype properties                  */
  98   t_block       cgs;            /* The charge groups                    */
  99   t_blocka      excls;          /* The exclusions                       */
 100 } gmx_localtop_t;
 101
 102 /* The old topology struct, completely written out, used in analysis tools */
 103 typedef struct {
 104   char          **name;         /* Name of the topology                 */
 105   t_idef        idef;           /* The interaction function definition  */
 106   t_atoms       atoms;          /* The atoms                            */
 107   t_atomtypes   atomtypes;      /* Atomtype properties                  */
 108   t_block       cgs;            /* The charge groups                    */
 109   t_block       mols;           /* The molecules                        */
 110   t_blocka      excls;          /* The exclusions                       */
 111   t_symtab      symtab;         /* The symbol table                     */
 112 } t_topology;