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
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   9  *                        VERSION 3.2.0
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  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
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  34  */
  35
  36 #include "atoms.h"
  37 #include "idef.h"
  38 #include "block.h"
  39 #include "simple.h"
  40 #include "symtab.h"
  41
  42 #ifdef __cplusplus
  43 extern "C" {
  44 #endif
  45
  46 enum {
  47   egcTC,    egcENER,   egcACC, egcFREEZE,
  48   egcUser1, egcUser2,  egcVCM, egcXTC,
  49   egcORFIT, egcQMMM,
  50   egcNR
  51 };
  52
  53 typedef struct {
  54   char          **name;         /* Name of the molecule type            */
  55   t_atoms       atoms;          /* The atoms                            */
  56   t_ilist       ilist[F_NRE];
  57   t_block       cgs;            /* The charge groups                    */
  58   t_blocka      excls;          /* The exclusions                       */
  59 } gmx_moltype_t;
  60
  61 typedef struct {
  62   int           type;           /* The molcule type index in mtop.moltype */
  63   int           nmol;           /* The number of molecules in this block  */
  64   int           natoms_mol;     /* The number of atoms in one molecule    */
  65   int           nposres_xA;     /* The number of posres coords for top A  */
  66   rvec          *posres_xA;     /* The posres coords for top A            */
  67   int           nposres_xB;     /* The number of posres coords for top B  */
  68   rvec          *posres_xB;     /* The posres coords for top B            */
  69 } gmx_molblock_t;
  70
  71 typedef struct {
  72   t_grps         grps[egcNR];   /* Groups of things                     */
  73   int            ngrpname;      /* Number of groupnames                 */
  74   char           ***grpname;    /* Names of the groups                  */
  75   int            ngrpnr[egcNR];
  76   unsigned char  *grpnr[egcNR]; /* Group numbers or NULL                */
  77 } gmx_groups_t;
  78
  79 /* This macro gives the group number of group type egc for atom i.
  80  * This macro is useful, since the grpnr pointers are NULL
  81  * for group types that have all entries 0.
  82  */
  83 #define ggrpnr(groups,egc,i) ((groups)->grpnr[egc] ? (groups)->grpnr[egc][i] : 0)
  84
  85 /* The global, complete system topology struct, based on molecule types.
  86    This structure should contain no data that is O(natoms) in memory. */
  87 typedef struct {
  88   char           **name;        /* Name of the topology                 */
  89   gmx_ffparams_t ffparams;
  90   int            nmoltype;
  91   gmx_moltype_t  *moltype;
  92   int            nmolblock;
  93   gmx_molblock_t *molblock;
  94   int            natoms;
  95   int            maxres_renum;  /* Parameter for residue numbering      */
  96   int            maxresnr;      /* The maximum residue number in moltype */
  97   t_atomtypes    atomtypes;     /* Atomtype properties                  */
  98   t_block        mols;          /* The molecules                        */
  99   gmx_groups_t   groups;
 100   t_symtab       symtab;        /* The symbol table                     */
 101 } gmx_mtop_t;
 102
 103 /* The mdrun node-local topology struct, completely written out */
 104 typedef struct {
 105   t_idef        idef;           /* The interaction function definition  */
 106   t_atomtypes   atomtypes;      /* Atomtype properties                  */
 107   t_block       cgs;            /* The charge groups                    */
 108   t_blocka      excls;          /* The exclusions                       */
 109 } gmx_localtop_t;
 110
 111 /* The old topology struct, completely written out, used in analysis tools */
 112 typedef struct {
 113   char          **name;         /* Name of the topology                 */
 114   t_idef        idef;           /* The interaction function definition  */
 115   t_atoms       atoms;          /* The atoms                            */
 116   t_atomtypes   atomtypes;      /* Atomtype properties                  */
 117   t_block       cgs;            /* The charge groups                    */
 118   t_block       mols;           /* The molecules                        */
 119   t_blocka      excls;          /* The exclusions                       */
 120   t_symtab      symtab;         /* The symbol table                     */
 121 } t_topology;
 122
 123 #ifdef __cplusplus
 124 }
 125 #endif
 126