include/mtop_util.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
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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "typedefs.h"
  40
  41 #ifdef __cplusplus
  42 extern "C" {
  43 #endif
  44
  45 /* Should be called after generating or reading mtop,
  46  * to set some compute intesive variables to avoid
  47  * N^2 operations later on.
  48  */
  49 extern void
  50 gmx_mtop_finalize(gmx_mtop_t *mtop);
  51
  52
  53 /* Returns the total number of charge groups in mtop */
  54 extern int
  55 ncg_mtop(const gmx_mtop_t *mtop);
  56
  57
  58 /* Returns a pointer to the t_atom struct belonging to atnr_global.
  59  * This can be an expensive operation, so if possible use
  60  * one of the atom loop constructs below.
  61  */
  62 extern void
  63 gmx_mtop_atomnr_to_atom(const gmx_mtop_t *mtop,int atnr_global,
  64                         t_atom **atom);
  65
  66
  67 /* Returns a pointer to the molecule interaction array ilist_mol[F_NRE]
  68  * and the local atom number in the molecule belonging to atnr_global.
  69  */
  70 extern void
  71 gmx_mtop_atomnr_to_ilist(const gmx_mtop_t *mtop,int atnr_global,
  72                          t_ilist **ilist_mol,int *atnr_offset);
  73
  74
  75 /* Returns the molecule block index
  76  * and the molecule number in the block
  77  * and the atom number offset for the atom indices in moltype
  78  * belonging to atnr_global.
  79  */
  80 extern void
  81 gmx_mtop_atomnr_to_molblock_ind(const gmx_mtop_t *mtop,int atnr_global,
  82                                 int *molb,int *molnr,int *atnr_mol);
  83
  84
  85 /* Returns atom name, global resnr and residue name  of atom atnr_global */
  86 extern void
  87 gmx_mtop_atominfo_global(const gmx_mtop_t *mtop,int atnr_global,
  88                          char **atomname,int *resnr,char **resname);
  89
  90
  91 /* Abstract type for atom loop over all atoms */
  92 typedef struct gmx_mtop_atomloop_all *gmx_mtop_atomloop_all_t;
  93
  94 /* Initialize an atom loop over all atoms in the system.
  95  * The order of the atoms will be as in the state struct.
  96  * Only use this when you really need to loop over all atoms,
  97  * i.e. when you use groups which might differ per molecule,
  98  * otherwise use gmx_mtop_atomloop_block.
  99  */
 100 extern gmx_mtop_atomloop_all_t
 101 gmx_mtop_atomloop_all_init(const gmx_mtop_t *mtop);
 102
 103 /* Loop to the next atom.
 104  * When not at the end:
 105  *   returns TRUE and at_global,
 106  *   writes the global atom number in *at_global
 107  *   and sets the pointer atom to the t_atom struct of that atom.
 108  * When at the end, destroys aloop and returns FALSE.
 109  * Use as:
 110  * gmx_mtop_atomloop_all_t aloop;
 111  * aloop = gmx_mtop_atomloop_all_init(mtop)
 112  * while (gmx_mtop_atomloop_all_next(aloop,&at_global,&atom)) {
 113  *     ...
 114  * }
 115  */
 116 extern bool
 117 gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
 118                            int *at_global,t_atom **atom);
 119
 120 /* Return the atomname, the residue number and residue name
 121  * of the current atom in the loop.
 122  */
 123 extern void
 124 gmx_mtop_atomloop_all_names(gmx_mtop_atomloop_all_t aloop,
 125                             char **atomname,int *resnr,char **resname);
 126
 127 /* Return the a pointer to the moltype struct of the current atom
 128  * in the loop and the atom number in the molecule.
 129  */
 130 extern void
 131 gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
 132                               gmx_moltype_t **moltype,int *at_mol);
 133
 134
 135 /* Abstract type for atom loop over atoms in all molecule blocks */
 136 typedef struct gmx_mtop_atomloop_block *gmx_mtop_atomloop_block_t;
 137
 138 /* Initialize an atom loop over atoms in all molecule blocks the system.
 139  */
 140 extern gmx_mtop_atomloop_block_t
 141 gmx_mtop_atomloop_block_init(const gmx_mtop_t *mtop);
 142
 143 /* Loop to the next atom.
 144  * When not at the end:
 145  *   returns TRUE
 146  *   sets the pointer atom to the t_atom struct of that atom
 147  *   and return the number of molecules corresponding to this atom.
 148  * When at the end, destroys aloop and returns FALSE.
 149  * Use as:
 150  * gmx_mtop_atomloop_block_t aloop;
 151  * aloop = gmx_mtop_atomloop_block_init(mtop)
 152  * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
 153  *     ...
 154  * }
 155  */
 156 extern bool
 157 gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
 158                              t_atom **atom,int *nmol);
 159
 160
 161 /* Abstract type for ilist loop over all ilists */
 162 typedef struct gmx_mtop_ilistloop *gmx_mtop_ilistloop_t;
 163
 164 /* Initialize an ilist loop over all molecule types in the system. */
 165 extern gmx_mtop_ilistloop_t
 166 gmx_mtop_ilistloop_init(const gmx_mtop_t *mtop);
 167
 168
 169 /* Loop to the next molecule,
 170  * When not at the end:
 171  *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 172  *   writes the number of molecules for this ilist in *nmol.
 173  * When at the end, destroys iloop and returns FALSE.
 174  */
 175 extern bool
 176 gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
 177                         t_ilist **ilist_mol,int *nmol);
 178
 179
 180 /* Abstract type for ilist loop over all ilists of all molecules */
 181 typedef struct gmx_mtop_ilistloop_all *gmx_mtop_ilistloop_all_t;
 182
 183 /* Initialize an ilist loop over all molecule types in the system.
 184  * Only use this when you really need to loop over all molecules,
 185  * i.e. when you use groups which might differ per molecule,
 186  * otherwise use gmx_mtop_ilistloop.
 187  */
 188 extern gmx_mtop_ilistloop_all_t
 189 gmx_mtop_ilistloop_all_init(const gmx_mtop_t *mtop);
 190
 191 /* Loop to the next molecule,
 192  * When not at the end:
 193  *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 194  *   writes the atom offset which should be added to iatoms in atnr_offset.
 195  * When at the end, destroys iloop and returns FALSE.
 196  */
 197 extern bool
 198 gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
 199                             t_ilist **ilist_mol,int *atnr_offset);
 200
 201
 202 /* Returns the total number of interactions in the system of type ftype */
 203 extern int
 204 gmx_mtop_ftype_count(const gmx_mtop_t *mtop,int ftype);
 205
 206
 207 /* Returns a charge group index for the whole system */
 208 extern t_block
 209 gmx_mtop_global_cgs(const gmx_mtop_t *mtop);
 210
 211
 212 /* Returns a single t_atoms struct for the whole system */
 213 extern t_atoms
 214 gmx_mtop_global_atoms(const gmx_mtop_t *mtop);
 215
 216
 217 /* Make all charge groups the size of one atom.
 218  * When bKeepSingleMolCG==TRUE keep charge groups for molecules
 219  * that consist of a single charge group.
 220  */
 221 extern void
 222 gmx_mtop_make_atomic_charge_groups(gmx_mtop_t *mtop,bool bKeepSingleMolCG);
 223
 224
 225 /* Generate a 'local' topology for the whole system.
 226  * When ir!=NULL the free energy interactions will be sorted to the end.
 227  */
 228 extern gmx_localtop_t *
 229 gmx_mtop_generate_local_top(const gmx_mtop_t *mtop,const t_inputrec *ir);
 230
 231
 232 /* Converts a gmx_mtop_t struct to t_topology.
 233  * All memory relating only to mtop will be freed.
 234  */
 235 extern t_topology
 236 gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop);
 237
 238 #ifdef __cplusplus
 239 }
 240 #endif
 241