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