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 /* Removes the charge groups, i.e. makes single atom charge groups, in mtop */
  54 void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop);
  55
  56
  57 /* Abstract data type for looking up atoms by global atom number */
  58 typedef struct gmx_mtop_atomlookup *gmx_mtop_atomlookup_t;
  59
  60 /* Initialize atom lookup by global atom number */
  61 gmx_mtop_atomlookup_t
  62 gmx_mtop_atomlookup_init(const gmx_mtop_t *mtop);
  63
  64 /* As gmx_mtop_atomlookup_init, but optimized for atoms involved in settle */
  65 gmx_mtop_atomlookup_t
  66 gmx_mtop_atomlookup_settle_init(const gmx_mtop_t *mtop);
  67
  68 /* Destroy a gmx_mtop_atomlookup_t data structure */
  69 void
  70 gmx_mtop_atomlookup_destroy(gmx_mtop_atomlookup_t alook);
  71
  72
  73 /* Returns a pointer to the t_atom struct belonging to atnr_global.
  74  * This can be an expensive operation, so if possible use
  75  * one of the atom loop constructs below.
  76  */
  77 void
  78 gmx_mtop_atomnr_to_atom(const gmx_mtop_atomlookup_t alook,
  79                         int atnr_global,
  80                         t_atom **atom);
  81
  82
  83 /* Returns a pointer to the molecule interaction array ilist_mol[F_NRE]
  84  * and the local atom number in the molecule belonging to atnr_global.
  85  */
  86 void
  87 gmx_mtop_atomnr_to_ilist(const gmx_mtop_atomlookup_t alook,
  88                          int atnr_global,
  89                          t_ilist **ilist_mol,int *atnr_offset);
  90
  91
  92 /* Returns the molecule block index
  93  * and the molecule number in the block
  94  * and the atom number offset for the atom indices in moltype
  95  * belonging to atnr_global.
  96  */
  97 void
  98 gmx_mtop_atomnr_to_molblock_ind(const gmx_mtop_atomlookup_t alook,
  99                                 int atnr_global,
 100                                 int *molb,int *molnr,int *atnr_mol);
 101
 102
 103 /* Returns atom name, global resnr and residue name  of atom atnr_global */
 104 void
 105 gmx_mtop_atominfo_global(const gmx_mtop_t *mtop,int atnr_global,
 106                          char **atomname,int *resnr,char **resname);
 107
 108
 109 /* Abstract type for atom loop over all atoms */
 110 typedef struct gmx_mtop_atomloop_all *gmx_mtop_atomloop_all_t;
 111
 112 /* Initialize an atom loop over all atoms in the system.
 113  * The order of the atoms will be as in the state struct.
 114  * Only use this when you really need to loop over all atoms,
 115  * i.e. when you use groups which might differ per molecule,
 116  * otherwise use gmx_mtop_atomloop_block.
 117  */
 118 gmx_mtop_atomloop_all_t
 119 gmx_mtop_atomloop_all_init(const gmx_mtop_t *mtop);
 120
 121 /* Loop to the next atom.
 122  * When not at the end:
 123  *   returns TRUE and at_global,
 124  *   writes the global atom number in *at_global
 125  *   and sets the pointer atom to the t_atom struct of that atom.
 126  * When at the end, destroys aloop and returns FALSE.
 127  * Use as:
 128  * gmx_mtop_atomloop_all_t aloop;
 129  * aloop = gmx_mtop_atomloop_all_init(mtop)
 130  * while (gmx_mtop_atomloop_all_next(aloop,&at_global,&atom)) {
 131  *     ...
 132  * }
 133  */
 134 gmx_bool
 135 gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
 136                            int *at_global,t_atom **atom);
 137
 138 /* Return the atomname, the residue number and residue name
 139  * of the current atom in the loop.
 140  */
 141 void
 142 gmx_mtop_atomloop_all_names(gmx_mtop_atomloop_all_t aloop,
 143                             char **atomname,int *resnr,char **resname);
 144
 145 /* Return the a pointer to the moltype struct of the current atom
 146  * in the loop and the atom number in the molecule.
 147  */
 148 void
 149 gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
 150                               gmx_moltype_t **moltype,int *at_mol);
 151
 152
 153 /* Abstract type for atom loop over atoms in all molecule blocks */
 154 typedef struct gmx_mtop_atomloop_block *gmx_mtop_atomloop_block_t;
 155
 156 /* Initialize an atom loop over atoms in all molecule blocks the system.
 157  */
 158 gmx_mtop_atomloop_block_t
 159 gmx_mtop_atomloop_block_init(const gmx_mtop_t *mtop);
 160
 161 /* Loop to the next atom.
 162  * When not at the end:
 163  *   returns TRUE
 164  *   sets the pointer atom to the t_atom struct of that atom
 165  *   and return the number of molecules corresponding to this atom.
 166  * When at the end, destroys aloop and returns FALSE.
 167  * Use as:
 168  * gmx_mtop_atomloop_block_t aloop;
 169  * aloop = gmx_mtop_atomloop_block_init(mtop)
 170  * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
 171  *     ...
 172  * }
 173  */
 174 gmx_bool
 175 gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
 176                              t_atom **atom,int *nmol);
 177
 178
 179 /* Abstract type for ilist loop over all ilists */
 180 typedef struct gmx_mtop_ilistloop *gmx_mtop_ilistloop_t;
 181
 182 /* Initialize an ilist loop over all molecule types in the system. */
 183 gmx_mtop_ilistloop_t
 184 gmx_mtop_ilistloop_init(const gmx_mtop_t *mtop);
 185
 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 number of molecules for this ilist in *nmol.
 191  * When at the end, destroys iloop and returns FALSE.
 192  */
 193 gmx_bool
 194 gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
 195                         t_ilist **ilist_mol,int *nmol);
 196
 197
 198 /* Abstract type for ilist loop over all ilists of all molecules */
 199 typedef struct gmx_mtop_ilistloop_all *gmx_mtop_ilistloop_all_t;
 200
 201 /* Initialize an ilist loop over all molecule types in the system.
 202  * Only use this when you really need to loop over all molecules,
 203  * i.e. when you use groups which might differ per molecule,
 204  * otherwise use gmx_mtop_ilistloop.
 205  */
 206 gmx_mtop_ilistloop_all_t
 207 gmx_mtop_ilistloop_all_init(const gmx_mtop_t *mtop);
 208
 209 /* Loop to the next molecule,
 210  * When not at the end:
 211  *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 212  *   writes the atom offset which should be added to iatoms in atnr_offset.
 213  * When at the end, destroys iloop and returns FALSE.
 214  */
 215 gmx_bool
 216 gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
 217                             t_ilist **ilist_mol,int *atnr_offset);
 218
 219
 220 /* Returns the total number of interactions in the system of type ftype */
 221 int
 222 gmx_mtop_ftype_count(const gmx_mtop_t *mtop,int ftype);
 223
 224
 225 /* Returns a charge group index for the whole system */
 226 t_block
 227 gmx_mtop_global_cgs(const gmx_mtop_t *mtop);
 228
 229
 230 /* Returns a single t_atoms struct for the whole system */
 231 t_atoms
 232 gmx_mtop_global_atoms(const gmx_mtop_t *mtop);
 233
 234
 235 /* Make all charge groups the size of one atom.
 236  * When bKeepSingleMolCG==TRUE keep charge groups for molecules
 237  * that consist of a single charge group.
 238  */
 239 void
 240 gmx_mtop_make_atomic_charge_groups(gmx_mtop_t *mtop,gmx_bool bKeepSingleMolCG);
 241
 242
 243 /* Generate a 'local' topology for the whole system.
 244  * When ir!=NULL the free energy interactions will be sorted to the end.
 245  */
 246 gmx_localtop_t *
 247 gmx_mtop_generate_local_top(const gmx_mtop_t *mtop,const t_inputrec *ir);
 248
 249
 250 /* Converts a gmx_mtop_t struct to t_topology.
 251  * All memory relating only to mtop will be freed.
 252  */
 253 t_topology
 254 gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop);
 255
 256 #ifdef __cplusplus
 257 }
 258 #endif
 259