src/gromacs/legacyheaders/mtop_util.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
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  37 #include "typedefs.h"
  38
  39 #ifdef __cplusplus
  40 extern "C" {
  41 #endif
  42
  43 /* Should be called after generating or reading mtop,
  44  * to set some compute intesive variables to avoid
  45  * N^2 operations later on.
  46  */
  47 void
  48 gmx_mtop_finalize(gmx_mtop_t *mtop);
  49
  50 /* Counts the number of atoms of each type. State should be 0 for
  51  * state A and 1 for state B types.  typecount should have at
  52  * least mtop->ffparams.atnr elements.
  53  */
  54 void
  55 gmx_mtop_count_atomtypes(const gmx_mtop_t *mtop, int state, int typecount[]);
  56
  57 /* Returns the total number of charge groups in mtop */
  58 int
  59 ncg_mtop(const gmx_mtop_t *mtop);
  60
  61 /* Removes the charge groups, i.e. makes single atom charge groups, in mtop */
  62 void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop);
  63
  64
  65 /* Abstract data type for looking up atoms by global atom number */
  66 typedef struct gmx_mtop_atomlookup *gmx_mtop_atomlookup_t;
  67
  68 /* Initialize atom lookup by global atom number */
  69 gmx_mtop_atomlookup_t
  70 gmx_mtop_atomlookup_init(const gmx_mtop_t *mtop);
  71
  72 /* As gmx_mtop_atomlookup_init, but optimized for atoms involved in settle */
  73 gmx_mtop_atomlookup_t
  74 gmx_mtop_atomlookup_settle_init(const gmx_mtop_t *mtop);
  75
  76 /* Destroy a gmx_mtop_atomlookup_t data structure */
  77 void
  78 gmx_mtop_atomlookup_destroy(gmx_mtop_atomlookup_t alook);
  79
  80
  81 /* Returns a pointer to the t_atom struct belonging to atnr_global.
  82  * This can be an expensive operation, so if possible use
  83  * one of the atom loop constructs below.
  84  */
  85 void
  86 gmx_mtop_atomnr_to_atom(const gmx_mtop_atomlookup_t alook,
  87                         int                         atnr_global,
  88                         t_atom                    **atom);
  89
  90
  91 /* Returns a pointer to the molecule interaction array ilist_mol[F_NRE]
  92  * and the local atom number in the molecule belonging to atnr_global.
  93  */
  94 void
  95 gmx_mtop_atomnr_to_ilist(const gmx_mtop_atomlookup_t alook,
  96                          int atnr_global,
  97                          t_ilist **ilist_mol, int *atnr_offset);
  98
  99
 100 /* Returns the molecule block index
 101  * and the molecule number in the block
 102  * and the atom number offset for the atom indices in moltype
 103  * belonging to atnr_global.
 104  */
 105 void
 106 gmx_mtop_atomnr_to_molblock_ind(const gmx_mtop_atomlookup_t alook,
 107                                 int atnr_global,
 108                                 int *molb, int *molnr, int *atnr_mol);
 109
 110
 111 /* Returns atom name, global resnr and residue name  of atom atnr_global */
 112 void
 113 gmx_mtop_atominfo_global(const gmx_mtop_t *mtop, int atnr_global,
 114                          char **atomname, int *resnr, char **resname);
 115
 116
 117 /* Abstract type for atom loop over all atoms */
 118 typedef struct gmx_mtop_atomloop_all *gmx_mtop_atomloop_all_t;
 119
 120 /* Initialize an atom loop over all atoms in the system.
 121  * The order of the atoms will be as in the state struct.
 122  * Only use this when you really need to loop over all atoms,
 123  * i.e. when you use groups which might differ per molecule,
 124  * otherwise use gmx_mtop_atomloop_block.
 125  */
 126 gmx_mtop_atomloop_all_t
 127 gmx_mtop_atomloop_all_init(const gmx_mtop_t *mtop);
 128
 129 /* Loop to the next atom.
 130  * When not at the end:
 131  *   returns TRUE and at_global,
 132  *   writes the global atom number in *at_global
 133  *   and sets the pointer atom to the t_atom struct of that atom.
 134  * When at the end, destroys aloop and returns FALSE.
 135  * Use as:
 136  * gmx_mtop_atomloop_all_t aloop;
 137  * aloop = gmx_mtop_atomloop_all_init(mtop)
 138  * while (gmx_mtop_atomloop_all_next(aloop,&at_global,&atom)) {
 139  *     ...
 140  * }
 141  */
 142 gmx_bool
 143 gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
 144                            int *at_global, t_atom **atom);
 145
 146 /* Return the atomname, the residue number and residue name
 147  * of the current atom in the loop.
 148  */
 149 void
 150 gmx_mtop_atomloop_all_names(gmx_mtop_atomloop_all_t aloop,
 151                             char **atomname, int *resnr, char **resname);
 152
 153 /* Return the a pointer to the moltype struct of the current atom
 154  * in the loop and the atom number in the molecule.
 155  */
 156 void
 157 gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
 158                               gmx_moltype_t **moltype, int *at_mol);
 159
 160
 161 /* Abstract type for atom loop over atoms in all molecule blocks */
 162 typedef struct gmx_mtop_atomloop_block *gmx_mtop_atomloop_block_t;
 163
 164 /* Initialize an atom loop over atoms in all molecule blocks the system.
 165  */
 166 gmx_mtop_atomloop_block_t
 167 gmx_mtop_atomloop_block_init(const gmx_mtop_t *mtop);
 168
 169 /* Loop to the next atom.
 170  * When not at the end:
 171  *   returns TRUE
 172  *   sets the pointer atom to the t_atom struct of that atom
 173  *   and return the number of molecules corresponding to this atom.
 174  * When at the end, destroys aloop and returns FALSE.
 175  * Use as:
 176  * gmx_mtop_atomloop_block_t aloop;
 177  * aloop = gmx_mtop_atomloop_block_init(mtop)
 178  * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
 179  *     ...
 180  * }
 181  */
 182 gmx_bool
 183 gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
 184                              t_atom **atom, int *nmol);
 185
 186
 187 /* Abstract type for ilist loop over all ilists */
 188 typedef struct gmx_mtop_ilistloop *gmx_mtop_ilistloop_t;
 189
 190 /* Initialize an ilist loop over all molecule types in the system. */
 191 gmx_mtop_ilistloop_t
 192 gmx_mtop_ilistloop_init(const gmx_mtop_t *mtop);
 193
 194
 195 /* Loop to the next molecule,
 196  * When not at the end:
 197  *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 198  *   writes the number of molecules for this ilist in *nmol.
 199  * When at the end, destroys iloop and returns FALSE.
 200  */
 201 gmx_bool
 202 gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
 203                         t_ilist **ilist_mol, int *nmol);
 204
 205
 206 /* Abstract type for ilist loop over all ilists of all molecules */
 207 typedef struct gmx_mtop_ilistloop_all *gmx_mtop_ilistloop_all_t;
 208
 209 /* Initialize an ilist loop over all molecule types in the system.
 210  * Only use this when you really need to loop over all molecules,
 211  * i.e. when you use groups which might differ per molecule,
 212  * otherwise use gmx_mtop_ilistloop.
 213  */
 214 gmx_mtop_ilistloop_all_t
 215 gmx_mtop_ilistloop_all_init(const gmx_mtop_t *mtop);
 216
 217 /* Loop to the next molecule,
 218  * When not at the end:
 219  *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 220  *   writes the atom offset which should be added to iatoms in atnr_offset.
 221  * When at the end, destroys iloop and returns FALSE.
 222  */
 223 gmx_bool
 224 gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
 225                             t_ilist **ilist_mol, int *atnr_offset);
 226
 227
 228 /* Returns the total number of interactions in the system of type ftype */
 229 int
 230 gmx_mtop_ftype_count(const gmx_mtop_t *mtop, int ftype);
 231
 232
 233 /* Returns a charge group index for the whole system */
 234 t_block
 235 gmx_mtop_global_cgs(const gmx_mtop_t *mtop);
 236
 237
 238 /* Returns a single t_atoms struct for the whole system */
 239 t_atoms
 240 gmx_mtop_global_atoms(const gmx_mtop_t *mtop);
 241
 242
 243 /* Make all charge groups the size of one atom.
 244  * When bKeepSingleMolCG==TRUE keep charge groups for molecules
 245  * that consist of a single charge group.
 246  */
 247 void
 248 gmx_mtop_make_atomic_charge_groups(gmx_mtop_t *mtop, gmx_bool bKeepSingleMolCG);
 249
 250
 251 /* Generate a 'local' topology for the whole system.
 252  * When ir!=NULL the free energy interactions will be sorted to the end.
 253  */
 254 gmx_localtop_t *
 255 gmx_mtop_generate_local_top(const gmx_mtop_t *mtop, const t_inputrec *ir);
 256
 257
 258 /* Converts a gmx_mtop_t struct to t_topology.
 259  * All memory relating only to mtop will be freed.
 260  */
 261 t_topology
 262 gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop);
 263
 264 #ifdef __cplusplus
 265 }
 266 #endif