src/gromacs/topology/mtop_util.h

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  37 #ifndef GMX_TOPOLOGY_MTOP_UTIL_H
  38 #define GMX_TOPOLOGY_MTOP_UTIL_H
  39
  40 #include <cstddef>
  41
  42 #include <vector>
  43
  44 #include "gromacs/utility/basedefinitions.h"
  45
  46 struct gmx_localtop_t;
  47 struct gmx_moltype_t;
  48 struct gmx_mtop_t;
  49 struct t_atom;
  50 struct t_atoms;
  51 struct t_block;
  52 struct t_ilist;
  53 struct t_symtab;
  54 struct t_topology;
  55
  56 /* Should be called after generating or reading mtop,
  57  * to set some compute intesive variables to avoid
  58  * N^2 operations later on.
  59  */
  60 void
  61 gmx_mtop_finalize(gmx_mtop_t *mtop);
  62
  63 /* Counts the number of atoms of each type. State should be 0 for
  64  * state A and 1 for state B types.  typecount should have at
  65  * least mtop->ffparams.atnr elements.
  66  */
  67 void
  68 gmx_mtop_count_atomtypes(const gmx_mtop_t *mtop, int state, int typecount[]);
  69
  70 /* Returns the total number of charge groups in mtop */
  71 int
  72 ncg_mtop(const gmx_mtop_t *mtop);
  73
  74 /* Removes the charge groups, i.e. makes single atom charge groups, in mtop */
  75 void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop);
  76
  77
  78 /* Abstract data type for looking up atoms by global atom number */
  79 typedef struct gmx_mtop_atomlookup *gmx_mtop_atomlookup_t;
  80
  81 /* Initialize atom lookup by global atom number */
  82 gmx_mtop_atomlookup_t
  83 gmx_mtop_atomlookup_init(const gmx_mtop_t *mtop);
  84
  85 /* As gmx_mtop_atomlookup_init, but optimized for atoms involved in settle */
  86 gmx_mtop_atomlookup_t
  87 gmx_mtop_atomlookup_settle_init(const gmx_mtop_t *mtop);
  88
  89 /* Destroy a gmx_mtop_atomlookup_t data structure */
  90 void
  91 gmx_mtop_atomlookup_destroy(gmx_mtop_atomlookup_t alook);
  92
  93
  94 /* Returns a pointer to the t_atom struct belonging to atnr_global.
  95  * This can be an expensive operation, so if possible use
  96  * one of the atom loop constructs below.
  97  */
  98 void
  99 gmx_mtop_atomnr_to_atom(const gmx_mtop_atomlookup_t alook,
 100                         int                         atnr_global,
 101                         t_atom                    **atom);
 102
 103
 104 /* Returns a pointer to the molecule interaction array ilist_mol[F_NRE]
 105  * and the local atom number in the molecule belonging to atnr_global.
 106  */
 107 void
 108 gmx_mtop_atomnr_to_ilist(const gmx_mtop_atomlookup_t alook,
 109                          int atnr_global,
 110                          t_ilist **ilist_mol, int *atnr_offset);
 111
 112
 113 /* Returns the molecule block index
 114  * and the molecule number in the block
 115  * and the atom number offset for the atom indices in moltype
 116  * belonging to atnr_global.
 117  */
 118 void
 119 gmx_mtop_atomnr_to_molblock_ind(const gmx_mtop_atomlookup_t alook,
 120                                 int atnr_global,
 121                                 int *molb, int *molnr, int *atnr_mol);
 122
 123
 124 /* Returns atom name, global resnr and residue name  of atom atnr_global */
 125 void
 126 gmx_mtop_atominfo_global(const gmx_mtop_t *mtop, int atnr_global,
 127                          char **atomname, int *resnr, char **resname);
 128
 129
 130 /* Abstract type for atom loop over all atoms */
 131 typedef struct gmx_mtop_atomloop_all *gmx_mtop_atomloop_all_t;
 132
 133 /* Initialize an atom loop over all atoms in the system.
 134  * The order of the atoms will be as in the state struct.
 135  * Only use this when you really need to loop over all atoms,
 136  * i.e. when you use groups which might differ per molecule,
 137  * otherwise use gmx_mtop_atomloop_block.
 138  */
 139 gmx_mtop_atomloop_all_t
 140 gmx_mtop_atomloop_all_init(const gmx_mtop_t *mtop);
 141
 142 /* Loop to the next atom.
 143  * When not at the end:
 144  *   returns TRUE and at_global,
 145  *   writes the global atom number in *at_global
 146  *   and sets the pointer atom to the t_atom struct of that atom.
 147  * When at the end, destroys aloop and returns FALSE.
 148  * Use as:
 149  * gmx_mtop_atomloop_all_t aloop;
 150  * aloop = gmx_mtop_atomloop_all_init(mtop)
 151  * while (gmx_mtop_atomloop_all_next(aloop,&at_global,&atom)) {
 152  *     ...
 153  * }
 154  */
 155 gmx_bool
 156 gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
 157                            int *at_global, t_atom **atom);
 158
 159 /* Return the atomname, the residue number and residue name
 160  * of the current atom in the loop.
 161  */
 162 void
 163 gmx_mtop_atomloop_all_names(gmx_mtop_atomloop_all_t aloop,
 164                             char **atomname, int *resnr, char **resname);
 165
 166 /* Return the a pointer to the moltype struct of the current atom
 167  * in the loop and the atom number in the molecule.
 168  */
 169 void
 170 gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
 171                               gmx_moltype_t **moltype, int *at_mol);
 172
 173
 174 /* Abstract type for atom loop over atoms in all molecule blocks */
 175 typedef struct gmx_mtop_atomloop_block *gmx_mtop_atomloop_block_t;
 176
 177 /* Initialize an atom loop over atoms in all molecule blocks the system.
 178  */
 179 gmx_mtop_atomloop_block_t
 180 gmx_mtop_atomloop_block_init(const gmx_mtop_t *mtop);
 181
 182 /* Loop to the next atom.
 183  * When not at the end:
 184  *   returns TRUE
 185  *   sets the pointer atom to the t_atom struct of that atom
 186  *   and return the number of molecules corresponding to this atom.
 187  * When at the end, destroys aloop and returns FALSE.
 188  * Use as:
 189  * gmx_mtop_atomloop_block_t aloop;
 190  * aloop = gmx_mtop_atomloop_block_init(mtop)
 191  * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
 192  *     ...
 193  * }
 194  */
 195 gmx_bool
 196 gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
 197                              t_atom **atom, int *nmol);
 198
 199
 200 /* Abstract type for ilist loop over all ilists */
 201 typedef struct gmx_mtop_ilistloop *gmx_mtop_ilistloop_t;
 202
 203 /* Initialize an ilist loop over all molecule types in the system. */
 204 gmx_mtop_ilistloop_t
 205 gmx_mtop_ilistloop_init(const gmx_mtop_t *mtop);
 206
 207
 208 /* Loop to the next molecule,
 209  * When not at the end:
 210  *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 211  *   writes the number of molecules for this ilist in *nmol.
 212  * When at the end, destroys iloop and returns FALSE.
 213  */
 214 gmx_bool
 215 gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
 216                         t_ilist **ilist_mol, int *nmol);
 217
 218
 219 /* Abstract type for ilist loop over all ilists of all molecules */
 220 typedef struct gmx_mtop_ilistloop_all *gmx_mtop_ilistloop_all_t;
 221
 222 /* Initialize an ilist loop over all molecule types in the system.
 223  * Only use this when you really need to loop over all molecules,
 224  * i.e. when you use groups which might differ per molecule,
 225  * otherwise use gmx_mtop_ilistloop.
 226  */
 227 gmx_mtop_ilistloop_all_t
 228 gmx_mtop_ilistloop_all_init(const gmx_mtop_t *mtop);
 229
 230 /* Loop to the next molecule,
 231  * When not at the end:
 232  *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 233  *   writes the atom offset which should be added to iatoms in atnr_offset.
 234  * When at the end, destroys iloop and returns FALSE.
 235  */
 236 gmx_bool
 237 gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
 238                             t_ilist **ilist_mol, int *atnr_offset);
 239
 240
 241 /* Returns the total number of interactions in the system of type ftype */
 242 int
 243 gmx_mtop_ftype_count(const gmx_mtop_t *mtop, int ftype);
 244
 245
 246 /* Returns a charge group index for the whole system */
 247 t_block
 248 gmx_mtop_global_cgs(const gmx_mtop_t *mtop);
 249
 250
 251 /* Returns a single t_atoms struct for the whole system */
 252 t_atoms
 253 gmx_mtop_global_atoms(const gmx_mtop_t *mtop);
 254
 255
 256 /* Generate a 'local' topology for the whole system.
 257  * When feeEnergyInteractionsAtEnd == true, the free energy interactions will
 258  * be sorted to the end.
 259  */
 260 gmx_localtop_t *
 261 gmx_mtop_generate_local_top(const gmx_mtop_t *mtop, bool freeEnergyInteractionsAtEnd);
 262
 263
 264 /* Converts a gmx_mtop_t struct to t_topology.
 265  * All memory relating only to mtop will be freed.
 266  */
 267 t_topology
 268 gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop);
 269
 270 /*! \brief Get vector of atoms indices from topology
 271  *
 272  * This function returns the indices of all particles with type
 273  * eptAtom, that is shells, vsites etc. are left out.
 274  * \param[in]  mtop Molecular topology
 275  * \returns Vector that will be filled with the atom indices
 276  */
 277 std::vector<size_t> get_atom_index(const gmx_mtop_t *mtop);
 278
 279 /*! \brief Converts a t_atoms struct to an mtop struct
 280  *
 281  * All pointers contained in \p atoms will be copied into \p mtop.
 282  * Note that this will produce one moleculetype encompassing the whole system.
 283  *
 284  * \param[in]  symtab  The symbol table
 285  * \param[in]  name    Pointer to the name for the topology
 286  * \param[in]  atoms   The atoms to convert
 287  * \param[out] mtop    The molecular topology output containing atoms.
 288  */
 289 void
 290 convertAtomsToMtop(t_symtab    *symtab,
 291                    char       **name,
 292                    t_atoms     *atoms,
 293                    gmx_mtop_t  *mtop);
 294
 295 #endif