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/topology/topology.h"
  45 #include "gromacs/utility/basedefinitions.h"
  46 #include "gromacs/utility/gmxassert.h"
  47
  48 struct gmx_localtop_t;
  49 struct t_atom;
  50 struct t_atoms;
  51 struct t_block;
  52 struct t_ilist;
  53 struct t_symtab;
  54
  55 /* Should be called after generating or reading mtop,
  56  * to set some compute intesive variables to avoid
  57  * N^2 operations later on.
  58  */
  59 void
  60 gmx_mtop_finalize(gmx_mtop_t *mtop);
  61
  62 /* Counts the number of atoms of each type. State should be 0 for
  63  * state A and 1 for state B types.  typecount should have at
  64  * least mtop->ffparams.atnr elements.
  65  */
  66 void
  67 gmx_mtop_count_atomtypes(const gmx_mtop_t *mtop, int state, int typecount[]);
  68
  69 /* Returns the total number of charge groups in mtop */
  70 int
  71 ncg_mtop(const gmx_mtop_t *mtop);
  72
  73 /*!\brief Returns the total number of molecules in mtop
  74  *
  75  * \param[in] mtop  The global topology
  76  */
  77 int gmx_mtop_num_molecules(const gmx_mtop_t &mtop);
  78
  79 /* Returns the total number of residues in mtop. */
  80 int gmx_mtop_nres(const gmx_mtop_t *mtop);
  81
  82 /* Removes the charge groups, i.e. makes single atom charge groups, in mtop */
  83 void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop);
  84
  85 /* Abstract type for atom loop over all atoms */
  86 typedef struct gmx_mtop_atomloop_all *gmx_mtop_atomloop_all_t;
  87
  88 /* Initialize an atom loop over all atoms in the system.
  89  * The order of the atoms will be as in the state struct.
  90  * Only use this when you really need to loop over all atoms,
  91  * i.e. when you use groups which might differ per molecule,
  92  * otherwise use gmx_mtop_atomloop_block.
  93  */
  94 gmx_mtop_atomloop_all_t
  95 gmx_mtop_atomloop_all_init(const gmx_mtop_t *mtop);
  96
  97 /* Loop to the next atom.
  98  * When not at the end:
  99  *   returns TRUE and at_global,
 100  *   writes the global atom number in *at_global
 101  *   and sets the pointer atom to the t_atom struct of that atom.
 102  * When at the end, destroys aloop and returns FALSE.
 103  * Use as:
 104  * gmx_mtop_atomloop_all_t aloop;
 105  * aloop = gmx_mtop_atomloop_all_init(mtop)
 106  * while (gmx_mtop_atomloop_all_next(aloop,&at_global,&atom)) {
 107  *     ...
 108  * }
 109  */
 110 gmx_bool
 111 gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
 112                            int *at_global, const t_atom **atom);
 113
 114 /* Return the atomname, the residue number and residue name
 115  * of the current atom in the loop.
 116  */
 117 void
 118 gmx_mtop_atomloop_all_names(gmx_mtop_atomloop_all_t aloop,
 119                             char **atomname, int *resnr, char **resname);
 120
 121 /* Return the a pointer to the moltype struct of the current atom
 122  * in the loop and the atom number in the molecule.
 123  */
 124 void
 125 gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
 126                               gmx_moltype_t **moltype, int *at_mol);
 127
 128
 129 /* Abstract type for atom loop over atoms in all molecule blocks */
 130 typedef struct gmx_mtop_atomloop_block *gmx_mtop_atomloop_block_t;
 131
 132 /* Initialize an atom loop over atoms in all molecule blocks the system.
 133  */
 134 gmx_mtop_atomloop_block_t
 135 gmx_mtop_atomloop_block_init(const gmx_mtop_t *mtop);
 136
 137 /* Loop to the next atom.
 138  * When not at the end:
 139  *   returns TRUE
 140  *   sets the pointer atom to the t_atom struct of that atom
 141  *   and return the number of molecules corresponding to this atom.
 142  * When at the end, destroys aloop and returns FALSE.
 143  * Use as:
 144  * gmx_mtop_atomloop_block_t aloop;
 145  * aloop = gmx_mtop_atomloop_block_init(mtop)
 146  * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
 147  *     ...
 148  * }
 149  */
 150 gmx_bool
 151 gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
 152                              const t_atom **atom, int *nmol);
 153
 154
 155 /* Abstract type for ilist loop over all ilists */
 156 typedef struct gmx_mtop_ilistloop *gmx_mtop_ilistloop_t;
 157
 158 /* Initialize an ilist loop over all molecule types in the system. */
 159 gmx_mtop_ilistloop_t
 160 gmx_mtop_ilistloop_init(const gmx_mtop_t *mtop);
 161
 162
 163 /* Loop to the next molecule,
 164  * When not at the end:
 165  *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 166  *   writes the number of molecules for this ilist in *nmol.
 167  * When at the end, destroys iloop and returns FALSE.
 168  */
 169 gmx_bool
 170 gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
 171                         t_ilist **ilist_mol, int *nmol);
 172
 173
 174 /* Abstract type for ilist loop over all ilists of all molecules */
 175 typedef struct gmx_mtop_ilistloop_all *gmx_mtop_ilistloop_all_t;
 176
 177 /* Initialize an ilist loop over all molecule types in the system.
 178  * Only use this when you really need to loop over all molecules,
 179  * i.e. when you use groups which might differ per molecule,
 180  * otherwise use gmx_mtop_ilistloop.
 181  */
 182 gmx_mtop_ilistloop_all_t
 183 gmx_mtop_ilistloop_all_init(const gmx_mtop_t *mtop);
 184
 185 /* Loop to the next molecule,
 186  * When not at the end:
 187  *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 188  *   writes the atom offset which should be added to iatoms in atnr_offset.
 189  * When at the end, destroys iloop and returns FALSE.
 190  */
 191 gmx_bool
 192 gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
 193                             t_ilist **ilist_mol, int *atnr_offset);
 194
 195
 196 /* Returns the total number of interactions in the system of type ftype */
 197 int
 198 gmx_mtop_ftype_count(const gmx_mtop_t *mtop, int ftype);
 199
 200
 201 /* Returns a charge group index for the whole system */
 202 t_block
 203 gmx_mtop_global_cgs(const gmx_mtop_t *mtop);
 204
 205
 206 /* Returns a single t_atoms struct for the whole system */
 207 t_atoms
 208 gmx_mtop_global_atoms(const gmx_mtop_t *mtop);
 209
 210
 211 /* Generate a 'local' topology for the whole system.
 212  * When freeEnergyInteractionsAtEnd == true, the free energy interactions will
 213  * be sorted to the end.
 214  */
 215 gmx_localtop_t *
 216 gmx_mtop_generate_local_top(const gmx_mtop_t *mtop, bool freeEnergyInteractionsAtEnd);
 217
 218
 219 /*!\brief Creates and returns a struct with begin/end atom indices of all molecules
 220  *
 221  * \param[in] mtop  The global topology
 222  * \returns A struct of type BlockRanges with numBlocks() equal to the number
 223  * of molecules and atom indices such that molecule m contains atoms a with:
 224  * index[m] <= a < index[m+1].
 225  */
 226 gmx::BlockRanges gmx_mtop_molecules(const gmx_mtop_t &mtop);
 227
 228
 229 /* Converts a gmx_mtop_t struct to t_topology.
 230  *
 231  * If freeMTop == true, memory related to mtop will be freed so that done_top()
 232  * on the result value will free all memory.
 233  * If freeMTop == false, mtop and the return value will share some of their
 234  * memory, and there is currently no way to consistently free all the memory.
 235  */
 236 t_topology
 237 gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop, bool freeMTop);
 238
 239 /*! \brief Get vector of atoms indices from topology
 240  *
 241  * This function returns the indices of all particles with type
 242  * eptAtom, that is shells, vsites etc. are left out.
 243  * \param[in]  mtop Molecular topology
 244  * \returns Vector that will be filled with the atom indices
 245  */
 246 std::vector<size_t> get_atom_index(const gmx_mtop_t *mtop);
 247
 248 /*! \brief Converts a t_atoms struct to an mtop struct
 249  *
 250  * All pointers contained in \p atoms will be copied into \p mtop.
 251  * Note that this will produce one moleculetype encompassing the whole system.
 252  *
 253  * \param[in]  symtab  The symbol table
 254  * \param[in]  name    Pointer to the name for the topology
 255  * \param[in]  atoms   The atoms to convert
 256  * \param[out] mtop    The molecular topology output containing atoms.
 257  */
 258 void
 259 convertAtomsToMtop(t_symtab    *symtab,
 260                    char       **name,
 261                    t_atoms     *atoms,
 262                    gmx_mtop_t  *mtop);
 263
 264 #endif