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