src/gromacs/topology/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) 2012,2013,2014,2015,2016,2018, 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
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  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_symtab;
  53 enum struct GmxQmmmMode;
  54
  55 // TODO All of the functions taking a const gmx_mtop * are deprecated
  56 // and should be replaced by versions taking const gmx_mtop & when
  57 // their callers are refactored similarly.
  58
  59 /* Should be called after generating or reading mtop,
  60  * to set some compute intesive variables to avoid
  61  * N^2 operations later on.
  62  */
  63 void
  64 gmx_mtop_finalize(gmx_mtop_t *mtop);
  65
  66 /* Counts the number of atoms of each type. State should be 0 for
  67  * state A and 1 for state B types.  typecount should have at
  68  * least mtop->ffparams.atnr elements.
  69  */
  70 void
  71 gmx_mtop_count_atomtypes(const gmx_mtop_t *mtop, int state, int typecount[]);
  72
  73 /* Returns the total number of charge groups in mtop */
  74 int
  75 ncg_mtop(const gmx_mtop_t *mtop);
  76
  77 /*!\brief Returns the total number of molecules in mtop
  78  *
  79  * \param[in] mtop  The global topology
  80  */
  81 int gmx_mtop_num_molecules(const gmx_mtop_t &mtop);
  82
  83 /* Returns the total number of residues in mtop. */
  84 int gmx_mtop_nres(const gmx_mtop_t *mtop);
  85
  86 /* Removes the charge groups, i.e. makes single atom charge groups, in mtop */
  87 void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop);
  88
  89 /* Abstract type for atom loop over all atoms */
  90 typedef struct gmx_mtop_atomloop_all *gmx_mtop_atomloop_all_t;
  91
  92 /* Initialize an atom loop over all atoms in the system.
  93  * The order of the atoms will be as in the state struct.
  94  * Only use this when you really need to loop over all atoms,
  95  * i.e. when you use groups which might differ per molecule,
  96  * otherwise use gmx_mtop_atomloop_block.
  97  */
  98 gmx_mtop_atomloop_all_t
  99 gmx_mtop_atomloop_all_init(const gmx_mtop_t *mtop);
 100
 101 /* Loop to the next atom.
 102  * When not at the end:
 103  *   returns TRUE and at_global,
 104  *   writes the global atom number in *at_global
 105  *   and sets the pointer atom to the t_atom struct of that atom.
 106  * When at the end, destroys aloop and returns FALSE.
 107  * Use as:
 108  * gmx_mtop_atomloop_all_t aloop;
 109  * aloop = gmx_mtop_atomloop_all_init(mtop)
 110  * while (gmx_mtop_atomloop_all_next(aloop,&at_global,&atom)) {
 111  *     ...
 112  * }
 113  */
 114 gmx_bool
 115 gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
 116                            int *at_global, const t_atom **atom);
 117
 118 /* Return the atomname, the residue number and residue name
 119  * of the current atom in the loop.
 120  */
 121 void
 122 gmx_mtop_atomloop_all_names(gmx_mtop_atomloop_all_t aloop,
 123                             char **atomname, int *resnr, char **resname);
 124
 125 /* Return the a pointer to the moltype struct of the current atom
 126  * in the loop and the atom number in the molecule.
 127  */
 128 void
 129 gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
 130                               const gmx_moltype_t **moltype, int *at_mol);
 131
 132
 133 /* Abstract type for atom loop over atoms in all molecule blocks */
 134 typedef struct gmx_mtop_atomloop_block *gmx_mtop_atomloop_block_t;
 135
 136 /* Initialize an atom loop over atoms in all molecule blocks the system.
 137  */
 138 gmx_mtop_atomloop_block_t
 139 gmx_mtop_atomloop_block_init(const gmx_mtop_t *mtop);
 140
 141 /* Loop to the next atom.
 142  * When not at the end:
 143  *   returns TRUE
 144  *   sets the pointer atom to the t_atom struct of that atom
 145  *   and return the number of molecules corresponding to this atom.
 146  * When at the end, destroys aloop and returns FALSE.
 147  * Use as:
 148  * gmx_mtop_atomloop_block_t aloop;
 149  * aloop = gmx_mtop_atomloop_block_init(mtop)
 150  * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
 151  *     ...
 152  * }
 153  */
 154 gmx_bool
 155 gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
 156                              const t_atom **atom, int *nmol);
 157
 158
 159 /* Abstract type for ilist loop over all ilists */
 160 typedef struct gmx_mtop_ilistloop *gmx_mtop_ilistloop_t;
 161
 162 /* Initialize an ilist loop over all molecule types in the system. */
 163 gmx_mtop_ilistloop_t
 164 gmx_mtop_ilistloop_init(const gmx_mtop_t *mtop);
 165
 166 /* Initialize an ilist loop over all molecule types in the system. */
 167 gmx_mtop_ilistloop_t
 168 gmx_mtop_ilistloop_init(const gmx_mtop_t &mtop);
 169
 170 /* Loop to the next molecule,
 171  * When not at the end:
 172  *   returns a valid pointer to the next array ilist_mol[F_NRE],
 173  *   writes the number of molecules for this ilist in *nmol.
 174  * When at the end, destroys iloop and returns nullptr.
 175  */
 176 const InteractionLists *
 177 gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t     iloop,
 178                         int                     *nmol);
 179
 180 /* Abstract type for ilist loop over all ilists of all molecules */
 181 typedef struct gmx_mtop_ilistloop_all *gmx_mtop_ilistloop_all_t;
 182
 183 /* Initialize an ilist loop over all molecule types in the system.
 184  * Only use this when you really need to loop over all molecules,
 185  * i.e. when you use groups which might differ per molecule,
 186  * otherwise use gmx_mtop_ilistloop.
 187  */
 188 gmx_mtop_ilistloop_all_t
 189 gmx_mtop_ilistloop_all_init(const gmx_mtop_t *mtop);
 190
 191 /* Loop to the next molecule,
 192  * When not at the end:
 193  *   returns a valid pointer to the next array ilist_mol[F_NRE],
 194  *   writes the atom offset which should be added to iatoms in atnr_offset.
 195  * When at the end, destroys iloop and returns nullptr.
 196  */
 197 const InteractionLists *
 198 gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t   iloop,
 199                             int                       *atnr_offset);
 200
 201
 202 /* Returns the total number of interactions in the system of type ftype */
 203 int
 204 gmx_mtop_ftype_count(const gmx_mtop_t *mtop, int ftype);
 205
 206 /* Returns the total number of interactions in the system of type ftype */
 207 int
 208 gmx_mtop_ftype_count(const gmx_mtop_t &mtop, int ftype);
 209
 210 /* Returns a charge group index for the whole system */
 211 t_block
 212 gmx_mtop_global_cgs(const gmx_mtop_t *mtop);
 213
 214
 215 /* Returns a single t_atoms struct for the whole system */
 216 t_atoms
 217 gmx_mtop_global_atoms(const gmx_mtop_t *mtop);
 218
 219
 220 /* Generate a 'local' topology for the whole system.
 221  * When freeEnergyInteractionsAtEnd == true, the free energy interactions will
 222  * be sorted to the end.
 223  */
 224 gmx_localtop_t *
 225 gmx_mtop_generate_local_top(const gmx_mtop_t *mtop, bool freeEnergyInteractionsAtEnd);
 226
 227
 228 /*!\brief Creates and returns a struct with begin/end atom indices of all molecules
 229  *
 230  * \param[in] mtop  The global topology
 231  * \returns A RangePartitioning object with numBlocks() equal to the number
 232  * of molecules and atom indices such that molecule m contains atoms a with:
 233  * index[m] <= a < index[m+1].
 234  */
 235 gmx::RangePartitioning gmx_mtop_molecules(const gmx_mtop_t &mtop);
 236
 237
 238 /* Converts a gmx_mtop_t struct to t_topology.
 239  *
 240  * If the lifetime of the returned topology should be longer than that
 241  * of mtop, your need to pass freeMtop==true.
 242  * If freeMTop == true, memory related to mtop will be freed so that done_top()
 243  * on the result value will free all memory.
 244  * If freeMTop == false, mtop and the return value will share some of their
 245  * memory, and there is currently no way to consistently free all the memory.
 246  */
 247 t_topology
 248 gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop, bool freeMTop);
 249
 250 /*! \brief Get vector of atoms indices from topology
 251  *
 252  * This function returns the indices of all particles with type
 253  * eptAtom, that is shells, vsites etc. are left out.
 254  * \param[in]  mtop Molecular topology
 255  * \returns Vector that will be filled with the atom indices
 256  */
 257 std::vector<int> get_atom_index(const gmx_mtop_t *mtop);
 258
 259 /*! \brief Converts a t_atoms struct to an mtop struct
 260  *
 261  * All pointers contained in \p atoms will be copied into \p mtop.
 262  * Note that this will produce one moleculetype encompassing the whole system.
 263  *
 264  * \param[in]  symtab  The symbol table
 265  * \param[in]  name    Pointer to the name for the topology
 266  * \param[in]  atoms   The atoms to convert
 267  * \param[out] mtop    The molecular topology output containing atoms.
 268  */
 269 void
 270 convertAtomsToMtop(t_symtab    *symtab,
 271                    char       **name,
 272                    t_atoms     *atoms,
 273                    gmx_mtop_t  *mtop);
 274
 275 #endif