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 by the GROMACS development team.
   7  * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   9  * and including many others, as listed in the AUTHORS file in the
  10  * top-level source directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
  18  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
  24  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
  28  * consider that scientific software is very special. Version
  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
  33  * official version at http://www.gromacs.org.
  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  38 #ifndef GMX_TOPOLOGY_MTOP_UTIL_H
  39 #define GMX_TOPOLOGY_MTOP_UTIL_H
  40
  41 #include <cstddef>
  42
  43 #include <array>
  44 #include <vector>
  45
  46 #include <boost/stl_interfaces/iterator_interface.hpp>
  47
  48 #include "gromacs/topology/topology.h"
  49 #include "gromacs/utility/basedefinitions.h"
  50
  51 struct gmx_localtop_t;
  52 struct t_atom;
  53 struct t_atoms;
  54 struct t_block;
  55 struct t_symtab;
  56
  57 // TODO All of the functions taking a const gmx_mtop * are deprecated
  58 // and should be replaced by versions taking const gmx_mtop & when
  59 // their callers are refactored similarly.
  60
  61 /* Counts the number of atoms of each type. State should be 0 for
  62  * state A and 1 for state B types.  typecount should have at
  63  * least mtop->ffparams.atnr elements.
  64  */
  65 void gmx_mtop_count_atomtypes(const gmx_mtop_t* mtop, int state, int typecount[]);
  66
  67 /*!\brief Returns the total number of molecules in mtop
  68  *
  69  * \param[in] mtop  The global topology
  70  */
  71 int gmx_mtop_num_molecules(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 class AtomIterator;
  77
  78 //! Proxy object returned from AtomIterator
  79 class AtomProxy
  80 {
  81 public:
  82     //! Default constructor.
  83     AtomProxy(const AtomIterator* it) : it_(it) {}
  84     //! Access current global atom number.
  85     int globalAtomNumber() const;
  86     //! Access current t_atom struct.
  87     const t_atom& atom() const;
  88     //! Access current name of the atom.
  89     const char* atomName() const;
  90     //! Access current name of the residue the atom is in.
  91     const char* residueName() const;
  92     //! Access current residue number.
  93     int residueNumber() const;
  94     //! Access current molecule type.
  95     const gmx_moltype_t& moleculeType() const;
  96     //! Access the position of the current atom in the molecule.
  97     int atomNumberInMol() const;
  98
  99 private:
 100     const AtomIterator* it_;
 101 };
 102
 103 /*! \brief
 104  * Object that allows looping over all atoms in an mtop.
 105  */
 106 class AtomIterator :
 107     public boost::stl_interfaces::proxy_iterator_interface<AtomIterator, std::forward_iterator_tag, t_atom, AtomProxy>
 108 {
 109     using Base =
 110             boost::stl_interfaces::proxy_iterator_interface<AtomIterator, std::forward_iterator_tag, t_atom, AtomProxy>;
 111
 112 public:
 113     //! Construct from topology and optionalally a global atom number.
 114     explicit AtomIterator(const gmx_mtop_t& mtop, int globalAtomNumber = 0);
 115
 116     //! Prefix increment.
 117     AtomIterator& operator++();
 118     using Base::  operator++;
 119
 120     //! Equality comparison.
 121     bool operator==(const AtomIterator& o) const;
 122
 123     //! Dereference operator. Returns proxy.
 124     AtomProxy operator*() const { return { this }; }
 125
 126 private:
 127     //! Global topology.
 128     const gmx_mtop_t* mtop_;
 129     //! Current molecule block.
 130     size_t mblock_;
 131     //! The atoms of the current molecule.
 132     const t_atoms* atoms_;
 133     //! The current molecule.
 134     int currentMolecule_;
 135     //! Current highest number for residues.
 136     int highestResidueNumber_;
 137     //! Current local atom number.
 138     int localAtomNumber_;
 139     //! Global current atom number.
 140     int globalAtomNumber_;
 141
 142     friend class AtomProxy;
 143 };
 144
 145 //! Range over all atoms of topology.
 146 class AtomRange
 147 {
 148 public:
 149     //! Default constructor.
 150     explicit AtomRange(const gmx_mtop_t& mtop) : begin_(mtop), end_(mtop, mtop.natoms) {}
 151     //! Iterator to begin of range.
 152     AtomIterator& begin() { return begin_; }
 153     //! Iterator to end of range.
 154     AtomIterator& end() { return end_; }
 155
 156 private:
 157     AtomIterator begin_, end_;
 158 };
 159
 160 /* Abstract type for atom loop over atoms in all molecule blocks */
 161 typedef struct gmx_mtop_atomloop_block* gmx_mtop_atomloop_block_t;
 162
 163 /* Initialize an atom loop over atoms in all molecule blocks the system.
 164  */
 165 gmx_mtop_atomloop_block_t gmx_mtop_atomloop_block_init(const gmx_mtop_t* mtop);
 166
 167 /* Loop to the next atom.
 168  * When not at the end:
 169  *   returns TRUE
 170  *   sets the pointer atom to the t_atom struct of that atom
 171  *   and return the number of molecules corresponding to this atom.
 172  * When at the end, destroys aloop and returns FALSE.
 173  * Use as:
 174  * gmx_mtop_atomloop_block_t aloop;
 175  * aloop = gmx_mtop_atomloop_block_init(mtop)
 176  * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
 177  *     ...
 178  * }
 179  */
 180 gmx_bool gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom** atom, int* nmol);
 181
 182
 183 /* Abstract type for ilist loop over all ilists */
 184 typedef struct gmx_mtop_ilistloop* gmx_mtop_ilistloop_t;
 185
 186 /* Initialize an ilist loop over all molecule types in the system. */
 187 gmx_mtop_ilistloop_t gmx_mtop_ilistloop_init(const gmx_mtop_t* mtop);
 188
 189 /* Initialize an ilist loop over all molecule types in the system. */
 190 gmx_mtop_ilistloop_t gmx_mtop_ilistloop_init(const gmx_mtop_t& mtop);
 191
 192 /* Loop to the next molecule,
 193  * When not at the end:
 194  *   returns a valid pointer to the next array ilist_mol[F_NRE],
 195  *   writes the number of molecules for this ilist in *nmol.
 196  * When at the end, destroys iloop and returns nullptr.
 197  */
 198 const InteractionLists* gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop, int* nmol);
 199
 200 /* Returns the total number of interactions in the system of type ftype */
 201 int gmx_mtop_ftype_count(const gmx_mtop_t* mtop, int ftype);
 202
 203 /* Returns the total number of interactions in the system of type ftype */
 204 int gmx_mtop_ftype_count(const gmx_mtop_t& mtop, int ftype);
 205
 206 /* Returns the total number of interactions in the system with all interaction flags that are set in \p if_flags set */
 207 int gmx_mtop_interaction_count(const gmx_mtop_t& mtop, int unsigned if_flags);
 208
 209 /* Returns the count of atoms for each particle type */
 210 std::array<int, eptNR> gmx_mtop_particletype_count(const gmx_mtop_t& mtop);
 211
 212 /* Returns a single t_atoms struct for the whole system */
 213 t_atoms gmx_mtop_global_atoms(const gmx_mtop_t* mtop);
 214
 215
 216 /*! \brief
 217  * Populate a 'local' topology for the whole system.
 218  *
 219  * When freeEnergyInteractionsAtEnd == true, the free energy interactions will
 220  * be sorted to the end.
 221  *
 222  * \param[in]     mtop                        The global topology used to populate the local one.
 223  * \param[in,out] top                         New local topology populated from global \p mtop.
 224  * \param[in]     freeEnergyInteractionsAtEnd If free energy interactions will be sorted.
 225  */
 226 void gmx_mtop_generate_local_top(const gmx_mtop_t& mtop, gmx_localtop_t* top, bool freeEnergyInteractionsAtEnd);
 227
 228
 229 /*!\brief Creates and returns a struct with begin/end atom indices of all molecules
 230  *
 231  * \param[in] mtop  The global topology
 232  * \returns A RangePartitioning object with numBlocks() equal to the number
 233  * of molecules and atom indices such that molecule m contains atoms a with:
 234  * index[m] <= a < index[m+1].
 235  */
 236 gmx::RangePartitioning gmx_mtop_molecules(const gmx_mtop_t& mtop);
 237
 238 /*! \brief
 239  * Returns the index range from residue begin to end for each residue in a molecule block.
 240  *
 241  * Note that residues will always have consecutive atoms numbers internally.
 242  *
 243  * \param[in] moltype  Molecule Type to parse for start and end.
 244  * \returns Vector of ranges for all residues.
 245  */
 246 std::vector<gmx::Range<int>> atomRangeOfEachResidue(const gmx_moltype_t& moltype);
 247
 248 /* Converts a gmx_mtop_t struct to t_topology.
 249  *
 250  * If the lifetime of the returned topology should be longer than that
 251  * of mtop, your need to pass freeMtop==true.
 252  * If freeMTop == true, memory related to mtop will be freed so that done_top()
 253  * on the result value will free all memory.
 254  * If freeMTop == false, mtop and the return value will share some of their
 255  * memory, and there is currently no way to consistently free all the memory.
 256  */
 257 t_topology gmx_mtop_t_to_t_topology(gmx_mtop_t* mtop, bool freeMTop);
 258
 259 /*! \brief Get vector of atoms indices from topology
 260  *
 261  * This function returns the indices of all particles with type
 262  * eptAtom, that is shells, vsites etc. are left out.
 263  * \param[in]  mtop Molecular topology
 264  * \returns Vector that will be filled with the atom indices
 265  */
 266 std::vector<int> get_atom_index(const gmx_mtop_t* mtop);
 267
 268 /*! \brief Converts a t_atoms struct to an mtop struct
 269  *
 270  * All pointers contained in \p atoms will be copied into \p mtop.
 271  * Note that this will produce one moleculetype encompassing the whole system.
 272  *
 273  * \param[in]  symtab  The symbol table
 274  * \param[in]  name    Pointer to the name for the topology
 275  * \param[in]  atoms   The atoms to convert
 276  * \param[out] mtop    The molecular topology output containing atoms.
 277  */
 278 void convertAtomsToMtop(t_symtab* symtab, char** name, t_atoms* atoms, gmx_mtop_t* mtop);
 279
 280 //! Checks and returns whether non-bonded interactions are perturbed for free-energy calculations
 281 bool haveFepPerturbedNBInteractions(const gmx_mtop_t& mtop);
 282
 283 //! Checks whether masses are perturbed for free-energy calculations
 284 bool haveFepPerturbedMasses(const gmx_mtop_t& mtop);
 285
 286 //! Checks whether constraints are perturbed for free-energy calculations
 287 bool havePerturbedConstraints(const gmx_mtop_t& mtop);
 288
 289 #endif