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 "gromacs/topology/topology.h"
  47 #include "gromacs/utility/basedefinitions.h"
  48
  49 struct gmx_localtop_t;
  50 struct t_atom;
  51 struct t_atoms;
  52 struct t_block;
  53 struct t_symtab;
  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 gmx_mtop_finalize(gmx_mtop_t* mtop);
  64
  65 /* Counts the number of atoms of each type. State should be 0 for
  66  * state A and 1 for state B types.  typecount should have at
  67  * least mtop->ffparams.atnr elements.
  68  */
  69 void gmx_mtop_count_atomtypes(const gmx_mtop_t* mtop, int state, int typecount[]);
  70
  71 /*!\brief Returns the total number of molecules in mtop
  72  *
  73  * \param[in] mtop  The global topology
  74  */
  75 int gmx_mtop_num_molecules(const gmx_mtop_t& mtop);
  76
  77 /* Returns the total number of residues in mtop. */
  78 int gmx_mtop_nres(const gmx_mtop_t* mtop);
  79
  80 class AtomIterator;
  81
  82 //! Proxy object returned from AtomIterator
  83 class AtomProxy
  84 {
  85 public:
  86     //! Default constructor.
  87     AtomProxy(const AtomIterator* it) : it_(it) {}
  88     //! Access current global atom number.
  89     int globalAtomNumber() const;
  90     //! Access current t_atom struct.
  91     const t_atom& atom() const;
  92     //! Access current name of the atom.
  93     const char* atomName() const;
  94     //! Access current name of the residue the atom is in.
  95     const char* residueName() const;
  96     //! Access current residue number.
  97     int residueNumber() const;
  98     //! Access current molecule type.
  99     const gmx_moltype_t& moleculeType() const;
 100     //! Access the position of the current atom in the molecule.
 101     int atomNumberInMol() const;
 102
 103 private:
 104     const AtomIterator* it_;
 105 };
 106
 107 //! Wrapper around proxy object to implement operator->
 108 template<typename T>
 109 class ProxyPtr
 110 {
 111 public:
 112     //! Construct with proxy object.
 113     ProxyPtr(T t) : t_(t) {}
 114     //! Member of pointer operator.
 115     T* operator->() { return &t_; }
 116
 117 private:
 118     T t_;
 119 };
 120
 121 /*! \brief
 122  * Object that allows looping over all atoms in an mtop.
 123  */
 124 class AtomIterator
 125 {
 126 public:
 127     //! Construct from topology and optionalally a global atom number.
 128     explicit AtomIterator(const gmx_mtop_t& mtop, int globalAtomNumber = 0);
 129
 130     //! Prefix increment.
 131     AtomIterator& operator++();
 132     //! Postfix increment.
 133     AtomIterator operator++(int);
 134
 135     //! Equality comparison.
 136     bool operator==(const AtomIterator& o) const;
 137     //! Non-equal comparison.
 138     bool operator!=(const AtomIterator& o) const;
 139
 140     //! Dereference operator. Returns proxy.
 141     AtomProxy operator*() const { return { this }; }
 142     //! Member of pointer operator.
 143     ProxyPtr<AtomProxy> operator->() const { return { this }; }
 144
 145 private:
 146     //! Global topology.
 147     const gmx_mtop_t* mtop_;
 148     //! Current molecule block.
 149     size_t mblock_;
 150     //! The atoms of the current molecule.
 151     const t_atoms* atoms_;
 152     //! The current molecule.
 153     int currentMolecule_;
 154     //! Current highest number for residues.
 155     int highestResidueNumber_;
 156     //! Current local atom number.
 157     int localAtomNumber_;
 158     //! Global current atom number.
 159     int globalAtomNumber_;
 160
 161     friend class AtomProxy;
 162 };
 163
 164 //! Range over all atoms of topology.
 165 class AtomRange
 166 {
 167 public:
 168     //! Default constructor.
 169     explicit AtomRange(const gmx_mtop_t& mtop) : begin_(mtop), end_(mtop, mtop.natoms) {}
 170     //! Iterator to begin of range.
 171     AtomIterator& begin() { return begin_; }
 172     //! Iterator to end of range.
 173     AtomIterator& end() { return end_; }
 174
 175 private:
 176     AtomIterator begin_, end_;
 177 };
 178
 179 /* Abstract type for atom loop over atoms in all molecule blocks */
 180 typedef struct gmx_mtop_atomloop_block* gmx_mtop_atomloop_block_t;
 181
 182 /* Initialize an atom loop over atoms in all molecule blocks the system.
 183  */
 184 gmx_mtop_atomloop_block_t gmx_mtop_atomloop_block_init(const gmx_mtop_t* mtop);
 185
 186 /* Loop to the next atom.
 187  * When not at the end:
 188  *   returns TRUE
 189  *   sets the pointer atom to the t_atom struct of that atom
 190  *   and return the number of molecules corresponding to this atom.
 191  * When at the end, destroys aloop and returns FALSE.
 192  * Use as:
 193  * gmx_mtop_atomloop_block_t aloop;
 194  * aloop = gmx_mtop_atomloop_block_init(mtop)
 195  * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
 196  *     ...
 197  * }
 198  */
 199 gmx_bool gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom** atom, int* nmol);
 200
 201
 202 /* Abstract type for ilist loop over all ilists */
 203 typedef struct gmx_mtop_ilistloop* gmx_mtop_ilistloop_t;
 204
 205 /* Initialize an ilist loop over all molecule types in the system. */
 206 gmx_mtop_ilistloop_t gmx_mtop_ilistloop_init(const gmx_mtop_t* mtop);
 207
 208 /* Initialize an ilist loop over all molecule types in the system. */
 209 gmx_mtop_ilistloop_t gmx_mtop_ilistloop_init(const gmx_mtop_t& mtop);
 210
 211 /* Loop to the next molecule,
 212  * When not at the end:
 213  *   returns a valid pointer to the next array ilist_mol[F_NRE],
 214  *   writes the number of molecules for this ilist in *nmol.
 215  * When at the end, destroys iloop and returns nullptr.
 216  */
 217 const InteractionLists* gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop, int* nmol);
 218
 219 /* Returns the total number of interactions in the system of type ftype */
 220 int gmx_mtop_ftype_count(const gmx_mtop_t* mtop, int ftype);
 221
 222 /* Returns the total number of interactions in the system of type ftype */
 223 int gmx_mtop_ftype_count(const gmx_mtop_t& mtop, int ftype);
 224
 225 /* Returns the total number of interactions in the system with all interaction flags that are set in \p if_flags set */
 226 int gmx_mtop_interaction_count(const gmx_mtop_t& mtop, int unsigned if_flags);
 227
 228 /* Returns the count of atoms for each particle type */
 229 std::array<int, eptNR> gmx_mtop_particletype_count(const gmx_mtop_t& mtop);
 230
 231 /* Returns a single t_atoms struct for the whole system */
 232 t_atoms gmx_mtop_global_atoms(const gmx_mtop_t* mtop);
 233
 234
 235 /*! \brief
 236  * Populate a 'local' topology for the whole system.
 237  *
 238  * When freeEnergyInteractionsAtEnd == true, the free energy interactions will
 239  * be sorted to the end.
 240  *
 241  * \param[in]     mtop                        The global topology used to populate the local one.
 242  * \param[in,out] top                         New local topology populated from global \p mtop.
 243  * \param[in]     freeEnergyInteractionsAtEnd If free energy interactions will be sorted.
 244  */
 245 void gmx_mtop_generate_local_top(const gmx_mtop_t& mtop, gmx_localtop_t* top, bool freeEnergyInteractionsAtEnd);
 246
 247
 248 /*!\brief Creates and returns a struct with begin/end atom indices of all molecules
 249  *
 250  * \param[in] mtop  The global topology
 251  * \returns A RangePartitioning object with numBlocks() equal to the number
 252  * of molecules and atom indices such that molecule m contains atoms a with:
 253  * index[m] <= a < index[m+1].
 254  */
 255 gmx::RangePartitioning gmx_mtop_molecules(const gmx_mtop_t& mtop);
 256
 257 /*! \brief
 258  * Returns the index range from residue begin to end for each residue in a molecule block.
 259  *
 260  * Note that residues will always have consecutive atoms numbers internally.
 261  *
 262  * \param[in] moltype  Molecule Type to parse for start and end.
 263  * \returns Vector of ranges for all residues.
 264  */
 265 std::vector<gmx::Range<int>> atomRangeOfEachResidue(const gmx_moltype_t& moltype);
 266
 267 /* Converts a gmx_mtop_t struct to t_topology.
 268  *
 269  * If the lifetime of the returned topology should be longer than that
 270  * of mtop, your need to pass freeMtop==true.
 271  * If freeMTop == true, memory related to mtop will be freed so that done_top()
 272  * on the result value will free all memory.
 273  * If freeMTop == false, mtop and the return value will share some of their
 274  * memory, and there is currently no way to consistently free all the memory.
 275  */
 276 t_topology gmx_mtop_t_to_t_topology(gmx_mtop_t* mtop, bool freeMTop);
 277
 278 /*! \brief Get vector of atoms indices from topology
 279  *
 280  * This function returns the indices of all particles with type
 281  * eptAtom, that is shells, vsites etc. are left out.
 282  * \param[in]  mtop Molecular topology
 283  * \returns Vector that will be filled with the atom indices
 284  */
 285 std::vector<int> get_atom_index(const gmx_mtop_t* mtop);
 286
 287 /*! \brief Converts a t_atoms struct to an mtop struct
 288  *
 289  * All pointers contained in \p atoms will be copied into \p mtop.
 290  * Note that this will produce one moleculetype encompassing the whole system.
 291  *
 292  * \param[in]  symtab  The symbol table
 293  * \param[in]  name    Pointer to the name for the topology
 294  * \param[in]  atoms   The atoms to convert
 295  * \param[out] mtop    The molecular topology output containing atoms.
 296  */
 297 void convertAtomsToMtop(t_symtab* symtab, char** name, t_atoms* atoms, gmx_mtop_t* mtop);
 298
 299 /*! \brief Checks if the non-bonded FEP should be performed in this run.
 300  *
 301  * \param[in]  mtop  Molecular topology.
 302  * \returns Whether FEP non-bonded is requested.
 303  */
 304 bool haveFepPerturbedNBInteractions(const gmx_mtop_t* mtop);
 305
 306 #endif