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38 #ifndef GMX_TOPOLOGY_MTOP_UTIL_H
39 #define GMX_TOPOLOGY_MTOP_UTIL_H
46 #include "gromacs/topology/topology.h"
47 #include "gromacs/utility/basedefinitions.h"
49 struct gmx_localtop_t;
54 enum struct GmxQmmmMode;
56 // TODO All of the functions taking a const gmx_mtop * are deprecated
57 // and should be replaced by versions taking const gmx_mtop & when
58 // their callers are refactored similarly.
60 /* Should be called after generating or reading mtop,
61 * to set some compute intesive variables to avoid
62 * N^2 operations later on.
64 void gmx_mtop_finalize(gmx_mtop_t* mtop);
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.
70 void gmx_mtop_count_atomtypes(const gmx_mtop_t* mtop, int state, int typecount[]);
72 /*!\brief Returns the total number of molecules in mtop
74 * \param[in] mtop The global topology
76 int gmx_mtop_num_molecules(const gmx_mtop_t& mtop);
78 /* Returns the total number of residues in mtop. */
79 int gmx_mtop_nres(const gmx_mtop_t* mtop);
83 //! Proxy object returned from AtomIterator
87 //! Default constructor.
88 AtomProxy(const AtomIterator* it) : it_(it) {}
89 //! Access current global atom number.
90 int globalAtomNumber() const;
91 //! Access current t_atom struct.
92 const t_atom& atom() const;
93 //! Access current name of the atom.
94 const char* atomName() const;
95 //! Access current name of the residue the atom is in.
96 const char* residueName() const;
97 //! Access current residue number.
98 int residueNumber() const;
99 //! Access current molecule type.
100 const gmx_moltype_t& moleculeType() const;
101 //! Access the position of the current atom in the molecule.
102 int atomNumberInMol() const;
105 const AtomIterator* it_;
108 //! Wrapper around proxy object to implement operator->
113 //! Construct with proxy object.
114 ProxyPtr(T t) : t_(t) {}
115 //! Member of pointer operator.
116 T* operator->() { return &t_; }
123 * Object that allows looping over all atoms in an mtop.
128 //! Construct from topology and optionalally a global atom number.
129 explicit AtomIterator(const gmx_mtop_t& mtop, int globalAtomNumber = 0);
131 //! Prefix increment.
132 AtomIterator& operator++();
133 //! Postfix increment.
134 AtomIterator operator++(int);
136 //! Equality comparison.
137 bool operator==(const AtomIterator& o) const;
138 //! Non-equal comparison.
139 bool operator!=(const AtomIterator& o) const;
141 //! Dereference operator. Returns proxy.
142 AtomProxy operator*() const { return { this }; }
143 //! Member of pointer operator.
144 ProxyPtr<AtomProxy> operator->() const { return { this }; }
148 const gmx_mtop_t* mtop_;
149 //! Current molecule block.
151 //! The atoms of the current molecule.
152 const t_atoms* atoms_;
153 //! The current molecule.
154 int currentMolecule_;
155 //! Current highest number for residues.
156 int highestResidueNumber_;
157 //! Current local atom number.
158 int localAtomNumber_;
159 //! Global current atom number.
160 int globalAtomNumber_;
162 friend class AtomProxy;
165 //! Range over all atoms of topology.
169 //! Default constructor.
170 explicit AtomRange(const gmx_mtop_t& mtop) : begin_(mtop), end_(mtop, mtop.natoms) {}
171 //! Iterator to begin of range.
172 AtomIterator& begin() { return begin_; }
173 //! Iterator to end of range.
174 AtomIterator& end() { return end_; }
177 AtomIterator begin_, end_;
180 /* Abstract type for atom loop over atoms in all molecule blocks */
181 typedef struct gmx_mtop_atomloop_block* gmx_mtop_atomloop_block_t;
183 /* Initialize an atom loop over atoms in all molecule blocks the system.
185 gmx_mtop_atomloop_block_t gmx_mtop_atomloop_block_init(const gmx_mtop_t* mtop);
187 /* Loop to the next atom.
188 * When not at the end:
190 * sets the pointer atom to the t_atom struct of that atom
191 * and return the number of molecules corresponding to this atom.
192 * When at the end, destroys aloop and returns FALSE.
194 * gmx_mtop_atomloop_block_t aloop;
195 * aloop = gmx_mtop_atomloop_block_init(mtop)
196 * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
200 gmx_bool gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom** atom, int* nmol);
203 /* Abstract type for ilist loop over all ilists */
204 typedef struct gmx_mtop_ilistloop* gmx_mtop_ilistloop_t;
206 /* Initialize an ilist loop over all molecule types in the system. */
207 gmx_mtop_ilistloop_t gmx_mtop_ilistloop_init(const gmx_mtop_t* mtop);
209 /* Initialize an ilist loop over all molecule types in the system. */
210 gmx_mtop_ilistloop_t gmx_mtop_ilistloop_init(const gmx_mtop_t& mtop);
212 /* Loop to the next molecule,
213 * When not at the end:
214 * returns a valid pointer to the next array ilist_mol[F_NRE],
215 * writes the number of molecules for this ilist in *nmol.
216 * When at the end, destroys iloop and returns nullptr.
218 const InteractionLists* gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop, int* nmol);
220 /* Abstract type for ilist loop over all ilists of all molecules */
221 typedef struct gmx_mtop_ilistloop_all* gmx_mtop_ilistloop_all_t;
223 /* Initialize an ilist loop over all molecule types in the system.
224 * Only use this when you really need to loop over all molecules,
225 * i.e. when you use groups which might differ per molecule,
226 * otherwise use gmx_mtop_ilistloop.
228 gmx_mtop_ilistloop_all_t gmx_mtop_ilistloop_all_init(const gmx_mtop_t* mtop);
230 /* Loop to the next molecule,
231 * When not at the end:
232 * returns a valid pointer to the next array ilist_mol[F_NRE],
233 * writes the atom offset which should be added to iatoms in atnr_offset.
234 * When at the end, destroys iloop and returns nullptr.
236 const InteractionLists* gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop, int* atnr_offset);
239 /* Returns the total number of interactions in the system of type ftype */
240 int gmx_mtop_ftype_count(const gmx_mtop_t* mtop, int ftype);
242 /* Returns the total number of interactions in the system of type ftype */
243 int gmx_mtop_ftype_count(const gmx_mtop_t& mtop, int ftype);
245 /* Returns the total number of interactions in the system with all interaction flags that are set in \p if_flags set */
246 int gmx_mtop_interaction_count(const gmx_mtop_t& mtop, int unsigned if_flags);
248 /* Returns the count of atoms for each particle type */
249 std::array<int, eptNR> gmx_mtop_particletype_count(const gmx_mtop_t& mtop);
251 /* Returns a single t_atoms struct for the whole system */
252 t_atoms gmx_mtop_global_atoms(const gmx_mtop_t* mtop);
256 * Populate a 'local' topology for the whole system.
258 * When freeEnergyInteractionsAtEnd == true, the free energy interactions will
259 * be sorted to the end.
261 * \param[in] mtop The global topology used to populate the local one.
262 * \param[in,out] top New local topology populated from global \p mtop.
263 * \param[in] freeEnergyInteractionsAtEnd If free energy interactions will be sorted.
265 void gmx_mtop_generate_local_top(const gmx_mtop_t& mtop, gmx_localtop_t* top, bool freeEnergyInteractionsAtEnd);
268 /*!\brief Creates and returns a struct with begin/end atom indices of all molecules
270 * \param[in] mtop The global topology
271 * \returns A RangePartitioning object with numBlocks() equal to the number
272 * of molecules and atom indices such that molecule m contains atoms a with:
273 * index[m] <= a < index[m+1].
275 gmx::RangePartitioning gmx_mtop_molecules(const gmx_mtop_t& mtop);
278 /* Converts a gmx_mtop_t struct to t_topology.
280 * If the lifetime of the returned topology should be longer than that
281 * of mtop, your need to pass freeMtop==true.
282 * If freeMTop == true, memory related to mtop will be freed so that done_top()
283 * on the result value will free all memory.
284 * If freeMTop == false, mtop and the return value will share some of their
285 * memory, and there is currently no way to consistently free all the memory.
287 t_topology gmx_mtop_t_to_t_topology(gmx_mtop_t* mtop, bool freeMTop);
289 /*! \brief Get vector of atoms indices from topology
291 * This function returns the indices of all particles with type
292 * eptAtom, that is shells, vsites etc. are left out.
293 * \param[in] mtop Molecular topology
294 * \returns Vector that will be filled with the atom indices
296 std::vector<int> get_atom_index(const gmx_mtop_t* mtop);
298 /*! \brief Converts a t_atoms struct to an mtop struct
300 * All pointers contained in \p atoms will be copied into \p mtop.
301 * Note that this will produce one moleculetype encompassing the whole system.
303 * \param[in] symtab The symbol table
304 * \param[in] name Pointer to the name for the topology
305 * \param[in] atoms The atoms to convert
306 * \param[out] mtop The molecular topology output containing atoms.
308 void convertAtomsToMtop(t_symtab* symtab, char** name, t_atoms* atoms, gmx_mtop_t* mtop);
310 /*! \brief Checks if the non-bonded FEP should be performed in this run.
312 * \param[in] mtop Molecular topology.
313 * \returns Whether FEP non-bonded is requested.
315 bool haveFepPerturbedNBInteractions(const gmx_mtop_t* mtop);