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37 #ifndef GMX_TOPOLOGY_MTOP_UTIL_H
38 #define GMX_TOPOLOGY_MTOP_UTIL_H
44 #include "gromacs/topology/topology.h"
45 #include "gromacs/utility/basedefinitions.h"
46 #include "gromacs/utility/gmxassert.h"
48 struct gmx_localtop_t;
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.
59 /* Should be called after generating or reading mtop,
60 * to set some compute intesive variables to avoid
61 * N^2 operations later on.
64 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.
71 gmx_mtop_count_atomtypes(const gmx_mtop_t *mtop, int state, int typecount[]);
73 /* Returns the total number of charge groups in mtop */
75 ncg_mtop(const gmx_mtop_t *mtop);
77 /*!\brief Returns the total number of molecules in mtop
79 * \param[in] mtop The global topology
81 int gmx_mtop_num_molecules(const gmx_mtop_t &mtop);
83 /* Returns the total number of residues in mtop. */
84 int gmx_mtop_nres(const gmx_mtop_t *mtop);
86 /* Removes the charge groups, i.e. makes single atom charge groups, in mtop */
87 void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop);
89 /* Abstract type for atom loop over all atoms */
90 typedef struct gmx_mtop_atomloop_all *gmx_mtop_atomloop_all_t;
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.
98 gmx_mtop_atomloop_all_t
99 gmx_mtop_atomloop_all_init(const gmx_mtop_t *mtop);
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.
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)) {
115 gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
116 int *at_global, const t_atom **atom);
118 /* Return the atomname, the residue number and residue name
119 * of the current atom in the loop.
122 gmx_mtop_atomloop_all_names(gmx_mtop_atomloop_all_t aloop,
123 char **atomname, int *resnr, char **resname);
125 /* Return the a pointer to the moltype struct of the current atom
126 * in the loop and the atom number in the molecule.
129 gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
130 const gmx_moltype_t **moltype, int *at_mol);
133 /* Abstract type for atom loop over atoms in all molecule blocks */
134 typedef struct gmx_mtop_atomloop_block *gmx_mtop_atomloop_block_t;
136 /* Initialize an atom loop over atoms in all molecule blocks the system.
138 gmx_mtop_atomloop_block_t
139 gmx_mtop_atomloop_block_init(const gmx_mtop_t *mtop);
141 /* Loop to the next atom.
142 * When not at the end:
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.
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)) {
155 gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
156 const t_atom **atom, int *nmol);
159 /* Abstract type for ilist loop over all ilists */
160 typedef struct gmx_mtop_ilistloop *gmx_mtop_ilistloop_t;
162 /* Initialize an ilist loop over all molecule types in the system. */
164 gmx_mtop_ilistloop_init(const gmx_mtop_t *mtop);
166 /* Initialize an ilist loop over all molecule types in the system. */
168 gmx_mtop_ilistloop_init(const gmx_mtop_t &mtop);
170 /* Loop to the next molecule,
171 * When not at the end:
172 * returns TRUE and a 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 FALSE.
177 gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
178 const t_ilist **ilist_mol, int *nmol);
181 /* Abstract type for ilist loop over all ilists of all molecules */
182 typedef struct gmx_mtop_ilistloop_all *gmx_mtop_ilistloop_all_t;
184 /* Initialize an ilist loop over all molecule types in the system.
185 * Only use this when you really need to loop over all molecules,
186 * i.e. when you use groups which might differ per molecule,
187 * otherwise use gmx_mtop_ilistloop.
189 gmx_mtop_ilistloop_all_t
190 gmx_mtop_ilistloop_all_init(const gmx_mtop_t *mtop);
192 /* Loop to the next molecule,
193 * When not at the end:
194 * returns TRUE and a pointer to the next array ilist_mol[F_NRE],
195 * writes the atom offset which should be added to iatoms in atnr_offset.
196 * When at the end, destroys iloop and returns FALSE.
199 gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
200 const t_ilist **ilist_mol, int *atnr_offset);
203 /* Returns the total number of interactions in the system of type ftype */
205 gmx_mtop_ftype_count(const gmx_mtop_t *mtop, int ftype);
207 /* Returns the total number of interactions in the system of type ftype */
209 gmx_mtop_ftype_count(const gmx_mtop_t &mtop, int ftype);
211 /* Returns a charge group index for the whole system */
213 gmx_mtop_global_cgs(const gmx_mtop_t *mtop);
216 /* Returns a single t_atoms struct for the whole system */
218 gmx_mtop_global_atoms(const gmx_mtop_t *mtop);
221 /* Generate a 'local' topology for the whole system.
222 * When freeEnergyInteractionsAtEnd == true, the free energy interactions will
223 * be sorted to the end.
226 gmx_mtop_generate_local_top(const gmx_mtop_t *mtop, bool freeEnergyInteractionsAtEnd);
229 /*!\brief Creates and returns a struct with begin/end atom indices of all molecules
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].
236 gmx::RangePartitioning gmx_mtop_molecules(const gmx_mtop_t &mtop);
239 /* Converts a gmx_mtop_t struct to t_topology.
241 * If the lifetime of the returned topology should be longer than that
242 * of mtop, your need to pass freeMtop==true.
243 * If freeMTop == true, memory related to mtop will be freed so that done_top()
244 * on the result value will free all memory.
245 * If freeMTop == false, mtop and the return value will share some of their
246 * memory, and there is currently no way to consistently free all the memory.
249 gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop, bool freeMTop);
251 /*! \brief Get vector of atoms indices from topology
253 * This function returns the indices of all particles with type
254 * eptAtom, that is shells, vsites etc. are left out.
255 * \param[in] mtop Molecular topology
256 * \returns Vector that will be filled with the atom indices
258 std::vector<size_t> get_atom_index(const gmx_mtop_t *mtop);
260 /*! \brief Converts a t_atoms struct to an mtop struct
262 * All pointers contained in \p atoms will be copied into \p mtop.
263 * Note that this will produce one moleculetype encompassing the whole system.
265 * \param[in] symtab The symbol table
266 * \param[in] name Pointer to the name for the topology
267 * \param[in] atoms The atoms to convert
268 * \param[out] mtop The molecular topology output containing atoms.
271 convertAtomsToMtop(t_symtab *symtab,