2 * This file is part of the GROMACS molecular simulation package.
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, 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.
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.
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.
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.
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.
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.
37 #ifndef GMX_TOPOLOGY_MTOP_UTIL_H
38 #define GMX_TOPOLOGY_MTOP_UTIL_H
40 #include "gromacs/legacyheaders/types/inputrec.h"
41 #include "gromacs/utility/basedefinitions.h"
43 /* Ugly hack to convince some compilers that returning t_topology (or other
44 * structs) from an extern "C" function is OK; can probably go when the extern
47 #include "gromacs/topology/topology.h"
53 struct gmx_localtop_t;
62 /* Should be called after generating or reading mtop,
63 * to set some compute intesive variables to avoid
64 * N^2 operations later on.
67 gmx_mtop_finalize(struct gmx_mtop_t *mtop);
69 /* Counts the number of atoms of each type. State should be 0 for
70 * state A and 1 for state B types. typecount should have at
71 * least mtop->ffparams.atnr elements.
74 gmx_mtop_count_atomtypes(const struct gmx_mtop_t *mtop, int state, int typecount[]);
76 /* Returns the total number of charge groups in mtop */
78 ncg_mtop(const struct gmx_mtop_t *mtop);
80 /* Removes the charge groups, i.e. makes single atom charge groups, in mtop */
81 void gmx_mtop_remove_chargegroups(struct gmx_mtop_t *mtop);
84 /* Abstract data type for looking up atoms by global atom number */
85 typedef struct gmx_mtop_atomlookup *gmx_mtop_atomlookup_t;
87 /* Initialize atom lookup by global atom number */
89 gmx_mtop_atomlookup_init(const struct gmx_mtop_t *mtop);
91 /* As gmx_mtop_atomlookup_init, but optimized for atoms involved in settle */
93 gmx_mtop_atomlookup_settle_init(const struct gmx_mtop_t *mtop);
95 /* Destroy a gmx_mtop_atomlookup_t data structure */
97 gmx_mtop_atomlookup_destroy(gmx_mtop_atomlookup_t alook);
100 /* Returns a pointer to the t_atom struct belonging to atnr_global.
101 * This can be an expensive operation, so if possible use
102 * one of the atom loop constructs below.
105 gmx_mtop_atomnr_to_atom(const gmx_mtop_atomlookup_t alook,
107 struct t_atom **atom);
110 /* Returns a pointer to the molecule interaction array ilist_mol[F_NRE]
111 * and the local atom number in the molecule belonging to atnr_global.
114 gmx_mtop_atomnr_to_ilist(const gmx_mtop_atomlookup_t alook,
116 struct t_ilist **ilist_mol, int *atnr_offset);
119 /* Returns the molecule block index
120 * and the molecule number in the block
121 * and the atom number offset for the atom indices in moltype
122 * belonging to atnr_global.
125 gmx_mtop_atomnr_to_molblock_ind(const gmx_mtop_atomlookup_t alook,
127 int *molb, int *molnr, int *atnr_mol);
130 /* Returns atom name, global resnr and residue name of atom atnr_global */
132 gmx_mtop_atominfo_global(const struct gmx_mtop_t *mtop, int atnr_global,
133 char **atomname, int *resnr, char **resname);
136 /* Abstract type for atom loop over all atoms */
137 typedef struct gmx_mtop_atomloop_all *gmx_mtop_atomloop_all_t;
139 /* Initialize an atom loop over all atoms in the system.
140 * The order of the atoms will be as in the state struct.
141 * Only use this when you really need to loop over all atoms,
142 * i.e. when you use groups which might differ per molecule,
143 * otherwise use gmx_mtop_atomloop_block.
145 gmx_mtop_atomloop_all_t
146 gmx_mtop_atomloop_all_init(const struct gmx_mtop_t *mtop);
148 /* Loop to the next atom.
149 * When not at the end:
150 * returns TRUE and at_global,
151 * writes the global atom number in *at_global
152 * and sets the pointer atom to the t_atom struct of that atom.
153 * When at the end, destroys aloop and returns FALSE.
155 * gmx_mtop_atomloop_all_t aloop;
156 * aloop = gmx_mtop_atomloop_all_init(mtop)
157 * while (gmx_mtop_atomloop_all_next(aloop,&at_global,&atom)) {
162 gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
163 int *at_global, struct t_atom **atom);
165 /* Return the atomname, the residue number and residue name
166 * of the current atom in the loop.
169 gmx_mtop_atomloop_all_names(gmx_mtop_atomloop_all_t aloop,
170 char **atomname, int *resnr, char **resname);
172 /* Return the a pointer to the moltype struct of the current atom
173 * in the loop and the atom number in the molecule.
176 gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
177 struct gmx_moltype_t **moltype, int *at_mol);
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
186 gmx_mtop_atomloop_block_init(const struct gmx_mtop_t *mtop);
188 /* Loop to the next atom.
189 * When not at the end:
191 * sets the pointer atom to the t_atom struct of that atom
192 * and return the number of molecules corresponding to this atom.
193 * When at the end, destroys aloop and returns FALSE.
195 * gmx_mtop_atomloop_block_t aloop;
196 * aloop = gmx_mtop_atomloop_block_init(mtop)
197 * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
202 gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
203 struct t_atom **atom, int *nmol);
206 /* Abstract type for ilist loop over all ilists */
207 typedef struct gmx_mtop_ilistloop *gmx_mtop_ilistloop_t;
209 /* Initialize an ilist loop over all molecule types in the system. */
211 gmx_mtop_ilistloop_init(const struct gmx_mtop_t *mtop);
214 /* Loop to the next molecule,
215 * When not at the end:
216 * returns TRUE and a pointer to the next array ilist_mol[F_NRE],
217 * writes the number of molecules for this ilist in *nmol.
218 * When at the end, destroys iloop and returns FALSE.
221 gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
222 struct t_ilist **ilist_mol, int *nmol);
225 /* Abstract type for ilist loop over all ilists of all molecules */
226 typedef struct gmx_mtop_ilistloop_all *gmx_mtop_ilistloop_all_t;
228 /* Initialize an ilist loop over all molecule types in the system.
229 * Only use this when you really need to loop over all molecules,
230 * i.e. when you use groups which might differ per molecule,
231 * otherwise use gmx_mtop_ilistloop.
233 gmx_mtop_ilistloop_all_t
234 gmx_mtop_ilistloop_all_init(const struct gmx_mtop_t *mtop);
236 /* Loop to the next molecule,
237 * When not at the end:
238 * returns TRUE and a pointer to the next array ilist_mol[F_NRE],
239 * writes the atom offset which should be added to iatoms in atnr_offset.
240 * When at the end, destroys iloop and returns FALSE.
243 gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
244 struct t_ilist **ilist_mol, int *atnr_offset);
247 /* Returns the total number of interactions in the system of type ftype */
249 gmx_mtop_ftype_count(const struct gmx_mtop_t *mtop, int ftype);
252 /* Returns a charge group index for the whole system */
254 gmx_mtop_global_cgs(const struct gmx_mtop_t *mtop);
257 /* Returns a single t_atoms struct for the whole system */
259 gmx_mtop_global_atoms(const struct gmx_mtop_t *mtop);
262 /* Make all charge groups the size of one atom.
263 * When bKeepSingleMolCG==TRUE keep charge groups for molecules
264 * that consist of a single charge group.
267 gmx_mtop_make_atomic_charge_groups(struct gmx_mtop_t *mtop, gmx_bool bKeepSingleMolCG);
270 /* Generate a 'local' topology for the whole system.
271 * When ir!=NULL the free energy interactions will be sorted to the end.
273 struct gmx_localtop_t *
274 gmx_mtop_generate_local_top(const struct gmx_mtop_t *mtop, const t_inputrec *ir);
277 /* Converts a gmx_mtop_t struct to t_topology.
278 * All memory relating only to mtop will be freed.
281 gmx_mtop_t_to_t_topology(struct gmx_mtop_t *mtop);