*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "typedefs.h"
+#ifndef GMX_LEGACYHEADERS_MTOP_UTIL_H
+#define GMX_LEGACYHEADERS_MTOP_UTIL_H
+
+#include "types/inputrec.h"
+#include "../utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct gmx_localtop_t;
+struct gmx_moltype_t;
+struct gmx_mtop_t;
+struct t_atom;
+struct t_atoms;
+struct t_block;
+struct t_ilist;
+struct t_topology;
+
/* Should be called after generating or reading mtop,
* to set some compute intesive variables to avoid
* N^2 operations later on.
*/
void
-gmx_mtop_finalize(gmx_mtop_t *mtop);
+gmx_mtop_finalize(struct gmx_mtop_t *mtop);
/* Counts the number of atoms of each type. State should be 0 for
* state A and 1 for state B types. typecount should have at
* least mtop->ffparams.atnr elements.
*/
void
-gmx_mtop_count_atomtypes(const gmx_mtop_t *mtop, int state, int typecount[]);
+gmx_mtop_count_atomtypes(const struct gmx_mtop_t *mtop, int state, int typecount[]);
/* Returns the total number of charge groups in mtop */
int
-ncg_mtop(const gmx_mtop_t *mtop);
+ncg_mtop(const struct gmx_mtop_t *mtop);
/* Removes the charge groups, i.e. makes single atom charge groups, in mtop */
-void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop);
+void gmx_mtop_remove_chargegroups(struct gmx_mtop_t *mtop);
/* Abstract data type for looking up atoms by global atom number */
/* Initialize atom lookup by global atom number */
gmx_mtop_atomlookup_t
-gmx_mtop_atomlookup_init(const gmx_mtop_t *mtop);
+gmx_mtop_atomlookup_init(const struct gmx_mtop_t *mtop);
/* As gmx_mtop_atomlookup_init, but optimized for atoms involved in settle */
gmx_mtop_atomlookup_t
-gmx_mtop_atomlookup_settle_init(const gmx_mtop_t *mtop);
+gmx_mtop_atomlookup_settle_init(const struct gmx_mtop_t *mtop);
/* Destroy a gmx_mtop_atomlookup_t data structure */
void
void
gmx_mtop_atomnr_to_atom(const gmx_mtop_atomlookup_t alook,
int atnr_global,
- t_atom **atom);
+ struct t_atom **atom);
/* Returns a pointer to the molecule interaction array ilist_mol[F_NRE]
void
gmx_mtop_atomnr_to_ilist(const gmx_mtop_atomlookup_t alook,
int atnr_global,
- t_ilist **ilist_mol, int *atnr_offset);
+ struct t_ilist **ilist_mol, int *atnr_offset);
/* Returns the molecule block index
/* Returns atom name, global resnr and residue name of atom atnr_global */
void
-gmx_mtop_atominfo_global(const gmx_mtop_t *mtop, int atnr_global,
+gmx_mtop_atominfo_global(const struct gmx_mtop_t *mtop, int atnr_global,
char **atomname, int *resnr, char **resname);
* otherwise use gmx_mtop_atomloop_block.
*/
gmx_mtop_atomloop_all_t
-gmx_mtop_atomloop_all_init(const gmx_mtop_t *mtop);
+gmx_mtop_atomloop_all_init(const struct gmx_mtop_t *mtop);
/* Loop to the next atom.
* When not at the end:
*/
gmx_bool
gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
- int *at_global, t_atom **atom);
+ int *at_global, struct t_atom **atom);
/* Return the atomname, the residue number and residue name
* of the current atom in the loop.
*/
void
gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
- gmx_moltype_t **moltype, int *at_mol);
+ struct gmx_moltype_t **moltype, int *at_mol);
/* Abstract type for atom loop over atoms in all molecule blocks */
/* Initialize an atom loop over atoms in all molecule blocks the system.
*/
gmx_mtop_atomloop_block_t
-gmx_mtop_atomloop_block_init(const gmx_mtop_t *mtop);
+gmx_mtop_atomloop_block_init(const struct gmx_mtop_t *mtop);
/* Loop to the next atom.
* When not at the end:
*/
gmx_bool
gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
- t_atom **atom, int *nmol);
+ struct t_atom **atom, int *nmol);
/* Abstract type for ilist loop over all ilists */
/* Initialize an ilist loop over all molecule types in the system. */
gmx_mtop_ilistloop_t
-gmx_mtop_ilistloop_init(const gmx_mtop_t *mtop);
+gmx_mtop_ilistloop_init(const struct gmx_mtop_t *mtop);
/* Loop to the next molecule,
*/
gmx_bool
gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
- t_ilist **ilist_mol, int *nmol);
+ struct t_ilist **ilist_mol, int *nmol);
/* Abstract type for ilist loop over all ilists of all molecules */
* otherwise use gmx_mtop_ilistloop.
*/
gmx_mtop_ilistloop_all_t
-gmx_mtop_ilistloop_all_init(const gmx_mtop_t *mtop);
+gmx_mtop_ilistloop_all_init(const struct gmx_mtop_t *mtop);
/* Loop to the next molecule,
* When not at the end:
*/
gmx_bool
gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
- t_ilist **ilist_mol, int *atnr_offset);
+ struct t_ilist **ilist_mol, int *atnr_offset);
/* Returns the total number of interactions in the system of type ftype */
int
-gmx_mtop_ftype_count(const gmx_mtop_t *mtop, int ftype);
+gmx_mtop_ftype_count(const struct gmx_mtop_t *mtop, int ftype);
/* Returns a charge group index for the whole system */
-t_block
-gmx_mtop_global_cgs(const gmx_mtop_t *mtop);
+struct t_block
+gmx_mtop_global_cgs(const struct gmx_mtop_t *mtop);
/* Returns a single t_atoms struct for the whole system */
-t_atoms
-gmx_mtop_global_atoms(const gmx_mtop_t *mtop);
+struct t_atoms
+gmx_mtop_global_atoms(const struct gmx_mtop_t *mtop);
/* Make all charge groups the size of one atom.
* that consist of a single charge group.
*/
void
-gmx_mtop_make_atomic_charge_groups(gmx_mtop_t *mtop, gmx_bool bKeepSingleMolCG);
+gmx_mtop_make_atomic_charge_groups(struct gmx_mtop_t *mtop, gmx_bool bKeepSingleMolCG);
/* Generate a 'local' topology for the whole system.
* When ir!=NULL the free energy interactions will be sorted to the end.
*/
-gmx_localtop_t *
-gmx_mtop_generate_local_top(const gmx_mtop_t *mtop, const t_inputrec *ir);
+struct gmx_localtop_t *
+gmx_mtop_generate_local_top(const struct gmx_mtop_t *mtop, const t_inputrec *ir);
/* Converts a gmx_mtop_t struct to t_topology.
* All memory relating only to mtop will be freed.
*/
-t_topology
-gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop);
+struct t_topology
+gmx_mtop_t_to_t_topology(struct gmx_mtop_t *mtop);
#ifdef __cplusplus
}
#endif
+
+#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff