libgromacs-dev 2018.1-1 / usr / include / gromacs / topology / mtop_util.h

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#ifndef GMX_TOPOLOGY_MTOP_UTIL_H
#define GMX_TOPOLOGY_MTOP_UTIL_H

#include <cstddef>

#include <vector>

#include "gromacs/topology/topology.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"

struct gmx_localtop_t;
struct t_atom;
struct t_atoms;
struct t_block;
struct t_ilist;
struct t_symtab;

/* 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);

/* 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[]);

/* Returns the total number of charge groups in mtop */
int
ncg_mtop(const gmx_mtop_t *mtop);

/* Returns the total number of residues in mtop. */
int gmx_mtop_nres(const 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);

/* Abstract type for atom loop over all atoms */
typedef struct gmx_mtop_atomloop_all *gmx_mtop_atomloop_all_t;

/* Initialize an atom loop over all atoms in the system.
 * The order of the atoms will be as in the state struct.
 * Only use this when you really need to loop over all atoms,
 * i.e. when you use groups which might differ per molecule,
 * otherwise use gmx_mtop_atomloop_block.
 */
gmx_mtop_atomloop_all_t
gmx_mtop_atomloop_all_init(const gmx_mtop_t *mtop);

/* Loop to the next atom.
 * When not at the end:
 *   returns TRUE and at_global,
 *   writes the global atom number in *at_global
 *   and sets the pointer atom to the t_atom struct of that atom.
 * When at the end, destroys aloop and returns FALSE.
 * Use as:
 * gmx_mtop_atomloop_all_t aloop;
 * aloop = gmx_mtop_atomloop_all_init(mtop)
 * while (gmx_mtop_atomloop_all_next(aloop,&at_global,&atom)) {
 *     ...
 * }
 */
gmx_bool
gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
                           int *at_global, const t_atom **atom);

/* Return the atomname, the residue number and residue name
 * of the current atom in the loop.
 */
void
gmx_mtop_atomloop_all_names(gmx_mtop_atomloop_all_t aloop,
                            char **atomname, int *resnr, char **resname);

/* Return the a pointer to the moltype struct of the current atom
 * in the loop and the atom number in the molecule.
 */
void
gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
                              gmx_moltype_t **moltype, int *at_mol);


/* Abstract type for atom loop over atoms in all molecule blocks */
typedef struct gmx_mtop_atomloop_block *gmx_mtop_atomloop_block_t;

/* 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);

/* Loop to the next atom.
 * When not at the end:
 *   returns TRUE
 *   sets the pointer atom to the t_atom struct of that atom
 *   and return the number of molecules corresponding to this atom.
 * When at the end, destroys aloop and returns FALSE.
 * Use as:
 * gmx_mtop_atomloop_block_t aloop;
 * aloop = gmx_mtop_atomloop_block_init(mtop)
 * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
 *     ...
 * }
 */
gmx_bool
gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
                             const t_atom **atom, int *nmol);


/* Abstract type for ilist loop over all ilists */
typedef struct gmx_mtop_ilistloop *gmx_mtop_ilistloop_t;

/* Initialize an ilist loop over all molecule types in the system. */
gmx_mtop_ilistloop_t
gmx_mtop_ilistloop_init(const gmx_mtop_t *mtop);


/* Loop to the next molecule,
 * When not at the end:
 *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 *   writes the number of molecules for this ilist in *nmol.
 * When at the end, destroys iloop and returns FALSE.
 */
gmx_bool
gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
                        t_ilist **ilist_mol, int *nmol);


/* Abstract type for ilist loop over all ilists of all molecules */
typedef struct gmx_mtop_ilistloop_all *gmx_mtop_ilistloop_all_t;

/* Initialize an ilist loop over all molecule types in the system.
 * Only use this when you really need to loop over all molecules,
 * i.e. when you use groups which might differ per molecule,
 * otherwise use gmx_mtop_ilistloop.
 */
gmx_mtop_ilistloop_all_t
gmx_mtop_ilistloop_all_init(const gmx_mtop_t *mtop);

/* Loop to the next molecule,
 * When not at the end:
 *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 *   writes the atom offset which should be added to iatoms in atnr_offset.
 * When at the end, destroys iloop and returns FALSE.
 */
gmx_bool
gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
                            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);


/* Returns a charge group index for the whole system */
t_block
gmx_mtop_global_cgs(const 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);


/* Generate a 'local' topology for the whole system.
 * When freeEnergyInteractionsAtEnd == true, the free energy interactions will
 * be sorted to the end.
 */
gmx_localtop_t *
gmx_mtop_generate_local_top(const gmx_mtop_t *mtop, bool freeEnergyInteractionsAtEnd);


/* Converts a gmx_mtop_t struct to t_topology.
 *
 * If freeMTop == true, memory related to mtop will be freed so that done_top()
 * on the result value will free all memory.
 * If freeMTop == false, mtop and the return value will share some of their
 * memory, and there is currently no way to consistently free all the memory.
 */
t_topology
gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop, bool freeMTop);

/*! \brief Get vector of atoms indices from topology
 *
 * This function returns the indices of all particles with type
 * eptAtom, that is shells, vsites etc. are left out.
 * \param[in]  mtop Molecular topology
 * \returns Vector that will be filled with the atom indices
 */
std::vector<size_t> get_atom_index(const gmx_mtop_t *mtop);

/*! \brief Converts a t_atoms struct to an mtop struct
 *
 * All pointers contained in \p atoms will be copied into \p mtop.
 * Note that this will produce one moleculetype encompassing the whole system.
 *
 * \param[in]  symtab  The symbol table
 * \param[in]  name    Pointer to the name for the topology
 * \param[in]  atoms   The atoms to convert
 * \param[out] mtop    The molecular topology output containing atoms.
 */
void
convertAtomsToMtop(t_symtab    *symtab,
                   char       **name,
                   t_atoms     *atoms,
                   gmx_mtop_t  *mtop);

#endif