gromacs-dev 4.6.5-1build1 / usr / include / gromacs / centerofmass.h

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/*! \file
 * \brief API for calculation of centers of mass/geometry.
 *
 * This header defines a few functions that can be used to calculate
 * centers of mass/geometry for a group of atoms.
 * These routines can be used independently of the other parts of the
 * library, but they are also used internally by the selection engine.
 * In most cases, it should not be necessary to call these functions
 * directly.
 * Instead, one should write an analysis tool such that it gets all
 * positions through selections.
 *
 * The functions in the header can be divided into a few groups based on the
 * parameters they take. The simplest group of functions calculates the center
 * of a single group of atoms:
 *  - gmx_calc_cog(): Calculates the center of geometry (COG) of a given
 *    group of atoms.
 *  - gmx_calc_com(): Calculates the center of mass (COM) of a given group
 *    of atoms.
 *  - gmx_calc_comg(): Calculates either the COM or COG, based on a
 *    gmx_boolean flag.
 *
 * A second set of routines is provided for calculating the centers for groups
 * that wrap over periodic boundaries (gmx_calc_cog_pbc(), gmx_calc_com_pbc(),
 * gmx_calc_comg_pbc()). These functions are slower, because they need to
 * adjust the center iteratively.
 *
 * It is also possible to calculate centers for several groups of atoms in
 * one call. The functions gmx_calc_cog_block(), gmx_calc_com_block() and
 * gmx_calc_comg_block() take an index group and a partitioning of that index
 * group (as a \c t_block structure), and calculate the centers for
 * each group defined by the \c t_block structure separately.
 *
 * Finally, there is a function gmx_calc_comg_blocka() that takes both the
 * index group and the partitioning as a single \c t_blocka structure.
 */
#ifndef CENTEROFMASS_H
#define CENTEROFMASS_H

#include "typedefs.h"

#ifdef __cplusplus
extern "C"
{
#endif

/** Calculate a single center of geometry. */
int
gmx_calc_cog(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xout);
/** Calculate a single center of mass. */
int
gmx_calc_com(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xout);
/** Calculate force on a single center of geometry. */
int
gmx_calc_cog_f(t_topology *top, rvec f[], int nrefat, atom_id index[], rvec fout);
/** Calculate a single center of mass/geometry. */
int
gmx_calc_comg(t_topology *top, rvec x[], int nrefat, atom_id index[],
              gmx_bool bMass, rvec xout);
/** Calculate force on a single center of mass/geometry. */
int
gmx_calc_comg_f(t_topology *top, rvec f[], int nrefat, atom_id index[],
                gmx_bool bMass, rvec fout);

/** Calculate a single center of geometry iteratively, taking PBC into account. */
int
gmx_calc_cog_pbc(t_topology *top, rvec x[], t_pbc *pbc,
                 int nrefat, atom_id index[], rvec xout);
/** Calculate a single center of mass iteratively, taking PBC into account. */
int
gmx_calc_com_pbc(t_topology *top, rvec x[], t_pbc *pbc,
                 int nrefat, atom_id index[], rvec xout);
/** Calculate a single center of mass/geometry iteratively with PBC. */
int
gmx_calc_comg_pbc(t_topology *top, rvec x[], t_pbc *pbc,
                  int nrefat, atom_id index[], gmx_bool bMass, rvec xout);

/** Calculate centers of geometry for a blocked index. */
int
gmx_calc_cog_block(t_topology *top, rvec x[], t_block *block,
                   atom_id index[], rvec xout[]);
/** Calculate centers of mass for a blocked index. */
int
gmx_calc_com_block(t_topology *top, rvec x[], t_block *block,
                   atom_id index[], rvec xout[]);
/** Calculate forces on centers of geometry for a blocked index. */
int
gmx_calc_cog_f_block(t_topology *top, rvec f[], t_block *block,
                     atom_id index[], rvec fout[]);
/** Calculate centers of mass/geometry for a blocked index. */
int
gmx_calc_comg_block(t_topology *top, rvec x[], t_block *block,
                    atom_id index[], gmx_bool bMass, rvec xout[]);
/** Calculate forces on centers of mass/geometry for a blocked index. */
int
gmx_calc_comg_f_block(t_topology *top, rvec f[], t_block *block,
                      atom_id index[], gmx_bool bMass, rvec fout[]);
/** Calculate centers of mass/geometry for a set of blocks; */
int
gmx_calc_comg_blocka(t_topology *top, rvec x[], t_blocka *block,
                     gmx_bool bMass, rvec xout[]);
/** Calculate forces on centers of mass/geometry for a set of blocks; */
int
gmx_calc_comg_f_blocka(t_topology *top, rvec x[], t_blocka *block,
                       gmx_bool bMass, rvec xout[]);

#ifdef __cplusplus
}
#endif

#endif