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36 * \brief API for calculation of centers of mass/geometry.
38 * This header defines a few functions that can be used to calculate
39 * centers of mass/geometry for a group of atoms.
40 * These routines can be used independently of the other parts of the
41 * library, but they are also used internally by the selection engine.
42 * In most cases, it should not be necessary to call these functions
44 * Instead, one should write an analysis tool such that it gets all
45 * positions through selections.
47 * The functions in the header can be divided into a few groups based on the
48 * parameters they take. The simplest group of functions calculates the center
49 * of a single group of atoms:
50 * - gmx_calc_cog(): Calculates the center of geometry (COG) of a given
52 * - gmx_calc_com(): Calculates the center of mass (COM) of a given group
54 * - gmx_calc_comg(): Calculates either the COM or COG, based on a
57 * A second set of routines is provided for calculating the centers for groups
58 * that wrap over periodic boundaries (gmx_calc_cog_pbc(), gmx_calc_com_pbc(),
59 * gmx_calc_comg_pbc()). These functions are slower, because they need to
60 * adjust the center iteratively.
62 * It is also possible to calculate centers for several groups of atoms in
63 * one call. The functions gmx_calc_cog_block(), gmx_calc_com_block() and
64 * gmx_calc_comg_block() take an index group and a partitioning of that index
65 * group (as a \c t_block structure), and calculate the centers for
66 * each group defined by the \c t_block structure separately.
68 * Finally, there is a function gmx_calc_comg_blocka() that takes both the
69 * index group and the partitioning as a single \c t_blocka structure.
71 * \author Teemu Murtola <teemu.murtola@gmail.com>
72 * \ingroup module_selection
74 #ifndef GMX_SELECTION_CENTEROFMASS_H
75 #define GMX_SELECTION_CENTEROFMASS_H
77 #include "../legacyheaders/typedefs.h"
80 * Calculate a single center of geometry.
82 * \param[in] top Topology structure (unused, can be NULL).
83 * \param[in] x Position vectors of all atoms.
84 * \param[in] nrefat Number of atoms in the index.
85 * \param[in] index Indices of atoms.
86 * \param[out] xout COG position for the indexed atoms.
87 * \returns 0 on success.
90 gmx_calc_cog(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xout);
91 /** Calculate a single center of mass. */
93 gmx_calc_com(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xout);
94 /** Calculate force on a single center of geometry. */
96 gmx_calc_cog_f(t_topology *top, rvec f[], int nrefat, atom_id index[], rvec fout);
98 * Calculate force on a single center of mass.
100 * \param[in] top Topology structure (unused, can be NULL).
101 * \param[in] f Forces on all atoms.
102 * \param[in] nrefat Number of atoms in the index.
103 * \param[in] index Indices of atoms.
104 * \param[out] fout Force on the COM position for the indexed atoms.
105 * \returns 0 on success.
108 gmx_calc_com_f(t_topology *top, rvec f[], int nrefat, atom_id index[], rvec fout);
109 /** Calculate a single center of mass/geometry. */
111 gmx_calc_comg(t_topology *top, rvec x[], int nrefat, atom_id index[],
112 bool bMass, rvec xout);
113 /** Calculate force on a single center of mass/geometry. */
115 gmx_calc_comg_f(t_topology *top, rvec f[], int nrefat, atom_id index[],
116 bool bMass, rvec fout);
118 /** Calculate a single center of geometry iteratively, taking PBC into account. */
120 gmx_calc_cog_pbc(t_topology *top, rvec x[], t_pbc *pbc,
121 int nrefat, atom_id index[], rvec xout);
122 /** Calculate a single center of mass iteratively, taking PBC into account. */
124 gmx_calc_com_pbc(t_topology *top, rvec x[], t_pbc *pbc,
125 int nrefat, atom_id index[], rvec xout);
126 /** Calculate a single center of mass/geometry iteratively with PBC. */
128 gmx_calc_comg_pbc(t_topology *top, rvec x[], t_pbc *pbc,
129 int nrefat, atom_id index[], bool bMass, rvec xout);
132 * Calculate centers of geometry for a blocked index.
134 * \param[in] top Topology structure (unused, can be NULL).
135 * \param[in] x Position vectors of all atoms.
136 * \param[in] block t_block structure that divides \p index into blocks.
137 * \param[in] index Indices of atoms.
138 * \param[out] xout \p block->nr COG positions.
139 * \returns 0 on success.
142 gmx_calc_cog_block(t_topology *top, rvec x[], t_block *block,
143 atom_id index[], rvec xout[]);
144 /** Calculate centers of mass for a blocked index. */
146 gmx_calc_com_block(t_topology *top, rvec x[], t_block *block,
147 atom_id index[], rvec xout[]);
148 /** Calculate forces on centers of geometry for a blocked index. */
150 gmx_calc_cog_f_block(t_topology *top, rvec f[], t_block *block,
151 atom_id index[], rvec fout[]);
153 * Calculate forces on centers of mass for a blocked index.
155 * \param[in] top Topology structure (unused, can be NULL).
156 * \param[in] f Forces on all atoms.
157 * \param[in] block t_block structure that divides \p index into blocks.
158 * \param[in] index Indices of atoms.
159 * \param[out] fout \p block->nr Forces on COM positions.
160 * \returns 0 on success.
163 gmx_calc_com_f_block(t_topology *top, rvec f[], t_block *block,
164 atom_id index[], rvec fout[]);
165 /** Calculate centers of mass/geometry for a blocked index. */
167 gmx_calc_comg_block(t_topology *top, rvec x[], t_block *block,
168 atom_id index[], bool bMass, rvec xout[]);
169 /** Calculate forces on centers of mass/geometry for a blocked index. */
171 gmx_calc_comg_f_block(t_topology *top, rvec f[], t_block *block,
172 atom_id index[], bool bMass, rvec fout[]);
173 /** Calculate centers of mass/geometry for a set of blocks; */
175 gmx_calc_comg_blocka(t_topology *top, rvec x[], t_blocka *block,
176 bool bMass, rvec xout[]);
177 /** Calculate forces on centers of mass/geometry for a set of blocks; */
179 gmx_calc_comg_f_blocka(t_topology *top, rvec x[], t_blocka *block,
180 bool bMass, rvec xout[]);