src/gromacs/selection/centerofmass.h

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  36 /*! \internal \file
  37  * \brief API for calculation of centers of mass/geometry.
  38  *
  39  * This header defines a few functions that can be used to calculate
  40  * centers of mass/geometry for a group of atoms.
  41  * These routines can be used independently of the other parts of the
  42  * library, but they are also used internally by the selection engine.
  43  * In most cases, it should not be necessary to call these functions
  44  * directly.
  45  * Instead, one should write an analysis tool such that it gets all
  46  * positions through selections.
  47  *
  48  * The functions in the header can be divided into a few groups based on the
  49  * parameters they take. The simplest group of functions calculates the center
  50  * of a single group of atoms:
  51  *  - gmx_calc_cog(): Calculates the center of geometry (COG) of a given
  52  *    group of atoms.
  53  *  - gmx_calc_com(): Calculates the center of mass (COM) of a given group
  54  *    of atoms.
  55  *  - gmx_calc_comg(): Calculates either the COM or COG, based on a
  56  *    boolean flag.
  57  *
  58  * A second set of routines is provided for calculating the centers for groups
  59  * that wrap over periodic boundaries (gmx_calc_cog_pbc(), gmx_calc_com_pbc(),
  60  * gmx_calc_comg_pbc()). These functions are slower, because they need to
  61  * adjust the center iteratively.
  62  *
  63  * It is also possible to calculate centers for several groups of atoms in
  64  * one call. The functions gmx_calc_cog_block(), gmx_calc_com_block() and
  65  * gmx_calc_comg_block() take an index group and a partitioning of that index
  66  * group (as a \c t_block structure), and calculate the centers for
  67  * each group defined by the \c t_block structure separately.
  68  *
  69  * Finally, there is a function gmx_calc_comg_blocka() that takes both the
  70  * index group and the partitioning as a single \c t_blocka structure.
  71  *
  72  * \author Teemu Murtola <teemu.murtola@gmail.com>
  73  * \ingroup module_selection
  74  */
  75 #ifndef GMX_SELECTION_CENTEROFMASS_H
  76 #define GMX_SELECTION_CENTEROFMASS_H
  77
  78 #include "gromacs/math/vectypes.h"
  79
  80 struct gmx_mtop_t;
  81 struct t_block;
  82 struct t_blocka;
  83 struct t_pbc;
  84
  85 /*! \brief
  86  * Calculate a single center of geometry.
  87  *
  88  * \param[in]  top    Topology structure (unused, can be NULL).
  89  * \param[in]  x      Position vectors of all atoms.
  90  * \param[in]  nrefat Number of atoms in the index.
  91  * \param[in]  index  Indices of atoms.
  92  * \param[out] xout   COG position for the indexed atoms.
  93  */
  94 void gmx_calc_cog(const gmx_mtop_t* top, rvec x[], int nrefat, const int index[], rvec xout);
  95 /** Calculate a single center of mass. */
  96 void gmx_calc_com(const gmx_mtop_t* top, rvec x[], int nrefat, const int index[], rvec xout);
  97 /** Calculate force on a single center of geometry. */
  98 void gmx_calc_cog_f(const gmx_mtop_t* top, rvec f[], int nrefat, const int index[], rvec fout);
  99 /*! \brief
 100  * Calculate force on a single center of mass.
 101  *
 102  * \param[in]  top    Topology structure (unused, can be NULL).
 103  * \param[in]  f      Forces on all atoms.
 104  * \param[in]  nrefat Number of atoms in the index.
 105  * \param[in]  index  Indices of atoms.
 106  * \param[out] fout   Force on the COM position for the indexed atoms.
 107  */
 108 void gmx_calc_com_f(const gmx_mtop_t* top, rvec f[], int nrefat, const int index[], rvec fout);
 109 /** Calculate a single center of mass/geometry. */
 110 void gmx_calc_comg(const gmx_mtop_t* top, rvec x[], int nrefat, const int index[], bool bMass, rvec xout);
 111 /** Calculate force on a single center of mass/geometry. */
 112 void gmx_calc_comg_f(const gmx_mtop_t* top, rvec f[], int nrefat, const int index[], bool bMass, rvec fout);
 113
 114 /** Calculate a single center of geometry iteratively, taking PBC into account. */
 115 void gmx_calc_cog_pbc(const gmx_mtop_t* top, rvec x[], const t_pbc* pbc, int nrefat, const int index[], rvec xout);
 116 /** Calculate a single center of mass iteratively, taking PBC into account. */
 117 void gmx_calc_com_pbc(const gmx_mtop_t* top, rvec x[], const t_pbc* pbc, int nrefat, const int index[], rvec xout);
 118 /** Calculate a single center of mass/geometry iteratively with PBC. */
 119 void gmx_calc_comg_pbc(const gmx_mtop_t* top,
 120                        rvec              x[],
 121                        const t_pbc*      pbc,
 122                        int               nrefat,
 123                        const int         index[],
 124                        bool              bMass,
 125                        rvec              xout);
 126
 127 /*! \brief
 128  * Calculate centers of geometry for a blocked index.
 129  *
 130  * \param[in]  top   Topology structure (unused, can be NULL).
 131  * \param[in]  x     Position vectors of all atoms.
 132  * \param[in]  block t_block structure that divides \p index into blocks.
 133  * \param[in]  index Indices of atoms.
 134  * \param[out] xout  \p block->nr COG positions.
 135  */
 136 void gmx_calc_cog_block(const gmx_mtop_t* top, rvec x[], const t_block* block, const int index[], rvec xout[]);
 137 /** Calculate centers of mass for a blocked index. */
 138 void gmx_calc_com_block(const gmx_mtop_t* top, rvec x[], const t_block* block, const int index[], rvec xout[]);
 139 /** Calculate forces on centers of geometry for a blocked index. */
 140 void gmx_calc_cog_f_block(const gmx_mtop_t* top, rvec f[], const t_block* block, const int index[], rvec fout[]);
 141 /*! \brief
 142  * Calculate forces on centers of mass for a blocked index.
 143  *
 144  * \param[in]  top   Topology structure (unused, can be NULL).
 145  * \param[in]  f     Forces on all atoms.
 146  * \param[in]  block t_block structure that divides \p index into blocks.
 147  * \param[in]  index Indices of atoms.
 148  * \param[out] fout  \p block->nr Forces on COM positions.
 149  */
 150 void gmx_calc_com_f_block(const gmx_mtop_t* top, rvec f[], const t_block* block, const int index[], rvec fout[]);
 151 /** Calculate centers of mass/geometry for a blocked index. */
 152 void gmx_calc_comg_block(const gmx_mtop_t* top,
 153                          rvec              x[],
 154                          const t_block*    block,
 155                          const int         index[],
 156                          bool              bMass,
 157                          rvec              xout[]);
 158 /** Calculate forces on centers of mass/geometry for a blocked index. */
 159 void gmx_calc_comg_f_block(const gmx_mtop_t* top,
 160                            rvec              f[],
 161                            const t_block*    block,
 162                            const int         index[],
 163                            bool              bMass,
 164                            rvec              fout[]);
 165 /** Calculate centers of mass/geometry for a set of blocks; */
 166 void gmx_calc_comg_blocka(const gmx_mtop_t* top, rvec x[], const t_blocka* block, bool bMass, rvec xout[]);
 167 /** Calculate forces on centers of mass/geometry for a set of blocks; */
 168 void gmx_calc_comg_f_blocka(const gmx_mtop_t* top, rvec x[], const t_blocka* block, bool bMass, rvec xout[]);
 169
 170 #endif