include/centerofmass.h

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  38 /*! \file
  39  * \brief API for calculation of centers of mass/geometry.
  40  *
  41  * This header defines a few functions that can be used to calculate
  42  * centers of mass/geometry for a group of atoms.
  43  * These routines can be used independently of the other parts of the
  44  * library, but they are also used internally by the selection engine.
  45  * In most cases, it should not be necessary to call these functions
  46  * directly.
  47  * Instead, one should write an analysis tool such that it gets all
  48  * positions through selections.
  49  *
  50  * The functions in the header can be divided into a few groups based on the
  51  * parameters they take. The simplest group of functions calculates the center
  52  * of a single group of atoms:
  53  *  - gmx_calc_cog(): Calculates the center of geometry (COG) of a given
  54  *    group of atoms.
  55  *  - gmx_calc_com(): Calculates the center of mass (COM) of a given group
  56  *    of atoms.
  57  *  - gmx_calc_comg(): Calculates either the COM or COG, based on a
  58  *    gmx_boolean flag.
  59  *
  60  * A second set of routines is provided for calculating the centers for groups
  61  * that wrap over periodic boundaries (gmx_calc_cog_pbc(), gmx_calc_com_pbc(),
  62  * gmx_calc_comg_pbc()). These functions are slower, because they need to
  63  * adjust the center iteratively.
  64  *
  65  * It is also possible to calculate centers for several groups of atoms in
  66  * one call. The functions gmx_calc_cog_block(), gmx_calc_com_block() and
  67  * gmx_calc_comg_block() take an index group and a partitioning of that index
  68  * group (as a \c t_block structure), and calculate the centers for
  69  * each group defined by the \c t_block structure separately.
  70  *
  71  * Finally, there is a function gmx_calc_comg_blocka() that takes both the
  72  * index group and the partitioning as a single \c t_blocka structure.
  73  */
  74 #ifndef CENTEROFMASS_H
  75 #define CENTEROFMASS_H
  76
  77 #include "typedefs.h"
  78
  79 #ifdef __cplusplus
  80 extern "C"
  81 {
  82 #endif
  83
  84 /** Calculate a single center of geometry. */
  85 int
  86 gmx_calc_cog(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xout);
  87 /** Calculate a single center of mass. */
  88 int
  89 gmx_calc_com(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xout);
  90 /** Calculate force on a single center of geometry. */
  91 int
  92 gmx_calc_cog_f(t_topology *top, rvec f[], int nrefat, atom_id index[], rvec fout);
  93 /** Calculate a single center of mass/geometry. */
  94 int
  95 gmx_calc_comg(t_topology *top, rvec x[], int nrefat, atom_id index[],
  96               gmx_bool bMass, rvec xout);
  97 /** Calculate force on a single center of mass/geometry. */
  98 int
  99 gmx_calc_comg_f(t_topology *top, rvec f[], int nrefat, atom_id index[],
 100                 gmx_bool bMass, rvec fout);
 101
 102 /** Calculate a single center of geometry iteratively, taking PBC into account. */
 103 int
 104 gmx_calc_cog_pbc(t_topology *top, rvec x[], t_pbc *pbc,
 105                  int nrefat, atom_id index[], rvec xout);
 106 /** Calculate a single center of mass iteratively, taking PBC into account. */
 107 int
 108 gmx_calc_com_pbc(t_topology *top, rvec x[], t_pbc *pbc,
 109                  int nrefat, atom_id index[], rvec xout);
 110 /** Calculate a single center of mass/geometry iteratively with PBC. */
 111 int
 112 gmx_calc_comg_pbc(t_topology *top, rvec x[], t_pbc *pbc,
 113                   int nrefat, atom_id index[], gmx_bool bMass, rvec xout);
 114
 115 /** Calculate centers of geometry for a blocked index. */
 116 int
 117 gmx_calc_cog_block(t_topology *top, rvec x[], t_block *block,
 118                    atom_id index[], rvec xout[]);
 119 /** Calculate centers of mass for a blocked index. */
 120 int
 121 gmx_calc_com_block(t_topology *top, rvec x[], t_block *block,
 122                    atom_id index[], rvec xout[]);
 123 /** Calculate forces on centers of geometry for a blocked index. */
 124 int
 125 gmx_calc_cog_f_block(t_topology *top, rvec f[], t_block *block,
 126                      atom_id index[], rvec fout[]);
 127 /** Calculate centers of mass/geometry for a blocked index. */
 128 int
 129 gmx_calc_comg_block(t_topology *top, rvec x[], t_block *block,
 130                     atom_id index[], gmx_bool bMass, rvec xout[]);
 131 /** Calculate forces on centers of mass/geometry for a blocked index. */
 132 int
 133 gmx_calc_comg_f_block(t_topology *top, rvec f[], t_block *block,
 134                       atom_id index[], gmx_bool bMass, rvec fout[]);
 135 /** Calculate centers of mass/geometry for a set of blocks; */
 136 int
 137 gmx_calc_comg_blocka(t_topology *top, rvec x[], t_blocka *block,
 138                      gmx_bool bMass, rvec xout[]);
 139 /** Calculate forces on centers of mass/geometry for a set of blocks; */
 140 int
 141 gmx_calc_comg_f_blocka(t_topology *top, rvec x[], t_blocka *block,
 142                        gmx_bool bMass, rvec xout[]);
 143
 144 #ifdef __cplusplus
 145 }
 146 #endif
 147
 148 #endif