include/centerofmass.h

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  31 /*! \file
  32  * \brief API for calculation of centers of mass/geometry.
  33  *
  34  * This header defines a few functions that can be used to calculate
  35  * centers of mass/geometry for a group of atoms.
  36  * These routines can be used independently of the other parts of the
  37  * library, but they are also used internally by the selection engine.
  38  * In most cases, it should not be necessary to call these functions
  39  * directly.
  40  * Instead, one should write an analysis tool such that it gets all
  41  * positions through selections.
  42  *
  43  * The functions in the header can be divided into a few groups based on the
  44  * parameters they take. The simplest group of functions calculates the center
  45  * of a single group of atoms:
  46  *  - gmx_calc_cog(): Calculates the center of geometry (COG) of a given
  47  *    group of atoms.
  48  *  - gmx_calc_com(): Calculates the center of mass (COM) of a given group
  49  *    of atoms.
  50  *  - gmx_calc_comg(): Calculates either the COM or COG, based on a
  51  *    gmx_boolean flag.
  52  *
  53  * A second set of routines is provided for calculating the centers for groups
  54  * that wrap over periodic boundaries (gmx_calc_cog_pbc(), gmx_calc_com_pbc(),
  55  * gmx_calc_comg_pbc()). These functions are slower, because they need to
  56  * adjust the center iteratively.
  57  *
  58  * It is also possible to calculate centers for several groups of atoms in
  59  * one call. The functions gmx_calc_cog_block(), gmx_calc_com_block() and
  60  * gmx_calc_comg_block() take an index group and a partitioning of that index
  61  * group (as a \c t_block structure), and calculate the centers for
  62  * each group defined by the \c t_block structure separately.
  63  *
  64  * Finally, there is a function gmx_calc_comg_blocka() that takes both the
  65  * index group and the partitioning as a single \c t_blocka structure.
  66  */
  67 #ifndef CENTEROFMASS_H
  68 #define CENTEROFMASS_H
  69
  70 #include "typedefs.h"
  71
  72 #ifdef __cplusplus
  73 extern "C"
  74 {
  75 #endif
  76
  77 /** Calculate a single center of geometry. */
  78 int
  79 gmx_calc_cog(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xout);
  80 /** Calculate a single center of mass. */
  81 int
  82 gmx_calc_com(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xout);
  83 /** Calculate force on a single center of geometry. */
  84 int
  85 gmx_calc_cog_f(t_topology *top, rvec f[], int nrefat, atom_id index[], rvec fout);
  86 /** Calculate a single center of mass/geometry. */
  87 int
  88 gmx_calc_comg(t_topology *top, rvec x[], int nrefat, atom_id index[],
  89               gmx_bool bMass, rvec xout);
  90 /** Calculate force on a single center of mass/geometry. */
  91 int
  92 gmx_calc_comg_f(t_topology *top, rvec f[], int nrefat, atom_id index[],
  93                 gmx_bool bMass, rvec fout);
  94
  95 /** Calculate a single center of geometry iteratively, taking PBC into account. */
  96 int
  97 gmx_calc_cog_pbc(t_topology *top, rvec x[], t_pbc *pbc,
  98                  int nrefat, atom_id index[], rvec xout);
  99 /** Calculate a single center of mass iteratively, taking PBC into account. */
 100 int
 101 gmx_calc_com_pbc(t_topology *top, rvec x[], t_pbc *pbc,
 102                  int nrefat, atom_id index[], rvec xout);
 103 /** Calculate a single center of mass/geometry iteratively with PBC. */
 104 int
 105 gmx_calc_comg_pbc(t_topology *top, rvec x[], t_pbc *pbc,
 106                   int nrefat, atom_id index[], gmx_bool bMass, rvec xout);
 107
 108 /** Calculate centers of geometry for a blocked index. */
 109 int
 110 gmx_calc_cog_block(t_topology *top, rvec x[], t_block *block,
 111                    atom_id index[], rvec xout[]);
 112 /** Calculate centers of mass for a blocked index. */
 113 int
 114 gmx_calc_com_block(t_topology *top, rvec x[], t_block *block,
 115                    atom_id index[], rvec xout[]);
 116 /** Calculate forces on centers of geometry for a blocked index. */
 117 int
 118 gmx_calc_cog_f_block(t_topology *top, rvec f[], t_block *block,
 119                      atom_id index[], rvec fout[]);
 120 /** Calculate centers of mass/geometry for a blocked index. */
 121 int
 122 gmx_calc_comg_block(t_topology *top, rvec x[], t_block *block,
 123                     atom_id index[], gmx_bool bMass, rvec xout[]);
 124 /** Calculate forces on centers of mass/geometry for a blocked index. */
 125 int
 126 gmx_calc_comg_f_block(t_topology *top, rvec f[], t_block *block,
 127                       atom_id index[], gmx_bool bMass, rvec fout[]);
 128 /** Calculate centers of mass/geometry for a set of blocks; */
 129 int
 130 gmx_calc_comg_blocka(t_topology *top, rvec x[], t_blocka *block,
 131                      gmx_bool bMass, rvec xout[]);
 132 /** Calculate forces on centers of mass/geometry for a set of blocks; */
 133 int
 134 gmx_calc_comg_f_blocka(t_topology *top, rvec x[], t_blocka *block,
 135                        gmx_bool bMass, rvec xout[]);
 136
 137 #ifdef __cplusplus
 138 }
 139 #endif
 140
 141 #endif