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  *    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 extern int
  79 gmx_calc_cog(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xref);
  80 //! Calculate a single center of mass.
  81 extern int
  82 gmx_calc_com(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xref);
  83 //! Calculate a single center of mass/geometry.
  84 extern int
  85 gmx_calc_comg(t_topology *top, rvec x[], int nrefat, atom_id index[],
  86               bool bMass, rvec xout);
  87
  88 //! Calculate a single center of geometry iteratively, taking PBC into account.
  89 extern int
  90 gmx_calc_cog_pbc(t_topology *top, rvec x[], t_pbc *pbc,
  91                  int nrefat, atom_id index[], rvec xout);
  92 //! Calculate a single center of mass iteratively, taking PBC into account.
  93 extern int
  94 gmx_calc_com_pbc(t_topology *top, rvec x[], t_pbc *pbc,
  95                  int nrefat, atom_id index[], rvec xout);
  96 //! Calculate a single center of mass/geometry iteratively with PBC.
  97 extern int
  98 gmx_calc_comg_pbc(t_topology *top, rvec x[], t_pbc *pbc,
  99                   int nrefat, atom_id index[], bool bMass, rvec xout);
 100
 101 //! Calculate centers of geometry for a blocked index.
 102 extern int
 103 gmx_calc_cog_block(t_topology *top, rvec x[], t_block *block,
 104                    atom_id index[], rvec xout[]);
 105 //! Calculate centers of mass for a blocked index.
 106 extern int
 107 gmx_calc_com_block(t_topology *top, rvec x[], t_block *block,
 108                    atom_id index[], rvec xout[]);
 109 //! Calculate centers of mass/geometry for a blocked index.
 110 extern int
 111 gmx_calc_comg_block(t_topology *top, rvec x[], t_block *block,
 112                     atom_id index[], bool bMass, rvec xout[]);
 113 //! Calculate centers of mass/geometry for a set of blocks;
 114 extern int
 115 gmx_calc_comg_blocka(t_topology *top, rvec x[], t_blocka *block,
 116                      bool bMass, rvec xout[]);
 117
 118 #ifdef __cplusplus
 119 }
 120 #endif
 121
 122 #endif