src/gromacs/gmxana/princ.h

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  37 #ifndef GMX_GMXANA_PRINC_H
  38 #define GMX_GMXANA_PRINC_H
  39
  40 #include "gromacs/math/vectypes.h"
  41 #include "gromacs/topology/idef.h"
  42 #include "gromacs/utility/basedefinitions.h"
  43
  44 struct t_atom;
  45 struct t_atoms;
  46
  47 void rotate_atoms(int gnx, const int index[], rvec x[], matrix trans);
  48 /* Rotate all atoms in index using matrix trans */
  49
  50 void principal_comp(int n, const int index[], t_atom atom[], rvec x[],
  51                     matrix trans, rvec d);
  52 /* Calculate the principal components of atoms in index. Atoms are
  53  * mass weighted. It is assumed that the center of mass is in the origin!
  54  */
  55
  56 void orient_princ(const t_atoms *atoms, int isize, const int *index,
  57                   int natoms, rvec x[], rvec *v, rvec d);
  58 /* rotates molecule to align principal axes with coordinate axes */
  59
  60 real calc_xcm(const rvec x[], int gnx, const int *index, const t_atom *atom, rvec xcm,
  61               gmx_bool bQ);
  62 /* Calculate the center of mass of the atoms in index. if bQ then the atoms
  63  * will be charge weighted rather than mass weighted.
  64  * Returns the total mass/charge.
  65  */
  66
  67 real sub_xcm(rvec x[], int gnx, const int *index, const t_atom atom[], rvec xcm,
  68              gmx_bool bQ);
  69 /* Calc. the center of mass and subtract it from all coordinates.
  70  * Returns the original center of mass in xcm
  71  * Returns the total mass
  72  */
  73
  74 void add_xcm(rvec x[], int gnx, const int *index, rvec xcm);
  75 /* Increment all atoms in index with xcm */
  76
  77 #endif