include/princ.h

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  38
  39 #ifndef _princ_h
  40 #define _princ_h
  41 #include "visibility.h"
  42 #include "typedefs.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 void rotate_atoms(int gnx, atom_id index[], rvec x[], matrix trans);
  49 /* Rotate all atoms in index using matrix trans */
  50
  51 GMX_LIBGMX_EXPORT
  52 void principal_comp(int n, atom_id index[], t_atom atom[], rvec x[],
  53                     matrix trans, rvec d);
  54 /* Calculate the principal components of atoms in index. Atoms are
  55  * mass weighted. It is assumed that the center of mass is in the origin!
  56  */
  57
  58 GMX_LIBGMX_EXPORT
  59 void orient_princ(t_atoms *atoms, int isize, atom_id *index,
  60                   int natoms, rvec x[], rvec *v, rvec d);
  61 /* rotates molecule to align principal axes with coordinate axes */
  62
  63 GMX_LIBGMX_EXPORT
  64 real calc_xcm(rvec x[], int gnx, atom_id *index, t_atom *atom, rvec xcm,
  65               gmx_bool bQ);
  66 /* Calculate the center of mass of the atoms in index. if bQ then the atoms
  67  * will be charge weighted rather than mass weighted.
  68  * Returns the total mass/charge.
  69  */
  70
  71 GMX_LIBGMX_EXPORT
  72 real sub_xcm(rvec x[], int gnx, atom_id *index, t_atom atom[], rvec xcm,
  73              gmx_bool bQ);
  74 /* Calc. the center of mass and subtract it from all coordinates.
  75  * Returns the original center of mass in xcm
  76  * Returns the total mass
  77  */
  78
  79 void add_xcm(rvec x[], int gnx, atom_id *index, rvec xcm);
  80 /* Increment all atoms in index with xcm */
  81
  82 #ifdef __cplusplus
  83 }
  84 #endif
  85
  86 #endif