include/princ.h

   1 /*
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   9  *                        VERSION 3.2.0
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  35
  36 #ifndef _princ_h
  37 #define _princ_h
  38
  39 #include "typedefs.h"
  40
  41 #ifdef __cplusplus
  42 extern "C" {
  43 #endif
  44
  45 void rotate_atoms(int gnx,atom_id index[],rvec x[],matrix trans);
  46 /* Rotate all atoms in index using matrix trans */
  47
  48 void principal_comp(int n,atom_id index[],t_atom atom[],rvec x[],
  49                            matrix trans,rvec d);
  50 /* Calculate the principal components of atoms in index. Atoms are
  51  * mass weighted. It is assumed that the center of mass is in the origin!
  52  */
  53
  54 void orient_princ(t_atoms *atoms, int isize, atom_id *index,
  55                          int natoms, rvec x[], rvec *v, rvec d);
  56 /* rotates molecule to align principal axes with coordinate axes */
  57
  58 real calc_xcm(rvec x[],int gnx,atom_id *index,t_atom *atom,rvec xcm,
  59                      gmx_bool bQ);
  60 /* Calculate the center of mass of the atoms in index. if bQ then the atoms
  61  * will be charge weighted rather than mass weighted.
  62  * Returns the total mass/charge.
  63  */
  64
  65 real sub_xcm(rvec x[],int gnx,atom_id *index,t_atom atom[],rvec xcm,
  66                     gmx_bool bQ);
  67 /* Calc. the center of mass and subtract it from all coordinates.
  68  * Returns the original center of mass in xcm
  69  * Returns the total mass
  70  */
  71
  72 void add_xcm(rvec x[],int gnx,atom_id *index,rvec xcm);
  73 /* Increment all atoms in index with xcm */
  74
  75 #ifdef __cplusplus
  76 }
  77 #endif
  78
  79 #endif