include/princ.h

   1 /*
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   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
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  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
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  15  * This program is free software; you can redistribute it and/or
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  35
  36 #ifndef _princ_h
  37 #define _princ_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include "typedefs.h"
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49 extern void rotate_atoms(int gnx,atom_id index[],rvec x[],matrix trans);
  50 /* Rotate all atoms in index using matrix trans */
  51
  52 extern 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 extern void orient_princ(t_atoms *atoms, int isize, atom_id *index,
  59                          int natoms, rvec x[], rvec *v, rvec d);
  60 /* rotates molecule to align principal axes with coordinate axes */
  61
  62 extern real calc_xcm(rvec x[],int gnx,atom_id *index,t_atom *atom,rvec xcm,
  63                      bool bQ);
  64 /* Calculate the center of mass of the atoms in index. if bQ then the atoms
  65  * will be charge weighted rather than mass weighted.
  66  * Returns the total mass/charge.
  67  */
  68
  69 extern real sub_xcm(rvec x[],int gnx,atom_id *index,t_atom atom[],rvec xcm,
  70                     bool bQ);
  71 /* Calc. the center of mass and subtract it from all coordinates.
  72  * Returns the original center of mass in xcm
  73  * Returns the total mass
  74  */
  75
  76 extern void add_xcm(rvec x[],int gnx,atom_id *index,rvec xcm);
  77 /* Increment all atoms in index with xcm */
  78
  79 #ifdef __cplusplus
  80 }
  81 #endif
  82
  83 #endif