include/princ.h

   1 /*
   2  * $Id$
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.1
  11  * Copyright (c) 1991-2001, University of Groningen, The Netherlands
  12  * This program is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU General Public License
  14  * as published by the Free Software Foundation; either version 2
  15  * of the License, or (at your option) any later version.
  16  *
  17  * If you want to redistribute modifications, please consider that
  18  * scientific software is very special. Version control is crucial -
  19  * bugs must be traceable. We will be happy to consider code for
  20  * inclusion in the official distribution, but derived work must not
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  22  * files - if they are missing, get the official version at www.gromacs.org.
  23  *
  24  * To help us fund GROMACS development, we humbly ask that you cite
  25  * the papers on the package - you can find them in the top README file.
  26  *
  27  * For more info, check our website at http://www.gromacs.org
  28  *
  29  * And Hey:
  30  * Getting the Right Output Means no Artefacts in Calculating Stuff
  31  */
  32
  33 #ifndef _princ_h
  34 #define _princ_h
  35
  36 static char *SRCID_princ_h = "$Id$";
  37 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include "typedefs.h"
  42
  43 extern void rotate_atoms(int gnx,atom_id index[],rvec x[],matrix trans);
  44 /* Rotate all atoms in index using matrix trans */
  45
  46 extern void principal_comp(int n,atom_id index[],t_atom atom[],rvec x[],
  47                            matrix trans,rvec d);
  48 /* Calculate the principal components of atoms in index. Atoms are
  49  * mass weighted. It is assumed that the center of mass is in the origin!
  50  */
  51
  52 extern void orient_princ(t_atoms *atoms, int isize, atom_id *index,
  53                          int natoms, rvec x[], rvec *v, rvec d);
  54 /* rotates molecule to align principal axes with coordinate axes */
  55
  56 extern real calc_xcm(rvec x[],int gnx,atom_id *index,t_atom *atom,rvec xcm,
  57                      bool bQ);
  58 /* Calculate the center of mass of the atoms in index. if bQ then the atoms
  59  * will be charge weighted rather than mass weighted.
  60  * Returns the total mass/charge.
  61  */
  62
  63 extern real sub_xcm(rvec x[],int gnx,atom_id *index,t_atom atom[],rvec xcm,
  64                     bool bQ);
  65 /* Calc. the center of mass and subtract it from all coordinates.
  66  * Returns the original center of mass in xcm
  67  * Returns the total mass
  68  */
  69
  70 extern void add_xcm(rvec x[],int gnx,atom_id *index,rvec xcm);
  71 /* Increment all atoms in index with xcm */
  72
  73 #endif