include/gbutil.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
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  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
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  32  * And Hey:
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  34  */
  35 #include "typedefs.h"
  36
  37 #ifdef __cplusplus
  38 extern "C" {
  39 #endif
  40
  41 void rotate_conf(int natom,rvec *x,rvec *v,real alfa, real beta,real gamma);
  42 /*rotate() rotates a configuration alfa degrees around the x_axis and beta degrees around the y_axis, *v can be NULL */
  43
  44 void orient(int natom,rvec *x,rvec *v, rvec angle,matrix box);
  45 /*orient() rotates a configuration until the largest atom-atom distance is
  46  *placed along the z-axis and the second largest distance is placed along
  47  *the y-axis. Finally the third longest distance is placed along the x-axis
  48  */
  49
  50 void genconf(t_atoms *atoms,rvec *x,rvec *v,real *r,matrix box,ivec n_box);
  51 /*genconf() generates a new configuration by adding boxes*/
  52 void gen_box(int NTB,int natoms,rvec *x, matrix box,rvec box_space,
  53                     gmx_bool bCenter);
  54 /* gen_box() generates a box around a configuration, box_space is optional
  55  * extra space around it. If NTB = 1 then a truncated octahedon will be
  56  * generated (don't!) if bCenter then coordinates will be centered in the
  57  * genereated box
  58  */
  59
  60 #ifdef __cplusplus
  61 }
  62 #endif