include/gbutil.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 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * Good ROcking Metal Altar for Chronical Sinners
  28  */
  29 static char *SRCID_gbutil_h = "$Id$";
  30
  31 extern int in_box(int NTB,matrix box,rvec x);
  32 /*in_box() returns zero if atom x is inside the box*/
  33
  34 extern void rotate_conf(int natom,rvec *x,rvec *v,real alfa, real beta,real gamma);
  35 /*rotate() rotates a configuration alfa degrees around the x_axis and beta degrees around the y_axis, *v can be NULL */
  36
  37 extern void orient(int natom,rvec *x,rvec *v, rvec angle,matrix box);
  38 /*orient() rotates a configuration until the largest atom-atom distance is
  39  *placed along the z-axis and the second largest distance is placed along
  40  *the y-axis. Finally the third longest distance is placed along the x-axis
  41  */
  42
  43 extern void genconf(t_atoms *atoms,rvec *x,real *r,matrix box,ivec n_box);
  44 /*genconf() generates a new configuration by adding boxes*/
  45 extern void gen_box(int NTB,int natoms,rvec *x, matrix box,rvec box_space,
  46                     bool bCenter);
  47 /* gen_box() generates a box around a configuration, box_space is optional
  48  * extra space around it. If NTB = 1 then a truncated octahedon will be
  49  * generated (don't!) if bCenter then coordinates will be centered in the
  50  * genereated box
  51  */