include/pbc.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 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
  18  * as published by the Free Software Foundation; either version 2
  19  * of the License, or (at your option) any later version.
  20  *
  21  * If you want to redistribute modifications, please consider that
  22  * scientific software is very special. Version control is crucial -
  23  * bugs must be traceable. We will be happy to consider code for
  24  * inclusion in the official distribution, but derived work must not
  25  * be called official GROMACS. Details are found in the README & COPYING
  26  * files - if they are missing, get the official version at www.gromacs.org.
  27  *
  28  * To help us fund GROMACS development, we humbly ask that you cite
  29  * the papers on the package - you can find them in the top README file.
  30  *
  31  * For more info, check our website at http://www.gromacs.org
  32  *
  33  * And Hey:
  34  * Gromacs Runs On Most of All Computer Systems
  35  */
  36
  37 #ifndef _pbc_h
  38 #define _pbc_h
  39
  40 #ifdef HAVE_CONFIG_H
  41 #include <config.h>
  42 #endif
  43
  44 #include "sysstuff.h"
  45 #include "typedefs.h"
  46
  47 #ifdef CPLUSPLUS
  48 extern "C" {
  49 #endif
  50
  51 #define BOX_MARGIN 0.5001
  52   /* margin factor for checking if the box is too skewed */
  53
  54 #define TRICLINIC(box) (box[YY][XX]!=0 || box[ZZ][XX]!=0 || box[ZZ][YY]!=0)
  55
  56 #define NTRICIMG 14
  57 #define NCUCVERT 24
  58 #define NCUCEDGE 36
  59
  60   extern char *check_box(matrix box);
  61   /* Returns NULL if the box is supported by Gromacs.
  62    * Otherwise is returns a string with the problem.
  63    */
  64
  65   extern void init_pbc(matrix box);
  66   /* Initiate the periodic boundary conditions. */
  67
  68   extern int pbc_dx(const rvec x1, const rvec x2, rvec dx);
  69   /* Calculate the correct distance vector from x2 to x1 and put it in dx.
  70    * Returns the ishift required to shift x1 at closest distance to x2;
  71    * i.e. if 0<=ishift<SHIFTS then x1 - x2 + shift_vec[ishift] = dx
  72    * (see calc_shifts below on how to obtain shift_vec)
  73    * init_pbc must be called before ever calling this routine
  74    * (this is done by put_charge_groups_in_box).
  75    */
  76
  77   extern bool image_rect(ivec xi,ivec xj,ivec box_size,
  78                          real rlong2,int *shift,real *r2);
  79   /* Calculate the distance between xi and xj for a rectangular box.
  80    * When the distance is SMALLER than rlong2 return TRUE, return
  81    * the shift code in shift and the distance in r2. When the distance is
  82    * >= rlong2 return FALSE;
  83    * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
  84    */
  85
  86   extern bool image_tri(ivec xi,ivec xj,imatrix box,
  87                         real rlong2,int *shift,real *r2);
  88   /* Calculate the distance between xi and xj for a triclinic box.
  89    * When the distance is SMALLER than rlong2 return TRUE, return
  90    * the shift code in shift and the distance in r2. When the distance is
  91    * >= rlong2 return FALSE;
  92    * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
  93    */
  94
  95   extern bool image_cylindric(ivec xi,ivec xj,ivec box_size,real rlong2,
  96                               int *shift,real *r2);
  97   /* Calculate the distance between xi and xj for a rectangular box
  98    * using a cylindric cutoff for long-range only.
  99    * When the distance is SMALLER than rlong2 (in X and Y dir.)
 100    * return TRUE, return
 101    * the shift code in shift and the distance in r2. When the distance is
 102    * >= rlong2 return FALSE;
 103    * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
 104    */
 105
 106   extern void calc_shifts(matrix box,rvec box_size,rvec shift_vec[]);
 107   /* This routine calculates ths shift vectors necessary to use the
 108    * ns routine.
 109    */
 110
 111   extern void calc_cgcm(FILE *log,int cg0,int cg1,t_block *cgs,
 112                         rvec pos[],rvec cg_cm[]);
 113   /* Routine to compute centers of geometry of charge groups. No periodicity
 114    * is used.
 115    */
 116
 117   extern void put_charge_groups_in_box (FILE *log,int cg0,int cg1,
 118                                         matrix box,rvec box_size,t_block *cgs,
 119                                         rvec pos[],
 120                                         rvec cg_cm[]);
 121
 122   /* This routine puts charge groups in the periodic box, keeping them
 123    * together.
 124    */
 125
 126   extern void calc_box_center(matrix box,rvec box_center);
 127   /* Calculates the center of the box */
 128
 129   extern void calc_triclinic_images(matrix box,rvec img[]);
 130   /* Calculates the NTRICIMG box images */
 131
 132   extern void calc_compact_unitcell_vertices(matrix box,rvec vert[]);
 133   /* Calculates the NCUCVERT vertices of a compact unitcell */
 134
 135   extern int *compact_unitcell_edges(void);
 136   /* Return an array of unitcell edges of length NCUCEDGE*2,
 137    * this is an index in vert[], which is calculated by calc_unitcell_vertices.
 138    * The index consists of NCUCEDGE pairs of vertex indices.
 139    * The index does not change, so it needs to be retrieved only once.
 140    */
 141
 142   extern void put_atoms_in_box(matrix box,int natoms,rvec x[]);
 143   /* This puts ALL atoms in the box, not caring about charge groups!
 144    * Also works for triclinic cells.
 145    */
 146
 147   extern void put_atoms_in_triclinic_unitcell(matrix box,int natoms,rvec x[]);
 148   /* This puts ALL atoms in the triclinic unit cell, centered around the
 149    * box center as calculated by calc_box_center.
 150    */
 151
 152   extern void put_atoms_in_compact_unitcell(matrix box,int natoms,rvec x[]);
 153   /* This puts ALL atoms at the closest distance for the center of the box
 154    * as calculated by calc_box_center.
 155    */
 156
 157   extern void set_gmx_full_pbc();
 158   /* Turn on full PBS calculation in the GROMACS bonded routines */
 159
 160 #ifdef CPLUSPLUS
 161 }
 162 #endif
 163
 164 #endif  /* _pbc_h */