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 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
  30 #ifndef _pbc_h
  31 #define _pbc_h
  32
  33 static char *SRCID_pbc_h = "$Id$";
  34
  35 #ifdef HAVE_IDENT
  36 #ident  "@(#) pbc.h 1.17 2/2/97"
  37 #endif /* HAVE_IDENT */
  38 #include "sysstuff.h"
  39 #include "typedefs.h"
  40
  41 #ifdef CPLUSPLUS
  42 extern "C" {
  43 #endif
  44
  45 extern void init_pbc(matrix box,bool bTruncOct);
  46 /* Initiate the periodic boundary conditions. Set bTruncOct to
  47  * TRUE when using a truncated octahedron box.
  48  */
  49
  50 extern void pbc_dx(rvec x1, rvec x2, rvec dx);
  51 /* Calculate the correct distance vector from x1 and x2 and put it in
  52  * dx. init_pbc must be called before ever calling this routine
  53  * (this is done by put_charge_groups_in_box).
  54  */
  55
  56 extern bool image_rect(ivec xi,ivec xj,ivec box_size,
  57                        real rlong2,int *shift,real *r2);
  58 /* Calculate the distance between xi and xj for a rectangular box.
  59  * When the distance is SMALLER than rlong2 return TRUE, return
  60  * the shift code in shift and the distance in r2. When the distance is
  61  * >= rlong2 return FALSE;
  62  * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
  63  */
  64
  65 extern bool image_tri(ivec xi,ivec xj,imatrix box,
  66                       real rlong2,int *shift,real *r2);
  67 /* Calculate the distance between xi and xj for a triclinic box.
  68  * When the distance is SMALLER than rlong2 return TRUE, return
  69  * the shift code in shift and the distance in r2. When the distance is
  70  * >= rlong2 return FALSE;
  71  * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
  72  */
  73
  74 extern bool image_cylindric(ivec xi,ivec xj,ivec box_size,real rlong2,
  75                             int *shift,real *r2);
  76 /* Calculate the distance between xi and xj for a rectangular box
  77  * using a cylindric cutoff for long-range only.
  78  * When the distance is SMALLER than rlong2 (in X and Y dir.)
  79  * return TRUE, return
  80  * the shift code in shift and the distance in r2. When the distance is
  81  * >= rlong2 return FALSE;
  82  * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
  83  */
  84
  85 extern void calc_shifts(matrix box,rvec box_size,rvec shift_vec[],
  86                         bool bTruncOct);
  87 /* This routine calculates ths shift vectors necessary to use the
  88  * ns routine. Note that for the truncated octahedron case too many
  89  * shift vectors can be calculated: The ones for which exactly
  90  * 2 of the k,l,m indexes are not 0 (12 vectors lying along the box
  91  * edges. This can be compensated for by removing all the shift_vecs with
  92  * (k+l+m) even. This is a feature of the way in which the counting is
  93  * done. It implies that, when using truncated octahedron,
  94  * the shift codes 1,3,5,7,9,11,15,17,19,21,23,25 should never occur,
  95  * that is, every second entry, EXCEPT the central box.
  96  */
  97
  98 extern void calc_cgcm(FILE *log,int cg0,int cg1,t_block *cgs,
  99                       rvec pos[],rvec cg_cm[]);
 100 /* Routine to compute centers of geometry of charge groups. No periodicity
 101  * is used.
 102  */
 103
 104 extern void put_charge_groups_in_box (FILE *log,int cg0,int cg1,bool bTruncOct,
 105                                       matrix box,rvec box_size,t_block *cgs,
 106                                       rvec pos[],rvec shift_vec[],
 107                                       rvec cg_cm[]);
 108
 109 /* This routine puts charge groups in the periodic box, keeping them
 110  * together. When bTruncOct==TRUE a truncated octahedron
 111  * box is used. There are no checks: the first element of the box matrix
 112  * is taken to be the box edge.
 113  */
 114
 115 extern void put_atoms_in_box(int natoms,matrix box,rvec x[]);
 116 /* This puts ALL atoms in the box, not caring about charge gorups! */
 117
 118 #ifdef CPLUSPLUS
 119 }
 120 #endif
 121
 122 #endif  /* _pbc_h */