src/gmxlib/rmpbc.c

   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  * GROningen Mixture of Alchemy and Childrens' Stories
  35  */
  36 #include "sysstuff.h"
  37 #include "typedefs.h"
  38 #include "smalloc.h"
  39 #include "mshift.h"
  40 #include "pbc.h"
  41 #include "gstat.h"
  42 #include "futil.h"
  43 #include "vec.h"
  44
  45 void rm_pbc(t_idef *idef,int natoms,matrix box,rvec x[],rvec x_s[])
  46 {
  47   typedef struct {
  48     int     natoms;
  49     t_graph *gr;
  50   } multi_graph;
  51
  52   static int ngraph=0;
  53   static multi_graph *mgraph=NULL;
  54   static bool bFirst=TRUE;
  55   rvec   sv[SHIFTS],box_size;
  56   int    n,i;
  57   bool   bNeedToCopy;
  58
  59   bNeedToCopy = (x != x_s);
  60
  61   if (box[0][0]) {
  62     if (idef->ntypes!=-1) {
  63       n=-1;
  64       for(i=0; i<ngraph; i++)
  65         if (mgraph[i].natoms==natoms)
  66           n=i;
  67       if (n==-1) {
  68         /* make a new graph if there isn't one with this number of atoms */
  69         n=ngraph;
  70         ngraph++;
  71         srenew(mgraph,ngraph);
  72         mgraph[n].natoms=natoms;
  73         mgraph[n].gr=mk_graph(idef,natoms,FALSE,FALSE);
  74       }
  75       mk_mshift(stdout,mgraph[n].gr,box,x);
  76       calc_shifts(box,box_size,sv);
  77       shift_x(mgraph[n].gr,box,x,x_s);
  78       bNeedToCopy=FALSE;
  79     } else if (bFirst) {
  80       fprintf(stderr,
  81               "\nWarning: can not make broken molecules whole without a run input file,\n         don't worry, mdrun doesn't write broken molecules\n\n");
  82       bFirst=FALSE;
  83     }
  84   }
  85   if (bNeedToCopy)
  86     for (i=0; i<natoms; i++)
  87       copy_rvec(x[i],x_s[i]);
  88 }
  89