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 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  * Green Red Orange Magenta Azure Cyan Skyblue
  28  */
  29 static char *SRCID_rmpbc_c = "$Id$";
  30
  31 #include "sysstuff.h"
  32 #include "typedefs.h"
  33 #include "smalloc.h"
  34 #include "mshift.h"
  35 #include "pbc.h"
  36 #include "gstat.h"
  37 #include "futil.h"
  38 #include "vec.h"
  39
  40 void rm_pbc(t_idef *idef,int natoms,matrix box,rvec x[],rvec x_s[])
  41 {
  42   typedef struct {
  43     int     natoms;
  44     t_graph *gr;
  45   } multi_graph;
  46
  47   static int ngraph=0;
  48   static multi_graph *mgraph=NULL;
  49   static bool bFirst=TRUE;
  50   rvec   sv[SHIFTS],box_size;
  51   int    n,i;
  52   bool   bNeedToCopy;
  53
  54   bNeedToCopy = (x != x_s);
  55
  56   if (box[0][0]) {
  57     if (idef->ntypes!=-1) {
  58       n=-1;
  59       for(i=0; i<ngraph; i++)
  60         if (mgraph[i].natoms==natoms)
  61           n=i;
  62       if (n==-1) {
  63         /* make a new graph if there isn't one with this number of atoms */
  64         n=ngraph;
  65         ngraph++;
  66         srenew(mgraph,ngraph);
  67         mgraph[n].natoms=natoms;
  68         mgraph[n].gr=mk_graph(idef,natoms,FALSE);
  69       }
  70       mk_mshift(stdout,mgraph[n].gr,box,x);
  71       calc_shifts(box,box_size,sv,FALSE);
  72       shift_x(mgraph[n].gr,sv,x,x_s);
  73       bNeedToCopy=FALSE;
  74     } else if (bFirst) {
  75       fprintf(stderr,
  76               "\nWarning: can not make broken molecules whole without a run input file\n");
  77       bFirst=FALSE;
  78     }
  79   }
  80   if (bNeedToCopy)
  81     for (i=0; i<natoms; i++)
  82       copy_rvec(x[i],x_s[i]);
  83 }
  84