src/gmxlib/rmpbc.c

   1 /*
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  10  *                        VERSION 3.2.0
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  14  * check out http://www.gromacs.org for more information.
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  35  */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include "sysstuff.h"
  41 #include "typedefs.h"
  42 #include "smalloc.h"
  43 #include "mshift.h"
  44 #include "pbc.h"
  45 #include "gstat.h"
  46 #include "futil.h"
  47 #include "vec.h"
  48
  49 void rm_pbc(t_idef *idef,int natoms,matrix box,rvec x[],rvec x_s[])
  50 {
  51   typedef struct {
  52     int     natoms;
  53     t_graph *gr;
  54   } multi_graph;
  55
  56   static int ngraph=0;
  57   static multi_graph *mgraph=NULL;
  58   static bool bFirst=TRUE;
  59   rvec   sv[SHIFTS],box_size;
  60   int    n,i;
  61   bool   bNeedToCopy;
  62
  63   bNeedToCopy = (x != x_s);
  64
  65   if (box[0][0]) {
  66     if (idef->ntypes!=-1) {
  67       n=-1;
  68       for(i=0; i<ngraph; i++)
  69         if (mgraph[i].natoms==natoms)
  70           n=i;
  71       if (n==-1) {
  72         /* make a new graph if there isn't one with this number of atoms */
  73         n=ngraph;
  74         ngraph++;
  75         srenew(mgraph,ngraph);
  76         mgraph[n].natoms=natoms;
  77         mgraph[n].gr=mk_graph(idef,natoms,FALSE,FALSE);
  78       }
  79       mk_mshift(stdout,mgraph[n].gr,box,x);
  80       calc_shifts(box,box_size,sv);
  81       shift_x(mgraph[n].gr,box,x,x_s);
  82       bNeedToCopy=FALSE;
  83     } else if (bFirst) {
  84       fprintf(stderr,
  85               "\nWarning: can not make broken molecules whole without a run input file,\n         don't worry, mdrun doesn't write broken molecules\n\n");
  86       bFirst=FALSE;
  87     }
  88   }
  89   if (bNeedToCopy)
  90     for (i=0; i<natoms; i++)
  91       copy_rvec(x[i],x_s[i]);
  92 }
  93