src/gmxlib/rmpbc.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * GROningen Mixture of Alchemy and Childrens' Stories
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "sysstuff.h"
  40 #include "typedefs.h"
  41 #include "smalloc.h"
  42 #include "mshift.h"
  43 #include "pbc.h"
  44 #include "gstat.h"
  45 #include "futil.h"
  46 #include "vec.h"
  47
  48 typedef struct {
  49     int     natoms;
  50     t_graph *gr;
  51 } multi_graph;
  52
  53
  54 void rm_pbc(t_idef *idef,int ePBC,int natoms,matrix box,rvec x[],rvec x_s[])
  55 {
  56   static int ngraph=0;
  57   static multi_graph *mgraph=NULL;
  58   static bool bFirst=TRUE;
  59   rvec   sv[SHIFTS];
  60   int    n,i;
  61   bool   bNeedToCopy;
  62
  63   if (ePBC == -1)
  64     ePBC = guess_ePBC(box);
  65
  66   bNeedToCopy = (x != x_s);
  67
  68   if (ePBC != epbcNONE) {
  69     if (idef->ntypes!=-1) {
  70       n=-1;
  71       for(i=0; i<ngraph; i++)
  72         if (mgraph[i].natoms==natoms)
  73           n=i;
  74       if (n==-1) {
  75         /* make a new graph if there isn't one with this number of atoms */
  76         n=ngraph;
  77         ngraph++;
  78         srenew(mgraph,ngraph);
  79         mgraph[n].natoms=natoms;
  80         mgraph[n].gr=mk_graph(NULL,idef,0,natoms,FALSE,FALSE);
  81       }
  82       mk_mshift(stdout,mgraph[n].gr,ePBC,box,x);
  83       calc_shifts(box,sv);
  84       shift_x(mgraph[n].gr,box,x,x_s);
  85       bNeedToCopy=FALSE;
  86     } else if (bFirst) {
  87       fprintf(stderr,
  88               "\nWarning: if there are broken molecules in the trajectory file,\n"
  89               "         they can not be made whole without a run input file\n\n");
  90       bFirst=FALSE;
  91     }
  92   }
  93   if (bNeedToCopy)
  94     for (i=0; i<natoms; i++)
  95       copy_rvec(x[i],x_s[i]);
  96 }
  97
  98 void rm_gropbc(t_atoms *atoms,rvec x[],matrix box)
  99 {
 100   real dist;
 101   int  n,m,d;
 102
 103   /* check periodic boundary */
 104   for(n=1;(n<atoms->nr);n++) {
 105     for(m=DIM-1; m>=0; m--) {
 106       dist = x[n][m]-x[n-1][m];
 107       if (fabs(dist) > 0.9*box[m][m]) {
 108         if ( dist >  0 )
 109           for(d=0; d<=m; d++)
 110             x[n][d] -= box[m][d];
 111         else
 112           for(d=0; d<=m; d++)
 113             x[n][d] += box[m][d];
 114       }
 115     }
 116   }
 117 }
 118