src/contrib/compnl.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
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   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
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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "ns.h"
  40 #include "gromacs/utility/smalloc.h"
  41 #include "wnblist.h"
  42 #include "gromacs/utility/futil.h"
  43 #include "macros.h"
  44 #include "gromacs/commandline/pargs.h"
  45 #include "copyrite.h"
  46 #include "gromacs/fileio/confio.h"
  47 #include "gromacs/pbcutil/pbc.h"
  48 #include "gromacs/math/vec.h"
  49
  50 int main(int argc,char *argv[])
  51 {
  52   static char *desc[] = {
  53     "[TT]compnl[tt] compares two neighborlists as generated by [TT]mdrun[tt]",
  54     "in the log file, when the environment variable DUMPNL is set to",
  55     "a number larger than 0. [TT]compnl[tt] is mainly used for debugging the",
  56     "[TT]mdrun[tt] internals and not for end-users."
  57   };
  58   FILE    *in,*out;
  59   int     i,j,nmiss,mod;
  60   char    **fn,title[256];
  61   int     ***mat,nnb;
  62   real    mb;
  63   gmx_bool    bConf;
  64   rvec    *x = NULL;
  65   rvec    dx;
  66   matrix  box;
  67   t_atoms atoms;
  68   t_pbc   pbc;
  69
  70   t_filenm fnm[] = {
  71     { efLOG, "-f1", NULL, ffREAD },
  72     { efLOG, "-f2", NULL, ffREAD },
  73     { efOUT, "-o",  "compnl", ffWRITE },
  74     { efSTX, "-c",  NULL, ffOPTRD }
  75   };
  76 #define NFILE asize(fnm)
  77   static int natoms=648;
  78   static gmx_bool bSymm=TRUE;
  79   static t_pargs pa[] = {
  80     { "-nat",  FALSE, etINT, { &natoms }, "Number of atoms" },
  81     { "-symm", FALSE, etBOOL,{ &bSymm  }, "Symmetrize the matrices" },
  82   };
  83
  84   CopyRight(stderr,argv[0]);
  85   parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
  86                     asize(desc),desc,0,NULL);
  87
  88   bConf = (opt2bSet("-c",NFILE,fnm));
  89   if (bConf) {
  90     get_stx_coordnum (opt2fn("-c",NFILE,fnm),&natoms);
  91     init_t_atoms(&atoms,natoms,FALSE);
  92     snew(x,natoms);
  93     read_stx_conf(opt2fn("-c",NFILE,fnm),title,&atoms,x,NULL,box);
  94     set_pbc(&pbc,box);
  95   }
  96   snew(fn,2);
  97   fn[0] = opt2fn("-f1",NFILE,fnm);
  98   fn[1] = opt2fn("-f2",NFILE,fnm);
  99
 100   snew(mat,2);
 101   out = gmx_fio_fopen(ftp2fn(efOUT,NFILE,fnm),"w");
 102   mb  = sizeof(int)*sqr(natoms/1024.0);
 103   for(i=0; (i<2); i++) {
 104     in = gmx_fio_fopen(fn[i],"r");
 105     fprintf(stderr,"Reading %s\n",fn[i]);
 106     fprintf(out,   "Reading %s\n",fn[i]);
 107     fprintf(stderr,"Going to allocate %.0f Mb of memory\n",mb);
 108     fprintf(out,   "Going to allocate %.0f Mb of memory\n",mb);
 109     snew(mat[i],natoms);
 110     for(j=0; (j<natoms); j++)
 111       snew(mat[i][j],natoms);
 112     nnb = read_nblist(in,out,mat[i],natoms,bSymm);
 113     gmx_fio_fclose(in);
 114     fprintf(stderr,"Interaction matrix %d has %d entries\n",i,nnb);
 115     fprintf(out,   "Interaction matrix %d has %d entries\n",i,nnb);
 116   }
 117   fprintf(stderr,"Comparing Interaction Matrices\n");
 118   mod=1;
 119   nmiss = 0;
 120   for(i=0; (i<natoms); i+=mod) {
 121     for(j=0; (j<natoms); j+=mod) {
 122       if (mat[0][i][j] != mat[1][i][j]) {
 123         fprintf(out,"i: %5d, j: %5d, shift[%s]: %3d, shift[%s]: %3d",
 124                 i,j,fn[0],mat[0][i][j]-1,fn[1],mat[1][i][j]-1);
 125         if (bConf) {
 126           pbc_dx(&pbc,x[i],x[j],dx);
 127           fprintf(out," dist: %8.3f\n",norm(dx));
 128         }
 129         else
 130           fprintf(out,"\n");
 131         nmiss++;
 132       }
 133     }
 134   }
 135   fprintf(out,"There were %d mismatches\n",nmiss);
 136   fprintf(out,"Done.\n");
 137   gmx_fio_fclose(out);
 138   fprintf(stderr,"There were %d mismatches\n",nmiss);
 139   fprintf(stderr,"Finished\n");
 140
 141   gmx_thanx(stdout);
 142
 143   return 0;
 144 }
 145
 146
 147