src/contrib/anaf.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 3.3.99_development_20071104
  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) 2001-2006, 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 Machine for Chemical Simulation
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <stdio.h>
  40 #include <string.h>
  41 #include <math.h>
  42
  43 #include "macros.h"
  44 #include "gromacs/utility/futil.h"
  45 #include "gromacs/commandline/pargs.h"
  46 #include "copyrite.h"
  47 #include "txtdump.h"
  48 #include "gromacs/utility/fatalerror.h"
  49 #include "gromacs/fileio/xtcio.h"
  50 #include "gromacs/fileio/enxio.h"
  51 #include "gromacs/utility/smalloc.h"
  52 #include "gromacs/fileio/gmxfio.h"
  53 #include "gromacs/fileio/tpxio.h"
  54 #include "gromacs/fileio/trnio.h"
  55 #include "txtdump.h"
  56 #include "gromacs/math/vec.h"
  57
  58 static char *nm[5]  = { "OW", "HW1", "HW2", "DW", "SW" };
  59
  60 static void list_trn(char *fn)
  61 {
  62   static real mass[5] = { 15.9994, 1.008, 1.008, 0.0, 0.0 };
  63   int         i,j=0,m,fpread,fpwrite,nframe;
  64   rvec        *x,*v,*f,fmol[2],xcm[2],torque[j],dx;
  65   real        mmm,len;
  66   matrix      box;
  67   t_trnheader trn;
  68   gmx_bool        bOK;
  69
  70   printf("Going to open %s\n",fn);
  71   fpread  = open_trn(fn,"r");
  72   fpwrite = open_tpx(NULL,"w");
  73   gmx_fio_setdebug(fpwrite,TRUE);
  74
  75   mmm=mass[0]+2*mass[1];
  76   for(i=0; (i<5); i++)
  77     mass[i] /= mmm;
  78
  79   nframe = 0;
  80   while (fread_trnheader(fpread,&trn,&bOK)) {
  81     snew(x,trn.natoms);
  82     snew(v,trn.natoms);
  83     snew(f,trn.natoms);
  84     if (fread_htrn(fpread,&trn,
  85                    trn.box_size ? box : NULL,
  86                    trn.x_size   ? x : NULL,
  87                    trn.v_size   ? v : NULL,
  88                    trn.f_size   ? f : NULL)) {
  89
  90       if (trn.x_size && trn.f_size) {
  91         printf("There are %d atoms\n",trn.natoms);
  92         for(j=0; (j<2); j++) {
  93           clear_rvec(xcm[j]);
  94           clear_rvec(fmol[j]);
  95           clear_rvec(torque[j]);
  96           for(i=5*j; (i<5*j+5); i++) {
  97             rvec_inc(fmol[j],f[i]);
  98             for(m=0; (m<DIM); m++)
  99               xcm[j][m] += mass[i%5]*x[i][m];
 100           }
 101           for(i=5*j; (i<5*j+5); i++) {
 102             rvec_dec(x[i],xcm[j]);
 103             cprod(x[i],f[i],dx);
 104             rvec_inc(torque[j],dx);
 105             rvec_inc(x[i],xcm[j]);
 106           }
 107         }
 108         pr_rvecs(stdout,0,"FMOL  ",fmol,2);
 109         pr_rvecs(stdout,0,"TORQUE",torque,2);
 110         printf("Distance matrix Water1-Water2\n%5s","");
 111         for(j=0; (j<5); j++)
 112           printf("  %10s",nm[j]);
 113         printf("\n");
 114         for(j=0; (j<5); j++) {
 115           printf("%5s",nm[j]);
 116           for(i=5; (i<10); i++) {
 117             rvec_sub(x[i],x[j],dx);
 118             len = sqrt(iprod(dx,dx));
 119             printf("  %10.7f",len);
 120           }
 121           printf("\n");
 122         }
 123       }
 124     }
 125     sfree(x);
 126     sfree(v);
 127     sfree(f);
 128     nframe++;
 129   }
 130   if (!bOK)
 131     fprintf(stderr,"\nWARNING: Incomplete frame header: nr %d, t=%g\n",
 132             nframe,trn.t);
 133   close_tpx(fpwrite);
 134   close_trn(fpread);
 135 }
 136
 137 int main(int argc,char *argv[])
 138 {
 139   static char *desc[] = {
 140     "[TT]gmxdump[tt] reads a run input file ([TT].tpr[tt]),",
 141     "a trajectory ([TT].trr[tt]/[TT].xtc[tt]) or an energy",
 142     "file ([TT].edr[tt]) and prints that to standard",
 143     "output in a readable format. This program is essential for",
 144     "checking your run input file in case of problems.[PAR]"
 145   };
 146   t_filenm fnm[] = {
 147     { efTRN, "-f", NULL, ffOPTRD }
 148   };
 149 #define NFILE asize(fnm)
 150   char *fn;
 151
 152   /* Command line options */
 153
 154   CopyRight(stdout,argv[0]);
 155   parse_common_args(&argc,argv,0,NFILE,fnm,0,NULL,
 156                     asize(desc),desc,0,NULL);
 157
 158   if (ftp2bSet(efTRN,NFILE,fnm)) {
 159     fn = ftp2fn(efTRN,NFILE,fnm);
 160     printf("Going to open %s\n",fn);
 161     list_trn(fn);
 162   }
 163
 164   gmx_thanx(stderr);
 165
 166   return 0;
 167 }