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 #include "main.h"
  43 #include "macros.h"
  44 #include "gromacs/fileio/futil.h"
  45 #include "gromacs/commandline/pargs.h"
  46 #include "copyrite.h"
  47 #include "sysstuff.h"
  48 #include "txtdump.h"
  49 #include "gmx_fatal.h"
  50 #include "gromacs/fileio/xtcio.h"
  51 #include "gromacs/fileio/enxio.h"
  52 #include "smalloc.h"
  53 #include "gromacs/fileio/gmxfio.h"
  54 #include "gromacs/fileio/tpxio.h"
  55 #include "gromacs/fileio/trnio.h"
  56 #include "txtdump.h"
  57 #include "vec.h"
  58
  59 static char *nm[5]  = { "OW", "HW1", "HW2", "DW", "SW" };
  60
  61 static void list_trn(char *fn)
  62 {
  63   static real mass[5] = { 15.9994, 1.008, 1.008, 0.0, 0.0 };
  64   int         i,j=0,m,fpread,fpwrite,nframe;
  65   rvec        *x,*v,*f,fmol[2],xcm[2],torque[j],dx;
  66   real        mmm,len;
  67   matrix      box;
  68   t_trnheader trn;
  69   gmx_bool        bOK;
  70
  71   printf("Going to open %s\n",fn);
  72   fpread  = open_trn(fn,"r");
  73   fpwrite = open_tpx(NULL,"w");
  74   gmx_fio_setdebug(fpwrite,TRUE);
  75
  76   mmm=mass[0]+2*mass[1];
  77   for(i=0; (i<5); i++)
  78     mass[i] /= mmm;
  79
  80   nframe = 0;
  81   while (fread_trnheader(fpread,&trn,&bOK)) {
  82     snew(x,trn.natoms);
  83     snew(v,trn.natoms);
  84     snew(f,trn.natoms);
  85     if (fread_htrn(fpread,&trn,
  86                    trn.box_size ? box : NULL,
  87                    trn.x_size   ? x : NULL,
  88                    trn.v_size   ? v : NULL,
  89                    trn.f_size   ? f : NULL)) {
  90
  91       if (trn.x_size && trn.f_size) {
  92         printf("There are %d atoms\n",trn.natoms);
  93         for(j=0; (j<2); j++) {
  94           clear_rvec(xcm[j]);
  95           clear_rvec(fmol[j]);
  96           clear_rvec(torque[j]);
  97           for(i=5*j; (i<5*j+5); i++) {
  98             rvec_inc(fmol[j],f[i]);
  99             for(m=0; (m<DIM); m++)
 100               xcm[j][m] += mass[i%5]*x[i][m];
 101           }
 102           for(i=5*j; (i<5*j+5); i++) {
 103             rvec_dec(x[i],xcm[j]);
 104             cprod(x[i],f[i],dx);
 105             rvec_inc(torque[j],dx);
 106             rvec_inc(x[i],xcm[j]);
 107           }
 108         }
 109         pr_rvecs(stdout,0,"FMOL  ",fmol,2);
 110         pr_rvecs(stdout,0,"TORQUE",torque,2);
 111         printf("Distance matrix Water1-Water2\n%5s","");
 112         for(j=0; (j<5); j++)
 113           printf("  %10s",nm[j]);
 114         printf("\n");
 115         for(j=0; (j<5); j++) {
 116           printf("%5s",nm[j]);
 117           for(i=5; (i<10); i++) {
 118             rvec_sub(x[i],x[j],dx);
 119             len = sqrt(iprod(dx,dx));
 120             printf("  %10.7f",len);
 121           }
 122           printf("\n");
 123         }
 124       }
 125     }
 126     sfree(x);
 127     sfree(v);
 128     sfree(f);
 129     nframe++;
 130   }
 131   if (!bOK)
 132     fprintf(stderr,"\nWARNING: Incomplete frame header: nr %d, t=%g\n",
 133             nframe,trn.t);
 134   close_tpx(fpwrite);
 135   close_trn(fpread);
 136 }
 137
 138 int main(int argc,char *argv[])
 139 {
 140   static char *desc[] = {
 141     "[TT]gmxdump[tt] reads a run input file ([TT].tpa[tt]/[TT].tpr[tt]/[TT].tpb[tt]),",
 142     "a trajectory ([TT].trj[tt]/[TT].trr[tt]/[TT].xtc[tt]) or an energy",
 143     "file ([TT].ene[tt]/[TT].edr[tt]) and prints that to standard",
 144     "output in a readable format. This program is essential for",
 145     "checking your run input file in case of problems.[PAR]"
 146   };
 147   t_filenm fnm[] = {
 148     { efTRN, "-f", NULL, ffOPTRD }
 149   };
 150 #define NFILE asize(fnm)
 151   char *fn;
 152
 153   /* Command line options */
 154
 155   CopyRight(stdout,argv[0]);
 156   parse_common_args(&argc,argv,0,NFILE,fnm,0,NULL,
 157                     asize(desc),desc,0,NULL);
 158
 159   if (ftp2bSet(efTRN,NFILE,fnm)) {
 160     fn = ftp2fn(efTRN,NFILE,fnm);
 161     printf("Going to open %s\n",fn);
 162     list_trn(fn);
 163   }
 164
 165   gmx_thanx(stderr);
 166
 167   return 0;
 168 }