src/contrib/test.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 -
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  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 <math.h>
  41 #include "typedefs.h"
  42 #include "gromacs/commandline/pargs.h"
  43 #include "copyrite.h"
  44 #include "gromacs/utility/fatalerror.h"
  45 #include "gromacs/fileio/xvgr.h"
  46 #include "viewit.h"
  47 #include "gromacs/fileio/pdbio.h"
  48 #include "macros.h"
  49 #include "gromacs/utility/smalloc.h"
  50 #include "gromacs/math/vec.h"
  51 #include "gromacs/math/units.h"
  52 #include "names.h"
  53 #include "txtdump.h"
  54 #include "gromacs/fileio/trnio.h"
  55 #include "gromacs/fileio/confio.h"
  56
  57 real pot(real x,real qq,real c6,real c12)
  58 {
  59   return c12*pow(x,-12)-c6*pow(x,-6)+qq*ONE_4PI_EPS0/x;
  60 }
  61
  62 real dpot(real x,real qq,real c6,real c12)
  63 {
  64   return -(12*c12*pow(x,-13)-6*c6*pow(x,-7)+qq*ONE_4PI_EPS0/sqr(x));
  65 }
  66
  67 int main(int argc,char *argv[])
  68 {
  69   static char *desc[] = {
  70     "Plot the potential"
  71   };
  72   static real c6=1.0e-3,c12=1.0e-6,qi=1,qj=2,sig=0.3,eps=1,sigfac=0.7;
  73   t_pargs pa[] = {
  74     { "-c6",   FALSE,  etREAL,  {&c6},  "c6"   },
  75     { "-c12",  FALSE,  etREAL,  {&c12}, "c12"  },
  76     { "-sig",  FALSE,  etREAL,  {&sig}, "sig"  },
  77     { "-eps",  FALSE,  etREAL,  {&eps}, "eps"  },
  78     { "-qi",   FALSE,  etREAL,  {&qi},  "qi"   },
  79     { "-qj",   FALSE,  etREAL,  {&qj},  "qj"   },
  80     { "-sigfac", FALSE, etREAL, {&sigfac}, "Factor in front of sigma for starting the plot" }
  81   };
  82   t_filenm fnm[] = {
  83     { efXVG, "-o", "potje", ffWRITE }
  84   };
  85 #define NFILE asize(fnm)
  86
  87   FILE      *fp;
  88   int       i;
  89   real      qq,x,oldx,minimum,mval,dp[2],pp[2];
  90   int       cur=0;
  91 #define next (1-cur)
  92
  93   /* CopyRight(stdout,argv[0]);*/
  94   parse_common_args(&argc,argv,PCA_CAN_VIEW,
  95                     NFILE,fnm,asize(pa),pa,asize(desc),
  96                     desc,0,NULL);
  97
  98   if (opt2parg_bSet("-sig",asize(pa),pa) ||
  99       opt2parg_bSet("-eps",asize(pa),pa)) {
 100     c6  = 4*eps*pow(sig,6);
 101     c12 = 4*eps*pow(sig,12);
 102   }
 103   else if ((c6 != 0) && (c12 != 0)) {
 104     sig = pow(c12/c6,1.0/6.0);
 105     eps = c6*c6/(4*c12);
 106   }
 107   else {
 108     sig = eps = 0;
 109   }
 110   printf("c6    = %12.5e, c12     = %12.5e\n",c6,c12);
 111   printf("sigma = %12.5f, epsilon = %12.5f\n",sig,eps);
 112   qq = qi*qj;
 113
 114   fp = xvgropen(ftp2fn(efXVG,NFILE,fnm),"Potential","r (nm)","E (kJ/mol)");
 115   if (sig == 0)
 116     sig=0.25;
 117   minimum = -1;
 118   mval    = 0;
 119   oldx    = 0;
 120   for(i=0; (i<100); i++) {
 121     x    = sigfac*sig+sig*i*0.02;
 122     dp[next] = dpot(x,qq,c6,c12);
 123     fprintf(fp,"%10g  %10g  %10g\n",x,pot(x,qq,c6,c12),
 124             dp[next]);
 125     if ((i > 0) && (dp[cur]*dp[next] < 0)) {
 126       minimum = oldx + dp[cur]*(x-oldx)/(dp[cur]-dp[next]);
 127       mval    = pot(minimum,qq,c6,c12);
 128       /*fprintf(stdout,"dp[cur] = %g, dp[next] = %g  oldx = %g, dx = %g\n",
 129         dp[cur],dp[next],oldx,x-oldx);*/
 130       printf("Minimum at r = %g (nm). Value = %g (kJ/mol)\n",
 131               minimum,mval);
 132     }
 133     cur = next;
 134     oldx = x;
 135
 136   }
 137   gmx_ffclose(fp);
 138
 139   do_view(ftp2fn(efXVG,NFILE,fnm),NULL);
 140
 141   gmx_thanx(stderr);
 142
 143   return 0;
 144 }
 145
 146