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