src/gromacs/gmxana/gmx_sigeps.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40 #include <cstdio>
  41
  42 #include "gromacs/commandline/pargs.h"
  43 #include "gromacs/commandline/viewit.h"
  44 #include "gromacs/fileio/xvgr.h"
  45 #include "gromacs/gmxana/gmx_ana.h"
  46 #include "gromacs/math/functions.h"
  47 #include "gromacs/math/units.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/mdtypes/md_enums.h"
  50 #include "gromacs/utility/arraysize.h"
  51 #include "gromacs/utility/smalloc.h"
  52
  53 static real pot(real x, real qq, real c6, real cn, int npow)
  54 {
  55     return cn*pow(x, -npow)-c6/gmx::power6(x)+qq*ONE_4PI_EPS0/x;
  56 }
  57
  58 static real bhpot(real x, real A, real B, real C)
  59 {
  60     return A*std::exp(-B*x) - C/gmx::power6(x);
  61 }
  62
  63 static real dpot(real x, real qq, real c6, real cn, int npow)
  64 {
  65     return -(npow*cn*std::pow(x, -npow-1)-6*c6/(x*gmx::power6(x))+qq*ONE_4PI_EPS0/gmx::square(x));
  66 }
  67
  68 int gmx_sigeps(int argc, char *argv[])
  69 {
  70     const char       *desc[] = {
  71         "[THISMODULE] is a simple utility that converts C6/C12 or C6/Cn combinations",
  72         "to [GRK]sigma[grk] and [GRK]epsilon[grk], or vice versa. It can also plot the potential",
  73         "in  file. In addition, it makes an approximation of a Buckingham potential",
  74         "to a Lennard-Jones potential."
  75     };
  76     static real       c6   = 1.0e-3, cn = 1.0e-6, qi = 0, qj = 0, sig = 0.3, eps = 1, sigfac = 0.7;
  77     static real       Abh  = 1e5, Bbh = 32, Cbh = 1e-3;
  78     static int        npow = 12;
  79     t_pargs           pa[] = {
  80         { "-c6",   FALSE,  etREAL,  {&c6},  "C6"   },
  81         { "-cn",   FALSE,  etREAL,  {&cn},  "Constant for repulsion"   },
  82         { "-pow",  FALSE,  etINT,   {&npow}, "Power of the repulsion term" },
  83         { "-sig",  FALSE,  etREAL,  {&sig}, "[GRK]sigma[grk]"  },
  84         { "-eps",  FALSE,  etREAL,  {&eps}, "[GRK]epsilon[grk]"  },
  85         { "-A",    FALSE,  etREAL,  {&Abh}, "Buckingham A" },
  86         { "-B",    FALSE,  etREAL,  {&Bbh}, "Buckingham B" },
  87         { "-C",    FALSE,  etREAL,  {&Cbh}, "Buckingham C" },
  88         { "-qi",   FALSE,  etREAL,  {&qi},  "qi"   },
  89         { "-qj",   FALSE,  etREAL,  {&qj},  "qj"   },
  90         { "-sigfac", FALSE, etREAL, {&sigfac}, "Factor in front of [GRK]sigma[grk] for starting the plot" }
  91     };
  92     t_filenm          fnm[] = {
  93         { efXVG, "-o", "potje", ffWRITE }
  94     };
  95     gmx_output_env_t *oenv;
  96 #define NFILE asize(fnm)
  97     const char       *legend[] = { "Lennard-Jones", "Buckingham" };
  98     FILE             *fp;
  99     int               i;
 100     gmx_bool          bBham;
 101     real              qq, x, oldx, minimum, mval, dp[2];
 102     int               cur = 0;
 103 #define next (1-cur)
 104
 105     if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
 106                            NFILE, fnm, asize(pa), pa, asize(desc),
 107                            desc, 0, nullptr, &oenv))
 108     {
 109         return 0;
 110     }
 111
 112     bBham = (opt2parg_bSet("-A", asize(pa), pa) ||
 113              opt2parg_bSet("-B", asize(pa), pa) ||
 114              opt2parg_bSet("-C", asize(pa), pa));
 115
 116     if (bBham)
 117     {
 118         c6  = Cbh;
 119         sig = std::pow((6.0/npow)*std::pow(npow/Bbh, npow-6), 1.0/(npow-6));
 120         eps = c6/(4*gmx::power6(sig));
 121         cn  = 4*eps*std::pow(sig, npow);
 122     }
 123     else
 124     {
 125         if (opt2parg_bSet("-sig", asize(pa), pa) ||
 126             opt2parg_bSet("-eps", asize(pa), pa))
 127         {
 128             c6  = 4*eps*gmx::power6(sig);
 129             cn  = 4*eps*std::pow(sig, npow);
 130         }
 131         else if (opt2parg_bSet("-c6", asize(pa), pa) ||
 132                  opt2parg_bSet("-cn", asize(pa), pa) ||
 133                  opt2parg_bSet("-pow", asize(pa), pa))
 134         {
 135             sig = std::pow(cn/c6, static_cast<real>(1.0/(npow-6)));
 136             eps = 0.25*c6/gmx::power6(sig);
 137         }
 138         else
 139         {
 140             sig = eps = 0;
 141         }
 142         printf("c6    = %12.5e, c%d    = %12.5e\n", c6, npow, cn);
 143         printf("sigma = %12.5f, epsilon = %12.5f\n", sig, eps);
 144
 145         minimum = std::pow(npow/6.0*std::pow(sig, npow-6), 1.0/(npow-6));
 146         printf("Van der Waals minimum at %g, V = %g\n\n",
 147                minimum, pot(minimum, 0, c6, cn, npow));
 148         printf("Fit of Lennard Jones (%d-6) to Buckingham:\n", npow);
 149         Bbh = npow/minimum;
 150         Cbh = c6;
 151         Abh = 4*eps*std::pow(sig/minimum, static_cast<real>(npow))*std::exp(static_cast<real>(npow));
 152         printf("A = %g, B = %g, C = %g\n", Abh, Bbh, Cbh);
 153     }
 154     qq = qi*qj;
 155
 156     fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Potential", "r (nm)", "E (kJ/mol)",
 157                   oenv);
 158     xvgr_legend(fp, asize(legend), legend,
 159                 oenv);
 160     if (sig == 0)
 161     {
 162         sig = 0.25;
 163     }
 164     oldx    = 0;
 165     for (i = 0; (i < 100); i++)
 166     {
 167         x        = sigfac*sig+sig*i*0.02;
 168         dp[next] = dpot(x, qq, c6, cn, npow);
 169         fprintf(fp, "%10g  %10g  %10g\n", x, pot(x, qq, c6, cn, npow),
 170                 bhpot(x, Abh, Bbh, Cbh));
 171         if (qq != 0)
 172         {
 173             if ((i > 0) && (dp[cur]*dp[next] < 0))
 174             {
 175                 minimum = oldx + dp[cur]*(x-oldx)/(dp[cur]-dp[next]);
 176                 mval    = pot(minimum, qq, c6, cn, npow);
 177                 printf("Van der Waals + Coulomb minimum at r = %g (nm). Value = %g (kJ/mol)\n",
 178                        minimum, mval);
 179             }
 180         }
 181         cur  = next;
 182         oldx = x;
 183
 184     }
 185     xvgrclose(fp);
 186
 187     do_view(oenv, ftp2fn(efXVG, NFILE, fnm), nullptr);
 188
 189     return 0;
 190 }