2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team,
6 * check out http://www.gromacs.org for more information.
7 * Copyright (c) 2012, by the GROMACS development team, led by
8 * David van der Spoel, Berk Hess, Erik Lindahl, and including many
9 * others, as listed in the AUTHORS file in the top-level source
10 * directory and at http://www.gromacs.org.
12 * GROMACS is free software; you can redistribute it and/or
13 * modify it under the terms of the GNU Lesser General Public License
14 * as published by the Free Software Foundation; either version 2.1
15 * of the License, or (at your option) any later version.
17 * GROMACS is distributed in the hope that it will be useful,
18 * but WITHOUT ANY WARRANTY; without even the implied warranty of
19 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 * Lesser General Public License for more details.
22 * You should have received a copy of the GNU Lesser General Public
23 * License along with GROMACS; if not, see
24 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
25 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
27 * If you want to redistribute modifications to GROMACS, please
28 * consider that scientific software is very special. Version
29 * control is crucial - bugs must be traceable. We will be happy to
30 * consider code for inclusion in the official distribution, but
31 * derived work must not be called official GROMACS. Details are found
32 * in the README & COPYING files - if they are missing, get the
33 * official version at http://www.gromacs.org.
35 * To help us fund GROMACS development, we humbly ask that you cite
36 * the research papers on the package. Check out http://www.gromacs.org.
47 #include "gmx_fatal.h"
61 real pot(real x, real qq, real c6, real cn, int npow)
63 return cn*pow(x, -npow)-c6*pow(x, -6)+qq*ONE_4PI_EPS0/x;
66 real bhpot(real x, real qq, real A, real B, real C)
68 return A*exp(-B*x) - C*pow(x, -6.0);
71 real dpot(real x, real qq, real c6, real cn, int npow)
73 return -(npow*cn*pow(x, -npow-1)-6*c6*pow(x, -7)+qq*ONE_4PI_EPS0/sqr(x));
76 int gmx_sigeps(int argc, char *argv[])
78 const char *desc[] = {
79 "[TT]g_sigeps[tt] is a simple utility that converts C6/C12 or C6/Cn combinations",
80 "to [GRK]sigma[grk] and [GRK]epsilon[grk], or vice versa. It can also plot the potential",
81 "in file. In addition, it makes an approximation of a Buckingham potential",
82 "to a Lennard-Jones potential."
84 static real c6 = 1.0e-3, cn = 1.0e-6, qi = 0, qj = 0, sig = 0.3, eps = 1, sigfac = 0.7;
85 static real Abh = 1e5, Bbh = 32, Cbh = 1e-3;
88 { "-c6", FALSE, etREAL, {&c6}, "C6" },
89 { "-cn", FALSE, etREAL, {&cn}, "Constant for repulsion" },
90 { "-pow", FALSE, etINT, {&npow}, "Power of the repulsion term" },
91 { "-sig", FALSE, etREAL, {&sig}, "[GRK]sigma[grk]" },
92 { "-eps", FALSE, etREAL, {&eps}, "[GRK]epsilon[grk]" },
93 { "-A", FALSE, etREAL, {&Abh}, "Buckingham A" },
94 { "-B", FALSE, etREAL, {&Bbh}, "Buckingham B" },
95 { "-C", FALSE, etREAL, {&Cbh}, "Buckingham C" },
96 { "-qi", FALSE, etREAL, {&qi}, "qi" },
97 { "-qj", FALSE, etREAL, {&qj}, "qj" },
98 { "-sigfac", FALSE, etREAL, {&sigfac}, "Factor in front of [GRK]sigma[grk] for starting the plot" }
101 { efXVG, "-o", "potje", ffWRITE }
104 #define NFILE asize(fnm)
105 const char *legend[] = { "Lennard-Jones", "Buckingham" };
109 real qq, x, oldx, minimum, mval, dp[2], pp[2];
113 parse_common_args(&argc, argv, PCA_CAN_VIEW,
114 NFILE, fnm, asize(pa), pa, asize(desc),
115 desc, 0, NULL, &oenv);
117 bBham = (opt2parg_bSet("-A", asize(pa), pa) ||
118 opt2parg_bSet("-B", asize(pa), pa) ||
119 opt2parg_bSet("-C", asize(pa), pa));
124 sig = pow((6.0/npow)*pow(npow/Bbh, npow-6.0), 1.0/(npow-6.0));
125 eps = c6/(4*pow(sig, 6.0));
126 cn = 4*eps*pow(sig, npow);
130 if (opt2parg_bSet("-sig", asize(pa), pa) ||
131 opt2parg_bSet("-eps", asize(pa), pa))
133 c6 = 4*eps*pow(sig, 6);
134 cn = 4*eps*pow(sig, npow);
136 else if (opt2parg_bSet("-c6", asize(pa), pa) ||
137 opt2parg_bSet("-cn", asize(pa), pa) ||
138 opt2parg_bSet("-pow", asize(pa), pa))
140 sig = pow(cn/c6, 1.0/(npow-6.0));
141 eps = 0.25*c6*pow(sig, -6.0);
147 printf("c6 = %12.5e, c%d = %12.5e\n", c6, npow, cn);
148 printf("sigma = %12.5f, epsilon = %12.5f\n", sig, eps);
150 minimum = pow(npow/6.0*pow(sig, npow-6.0), 1.0/(npow-6));
151 printf("Van der Waals minimum at %g, V = %g\n\n",
152 minimum, pot(minimum, 0, c6, cn, npow));
153 printf("Fit of Lennard Jones (%d-6) to Buckingham:\n", npow);
156 Abh = 4*eps*pow(sig/minimum, npow)*exp(npow);
157 printf("A = %g, B = %g, C = %g\n", Abh, Bbh, Cbh);
161 fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Potential", "r (nm)", "E (kJ/mol)",
163 xvgr_legend(fp, asize(legend), legend,
172 for (i = 0; (i < 100); i++)
174 x = sigfac*sig+sig*i*0.02;
175 dp[next] = dpot(x, qq, c6, cn, npow);
176 fprintf(fp, "%10g %10g %10g\n", x, pot(x, qq, c6, cn, npow),
177 bhpot(x, qq, Abh, Bbh, Cbh));
180 if ((i > 0) && (dp[cur]*dp[next] < 0))
182 minimum = oldx + dp[cur]*(x-oldx)/(dp[cur]-dp[next]);
183 mval = pot(minimum, qq, c6, cn, npow);
184 printf("Van der Waals + Coulomb minimum at r = %g (nm). Value = %g (kJ/mol)\n",
194 do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);