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 * Copyright (c) 2013,2014, 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.
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.
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.
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.
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.
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.
48 #include "gromacs/utility/smalloc.h"
53 #include "gmx_fatal.h"
55 #include "gromacs/fileio/futil.h"
56 #include "gromacs/math/gmxcomplex.h"
57 #include "gromacs/math/utilities.h"
59 /* Determines at which point in the array the fit should start */
60 int calc_nbegin(int nx, real x[], real tbegin)
65 /* Assume input x is sorted */
66 for (nbegin = 0; (nbegin < nx) && (x[nbegin] <= tbegin); nbegin++)
70 if ((nbegin == nx) || (nbegin == 0))
72 gmx_fatal(FARGS, "Begin time %f not in x-domain [%f through %f]\n",
73 tbegin, x[0], x[nx-1]);
76 /* Take the one closest to tbegin */
77 if (fabs(x[nbegin]-tbegin) > fabs(x[nbegin-1]-tbegin))
82 printf("nbegin = %d, x[nbegin] = %g, tbegin = %g\n",
83 nbegin, x[nbegin], tbegin);
88 real numerical_deriv(int nx, real x[], real y[], real fity[], real combined[], real dy[],
89 real tendInt, int nsmooth)
92 int i, nbegin, i0, i1;
93 real fac, fx, fy, integralSmth;
95 nbegin = calc_nbegin(nx, x, tendInt);
98 for (i = 0; (i < nbegin); i++)
102 fac = y[nbegin]/fity[nbegin];
103 printf("scaling fitted curve by %g\n", fac);
104 for (i = nbegin; (i < nx); i++)
106 combined[i] = fity[i]*fac;
112 i1 = min(nx-1, nbegin+nsmooth);
113 printf("Making smooth transition from %d through %d\n", i0, i1);
114 for (i = 0; (i < i0); i++)
118 for (i = i0; (i <= i1); i++)
120 fx = (i1-i)/(real)(i1-i0);
121 fy = (i-i0)/(real)(i1-i0);
124 fprintf(debug, "x: %g factors for smoothing: %10g %10g\n", x[i], fx, fy);
126 combined[i] = fx*y[i] + fy*fity[i];
128 for (i = i1+1; (i < nx); i++)
130 combined[i] = fity[i];
134 tmpfp = gmx_ffopen("integral_smth.xvg", "w");
135 integralSmth = print_and_integrate(tmpfp, nx, x[1]-x[0], combined, NULL, 1);
136 printf("SMOOTH integral = %10.5e\n", integralSmth);
138 dy[0] = (combined[1]-combined[0])/(x[1]-x[0]);
139 for (i = 1; (i < nx-1); i++)
141 dy[i] = (combined[i+1]-combined[i-1])/(x[i+1]-x[i-1]);
143 dy[nx-1] = (combined[nx-1]-combined[nx-2])/(x[nx-1]-x[nx-2]);
145 for (i = 0; (i < nx); i++)
153 void do_four(const char *fn, const char *cn, int nx, real x[], real dy[],
154 real eps0, real epsRF, const output_env_t oenv)
157 t_complex *tmp, gw, hw, kw;
159 real fac, nu, dt, *ptr, maxeps, numax;
162 /*while ((dy[nx-1] == 0.0) && (nx > 0))
166 gmx_fatal(FARGS, "Empty dataset in %s, line %d!", __FILE__, __LINE__);
175 printf("Doing FFT of %d points\n", nnx);
176 for (i = 0; (i < nx); i++)
181 four1(ptr-1, nnx, -1);
186 fac = (eps0-1)/tmp[0].re;
190 fac = ((eps0-1)/(2*epsRF+eps0))/tmp[0].re;
192 fp = xvgropen(fn, "Epsilon(\\8w\\4)", "Freq. (GHz)", "eps", oenv);
193 cp = xvgropen(cn, "Cole-Cole plot", "Eps'", "Eps''", oenv);
196 for (i = 0; (i < nxsav); i++)
200 kw.re = 1+fac*tmp[i].re;
201 kw.im = 1+fac*tmp[i].im;
205 gw = rcmul(fac, tmp[i]);
206 hw = rcmul(2*epsRF, gw);
214 nu = (i+1)*1000.0/(nnx*dt);
221 fprintf(fp, "%10.5e %10.5e %10.5e\n", nu, kw.re, kw.im);
222 fprintf(cp, "%10.5e %10.5e\n", kw.re, kw.im);
224 printf("MAXEPS = %10.5e at frequency %10.5e GHz (tauD = %8.1f ps)\n",
225 maxeps, numax, 1000/(2*M_PI*numax));
231 int gmx_dielectric(int argc, char *argv[])
233 const char *desc[] = {
234 "[THISMODULE] calculates frequency dependent dielectric constants",
235 "from the autocorrelation function of the total dipole moment in",
236 "your simulation. This ACF can be generated by [gmx-dipoles].",
237 "The functional forms of the available functions are:[PAR]",
238 "One parameter: y = [EXP]-a[SUB]1[sub] x[exp],[BR]",
239 "Two parameters: y = a[SUB]2[sub] [EXP]-a[SUB]1[sub] x[exp],[BR]",
240 "Three parameters: y = a[SUB]2[sub] [EXP]-a[SUB]1[sub] x[exp] + (1 - a[SUB]2[sub]) [EXP]-a[SUB]3[sub] x[exp].[BR]",
241 "Start values for the fit procedure can be given on the command line.",
242 "It is also possible to fix parameters at their start value, use [TT]-fix[tt]",
243 "with the number of the parameter you want to fix.",
245 "Three output files are generated, the first contains the ACF,",
246 "an exponential fit to it with 1, 2 or 3 parameters, and the",
247 "numerical derivative of the combination data/fit.",
248 "The second file contains the real and imaginary parts of the",
249 "frequency-dependent dielectric constant, the last gives a plot",
250 "known as the Cole-Cole plot, in which the imaginary",
251 "component is plotted as a function of the real component.",
252 "For a pure exponential relaxation (Debye relaxation) the latter",
253 "plot should be one half of a circle."
256 { efXVG, "-f", "dipcorr", ffREAD },
257 { efXVG, "-d", "deriv", ffWRITE },
258 { efXVG, "-o", "epsw", ffWRITE },
259 { efXVG, "-c", "cole", ffWRITE }
261 #define NFILE asize(fnm)
263 int i, j, nx, ny, nxtail, eFitFn, nfitparm;
264 real dt, integral, fitintegral, *fitparms, fac, rffac;
267 const char *legend[] = { "Correlation", "Std. Dev.", "Fit", "Combined", "Derivative" };
268 static int fix = 0, bFour = 0, bX = 1, nsmooth = 3;
269 static real tendInt = 5.0, tbegin = 5.0, tend = 500.0;
270 static real A = 0.5, tau1 = 10.0, tau2 = 1.0, eps0 = 80, epsRF = 78.5, tail = 500.0;
273 { "-fft", FALSE, etBOOL, {&bFour},
274 "use fast fourier transform for correlation function" },
275 { "-x1", FALSE, etBOOL, {&bX},
276 "use first column as [IT]x[it]-axis rather than first data set" },
277 { "-eint", FALSE, etREAL, {&tendInt},
278 "Time to end the integration of the data and start to use the fit"},
279 { "-bfit", FALSE, etREAL, {&tbegin},
280 "Begin time of fit" },
281 { "-efit", FALSE, etREAL, {&tend},
283 { "-tail", FALSE, etREAL, {&tail},
284 "Length of function including data and tail from fit" },
285 { "-A", FALSE, etREAL, {&A},
286 "Start value for fit parameter A" },
287 { "-tau1", FALSE, etREAL, {&tau1},
288 "Start value for fit parameter [GRK]tau[grk]1" },
289 { "-tau2", FALSE, etREAL, {&tau2},
290 "Start value for fit parameter [GRK]tau[grk]2" },
291 { "-eps0", FALSE, etREAL, {&eps0},
292 "[GRK]epsilon[grk]0 of your liquid" },
293 { "-epsRF", FALSE, etREAL, {&epsRF},
294 "[GRK]epsilon[grk] of the reaction field used in your simulation. A value of 0 means infinity." },
295 { "-fix", FALSE, etINT, {&fix},
296 "Fix parameters at their start values, A (2), tau1 (1), or tau2 (4)" },
297 { "-ffn", FALSE, etENUM, {s_ffn},
299 { "-nsmooth", FALSE, etINT, {&nsmooth},
300 "Number of points for smoothing" }
303 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
304 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
308 please_cite(stdout, "Spoel98a");
309 printf("WARNING: non-polarizable models can never yield an infinite\n"
310 "dielectric constant that is different from 1. This is incorrect\n"
311 "in the reference given above (Spoel98a).\n\n");
314 nx = read_xvg(opt2fn("-f", NFILE, fnm), &yd, &ny);
315 dt = yd[0][1] - yd[0][0];
316 nxtail = min(tail/dt, nx);
318 printf("Read data set containing %d colums and %d rows\n", ny, nx);
319 printf("Assuming (from data) that timestep is %g, nxtail = %d\n",
322 for (i = 0; (i < ny); i++)
324 snew(y[i], max(nx, nxtail));
326 for (i = 0; (i < nx); i++)
329 for (j = 1; (j < ny); j++)
336 for (i = nx; (i < nxtail); i++)
338 y[0][i] = dt*i+y[0][0];
339 for (j = 1; (j < ny); j++)
348 /* We have read a file WITHOUT standard deviations, so we make our own... */
351 printf("Creating standard deviation numbers ...\n");
355 fac = 1.0/((real)nx);
356 for (i = 0; (i < nx); i++)
362 eFitFn = sffn2effn(s_ffn);
363 nfitparm = nfp_ffn[eFitFn];
380 integral = print_and_integrate(NULL, calc_nbegin(nx, y[0], tbegin),
382 integral += do_lmfit(nx, y[1], y[2], dt, y[0], tbegin, tend,
383 oenv, TRUE, eFitFn, fitparms, fix);
384 for (i = 0; i < nx; i++)
386 y[3][i] = fit_function(eFitFn, fitparms, y[0][i]);
391 /* This means infinity! */
397 lambda = (eps0 - 1.0)/(2*epsRF - 1.0);
398 rffac = (2*epsRF+eps0)/(2*epsRF+1);
400 printf("DATA INTEGRAL: %5.1f, tauD(old) = %5.1f ps, "
401 "tau_slope = %5.1f, tau_slope,D = %5.1f ps\n",
402 integral, integral*rffac, fitparms[0], fitparms[0]*rffac);
404 printf("tau_D from tau1 = %8.3g , eps(Infty) = %8.3f\n",
405 fitparms[0]*(1 + fitparms[1]*lambda),
406 1 + ((1 - fitparms[1])*(eps0 - 1))/(1 + fitparms[1]*lambda));
408 fitintegral = numerical_deriv(nx, y[0], y[1], y[3], y[4], y[5], tendInt, nsmooth);
409 printf("FIT INTEGRAL (tau_M): %5.1f, tau_D = %5.1f\n",
410 fitintegral, fitintegral*rffac);
412 /* Now we have the negative gradient of <Phi(0) Phi(t)> */
413 write_xvg(opt2fn("-d", NFILE, fnm), "Data", nx-1, 6, y, legend, oenv);
415 /* Do FFT and analysis */
416 do_four(opt2fn("-o", NFILE, fnm), opt2fn("-c", NFILE, fnm),
417 nx-1, y[0], y[5], eps0, epsRF, oenv);
419 do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
420 do_view(oenv, opt2fn("-c", NFILE, fnm), NULL);
421 do_view(oenv, opt2fn("-d", NFILE, fnm), "-nxy");