/* Determines at which point in the array the fit should start */
static int calc_nbegin(int nx, real x[], real tbegin)
{
- int nbegin;
+ int nbegin;
/* Assume input x is sorted */
for (nbegin = 0; (nbegin < nx) && (x[nbegin] <= tbegin); nbegin++)
}
if ((nbegin == nx) || (nbegin == 0))
{
- gmx_fatal(FARGS, "Begin time %f not in x-domain [%f through %f]\n",
- tbegin, x[0], x[nx-1]);
+ gmx_fatal(FARGS, "Begin time %f not in x-domain [%f through %f]\n", tbegin, x[0], x[nx - 1]);
}
/* Take the one closest to tbegin */
- if (std::abs(x[nbegin]-tbegin) > std::abs(x[nbegin-1]-tbegin))
+ if (std::abs(x[nbegin] - tbegin) > std::abs(x[nbegin - 1] - tbegin))
{
nbegin--;
}
- printf("nbegin = %d, x[nbegin] = %g, tbegin = %g\n",
- nbegin, x[nbegin], tbegin);
+ printf("nbegin = %d, x[nbegin] = %g, tbegin = %g\n", nbegin, x[nbegin], tbegin);
return nbegin;
}
-static real numerical_deriv(int nx, real x[], const real y[], const real fity[], real combined[], real dy[],
- real tendInt, int nsmooth)
+static real
+numerical_deriv(int nx, real x[], const real y[], const real fity[], real combined[], real dy[], real tendInt, int nsmooth)
{
- FILE *tmpfp;
+ FILE* tmpfp;
int i, nbegin, i0, i1;
real fac, fx, fy, integralSmth;
{
combined[i] = y[i];
}
- fac = y[nbegin]/fity[nbegin];
+ fac = y[nbegin] / fity[nbegin];
printf("scaling fitted curve by %g\n", fac);
for (i = nbegin; (i < nx); i++)
{
- combined[i] = fity[i]*fac;
+ combined[i] = fity[i] * fac;
}
}
else
{
i0 = std::max(0, nbegin);
- i1 = std::min(nx-1, nbegin+nsmooth);
+ i1 = std::min(nx - 1, nbegin + nsmooth);
printf("Making smooth transition from %d through %d\n", i0, i1);
for (i = 0; (i < i0); i++)
{
}
for (i = i0; (i <= i1); i++)
{
- fx = static_cast<real>(i1-i)/(i1-i0);
- fy = static_cast<real>(i-i0)/(i1-i0);
+ fx = static_cast<real>(i1 - i) / (i1 - i0);
+ fy = static_cast<real>(i - i0) / (i1 - i0);
if (debug)
{
fprintf(debug, "x: %g factors for smoothing: %10g %10g\n", x[i], fx, fy);
}
- combined[i] = fx*y[i] + fy*fity[i];
+ combined[i] = fx * y[i] + fy * fity[i];
}
- for (i = i1+1; (i < nx); i++)
+ for (i = i1 + 1; (i < nx); i++)
{
combined[i] = fity[i];
}
}
tmpfp = gmx_ffopen("integral_smth.xvg", "w");
- integralSmth = print_and_integrate(tmpfp, nx, x[1]-x[0], combined, nullptr, 1);
+ integralSmth = print_and_integrate(tmpfp, nx, x[1] - x[0], combined, nullptr, 1);
printf("SMOOTH integral = %10.5e\n", integralSmth);
- dy[0] = (combined[1]-combined[0])/(x[1]-x[0]);
- for (i = 1; (i < nx-1); i++)
+ dy[0] = (combined[1] - combined[0]) / (x[1] - x[0]);
+ for (i = 1; (i < nx - 1); i++)
{
- dy[i] = (combined[i+1]-combined[i-1])/(x[i+1]-x[i-1]);
+ dy[i] = (combined[i + 1] - combined[i - 1]) / (x[i + 1] - x[i - 1]);
}
- dy[nx-1] = (combined[nx-1]-combined[nx-2])/(x[nx-1]-x[nx-2]);
+ dy[nx - 1] = (combined[nx - 1] - combined[nx - 2]) / (x[nx - 1] - x[nx - 2]);
for (i = 0; (i < nx); i++)
{
return integralSmth;
}
-static void do_four(const char *fn, const char *cn, int nx, const real x[], const real dy[],
- real eps0, real epsRF, const gmx_output_env_t *oenv)
+static void do_four(const char* fn,
+ const char* cn,
+ int nx,
+ const real x[],
+ const real dy[],
+ real eps0,
+ real epsRF,
+ const gmx_output_env_t* oenv)
{
- FILE *fp, *cp;
+ FILE * fp, *cp;
t_complex *tmp, gw, hw, kw;
int i, nnx, nxsav;
real fac, nu, dt, maxeps, numax;
}
nnx = 1;
- while (nnx < 2*nx)
+ while (nnx < 2 * nx)
{
nnx *= 2;
}
- snew(tmp, 2*nnx);
+ snew(tmp, 2 * nnx);
printf("Doing FFT of %d points\n", nnx);
for (i = 0; (i < nx); i++)
{
tmp[i].re = dy[i];
}
- if ((fftcode = gmx_fft_init_1d_real(&fft, nnx,
- GMX_FFT_FLAG_NONE)) != 0)
+ if ((fftcode = gmx_fft_init_1d_real(&fft, nnx, GMX_FFT_FLAG_NONE)) != 0)
{
gmx_fatal(FARGS, "gmx_fft_init_1d_real returned %d", fftcode);
}
- if ((fftcode = gmx_fft_1d_real(fft, GMX_FFT_COMPLEX_TO_REAL,
- tmp, tmp)) != 0)
+ if ((fftcode = gmx_fft_1d_real(fft, GMX_FFT_COMPLEX_TO_REAL, tmp, tmp)) != 0)
{
gmx_fatal(FARGS, "gmx_fft_1d_real returned %d", fftcode);
}
gmx_fft_destroy(fft);
- dt = x[1]-x[0];
+ dt = x[1] - x[0];
if (epsRF == 0)
{
- fac = (eps0-1)/tmp[0].re;
+ fac = (eps0 - 1) / tmp[0].re;
}
else
{
- fac = ((eps0-1)/(2*epsRF+eps0))/tmp[0].re;
+ fac = ((eps0 - 1) / (2 * epsRF + eps0)) / tmp[0].re;
}
fp = xvgropen(fn, "Epsilon(\\8w\\4)", "Freq. (GHz)", "eps", oenv);
cp = xvgropen(cn, "Cole-Cole plot", "Eps'", "Eps''", oenv);
{
if (epsRF == 0)
{
- kw.re = 1+fac*tmp[i].re;
- kw.im = 1+fac*tmp[i].im;
+ kw.re = 1 + fac * tmp[i].re;
+ kw.im = 1 + fac * tmp[i].im;
}
else
{
- gw = rcmul(fac, tmp[i]);
- hw = rcmul(2*epsRF, gw);
+ gw = rcmul(fac, tmp[i]);
+ hw = rcmul(2 * epsRF, gw);
hw.re += 1.0;
- gw.re = 1.0 - gw.re;
- gw.im = -gw.im;
- kw = cdiv(hw, gw);
+ gw.re = 1.0 - gw.re;
+ gw.im = -gw.im;
+ kw = cdiv(hw, gw);
}
kw.im *= -1;
- nu = (i+1)*1000.0/(nnx*dt);
+ nu = (i + 1) * 1000.0 / (nnx * dt);
if (kw.im > maxeps)
{
maxeps = kw.im;
fprintf(fp, "%10.5e %10.5e %10.5e\n", nu, kw.re, kw.im);
fprintf(cp, "%10.5e %10.5e\n", kw.re, kw.im);
}
- printf("MAXEPS = %10.5e at frequency %10.5e GHz (tauD = %8.1f ps)\n",
- maxeps, numax, 1000/(2*M_PI*numax));
+ printf("MAXEPS = %10.5e at frequency %10.5e GHz (tauD = %8.1f ps)\n", maxeps, numax,
+ 1000 / (2 * M_PI * numax));
xvgrclose(fp);
xvgrclose(cp);
sfree(tmp);
}
-int gmx_dielectric(int argc, char *argv[])
+int gmx_dielectric(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"[THISMODULE] calculates frequency dependent dielectric constants",
"from the autocorrelation function of the total dipole moment in",
"your simulation. This ACF can be generated by [gmx-dipoles].",
"",
" * One parameter: y = [EXP]-a[SUB]1[sub] x[exp],",
" * Two parameters: y = a[SUB]2[sub] [EXP]-a[SUB]1[sub] x[exp],",
- " * 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].",
+ " * 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].",
"",
"Start values for the fit procedure can be given on the command line.",
"It is also possible to fix parameters at their start value, use [TT]-fix[tt]",
"For a pure exponential relaxation (Debye relaxation) the latter",
"plot should be one half of a circle."
};
- t_filenm fnm[] = {
- { efXVG, "-f", "dipcorr", ffREAD },
- { efXVG, "-d", "deriv", ffWRITE },
- { efXVG, "-o", "epsw", ffWRITE },
- { efXVG, "-c", "cole", ffWRITE }
- };
+ t_filenm fnm[] = { { efXVG, "-f", "dipcorr", ffREAD },
+ { efXVG, "-d", "deriv", ffWRITE },
+ { efXVG, "-o", "epsw", ffWRITE },
+ { efXVG, "-c", "cole", ffWRITE } };
#define NFILE asize(fnm)
- gmx_output_env_t *oenv;
+ gmx_output_env_t* oenv;
int i, j, nx, ny, nxtail, eFitFn, nfitparm;
real dt, integral, fitintegral, fac, rffac;
- double *fitparms;
- double **yd;
- real **y;
- const char *legend[] = { "Correlation", "Std. Dev.", "Fit", "Combined", "Derivative" };
- static int fix = 0, bX = 1, nsmooth = 3;
- static real tendInt = 5.0, tbegin = 5.0, tend = 500.0;
- static real A = 0.5, tau1 = 10.0, tau2 = 1.0, eps0 = 80, epsRF = 78.5, tail = 500.0;
+ double* fitparms;
+ double** yd;
+ real** y;
+ const char* legend[] = { "Correlation", "Std. Dev.", "Fit", "Combined", "Derivative" };
+ static int fix = 0, bX = 1, nsmooth = 3;
+ static real tendInt = 5.0, tbegin = 5.0, tend = 500.0;
+ static real A = 0.5, tau1 = 10.0, tau2 = 1.0, eps0 = 80, epsRF = 78.5, tail = 500.0;
real lambda;
t_pargs pa[] = {
- { "-x1", FALSE, etBOOL, {&bX},
+ { "-x1",
+ FALSE,
+ etBOOL,
+ { &bX },
"use first column as [IT]x[it]-axis rather than first data set" },
- { "-eint", FALSE, etREAL, {&tendInt},
- "Time to end the integration of the data and start to use the fit"},
- { "-bfit", FALSE, etREAL, {&tbegin},
- "Begin time of fit" },
- { "-efit", FALSE, etREAL, {&tend},
- "End time of fit" },
- { "-tail", FALSE, etREAL, {&tail},
- "Length of function including data and tail from fit" },
- { "-A", FALSE, etREAL, {&A},
- "Start value for fit parameter A" },
- { "-tau1", FALSE, etREAL, {&tau1},
- "Start value for fit parameter [GRK]tau[grk]1" },
- { "-tau2", FALSE, etREAL, {&tau2},
- "Start value for fit parameter [GRK]tau[grk]2" },
- { "-eps0", FALSE, etREAL, {&eps0},
- "[GRK]epsilon[grk]0 of your liquid" },
- { "-epsRF", FALSE, etREAL, {&epsRF},
- "[GRK]epsilon[grk] of the reaction field used in your simulation. A value of 0 means infinity." },
- { "-fix", FALSE, etINT, {&fix},
+ { "-eint",
+ FALSE,
+ etREAL,
+ { &tendInt },
+ "Time to end the integration of the data and start to use the fit" },
+ { "-bfit", FALSE, etREAL, { &tbegin }, "Begin time of fit" },
+ { "-efit", FALSE, etREAL, { &tend }, "End time of fit" },
+ { "-tail", FALSE, etREAL, { &tail }, "Length of function including data and tail from fit" },
+ { "-A", FALSE, etREAL, { &A }, "Start value for fit parameter A" },
+ { "-tau1", FALSE, etREAL, { &tau1 }, "Start value for fit parameter [GRK]tau[grk]1" },
+ { "-tau2", FALSE, etREAL, { &tau2 }, "Start value for fit parameter [GRK]tau[grk]2" },
+ { "-eps0", FALSE, etREAL, { &eps0 }, "[GRK]epsilon[grk]0 of your liquid" },
+ { "-epsRF",
+ FALSE,
+ etREAL,
+ { &epsRF },
+ "[GRK]epsilon[grk] of the reaction field used in your simulation. A value of 0 means "
+ "infinity." },
+ { "-fix",
+ FALSE,
+ etINT,
+ { &fix },
"Fix parameters at their start values, A (2), tau1 (1), or tau2 (4)" },
- { "-ffn", FALSE, etENUM, {s_ffn},
- "Fit function" },
- { "-nsmooth", FALSE, etINT, {&nsmooth},
- "Number of points for smoothing" }
+ { "-ffn", FALSE, etENUM, { s_ffn }, "Fit function" },
+ { "-nsmooth", FALSE, etINT, { &nsmooth }, "Number of points for smoothing" }
};
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
nx = read_xvg(opt2fn("-f", NFILE, fnm), &yd, &ny);
dt = yd[0][1] - yd[0][0];
- nxtail = std::min(static_cast<int>(tail/dt), nx);
+ nxtail = std::min(static_cast<int>(tail / dt), nx);
printf("Read data set containing %d colums and %d rows\n", ny, nx);
- printf("Assuming (from data) that timestep is %g, nxtail = %d\n",
- dt, nxtail);
+ printf("Assuming (from data) that timestep is %g, nxtail = %d\n", dt, nxtail);
snew(y, 6);
for (i = 0; (i < ny); i++)
{
{
for (i = nx; (i < nxtail); i++)
{
- y[0][i] = dt*i+y[0][0];
+ y[0][i] = dt * i + y[0][0];
for (j = 1; (j < ny); j++)
{
y[j][i] = 0.0;
printf("Creating standard deviation numbers ...\n");
snew(y[2], nx);
- fac = 1.0/nx;
+ fac = 1.0 / nx;
for (i = 0; (i < nx); i++)
{
y[2][i] = fac;
snew(y[4], nx);
snew(y[5], nx);
- integral = print_and_integrate(nullptr, calc_nbegin(nx, y[0], tbegin),
- dt, y[1], nullptr, 1);
- integral += do_lmfit(nx, y[1], y[2], dt, y[0], tbegin, tend,
- oenv, TRUE, eFitFn, fitparms, fix, nullptr);
+ integral = print_and_integrate(nullptr, calc_nbegin(nx, y[0], tbegin), dt, y[1], nullptr, 1);
+ integral += do_lmfit(nx, y[1], y[2], dt, y[0], tbegin, tend, oenv, TRUE, eFitFn, fitparms, fix, nullptr);
for (i = 0; i < nx; i++)
{
y[3][i] = fit_function(eFitFn, fitparms, y[0][i]);
}
else
{
- lambda = (eps0 - 1.0)/(2*epsRF - 1.0);
- rffac = (2*epsRF+eps0)/(2*epsRF+1);
+ lambda = (eps0 - 1.0) / (2 * epsRF - 1.0);
+ rffac = (2 * epsRF + eps0) / (2 * epsRF + 1);
}
printf("DATA INTEGRAL: %5.1f, tauD(old) = %5.1f ps, "
"tau_slope = %5.1f, tau_slope,D = %5.1f ps\n",
- integral, integral*rffac, fitparms[0], fitparms[0]*rffac);
+ integral, integral * rffac, fitparms[0], fitparms[0] * rffac);
- printf("tau_D from tau1 = %8.3g , eps(Infty) = %8.3f\n",
- fitparms[0]*(1 + fitparms[1]*lambda),
- 1 + ((1 - fitparms[1])*(eps0 - 1))/(1 + fitparms[1]*lambda));
+ printf("tau_D from tau1 = %8.3g , eps(Infty) = %8.3f\n", fitparms[0] * (1 + fitparms[1] * lambda),
+ 1 + ((1 - fitparms[1]) * (eps0 - 1)) / (1 + fitparms[1] * lambda));
fitintegral = numerical_deriv(nx, y[0], y[1], y[3], y[4], y[5], tendInt, nsmooth);
- printf("FIT INTEGRAL (tau_M): %5.1f, tau_D = %5.1f\n",
- fitintegral, fitintegral*rffac);
+ printf("FIT INTEGRAL (tau_M): %5.1f, tau_D = %5.1f\n", fitintegral, fitintegral * rffac);
/* Now we have the negative gradient of <Phi(0) Phi(t)> */
- write_xvg(opt2fn("-d", NFILE, fnm), "Data", nx-1, 6, y, legend, oenv);
+ write_xvg(opt2fn("-d", NFILE, fnm), "Data", nx - 1, 6, y, legend, oenv);
/* Do FFT and analysis */
- do_four(opt2fn("-o", NFILE, fnm), opt2fn("-c", NFILE, fnm),
- nx-1, y[0], y[5], eps0, epsRF, oenv);
+ do_four(opt2fn("-o", NFILE, fnm), opt2fn("-c", NFILE, fnm), nx - 1, y[0], y[5], eps0, epsRF, oenv);
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
do_view(oenv, opt2fn("-c", NFILE, fnm), nullptr);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff