/*! \brief Print chi-squared value and the parameters */
static void print_chi2_params(FILE *fp,
const int eFitFn,
const double fitparms[],
const char *label,
const int nfitpnts,
const double x[],
const double y[])
{
int i;
double chi2 = 0;
for (i = 0; (i < nfitpnts); i++)
{
double yfit = lmcurves[eFitFn](x[i], fitparms);
chi2 += gmx::square(y[i] - yfit);
}
fprintf(fp, "There are %d data points, %d parameters, %s chi2 = %g\nparams:",
nfitpnts, effnNparams(eFitFn), label, chi2);
for (i = 0; (i < effnNparams(eFitFn)); i++)
{
fprintf(fp, " %10g", fitparms[i]);
}
fprintf(fp, "\n");
}
bool lmfit_exp(int nfit,
const double x[],
const double y[],
const double dy[],
double parm[], // NOLINT(readability-non-const-parameter)
bool bVerbose,
int eFitFn,
int nfix)
{
if ((eFitFn < 0) || (eFitFn >= effnNR))
{
fprintf(stderr, "fitfn = %d, should be in the range 0..%d\n",
eFitFn, effnNR-1);
return false;
}
#if HAVE_LMFIT
double chisq, ochisq;
gmx_bool bCont;
int j;
int maxiter = 100;
lm_control_struct control;
lm_status_struct *status;
int nparam = effnNparams(eFitFn);
int p2;
gmx_bool bSkipLast;
/* Using default control structure for double precision fitting that
* comes with the lmfit package (i.e. from the include file).
*/
control = lm_control_double;
control.verbosity = (bVerbose ? 1 : 0);
control.n_maxpri = 0;
control.m_maxpri = 0;
snew(status, 1);
/* Initial params */
chisq = 1e12;
j = 0;
if (bVerbose)
{
printf("%4s %10s Parameters\n", "Step", "chi^2");
}
/* Check whether we have to skip some params */
if (nfix > 0)
{
do
{
p2 = 1 << (nparam-1);
bSkipLast = ((p2 & nfix) == p2);
if (bSkipLast)
{
nparam--;
nfix -= p2;
}
}
while ((nparam > 0) && (bSkipLast));
if (bVerbose)
{
printf("Using %d out of %d parameters\n", nparam, effnNparams(eFitFn));
}
}
do
{
ochisq = chisq;
gmx_lmcurve(nparam, parm, nfit, x, y, dy,
lmcurves[eFitFn], &control, status);
chisq = gmx::square(status->fnorm);
if (bVerbose)
{
printf("status: fnorm = %g, nfev = %d, userbreak = %d\noutcome = %s\n",
status->fnorm, status->nfev, status->userbreak,
lm_infmsg[status->outcome]);
}
if (bVerbose)
{
int mmm;
printf("%4d %8g", j, chisq);
for (mmm = 0; (mmm < effnNparams(eFitFn)); mmm++)
{
printf(" %8g", parm[mmm]);
}
printf("\n");
}
j++;
bCont = (fabs(ochisq - chisq) > fabs(control.ftol*chisq));
}
while (bCont && (j < maxiter));
sfree(status);
#else
gmx_fatal(FARGS, "This build of GROMACS was not configured with support "
"for lmfit, so the requested fitting cannot be performed. "
"See the install guide for instructions on how to build "
"GROMACS with lmfit supported.");
GMX_UNUSED_VALUE(nfit);
GMX_UNUSED_VALUE(x);
GMX_UNUSED_VALUE(y);
GMX_UNUSED_VALUE(dy);
GMX_UNUSED_VALUE(parm);
GMX_UNUSED_VALUE(bVerbose);
GMX_UNUSED_VALUE(eFitFn);
GMX_UNUSED_VALUE(nfix);
#endif
return true;
}
real fit_acf(int ncorr, int fitfn, const gmx_output_env_t *oenv, gmx_bool bVerbose,
real tbeginfit, real tendfit, real dt, real c1[], real *fit)
{
double fitparm[3];
double tStart, tail_corr, sum, sumtot = 0, c_start, ct_estimate;
real *sig;
int i, j, jmax, nf_int;
gmx_bool bPrint;
bPrint = bVerbose || bDebugMode();
if (bPrint)
{
printf("COR:\n");
}
if (tendfit <= 0)
{
tendfit = ncorr*dt;
}
nf_int = std::min(ncorr, (int)(tendfit/dt));
sum = print_and_integrate(debug, nf_int, dt, c1, NULL, 1);
if (bPrint)
{
printf("COR: Correlation time (plain integral from %6.3f to %6.3f ps) = %8.5f ps\n",
0.0, dt*nf_int, sum);
printf("COR: Relaxation times are computed as fit to an exponential:\n");
printf("COR: %s\n", effnDescription(fitfn));
printf("COR: Fit to correlation function from %6.3f ps to %6.3f ps, results in a\n", tbeginfit, std::min(ncorr*dt, tendfit));
}
tStart = 0;
if (bPrint)
{
printf("COR:%11s%11s%11s%11s%11s%11s%11s\n",
"Fit from", "Integral", "Tail Value", "Sum (ps)", " a1 (ps)",
(effnNparams(fitfn) >= 2) ? " a2 ()" : "",
(effnNparams(fitfn) >= 3) ? " a3 (ps)" : "");
}
snew(sig, ncorr);
if (tbeginfit > 0)
{
jmax = 3;
}
else
{
jmax = 1;
}
for (j = 0; ((j < jmax) && (tStart < tendfit) && (tStart < ncorr*dt)); j++)
{
/* Estimate the correlation time for better fitting */
c_start = -1;
ct_estimate = 0;
for (i = 0; (i < ncorr) && (dt*i < tStart || c1[i] > 0); i++)
{
if (c_start < 0)
{
if (dt*i >= tStart)
{
c_start = c1[i];
ct_estimate = 0.5*c1[i];
}
}
else
{
ct_estimate += c1[i];
}
}
if (c_start > 0)
{
ct_estimate *= dt/c_start;
}
else
{
/* The data is strange, so we need to choose somehting */
ct_estimate = tendfit;
}
if (debug)
{
fprintf(debug, "tStart %g ct_estimate: %g\n", tStart, ct_estimate);
}
if (fitfn == effnEXPEXP)
{
fitparm[0] = 0.002*ncorr*dt;
fitparm[1] = 0.95;
fitparm[2] = 0.2*ncorr*dt;
}
else
{
/* Good initial guess, this increases the probability of convergence */
fitparm[0] = ct_estimate;
fitparm[1] = 1.0;
fitparm[2] = 1.0;
}
/* Generate more or less appropriate sigma's */
for (i = 0; i < ncorr; i++)
{
sig[i] = sqrt(ct_estimate+dt*i);
}
nf_int = std::min(ncorr, (int)((tStart+1e-4)/dt));
sum = print_and_integrate(debug, nf_int, dt, c1, NULL, 1);
tail_corr = do_lmfit(ncorr, c1, sig, dt, NULL, tStart, tendfit, oenv,
bDebugMode(), fitfn, fitparm, 0, NULL);
sumtot = sum+tail_corr;
if (fit && ((jmax == 1) || (j == 1)))
{
double mfp[3];
for (i = 0; (i < 3); i++)
{
mfp[i] = fitparm[i];
}
for (i = 0; (i < ncorr); i++)
{
fit[i] = lmcurves[fitfn](i*dt, mfp);
}
}
if (bPrint)
{
printf("COR:%11.4e%11.4e%11.4e%11.4e", tStart, sum, tail_corr, sumtot);
for (i = 0; (i < effnNparams(fitfn)); i++)
{
printf(" %11.4e", fitparm[i]);
}
printf("\n");
}
tStart += tbeginfit;
}
sfree(sig);
return sumtot;
}
real do_lmfit(int ndata, real c1[], real sig[], real dt, real *x0,
real begintimefit, real endtimefit, const gmx_output_env_t *oenv,
gmx_bool bVerbose, int eFitFn, double fitparms[], int fix,
const char *fn_fitted)
{
FILE *fp;
int i, j, nfitpnts;
double integral, ttt;
double *x, *y, *dy;
if (0 != fix)
{
fprintf(stderr, "Using fixed parameters in curve fitting is temporarily not working.\n");
}
if (debug)
{
fprintf(debug, "There are %d points to fit %d vars!\n", ndata, effnNparams(eFitFn));
fprintf(debug, "Fit to function %d from %g through %g, dt=%g\n",
eFitFn, begintimefit, endtimefit, dt);
}
snew(x, ndata);
snew(y, ndata);
snew(dy, ndata);
j = 0;
for (i = 0; i < ndata; i++)
{
ttt = x0 ? x0[i] : dt*i;
if (ttt >= begintimefit && ttt <= endtimefit)
{
x[j] = ttt;
y[j] = c1[i];
if (NULL == sig)
{
// No weighting if all values are divided by 1.
dy[j] = 1;
}
else
{
dy[j] = std::max(1.0e-7, (double)sig[i]);
}
if (debug)
{
fprintf(debug, "j= %d, i= %d, x= %g, y= %g, dy=%g, ttt=%g\n",
j, i, x[j], y[j], dy[j], ttt);
}
j++;
}
}
nfitpnts = j;
integral = 0;
if (nfitpnts < effnNparams(eFitFn))
{
fprintf(stderr, "Not enough (%d) data points for fitting, dt = %g!\n",
nfitpnts, dt);
}
else
{
gmx_bool bSuccess;
if (bVerbose)
{
print_chi2_params(stdout, eFitFn, fitparms, "initial", nfitpnts, x, y);
}
initiate_fit_params(eFitFn, fitparms);
bSuccess = lmfit_exp(nfitpnts, x, y, dy, fitparms, bVerbose, eFitFn, fix);
extract_fit_params(eFitFn, fitparms);
if (!bSuccess)
{
fprintf(stderr, "Fit failed!\n");
}
else
{
if (bVerbose)
{
print_chi2_params(stdout, eFitFn, fitparms, "final", nfitpnts, x, y);
}
switch (eFitFn)
{
case effnEXP1:
integral = fitparms[0]*myexp(begintimefit, 1, fitparms[0]);
break;
case effnEXP2:
integral = fitparms[0]*myexp(begintimefit, fitparms[1], fitparms[0]);
break;
case effnEXPEXP:
integral = (fitparms[0]*myexp(begintimefit, fitparms[1], fitparms[0]) +
fitparms[2]*myexp(begintimefit, 1-fitparms[1], fitparms[2]));
break;
case effnEXP5:
case effnEXP7:
case effnEXP9:
integral = 0;
for (i = 0; (i < (effnNparams(eFitFn)-1)/2); i++)
{
integral += fitparms[2*i]*myexp(begintimefit, fitparms[2*i+1], fitparms[2*i]);
}
break;
default:
/* Do numerical integration */
integral = 0;
for (i = 0; (i < nfitpnts-1); i++)
{
double y0 = lmcurves[eFitFn](x[i], fitparms);
double y1 = lmcurves[eFitFn](x[i+1], fitparms);
integral += (x[i+1]-x[i])*(y1+y0)*0.5;
}
break;
}
if (bVerbose)
{
printf("FIT: Integral of fitted function: %g\n", integral);
if ((effnEXP5 == eFitFn) || (effnEXP7 == eFitFn) || (effnEXP9 == eFitFn))
{
printf("FIT: Note that the constant term is not taken into account when computing integral.\n");
}
}
/* Generate debug output */
if (NULL != fn_fitted)
{
fp = xvgropen(fn_fitted, "Data + Fit", "Time (ps)",
"Data (t)", oenv);
for (i = 0; (i < effnNparams(eFitFn)); i++)
{
fprintf(fp, "# fitparms[%d] = %g\n", i, fitparms[i]);
}
for (j = 0; (j < nfitpnts); j++)
{
real ttt = x0 ? x0[j] : dt*j;
fprintf(fp, "%10.5e %10.5e %10.5e\n",
x[j], y[j], (lmcurves[eFitFn])(ttt, fitparms));
}
xvgrclose(fp);
}
}
}
sfree(x);
sfree(y);
sfree(dy);
return integral;
}
/*! \brief Process the fitting parameters to get output parameters.
*
* See comment at the previous function.
*/
static void extract_fit_params(int eFitFn,
double params[])
{
int i, nparm;
nparm = effnNparams(eFitFn);
switch (eFitFn)
{
case effnVAC:
params[0] = fabs(params[0]);
break;
case effnEXP1:
case effnEXP2:
case effnEXPEXP:
params[0] = fabs(params[0]);
if (nparm > 2)
{
/* Back conversion of parameters from the fitted difference
* to the absolute value.
*/
params[2] = fabs(params[2])+params[0];
}
break;
case effnEXP5:
case effnEXP7:
case effnEXP9:
params[1] = fabs(params[1]);
if (nparm > 3)
{
/* See comment under effnEXPEXP */
params[3] = fabs(params[3])+params[1];
if (nparm > 5)
{
/* See comment under effnEXPEXP */
params[5] = fabs(params[5])+params[3];
if (nparm > 7)
{
/* See comment under effnEXPEXP */
params[7] = fabs(params[7])+params[5];
}
}
}
break;
case effnERREST:
params[0] = fabs(params[0]);
if (params[1] < 0)
{
params[1] = 0;
}
else if (params[1] > 1)
{
params[1] = 1;
}
/* See comment under effnEXPEXP */
params[2] = params[0]+fabs(params[2]);
break;
case effnPRES:
for (i = 1; (i < nparm); i++)
{
params[i] = fabs(params[i]);
}
break;
default:
break;
}
}
/*! \brief Ensure the fitting parameters are well-behaved.
*
* In order to make sure that fitting behaves according to the
* constraint that time constants are positive and increasing
* we enforce this here by setting all time constants to their
* absolute value and by adding e.g. |a_0| to |a_2|. This is
* done in conjunction with the fitting functions themselves.
* When there are multiple time constants we make sure that
* the successive time constants are at least double the
* previous ones and during fitting we enforce the they remain larger.
* It may very well help the convergence of the fitting routine.
*/
static void initiate_fit_params(int eFitFn,
double params[])
{
int i, nparm;
nparm = effnNparams(eFitFn);
switch (eFitFn)
{
case effnVAC:
GMX_ASSERT(params[0] >= 0, "parameters should be >= 0");
break;
case effnEXP1:
case effnEXP2:
case effnEXPEXP:
GMX_ASSERT(params[0] >= 0, "parameters should be >= 0");
if (nparm > 2)
{
GMX_ASSERT(params[2] >= 0, "parameters should be >= 0");
/* In order to maintain params[2] >= params[0] in the final
* result, we fit the difference between the two, that is
* params[2]-params[0] and in the add add in params[0]
* again.
*/
params[2] = std::max(fabs(params[2])-params[0], params[0]);
}
break;
case effnEXP5:
case effnEXP7:
case effnEXP9:
GMX_ASSERT(params[1] >= 0, "parameters should be >= 0");
params[1] = fabs(params[1]);
if (nparm > 3)
{
GMX_ASSERT(params[3] >= 0, "parameters should be >= 0");
/* See comment under effnEXPEXP */
params[3] = std::max(fabs(params[3])-params[1], params[1]);
if (nparm > 5)
{
GMX_ASSERT(params[5] >= 0, "parameters should be >= 0");
/* See comment under effnEXPEXP */
params[5] = std::max(fabs(params[5])-params[3], params[3]);
if (nparm > 7)
{
GMX_ASSERT(params[7] >= 0, "parameters should be >= 0");
/* See comment under effnEXPEXP */
params[7] = std::max(fabs(params[7])-params[5], params[5]);
}
}
}
break;
case effnERREST:
GMX_ASSERT(params[0] >= 0, "parameters should be >= 0");
GMX_ASSERT(params[1] >= 0 && params[1] <= 1, "parameter 1 should in 0 .. 1");
GMX_ASSERT(params[2] >= 0, "parameters should be >= 0");
/* See comment under effnEXPEXP */
params[2] = fabs(params[2])-params[0];
break;
case effnPRES:
for (i = 1; (i < nparm); i++)
{
GMX_ASSERT(params[i] >= 0, "parameters should be >= 0");
}
break;
default:
break;
}
}
/*! \brief lmfit_exp supports fitting of different functions
*
* This routine calls the Levenberg-Marquardt non-linear fitting
* routine for fitting a data set with errors to a target function.
* Fitting routines included in gromacs in src/external/lmfit.
*/
static gmx_bool lmfit_exp(int nfit,
const double x[],
const double y[],
const double dy[],
double parm[],
gmx_bool bVerbose,
int eFitFn,
int nfix)
{
double chisq, ochisq;
gmx_bool bCont;
int j;
int maxiter = 100;
lm_control_struct control;
lm_status_struct *status;
int nparam = effnNparams(eFitFn);
int p2;
gmx_bool bSkipLast;
if ((eFitFn < 0) || (eFitFn >= effnNR))
{
fprintf(stderr, "fitfn = %d, should be in the range 0..%d\n",
eFitFn, effnNR-1);
return FALSE;
}
/* Using default control structure for double precision fitting that
* comes with the lmfit package (i.e. from the include file).
*/
control = lm_control_double;
control.verbosity = (bVerbose ? 1 : 0);
control.n_maxpri = 0;
control.m_maxpri = 0;
snew(status, 1);
/* Initial params */
chisq = 1e12;
j = 0;
if (bVerbose)
{
printf("%4s %10s Parameters\n", "Step", "chi^2");
}
/* Check whether we have to skip some params */
if (nfix > 0)
{
do
{
p2 = 1 << (nparam-1);
bSkipLast = ((p2 & nfix) == p2);
if (bSkipLast)
{
nparam--;
nfix -= p2;
}
}
while ((nparam > 0) && (bSkipLast));
if (bVerbose)
{
printf("Using %d out of %d parameters\n", nparam, effnNparams(eFitFn));
}
}
do
{
ochisq = chisq;
gmx_lmcurve(nparam, parm, nfit, x, y, dy,
lmcurves[eFitFn], &control, status);
chisq = gmx::square(status->fnorm);
if (bVerbose)
{
printf("status: fnorm = %g, nfev = %d, userbreak = %d\noutcome = %s\n",
status->fnorm, status->nfev, status->userbreak,
lm_infmsg[status->outcome]);
}
if (bVerbose)
{
int mmm;
printf("%4d %8g", j, chisq);
for (mmm = 0; (mmm < effnNparams(eFitFn)); mmm++)
{
printf(" %8g", parm[mmm]);
}
printf("\n");
}
j++;
bCont = (fabs(ochisq - chisq) > fabs(control.ftol*chisq));
}
while (bCont && (j < maxiter));
sfree(status);
return TRUE;
}
int gmx_dielectric(int argc, char *argv[])
{
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].",
"The functional forms of the available functions are:[PAR]",
"One parameter: y = [EXP]-a[SUB]1[sub] x[exp],[BR]",
"Two parameters: y = a[SUB]2[sub] [EXP]-a[SUB]1[sub] x[exp],[BR]",
"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]",
"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]",
"with the number of the parameter you want to fix.",
"[PAR]",
"Three output files are generated, the first contains the ACF,",
"an exponential fit to it with 1, 2 or 3 parameters, and the",
"numerical derivative of the combination data/fit.",
"The second file contains the real and imaginary parts of the",
"frequency-dependent dielectric constant, the last gives a plot",
"known as the Cole-Cole plot, in which the imaginary",
"component is plotted as a function of the real component.",
"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 }
};
#define NFILE asize(fnm)
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;
real lambda;
t_pargs pa[] = {
{ "-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},
"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" }
};
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
please_cite(stdout, "Spoel98a");
printf("WARNING: non-polarizable models can never yield an infinite\n"
"dielectric constant that is different from 1. This is incorrect\n"
"in the reference given above (Spoel98a).\n\n");
nx = read_xvg(opt2fn("-f", NFILE, fnm), &yd, &ny);
dt = yd[0][1] - yd[0][0];
nxtail = min(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);
snew(y, 6);
for (i = 0; (i < ny); i++)
{
snew(y[i], max(nx, nxtail));
}
for (i = 0; (i < nx); i++)
{
y[0][i] = yd[0][i];
for (j = 1; (j < ny); j++)
{
y[j][i] = yd[j][i];
}
}
if (nxtail > nx)
{
for (i = nx; (i < nxtail); i++)
{
y[0][i] = dt*i+y[0][0];
for (j = 1; (j < ny); j++)
{
y[j][i] = 0.0;
}
}
nx = nxtail;
}
/* We have read a file WITHOUT standard deviations, so we make our own... */
if (ny == 2)
{
printf("Creating standard deviation numbers ...\n");
srenew(y, 3);
snew(y[2], nx);
fac = 1.0/((real)nx);
for (i = 0; (i < nx); i++)
{
y[2][i] = fac;
}
}
eFitFn = sffn2effn(s_ffn);
nfitparm = effnNparams(eFitFn);
snew(fitparms, 4);
fitparms[0] = tau1;
if (nfitparm > 1)
{
fitparms[1] = A;
}
if (nfitparm > 2)
{
fitparms[2] = tau2;
}
snew(y[3], nx);
snew(y[4], nx);
snew(y[5], nx);
integral = print_and_integrate(NULL, calc_nbegin(nx, y[0], tbegin),
dt, y[1], NULL, 1);
integral += do_lmfit(nx, y[1], y[2], dt, y[0], tbegin, tend,
oenv, TRUE, eFitFn, fitparms, fix);
for (i = 0; i < nx; i++)
{
y[3][i] = fit_function(eFitFn, fitparms, y[0][i]);
}
if (epsRF == 0)
{
/* This means infinity! */
lambda = 0;
rffac = 1;
}
else
{
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);
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);
/* Now we have the negative gradient of <Phi(0) Phi(t)> */
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_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
do_view(oenv, opt2fn("-c", NFILE, fnm), NULL);
do_view(oenv, opt2fn("-d", NFILE, fnm), "-nxy");
return 0;
}
static void do_fit(FILE *out, int n, gmx_bool bYdy,
int ny, real *x0, real **val,
int npargs, t_pargs *ppa, const gmx_output_env_t *oenv,
const char *fn_fitted)
{
real *c1 = NULL, *sig = NULL;
double *fitparm;
real tendfit, tbeginfit;
int i, efitfn, nparm;
efitfn = get_acffitfn();
nparm = effnNparams(efitfn);
fprintf(out, "Will fit to the following function:\n");
fprintf(out, "%s\n", effnDescription(efitfn));
c1 = val[n];
if (bYdy)
{
c1 = val[n];
sig = val[n+1];
fprintf(out, "Using two columns as y and sigma values\n");
}
else
{
snew(sig, ny);
}
if (opt2parg_bSet("-beginfit", npargs, ppa))
{
tbeginfit = opt2parg_real("-beginfit", npargs, ppa);
}
else
{
tbeginfit = x0[0];
}
if (opt2parg_bSet("-endfit", npargs, ppa))
{
tendfit = opt2parg_real("-endfit", npargs, ppa);
}
else
{
tendfit = x0[ny-1];
}
snew(fitparm, nparm);
switch (efitfn)
{
case effnEXP1:
fitparm[0] = 0.5;
break;
case effnEXP2:
fitparm[0] = 0.5;
fitparm[1] = c1[0];
break;
case effnEXPEXP:
fitparm[0] = 1.0;
fitparm[1] = 0.5*c1[0];
fitparm[2] = 10.0;
break;
case effnEXP5:
fitparm[0] = fitparm[2] = 0.5*c1[0];
fitparm[1] = 10;
fitparm[3] = 40;
fitparm[4] = 0;
break;
case effnEXP7:
fitparm[0] = fitparm[2] = fitparm[4] = 0.33*c1[0];
fitparm[1] = 1;
fitparm[3] = 10;
fitparm[5] = 100;
fitparm[6] = 0;
break;
case effnEXP9:
fitparm[0] = fitparm[2] = fitparm[4] = fitparm[6] = 0.25*c1[0];
fitparm[1] = 0.1;
fitparm[3] = 1;
fitparm[5] = 10;
fitparm[7] = 100;
fitparm[8] = 0;
break;
default:
fprintf(out, "Warning: don't know how to initialize the parameters\n");
for (i = 0; (i < nparm); i++)
{
fitparm[i] = 1;
}
}
fprintf(out, "Starting parameters:\n");
for (i = 0; (i < nparm); i++)
{
fprintf(out, "a%-2d = %12.5e\n", i+1, fitparm[i]);
}
if (do_lmfit(ny, c1, sig, 0, x0, tbeginfit, tendfit,
oenv, bDebugMode(), efitfn, fitparm, 0,
fn_fitted) > 0)
{
for (i = 0; (i < nparm); i++)
{
fprintf(out, "a%-2d = %12.5e\n", i+1, fitparm[i]);
}
}
else
{
fprintf(out, "No solution was found\n");
}
}