real do_lmfit(int ndata, real c1[], real sig[], real dt, real x0[],
real begintimefit, real endtimefit, const output_env_t oenv,
gmx_bool bVerbose, int eFitFn, real fitparms[], int fix)
{
FILE *fp;
char buf[32];
int i, j, nparm, nfitpnts;
real integral, ttt;
real *parm, *dparm;
real *x, *y, *dy;
real ftol = 1e-4;
nparm = nfp_ffn[eFitFn];
if (debug)
{
fprintf(debug, "There are %d points to fit %d vars!\n", ndata, nparm);
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];
/* mrqmin does not like sig to be zero */
if (sig[i] < 1.0e-7)
{
dy[j] = 1.0e-7;
}
else
{
dy[j] = sig[i];
}
if (debug)
{
fprintf(debug, "j= %d, i= %d, x= %g, y= %g, dy= %g\n",
j, i, x[j], y[j], dy[j]);
}
j++;
}
}
nfitpnts = j;
integral = 0;
if (nfitpnts < nparm)
{
fprintf(stderr, "Not enough data points for fitting!\n");
}
else
{
snew(parm, nparm);
snew(dparm, nparm);
if (fitparms)
{
for (i = 0; (i < nparm); i++)
{
parm[i] = fitparms[i];
}
}
if (!lmfit_exp(nfitpnts, x, y, dy, ftol, parm, dparm, bVerbose, eFitFn, fix))
{
fprintf(stderr, "Fit failed!\n");
}
else if (nparm <= 3)
{
/* Compute the integral from begintimefit */
if (nparm == 3)
{
integral = (parm[0]*myexp(begintimefit, parm[1], parm[0]) +
parm[2]*myexp(begintimefit, 1-parm[1], parm[2]));
}
else if (nparm == 2)
{
integral = parm[0]*myexp(begintimefit, parm[1], parm[0]);
}
else if (nparm == 1)
{
integral = parm[0]*myexp(begintimefit, 1, parm[0]);
}
else
{
gmx_fatal(FARGS, "nparm = %d in file %s, line %d",
nparm, __FILE__, __LINE__);
}
/* Generate THE output */
if (bVerbose)
{
fprintf(stderr, "FIT: # points used in fit is: %d\n", nfitpnts);
fprintf(stderr, "FIT: %21s%21s%21s\n",
"parm0 ", "parm1 (ps) ", "parm2 (ps) ");
fprintf(stderr, "FIT: ------------------------------------------------------------\n");
fprintf(stderr, "FIT: %8.3g +/- %8.3g%9.4g +/- %8.3g%8.3g +/- %8.3g\n",
parm[0], dparm[0], parm[1], dparm[1], parm[2], dparm[2]);
fprintf(stderr, "FIT: Integral (calc with fitted function) from %g ps to inf. is: %g\n",
begintimefit, integral);
sprintf(buf, "test%d.xvg", nfitpnts);
fp = xvgropen(buf, "C(t) + Fit to C(t)", "Time (ps)", "C(t)", oenv);
fprintf(fp, "# parm0 = %g, parm1 = %g, parm2 = %g\n",
parm[0], parm[1], parm[2]);
for (j = 0; (j < nfitpnts); j++)
{
ttt = x0 ? x0[j] : dt*j;
fprintf(fp, "%10.5e %10.5e %10.5e\n",
ttt, c1[j], fit_function(eFitFn, parm, ttt));
}
xvgrclose(fp);
}
}
if (fitparms)
{
for (i = 0; (i < nparm); i++)
{
fitparms[i] = parm[i];
}
}
sfree(parm);
sfree(dparm);
}
sfree(x);
sfree(y);
sfree(dy);
return integral;
}
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;
}
