expfit.h File Reference

#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"

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Description

Declares routine for fitting a data set to a curve.

Author

David van der Spoel david.nosp@m..van.nosp@m.dersp.nosp@m.oel@.nosp@m.icm.u.nosp@m.u.se

Enumerations
enum	{   effnNONE, effnEXP1, effnEXP2, effnEXPEXP,   effnEXP5, effnEXP7, effnEXP9, effnVAC,   effnERF, effnERREST, effnPRES, effnNR }
	Enum to select fitting functions.

Functions
const char *	effnDescription (int effn)
	Returns description corresponding to the enum above, or NULL if out of range. More...
int	effnNparams (int effn)
	Returns number of function parameters associated with a fitting function. More...
int	sffn2effn (const char **sffn)
	Returns corresponding to the selected enum option in sffn. More...
double	fit_function (int eFitFn, const double parm[], double x)
	Returns the value of fit function eFitFn at x. More...
real	do_lmfit (int ndata, const real c1[], real sig[], real dt, const 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)
	Use Levenberg-Marquardt method to fit to a nfitparm parameter exponential or to a transverse current autocorrelation function. More...
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)
	Fit an autocorrelation function to a pre-defined functional form. More...

Variables
const char *	s_ffn [effnNR+2]
	Short name of each function type. This is exported for now in order to use when calling parse_common_args.

Function Documentation

real do_lmfit	(	int	ndata,
		const real	c1[],
		real	sig[],
		real	dt,
		const 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
	)

Use Levenberg-Marquardt method to fit to a nfitparm parameter exponential or to a transverse current autocorrelation function.

If x == NULL, the timestep dt will be used to create a time axis.

Parameters

[in]	ndata	Number of data points
[in]	c1	The data points
[in]	sig	The standard deviation in the points (can be NULL)
[in]	dt	The time step
[in]	x0	The X-axis (may be NULL, see above)
[in]	begintimefit	Starting time for fitting
[in]	endtimefit	Ending time for fitting
[in]	oenv	Output formatting information
[in]	bVerbose	Should the routine write to console?
[in]	eFitFn	Fitting function (0 .. effnNR)
[in,out]	fitparms[]	Fitting parameters, see printed manual for a detailed description. Note that in all implemented cases the parameters corresponding to time constants will be generated with increasing values. Such input parameters should therefore be provided in increasing order. If this is not the case or if subsequent time parameters differ by less than a factor of 2, they will be modified to ensure tau_i+1 >= 2 tau_i.
[in]	fix	Constrains fit parameter i at it's starting value, when the i'th bit of fix is set. This works only when the N last parameters are fixed but not when a parameter somewhere in the middle needs to be fixed.
[in]	fn_fitted	If not NULL file to print the data and fitted curve to

Returns

integral.

const char* effnDescription

(

int

effn

)

Returns description corresponding to the enum above, or NULL if out of range.

Parameters

[in]

effn

Index

Returns

Description or NULL

int effnNparams

(

int

effn

)

Returns number of function parameters associated with a fitting function.

Parameters

[in]

effn

Index

Returns

number or -1 if index out of range

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
	)

Fit an autocorrelation function to a pre-defined functional form.

Todo:

check parameters

Parameters

[in]	ncorr
[in]	fitfn	Fitting function (0 .. effnNR)
[in]	oenv	Output formatting information
[in]	bVerbose	Should the routine write to console?
[in]	tbeginfit	Starting time for fitting
[in]	tendfit	Ending time for fitting
[in]	dt	The time step
[in]	c1	The data points
[in,out]	fit	The fitting parameters

Returns

the integral over the autocorrelation function?

double fit_function	(	int	eFitFn,
		const double	parm[],
		double	x
	)

Returns the value of fit function eFitFn at x.

Parameters

[in]	eFitFn	the index to the fitting function (0 .. effnNR)
[in]	parm	Array of parameters, the length of which depends on eFitFn
[in]	x	The value of x

Returns

the value of the fit

int sffn2effn

(

const char **

sffn

)

Returns corresponding to the selected enum option in sffn.

Parameters

[in]

sffn

Two dimensional string array coming from parse_common_args

Returns

the ffn enum