g_dielectric

VERSION 3.2.0
Sun 25 Jan 2004

Description

dielectric calculates frequency dependent dielectric constants from the autocorrelation function of the total dipole moment in your simulation. This ACF can be generated by g_dipoles. For an estimate of the error you can run g_statistics on the ACF, and use the output thus generated for this program. The functional forms of the available functions are:

One parmeter : y = Exp[-a1 x] Two parmeters : y = a2 Exp[-a1 x] Three parmeter: y = a2 Exp[-a1 x] + (1 - a2) Exp[-a3 x] Startvalues for the fit procedure can be given on the commandline. It is also possible to fix parameters at their start value, use -fix with the number of the parameter you want to fix.

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

Files

option	filename	type	description
`-f`	`Mtot.xvg`	Input	xvgr/xmgr file
`-d`	`deriv.xvg`	Output	xvgr/xmgr file
`-o`	`epsw.xvg`	Output	xvgr/xmgr file
`-c`	`cole.xvg`	Output	xvgr/xmgr file

Other options

option	type	default	description
`-[no]h`	bool	`no`	Print help info and quit
`-nice`	int	`19`	Set the nicelevel
`-b`	time	`-1`	First frame (ps) to read from trajectory
`-e`	time	`-1`	Last frame (ps) to read from trajectory
`-dt`	time	`-1`	Only use frame when t MOD dt = first time (ps)
`-[no]w`	bool	`no`	View output xvg, xpm, eps and pdb files
`-[no]fft`	bool	`no`	use fast fourier transform for correlation function
`-[no]x1`	bool	`yes`	use first column as X axis rather than first data set
`-eint`	real	`5`	Time were to end the integration of the data and start to use the fit
`-bfit`	real	`5`	Begin time of fit
`-efit`	real	`500`	End time of fit
`-tail`	real	`500`	Length of function including data and tail from fit
`-A`	real	`0.5`	Start value for fit parameter A
`-tau1`	real	`10`	Start value for fit parameter tau1
`-tau2`	real	`1`	Start value for fit parameter tau2
`-eps0`	real	`80`	Epsilon 0 of your liquid
`-epsRF`	real	`78.5`	Epsilon of the reaction field used in your simulation. A value of 0 means infinity.
`-fix`	int	`0`	Fix parameters at their start values, A (2), tau1 (1), or tau2 (4)
`-ffn`	enum	`none`	Fit function: `none`, `exp`, `aexp`, `exp_exp`, `vac`, `exp5`, `exp7` or `exp9`
`-nsmooth`	int	`3`	Number of points for smoothing

http://www.gromacs.org
gromacs@gromacs.org