StepModel¶

class poreana.model.StepModel(data_link, n_diff=6, n_df=10, n_diff_radial=6, d0=1, is_print=False)¶

This class sets the Step Model to calculate the free energy profile and the diffusion profile. This model based on a spline calculation. In contrast to the Cosine Model the determined profile has not the typical oscillation and receives a profile which is better interpretable. The profile will be determined with the following equations

\[\ln \left(D_{i+\frac{1}{2}}\right) = a_{k} \cdot \mathrm{basis}_{\mathrm{diff}}\]

\[F_i = a_{k} \cdot \mathrm{basis}_{\mathrm{df}}\]

with \(a_k\) as the coefficients and the \(\mathrm{basis}\). The basis of the modell is calculated with

StepModel

Parameters:

data_linkstring: Data link to the pickle data from poreana.sample.Sample.init_diffusion_mc()
n_diffinteger, optional: Number of the Fourier coefficients for the diffusion profile
n_dfinteger, optional: Number of the Fourier coefficients for the free energy profile
n_diff_radialinteger, optional: Number of the Fourier coefficients for the radial diffusion profile
d0double, optional: Initial guess of diffusion coefficient \(\left( 10^{-9} \frac{m^2}{s}\right)\)
is_printbool, optional: True to print output

Methods

`_calc_profile`(coeff, basis)	This function calculates the diffusion and free energy profile over the bins.
`_create_basis_border`()	This function creates the basis part in every bin of the Step model for the diffusion profile.
`_create_basis_center`()	This function creates the basis part in every bin of the Step model for the free energy and the radial diffusion profile.
`_init_model`()	This function initializes the coefficient list for the Step Model and the profile list for the free energy and diffusion profile.
`_init_profiles`()	This function initializes the normal diffusion, radial diffusion and free energy profile over the bins.
`_step_model`()	This function set a Step Model for the MC Diffusion Calculation and determine the initialize profiles.