plot_state_lifetime_discrete

Plot the lifetime autocorrelation function of discrete states as function of another set of discrete states.

Todo

Finish docstring

This script is designed to plot the output of scripts.discretization.state_lifetime_discrete.

Options

-f

Input filename. The output file of scripts.discretization.state_lifetime_discrete.

-o

Output filename pattern. There are created two or three output files:

<OUTFILE>.pdf containing the lifetime autocorrelation functions as function of lag time and secondary state as well as the average lifetimes as function of the secondary states.

<OUTFILE>_fit.pdf containing the lifetime autocorrelation functions for each secondary state as function of lag time with its respective fit.

<OUTFILE>_fit.txt containing the fit parameters for each secondary state. Only created if --refit is given.

--cols

The columns of the input file that should be plotted. Column numbering starts at zero. Note that all given columns are treated as y data. The 0-th column is always read automatically and treated as x data. Default: None (this means read all columns).

--refit

Do not read the fitting parameters from the input file but redo the fitting of the data.

--end-fit

End time for fitting the remain probability in data units. This is inclusive, i.e. the time given here is still included in the fit. Is meaningless if --refit is not given. Default: None (this means end at 90% of the lag times).

--stop-fit

Stop fitting the remain probability as soon as it falls below this value. The fitting is stopped by whatever happens earlier: --end-fit or --stop-fit. Is meaningless if --refit is not given. Default: 0.01.

--xlim

Left and right limit of the x-axis in data coordinates. If the right limit is None, plot until the maximum lag time. Default: [0, None].

--ylim

Lower and upper limit of the y-axis in data coordinates. Pass ‘None’ to adjust the limit(s) automatically. Default: [0, 1].

--time-conv

Multiply all times by this factor. Default: 1.

--time-unit

Time unit. Default: 'steps'.