plot_msd_layer_cross_section_xyz_at_constant_msd

Plot the diffusion time at which the x-, y- and z-component of the MSD reach a certain value as function of the initial particle position.

Todo

Finish docstring

This script is designed to plot cross sections from the output of scripts.dynamics.msd_layer_serial (or scripts.dynamics.msd_layer_parallel) for all three spatial components x, y and z in one plot.

Options

-f: Input files. The three output files of scripts.dynamics.msd_layer_serial (or scripts.dynamics.msd_layer_parallel) containing the MSDs for all three spatial directions as space separated list in the order x y z.
--fmd: Optional further input files. The three output files of scripts.dynamics.msd_layer_serial (or scripts.dynamics.msd_layer_parallel) containing the mean displacements for all three spatial directions as space separated list in the order x y z. If provided, the square of the mean displacements will be subtracted from the MSDs to correct for a potential particle drift by calculating the variance \(\langle \Delta\mathbf{r}^2 \rangle - \langle \Delta\mathbf{r} \rangle^2\).
-o: Output filename.
--msd: MSD in data units for which to plot the diffusion times as function of the initial particle position. Default: 1.
--msd-eq-bins: Instead of choosing the MSD manually with --msd, set the MSD for each individual bin to the square of the respective bin width. Must not be used together with --msd.
-d: The spatial direction that was used to dicretize the MSD. Default: 'z'.
--f2: An optional further input file providing additional 1-dimensional data as a function of the spatial direction given with -d, e.g. a density profile. This data will be plotted above the original plot.
--cols: From which columns of INFILE2 to read the additional data. Column numbering starts at zero. The first given number determines the column containing the x values, the second is for the y values. Default: [0, 1].
--xlim: Left and right limit of the x-axis in data coordinates. Pass ‘None’ to set the limits to the leftmost and rightmost bin edges. Default:[None, None].
--ylim: Lower and upper limit of the y-axis in data coordinates. Pass ‘None’ to adjust the limit(s) automatically. Default: [None, None].
--logy: Use logarithmic scale for the y-axis.
--time-conv: Multiply all times by this factor. Default: 1.
--time-unit: Time unit. Default: 'ps'.
--length-conv: Multiply all lengths by this factor. Default: 1.
--length-unit: Lengh unit. Default: A.