plot_msd_layer_cross_section_xyz_at_constant_time

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

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.
-t: Diffusion time in data units for which to plot the MSDs as function of the initial particle position. If no data are present at the given diffusion time, the next nearest diffusion time for which data are present is used. Default: 1.
-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.