plot_msd_layer_heatmap

Plot the MSD as function of the initial particle position and the diffusion time in a heatmap.

Todo

Finish docstring

This script is designed to plot the output of scripts.dynamics.msd_layer_serial (or scripts.dynamics.msd_layer_parallel).

Options

-f

Input file. One of the output files of scripts.dynamics.msd_layer_serial (or scripts.dynamics.msd_layer_parallel).

--fmd

Optional further input file(s). The output file(s) of scripts.dynamics.msd_layer_serial (or scripts.dynamics.msd_layer_parallel) that contain(s) the mean displacement. If provided the square of the mean displacement will be subtracted from the MSD to correct for a potential particle drift by calculating the variance \(\langle \Delta\mathbf{r}^2 \rangle - \langle \Delta\mathbf{r} \rangle^2\). You can either provide the mean displacement in a single spatial direction or in all three spatial directions.

-o

Output filename.

--d1

{‘r’, ‘x’, ‘y’, ‘z’}

The component of the MSD that is contained in the input file. 'r' stands for the entire displacement vector. Default: 'r'.

--d2

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 adjust the limit(s) automatically. 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].

--vlim

The colorbar range. Pass ‘None’ to adjust the limit(s) automatically. Default: [None, None].

--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.