plot_discrete_hex_trj

Plot on which discrete hexagonal site a compounds resides as function of time and space in a scatter plot.

Todo

Finish docstring

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

Options

-f

Input filename. The output file of scripts.discretization.discrete_hex containing the discrete trajectory.

--lf

Second input file. The output file of scripts.discretization.discrete_hex containing the hexagonal lattice faces.

--lv

Third input file. The output file of scripts.discretization.discrete_hex containing the hexagonal lattice vertices.

-o

Output filename.

-i

The index of the compound for which to plot the discrete trajectory. Indexing starts at zero. Default: The compound that has the fewest negative elements in its discrete trajectory.

--every

Plot only every n-th frame. Default: 1.

--msize

If given, the size of the scatter points will be proportional to the number of times the compound visited the respective lattice face.

--xlim

Left and right limit of the x-axis in data coordinates. Pass ‘None’ to adjust the limit(s) automatically. 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, None].

--length-conv

Multiply all lengths by this factor. Default: 1.

--length-unit

Lengh unit. Default: A.

Examples

TODO