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