plot_msd_layer_cross_section_at_constant_time
Plot (one component of) the MSD as function of the initial particle position at a constant diffusion time(s).
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
).
Options
- -f
Input file. One of the output files of
scripts.dynamics.msd_layer_serial
(orscripts.dynamics.msd_layer_parallel
).- --fmd
Optional further input file(s). The output file(s) of
scripts.dynamics.msd_layer_serial
(orscripts.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.
- -t
Diffusion time(s) in data units for which to plot the MSD as function of the initial particle position. If no data are present at a given diffusion time, the next nearest diffusion time for which data are present is used. Default:
1
.- --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 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
.
See also
plot_msd_layer
Plot the MSD as function of diffusion time for different initial particle positions
plot_msd_layer_heatmap
Plot the MSD as function of the initial particle position and the diffusion time in a heatmap
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
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
Examples
TODO