CubePy is under CC BY-NC-SA license

AdditionalFunctions.py is a collection of functions that do not work directly with cube files, but with data produced by the other scripts.

Requirements

Python
Matplotlib

An easy way to obtain Python with the required modules is by installing Anaconda.

Anaconda comes with Spyder, which is a Python editor that you can use to write and run Python codes (Applications $\to$ Anaconda Navigator $\to$ spyder $\to$ Launch)

Instructions

Running the code

The plotting functions can be run from the terminal window by typing:

python AdditionalFunctions.py function_name file_path1 file_path2... arg1=val1 arg2=val2...

Functions

OverlapKDEs

This function plots overlapping KDEs as read from _kde.out files written by PlotHistogram from PlotCube.py (when save is True).

Required arguments

fpaths (string) = paths for _kde.out files

Optional arguments

value_type (string, default='esp') = can be ‘esp’/’potential’ or ‘dens’/’density’ (or any uppercase version of the aforementioned); used in conjunction with the keywords au and units in order to convert the values to the appropriate units
xlim (list, default=None) = x axis limits
ylim (list, default=None) = y axis limits
log (boolean, default=True) = if True, it saves a .log file of the command used to run the functions (the command is tidied-up before saving i.e. unnecessary spaces are removed, argument values are converted to their usual uppercase/lowercase versions, file lists are explicit - instead of using wildcard symbols such as *)
logfile (string, default=None) = the name of the log file (if log is True); by default the file name is the input file name followed by the function name

Observations

if you only want to specify one limit for either of the axis, use None for the other (e.g. xlim=[None,3.5])

Example

python AdditionalFunctions.py OverlapKDEs NH3CH2Cl_esp_kde.out NH3CH2OH_esp_kde.out NH3CH2BH2_esp_kde.out xlim=[2,10]

The resulting plot is shown in figure 1.

PlotHistogram

This function plots one KDE and/or one histogram as read from _kde.out and _hist.out files written by PlotHistogram from PlotCube.py (when save is True).

Required arguments

fpaths (string) = paths for _kde.out and _hist.out files (should be one of each at most)

Optional arguments

value_type (string, default='esp') = can be ‘esp’/’potential’ or ‘dens’/’density’ (or any uppercase version of the aforementioned); used in conjunction with the keywords au and units in order to convert the values to the appropriate units
colour (string, default='rainbow') = colour scheme ('rainbow' by default, change it to 'bwr' for blue-white-red) - full list here
cb_lim (list, default=None) = limits for the colour bar (list of two floats; if not specified, the limits will be the min and max of the values; if the limits do not cover the whole range of values, a warning is printed)
xlim (list, default=None) = x axis limits
ylim (list, default=None) = y axis limits
log (boolean, default=True) = if True, it saves a .log file of the command used to run the functions (the command is tidied-up before saving i.e. unnecessary spaces are removed, argument values are converted to their usual uppercase/lowercase versions, file lists are explicit - instead of using wildcard symbols such as *)
logfile (string, default=None) = the name of the log file (if log is True); by default the file name is the input file name followed by the function name
cb_sym (boolean, default=False) = if True, the colour bar limits are chosen to be symmetric around 0 (cb_lim, if specified, overrides cb_sym)

Observations

if you only want to specify one limit for either of the axis, use None for the other (e.g. xlim=[None,3.5])
the function only works for one histogram file and/or one KDE file. If multiple files of either type are specified as arguments, the execution of the program is stopped and a warning is printed.
the data in the files specified as arguments must be in the same units. If that is not the case, the execution of the program is stopped and a warning is printed.

Example

python AdditionalFunctions.py PlotHistogram test_emim_oac_esp_kde.out test_emim_oac_esp_hist.out

The resulting plot is shown in figure 2.