dylanbmorgan / ims-plot Goto Github PK

Enable generation of matplotlib 1D plots so they appear like in the Stanger paper where multiple molecules/excited states/etc appear on the same plot

• Automatically add a title, axes titles, and units
• Include optional flag so user can specify above criteria if desired

When testing the 2d_ga_gen script, it was discovered that it would only append Bq coors correctly if they were specified in the xy plane. If attempting to append in other planes, it would only generate a 1d array and many atoms were duplicated. I have written a quick fix utilising argparse, but I would prefer if it could work as intended without the usr having to specify the plane themselves with an argparse argument.

Details of the current fix can be found in 38f54ac

@felixplasser if it's ok with you, I'm going to leave this for now and focus on finishing the 2d contour plot

• Pull test files for anthracene and benzene in singlet and triplet states generated using 1D scripts
• Complete above for 2D
• Complete above for 3D

Include the following:

• docs/conf.py
• docs/index.rst
• module/init.py
• module/core.py
• tests/core.py
• requirements.txt
• setup.py

And incorporate other practices as found in https://data-flair.training/blogs/python-best-practices/

Instead of quoting the name of script again at the top of the file, just give the title of the script.

Include title, axis labels, legend, etc.

Completed for:

• Contour
• Isosurface

• Modify these scripts so plotter automatically calls parser (maybe as a module)
  • Only one script will need to be called, not both
• Change how parsed_log_data.txt is created. Enable auto deletion once graph has been plotted

• Assess whether import or using dictionaries is better
• Add functionality for if x and y are different lengths
• Automatically move input_data.txt to parsed_data directory upon creation

As the title says. Maybe need to look at json files?

• Swap the sign of isotropic values so they become chemical shift
• Give option as a CLI argument to plot graph as shielding value

• Update README to provide information on how to use scripts once they are finished
• Correct figure 1
• Improve in-text documentation

Improve front end and argparse statements so it matches the 2d_graph.py

TODO:

• Add shebangs to scripts so paths can be set and called from anywhere in cli
• Include script to automatically add script to path (see
• Modify scripts so filenames can be written in cli, like username@hostname$<name_of_script> <original_filename> <copy_filename> (see https://sourceforge.net/p/theodore-qc/code/ci/master/tree/bin/babel.py and https://www.geeksforgeeks.org/how-to-use-sys-argv-in-python/)
• Include plots like those found here: https://pubs.acs.org/doi/10.1021/jo051746o

Complete for each:

• 2D ghost atom generator

• 3D ghost atom generator

• 2D log file parser

• 3D log file parser

• 2D graph plotter

• 3D graph plotter

Gaussian doesn't like files containing more than 100 or so Bq atoms, so the generator scripts are going to split the job into files containing maximum 100 Bqs

• Write script to automatically add scripts/repository to $PATH
• Write script to automatically set up everything
  • low priority, possibly wait until later release

For doing a 1D scan we'd need the following

• Generate input file for 0D script

• Generate input file for 1D script

• Parse the information from the output file

• Convert into a graphical representation (xy plot)

edits by @dylanbmorgan : added separate completion tasks for 0D and 1D scripts

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