Add Quickstart notebook #202
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TODO: The periodic grid brief explanation is missing.
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@marco-2023, thanks for your PR. The content and logic of your notebook were great; I working through it. I added my revisions in b734bbc. Some of the changes were made automatically by my editor, and the changes I made addressed (the list is not complete):
- The links should be to the webpage not the
rstfiles in the repo. Unless I am missing sth, your links didn't work for me. - When making an instance of a class like
MolGrid, it would be good to showcase its attributes by printing some information about the grid. I changed the print statements to do that. - It is better for
MolGridexample to show an example of a molecule (instead of H atom, which is useful but can be confusing as a quick start example). Then, we don't need to remake the MolGrid for H2+ when using the grid for computations. - Sometimes the markdown description did not match the code block, so I updated that. For example, Formaldehyde was mentioned in the comments when H2+ was used in the code/markdown.
- Let's keep our variable names consistent across notebooks and packages. For example, we have been using
rgrid,atgrid, andoned(probably we should make a glossary). It is important to stay consistent for easier understanding and use. - Sometimes the text in the markdown and comments repeated the same thing. I would keep the comments minimal, so that code is simpler and easier to maintain. I updated the notebook to fix these.
- I added a small section to check the accuracy of interpolated density against the analytical value.
- Moved Cubic and Periodic grids to the end of the notebook to move using the grid for computation (integration and interpolation closer to MolGrid section).
After @Ali-Tehrani has reviewed the notebook, we can merge it, and you can make a new PR when the cubic/periodic parts are done.
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@FarnazH Thanks for the review and the comments. The guidelines you shared will help me a lot in the upcoming notebooks! I have a doubt regarding the first point. I made the links pointing to the corresponding |
An example was added for calculating, visualizing and integrating the lobes of formaldehyde dual descriptor. Notes The example is a little bit long and perhaps even complicated.
The fchk files necessary for calculating formaldehyde dual descriptor are added.
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1. The cubic grid section showcased a great example, but was too elaborate and complicated to be suitable for a short quickstart. I believe the Quickstart.ipynb does not need to cover all the functionality, so it is best to add this example to the notebook dedicated to Cubic grid. 2. Add a section for differentiation on the grid.
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