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exa-analytics / exatomic

A unified platform for theoretical and computational chemists
https://exa-analytics.github.io/exatomic
Apache License 2.0
19 stars 12 forks source link

Features to atom_two #205

Open herbertludowieg opened 3 years ago

herbertludowieg commented 3 years ago

Is your feature request related to a problem? Please describe. I think it'd be good if we were to add the frame index to the atom_two table. This would allow users to access the bond distances for specific frames in the atom table which is useful for tracking the bond distance between certain atoms.

Something that I'm not sure if it would be useful would be to change the indexing for the atom0 and atom1 columns to match the set column on the atom table as, again, might make things useful for tracking changes in bond distances.

Edit: Since the set column in ADF is not the same as an atomic index I think we would need to add a new column such as adx to keep track of the atomic index within each frame. This would require us to add that column into every parse_atom method.

Describe the solution you'd like Just adding a new column.

Describe alternatives you've considered None so far really. Not sure if we can do it with the current implementation unless we get the min and max index in each of the atom frames.

Additional context Not sure yet what this would mean for any of the javascript code. Edit: From the small number of tests with visualizing the molecule this does not seem to be an issue.

Would need features addressed in #211

tjduigna commented 2 years ago

I am confused about references to the set column in the atom table. I believe this column is usually used as a foreign key into the basis_set table. I am not sure how it is related to the atom_two table. Could you clarify?