Align atom on arbitrary axis and addition of new centering methods

exa-analytics / exatomic

A unified platform for theoretical and computational chemists

https://exa-analytics.github.io/exatomic

Apache License 2.0

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Align atom on arbitrary axis and addition of new centering methods #168

Closed herbertludowieg closed 4 years ago

herbertludowieg commented 5 years ago

This closes #166 and closes #167.

Fixed bug in Atom.center

Additions:

New code to center the molecule to the center of nuclear charge
Align molecule along an arbitrary axis
- This will also center the molecule
Some possible zero division error handling when normalizing vector in Atom.rotate

herbertludowieg commented 5 years ago

Should we consider adding return Atom(return_var) for the center, rotate, translate and align methods. As it is right now it only returns an instance of pandas.DataFrame instead of Atom.

herbertludowieg commented 5 years ago

I just noticed that the new Atom.align method may have overwritten a pre-existing method in pandas.DataFrame. Also, I would like to add tests to this PR.

avmarchenko commented 5 years ago

Given your last comment, lets rename the method so that it doesn't mess with pandas API.

herbertludowieg commented 5 years ago

I agree I'll rename it to align_mol. Seems to make enough sense to me.

avmarchenko commented 4 years ago

@herbertludowieg , lets merge master into this PR, resolve conflicts, and then see what the build system reports.