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theochem / iodata

Python library for reading, writing, and converting computational chemistry file formats and generating input files.
https://iodata.readthedocs.io/
GNU Lesser General Public License v3.0
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Add support for fractional bond orders #222

Open tovrstra opened 3 years ago

tovrstra commented 3 years ago

At the moment, bond orders are force to be integer because they are stored in the same array containing the atomic indices. This can be fixed easily with a structured data type: np.dtype("int, int, float").

tovrstra commented 3 years ago

I've added a few PRs adding support for bond information to a few more file formats, just to get a better feel of what is needed, see #248 and #250. There are a few different things needed by various formats. Splitting up the current bonds array into a three attributes seems most appropriate:

  1. bonds just becomes an array with two columns for pairs for atoms (first two columns of the current bonds attribute.
  2. bondtypes is a vector with an integer kind for each bond. Integers can be mapped to various string representations of bond types, to deal with incompatible nomenclatures.
  3. bondorders is a floating point vector with just the bond orders of the bonds listed in bonds. This is needed e.g. by QCSchema.

The usual validation mechanisms can impose consistent sizes of these arrays and a read-only nbond property can be added in line with natom.

In the long run, we can add machinery to deduce a decent bondorders vector from the bondtypes (and vice versa), but that is a secondary concern. (This would make more sense after addressing #191.) Just getting the right attributes in place should be done first because it affects API and blocks a 1.0 release.