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QChASM / AaronTools.py

Python tools for automating routine tasks encountered when running quantum chemistry computations.
https://aarontools.readthedocs.io/en/latest/
GNU General Public License v3.0
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Radii for lanthanides/actinides #6

Closed swheele2 closed 2 years ago

swheele2 commented 2 years ago

AaronTools is missing radii for the lanthanides and actinides, which prevents SEQCROW from opening ORCA output files for molecules containing such atoms.

swheele2 commented 2 years ago

Radii have been added to const.py, but we should make sure that we can now open such ORCA files in SEQCROW before closing issue (I put a sample output file in DropBox).

ajs99778 commented 2 years ago

We should be able to open any file with actinides and lanthanides. I also made the radius default to 1.5 in case we are still missing some elements. Missing the radii affected determining connectivity, not parsing the file. This means you were able to printXYZ.py the file, but not findAtoms.py the file because printXYZ does not determine connectivity and findAtoms does. Elements are parsed from files according to white space, a regular expression, or using the element number depending on the type of file.

I am able to open the ORCA file with the version of SEQCROW that's on the dev branch.