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Oxo handling #22

Merged
merged 7 commits into from
Jul 12, 2023
Merged

Oxo handling #22

merged 7 commits into from
Jul 12, 2023

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mgt16-LANL
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This branch adds additional handling for OXO-bound complexes.

OXO ligand compounds are particularly relevant for actinides and catalytic water-based systems.

This change adds 4 basic functionalities:

  1. Change logic of handling oxos to force trans oxos by default for only actinide systems with the option to turn this off.
  2. Add tabulated experimental metal-oxo distances and enable setting of average experimental distance for oxos.
  3. Enable 'ff_preopt' for oxos and keywords options allowing for cleaning more crowded ligands around metal-oxo centers.
  4. Allow (though not recommended) for 'override_oxo_opt' to still perform XTB or UFF optimization of fully build molecules with oxos.

If you are running actinides with oxos - the following parameters are suggested for MOST cases:
parameters = { 'force_trans_oxos':True,
'ff_preopt':True,
'override_oxo_opt':False}

@mgt16-LANL mgt16-LANL self-assigned this Jul 12, 2023
@mgt16-LANL mgt16-LANL merged commit 466bf75 into main Jul 12, 2023
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@mgt16-LANL mgt16-LANL deleted the Oxo_handling branch July 12, 2023 23:22
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