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| coords = np.asarray(molecule.coords) | ||
| charge = molecule.charge | ||
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| atomicInfo = [] |
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Check the cs.atom_EOL_string() method. I builds exactly this string of regions + atomic properties that you need here.
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Great thanks, that works perfectly and is much simpler
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Description
This PR adds support for passing
scm.base.ChemicalSystemtoAMSWorker, alongside PLAMS Molecule, and addsAMSWorkerResults.get_input_system()/get_main_system()in line withAMSResults.Changes
Main updates:
ChemicalSystemhandling inAMSWorker._prepare_system()via type branching (Molecule vs ChemicalSystem), including serialization of coordinates, charge, lattice, bonds, and atomicInfoAMSWorkerResultsfor_input_moleculeand_input_system, with conversion between representations using same logic as in scm.utils (not used to avoid dependency)AMSWorkerResults.get_input_system()andAMSWorkerResults.get_main_system()AMSWorkerResults.get_input_moleculeandget_main_moleculenow always return copiesPoints for Comment
atomicInfoextraction forChemicalSystemwas a bit tricky to implement - is this the best and most reliable way of doing it?get_main_ase_atoms()based on molecule conversion (toASE(get_main_molecule())), notChemicalSystem.to_ase_atoms()