Visualizing QM/MM systems

Once the method object has been initialized with the corresponding potential file, which describes the surroundings, the geometry of the full system can be visualized by using the show_pe function. Note that all visualizations requires installation of the py3dmol package.

import penguin
import veloxchem as vlx

molecule = penguin.get_molecule("""
    C  0.997930 -0.087600 -0.014220
    O  2.222560 -0.087600 -0.014220
    H  0.410270 -0.803000  0.582940
    H  0.410270 0.6278000 -0.611380"""
)

basis = penguin.get_molecular_basis(molecule, "cc-pVDZ")

scf_drv = vlx.ScfRestrictedDriver()

pe_dict = {'potfile': '../../data/potfiles/50water.pot'}
scf_drv.update_settings({},method_dict=pe_dict)
scf_drv.ostream.mute()

scf_results = scf_drv.compute(molecule, basis)

ref_state = penguin.create_reference_state(molecule, basis, scf_drv)

ccsd_drv = penguin.CCSD()
settings_dict = {
    'reference_state': ref_state,
}
ccsd_drv.update_settings(settings_dict,pe_dict=pe_dict)

ccsd_drv.show_pe()

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