I performed optimization of my moleclue via
geo = psi4.geometry(mol_input)
energy, wf_o = psi4.optimize(level, molecule=geo, return_wfn=True)
I can save this file via
with open(geo_file+"_geometry.xyz", 'w') as file:
print(geo.save_string_xyz_file(), file=file)
Is it actully possible to use this file for energy and frequency calculation? something like…
mol = Chem.MolFromXYZFile(optimized_geo_file)
mol_input = str(charge) + " " + str(spinmulti)
for atom in mol.GetAtoms():
mol_input += "\n" + atom.GetSymbol() \
+ " " + str(conf.GetAtomPosition(atom.GetIdx()).x)\
+ " " + str(conf.GetAtomPosition(atom.GetIdx()).y)\
+ " " + str(conf.GetAtomPosition(atom.GetIdx()).z)
try:
geo = psi4.geometry(mol_input)
# no opimization, here
# single poinr energy calc.
energy, wf_e = psi4.energy(level, molecule=geo, return_wfn=True)
energy, wf_f = psi4.frequency(level, molecule=geo, return_wfn=True)
I actully did two cases
“with an already optimized_geo_file” and “without an already optimized_geo_file”
Frequencies and results of Thermochemistry_Energy_Analysis such as zero-point-energy are slightly different. I’m worring if this difference is just flucutuation or critical calculation error.