Dear experts on Psi4
I’d like to somehow get/calculate these physical parameters. but, I could not find example or information about it. Could you someone instrcuct me how one can get these information from certain moleclue with Psi4?
Best regards.
What quantum chemical method do you want to use?
Below is a part of my source code using MP2
# compatible with "removeHs=False"
mol = Chem.AddHs(mol) #水素付加
#level = "hf/sto-3g"
level = "mp2"
#level = "b3lyp"
mixbasis2 = """
assign 6-311G
assign I 3-21G
assign XE 3-21G
"""
psi4.basis_helper(mixbasis2, name='mixbasis')
store_dir = "wavefunctions_MP2_6-311G+3-21G/"
wf_file = store_dir + "wavefunction_{}".format(ID)
if os.path.exists(wf_file+"_spointene.npy"):
continue;
params = ETKDGv3()
params.randomseed = int(dt_now.microsecond)
EmbedMolecule(mol, params)
if 1:
MMFFOptimizeMolecule(mol)
conf = mol.GetConformer()
series = ORIGINAL_df.query(f"CIDNUM == {ID}")
try:
smile = series["CanonicalSMILES"].iloc[-1]
plus = smile.count('+')
minus = smile.count('-')
charge = plus - minus + 0
spinmulti = GetSpinMultiplicity(mol)
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)
print(f"mol_input = {mol_input}
psi4.set_options({'MAXITER': 1000}) # Default is 100
psi4.set_options({'GEOM_MAXITER': 1000}) # Default is 50
if 1:
energy, wf_o = psi4.optimize(level, molecule=geo, return_wfn=True)
# single poinr energy calc.
energy, wf_e = psi4.energy(level, molecule=geo, return_wfn=True)
print("\t>>>>> frequency calculation will start, here")
energy, wf_f = psi4.frequency(level, molecule=geo, return_wfn=True, ref_gradient=wf_o.gradient())
According to this page Property
Depending on the methond of calculation, available properties are restlicted.
“polarizability” is not supported for the mp2 method…
and it must be re-calculated with, for istance,
polar = psi4.properties(“cc2/3-21g”, properties=[‘polarizability’], molecule=molecule)
correct?
I checked diploe and polarizability with H2O, I also found the reference here, Untitled Document where diploe and polarizability with H2O are 6.17 and 14.8.
Values I got are different a bit, Do I mistook something? The data i got is following
==> Integral Setup <==
Using in-core PK algorithm.
Calculation information:
Number of atoms: 3
Number of AO shells: 13
Number of primitives: 26
Number of atomic orbitals: 19
Number of basis functions: 19
Integral cutoff 1.00e-12
Number of threads: 1
...
...
Multipole Moments:
------------------------------------------------------------------------------------
Multipole Electronic (a.u.) Nuclear (a.u.) Total (a.u.)
------------------------------------------------------------------------------------
L = 1. Multiply by 2.5417464519 to convert [e a0] to [Debye]
Dipole X : 0.0000000 0.0000000 0.0000000
Dipole Y : 0.0000000 0.0000000 0.0000000
Dipole Z : 0.0694819 0.9246863 0.9941683
Magnitude : 0.9941683
..
..
..
Input parameters:
-----------------
Property = POLARIZABILITY
Reference wfn = RHF
Memory (Mbytes) = 524.3
Cache Level = 0
Print Level = 1
Maxiter = 50
Convergence = 1.0e-07
Restart = Allowed
DIIS = Yes
Model III = No
Linear Model = No
ABCD = NEW
Irrep X = B1
Irrep Y = B2
Irrep Z = A1
Irrep RX = B2
Irrep RY = B1
Irrep RZ = A2
Gauge = LENGTH
Applied field 0 = 0.000
Analyze X2 Amps = No
Local CC = No
..
..
CC2 Dipole Polarizability (Length Gauge) [(e^2 a0^2)/E_h]:
-------------------------------------------------------------------------
Evaluated at omega = 0.000000 E_h (Inf nm, 0.000 eV, 0.00 cm-1)
-------------------------------------------------------------------------
0 1 2
0 2.763744610766417 0.000000000000000 0.000000000000000
1 0.000000000000000 7.912034229646018 0.000000000000000
2 0.000000000000000 0.000000000000000 4.993179599400994
alpha_(0.000) = 5.222986146604 a.u.
The dipole moment and polarizability depend on numerous factors, and I have no idea either what parameters you used in your calculation or where the numbers in the table you cite came from (they don’t even give units, so no reasonable comparison is possible).
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