def frequencies(molecule, config):
print("Determining normal modes and running frequency analysis...")
total_energy, wavefunc = psi4.frequency(config['config_generator']['method'] + '/' + config['config_generator']['basis'], molecule=molecule, return_wfn=True)
vib_info_raw = wavefunc.frequency_analysis
vib_info = psi4.qcdb.vib.filter_nonvib(vib_info_raw)
frequencies = wavefunc.frequencies().to_array()
red_masses = vib_info["mu"].data
normal_modes_raw = vib_info['x'].data
normal_modes = []
num_modes = len(frequencies)
num_atoms = molecule.natom()
for i in range(num_modes):
geometry = np.zeros((num_atoms, 3))
for atom in range(num_atoms):
geometry[atom][0] = float(normal_modes_raw[3 * atom + 0][i])
geometry[atom][1] = float(normal_modes_raw[3 * atom + 1][i])
geometry[atom][2] = float(normal_modes_raw[3 * atom + 2][i])
normal_modes.append(geometry)
print("Normal mode/frequency analysis complete.")
print("")
return normal_modes, frequencies, red_masses
def calc_vib_freq(smiles):
mol = Chem.MolFromSmiles(smiles)
xyz, mol = mol_to_xyz(mol)
psi4.set_memory('4 GB')
psi4.set_num_threads(4)
method_basis = args.method + '/' + args.basis
geom = psi4.geometry(xyz)
e, wfn = psi4.frequency(method_basis, molecule=geom, return_wfn=True)
print("SMILES: " + smiles + ", Vibrational Frequency Energy: " + str(e))
return e
def main():
psi4.set_output_file("pbeh3c_mol.dat", True)
#psi4.set_memory('500 MB')
numpy_memory = 2
mol = psi4.geometry("""
1 1
C 3.533276577335 0.297516950079 -0.033740208753
C 2.574760938246 1.278066479179 -0.069835787116
C 1.253218752224 0.849739147834 -0.039258570370
C 0.899019257306 -0.495860874701 0.032550031024
C 1.888860870465 -1.490197119704 0.067078565308
C 3.204596438039 -1.081456560919 0.033430560670
O 4.250570460820 -1.915645303151 0.060360861113
C -0.521891091036 -0.526599835195 0.052806016194
C -0.907216553266 0.796770182506 -0.010855959829
O 0.163856617883 1.625333309480 -0.070535693831
C -2.142468145732 1.509067711325 -0.077871153394
O -2.328114248487 2.665835310257 -0.269517118360
N -3.421527194392 0.695313957156 0.191159341639
C -3.581807216427 -0.692769910170 -0.352292538279
C -2.772392782598 -1.705499205563 0.431794190569
C -1.307831296645 -1.790976049117 0.040569332872
H 4.581064582865 0.566654620917 -0.057341951344
H 2.837749742920 2.324943817097 -0.122662938228
H 1.625749586779 -2.540289226583 0.117596634162
H 3.972628181395 -2.834781214964 0.105049915868
H -3.557445242160 0.671475310656 1.206814356133
H -4.167512313144 1.297833117167 -0.169560281990
H -4.646108631113 -0.913660797798 -0.283335352767
H -3.313356183445 -0.663729781207 -1.408465575248
H -2.877036964703 -1.518274278002 1.505474270168
H -3.228135005269 -2.682198217407 0.265368459879
H -1.225392070756 -2.220062054576 -0.963992292922
H -0.817581075574 -2.508114264473 0.702369958893
""")
#psi4.energy('mp2/cc-pvdz', molecule=mol)
#psi4.energy('scf/cc-pvdz', molecule=mol)
psi4.energy('pbeh3c/', molecule=mol) # default is def2-mSVP
#psi4.optimize('pbeh3c/', molecule=mol) # default is def2-mSVP
psi4.frequency('pbeh3c/', molecule=mol) # default is def2-mSVP
H 0.21028 2.41258 0.00000
H -1.21638 2.69390 -0.96879
H -1.21639 3.11091 0.72802
H -1.21639 1.43293 0.24076
""")
# Geometry optimization
psi4.set_output_file(file_prefix + '_geomopt.dat', False)
psi4.set_options({'g_convergence': 'gau_tight'})
psi4.optimize('scf/cc-pVDZ', molecule=ch4)
# Run vibrational frequency analysis
psi4.set_output_file(file_prefix + '_vibfreq.dat', False)
scf_energy, scf_wfn = psi4.frequency('scf/cc-pVDZ', molecule=ch4, return_wfn=True, dertype='gradient')
# Save "raw" frequencies into a variable
scf_wfn_freq = scf_wfn.frequency_analysis['omega'][2]
print(scf_wfn_freq)
# Eliminate imaginary parts of frequencies,
scf_wfn_real=scf_wfn_freq.real
# round the frequencies (to the nearest whole number),
scf_wfn_round=np.rint(scf_wfn_real)
# and extract only the *non-zero* frequencies
scf_wfn_nonzero=np.extract(scf_wfn_round>0, scf_wfn_round)
# Determine the unique non-zero frequencies and
def calculate_frequency(mol: psi4.core.Molecule, method: str = "wB97X/6-31g*"):
e, wfn = psi4.frequency(method, molecule=mol, return_wfn=True)
return (e * hartree_to_kJ_mol) * unit.kilojoule_per_mole, wfn
import psi4 #as psi4
import numpy as np
psi4.set_output_file("output.dat", True)
psi4.set_memory('500 MB')
numpy_memory = 2
h2o = psi4.geometry("""
O 0.0 0.0 0.0
H 1.0 0.0 0.0
H 0.0 1.0 0.0
symmetry c1
""")
#psi4.set_options({'basis': 'cc-pcdz'})
psi4.energy('scf/cc-pvdz', molecule=h2o)
psi4.optimize('scf/cc-pvdz', molecule=h2o)
scf_e, scf_wfn = psi4.frequency('scf/cc-pvdz',
molecule=h2o,
return_wfn=True,
dertype=1)
def cmd(method, mol):
frequency(method, molecule=mol)
SP 3 1.00
5.0331513 -0.09996723 0.15591627
1.1695961 0.39951283 0.60768372
0.3803890 0.70011547 0.39195739
****
"""
return basstrings
qcdb.libmintsbasisset.basishorde['STO-3G_DALTON'] = define_custom_basis
core.set_global_option("BASIS", "STO-3G_dalton")
psi4.set_options(options)
# Perform SCF Energy Calculation
rhf_e, wfn = psi4.frequency('SCF', return_wfn=True)
# Relevant Variables
natoms = mol.natom()
nmo = wfn.nmo()
nocc = wfn.doccpi()[0]
nvir = nmo - nocc
# MO Coefficients
C = wfn.Ca_subset("AO", "ALL")
npC = psi4.core.Matrix.to_array(C)
# Integral generation from Psi4's MintsHelper
mints = psi4.core.MintsHelper(wfn.basisset())
# Build T, V, and S
