def test_orca_mock(mocker: MockFixture):
"""Mock a call to orca."""
methanol = Molecule(PATH_MOLECULES / "methanol.xyz")
s = Settings()
s.specific.orca.main = "RKS B3LYP SVP Opt NumFreq TightSCF SmallPrint"
# print the orbitals
s.specific.orca.scf = " print[p_mos] 1"
job = orca(s, methanol)
run_mocked = mocker.patch("qmflows.run")
jobname = "ORCAjob"
dill_path = WORKDIR / jobname / "ORCAjob.dill"
plams_dir = WORKDIR / jobname
run_mocked.return_value = ORCA_Result(s,
methanol,
jobname,
dill_path=dill_path,
plams_dir=plams_dir)
rs = run_mocked(job)
assertion.isfinite(rs.energy)
assertion.isfinite(rs.runtime)
assertion.isfinite(np.sum(rs.dipole))
# steps until convergence
assertion.eq(rs.optcycles, 8)
# Check that hessian is symmetric
hess = rs.hessian
assertion.isclose(np.sum(hess - hess.T), 0.0)
# frequencies
frequencies = rs.frequencies
assertion.len_eq(frequencies, 18)
# Normal modes
normal_modes = rs.normal_modes
assertion.shape_eq(normal_modes, (18, 18))
# Orbitals
orbs = rs.orbitals
assert np.isfinite(np.sum(orbs.eigenvalues)) # eigenvalues
# Molecule
mol = rs.molecule
assertion.isinstance(mol, Molecule)
assertion.len_eq(mol, 6) # there are 6 atoms
def example_H2O2_TS():
"""
This example generates an approximate TS for rotation in hydrogen peroxide
using DFTB, and performs a full TS optimization in Orca.
It illustrates using a hessian from one package, DFTB in this case,
to initialize a TS optimization in another, i.e. Orca in this case
"""
# Generate hydrogen peroxide molecule
h2o2 = molkit.from_smarts('[H]OO[H]')
# Define dihedral angle
dihe = Dihedral(1, 2, 3, 4)
# Constrained geometry optimization with DFTB
# The dihedral is set to 0.0 to obtain an approximate TS
s1 = Settings()
s1.constraint.update(dihe.get_settings(0.0))
dftb_opt = dftb(templates.geometry.overlay(s1), h2o2)
# Calculate the DFTB hessian
dftb_freq = dftb(templates.freq, dftb_opt.molecule)
# Transition state calculation using the DFTB hessian as starting point
s2 = Settings()
s2.inithess = dftb_freq.hessian
orca_ts = orca(templates.ts.overlay(s2), dftb_opt.molecule)
# Execute the workflow
result = run(orca_ts)
# Analyse the result
ts_dihe = round(dihe.get_current_value(result.molecule))
n_optcycles = result.optcycles
print('Dihedral angle (degrees): {:.0f}'.format(ts_dihe))
print('Number of optimization cycles: {:d}'.format(n_optcycles))
return ts_dihe, n_optcycles
# DFTB optimization
dftb_jobs = {
n: dftb(templates.geometry, mol, job_name='dftb_{}'.format(n))
for n, mol in molecules.items()
}
# Check preoptimized molecules
opt_mols = {n: skip_dftb(job, molecules[n]) for n, job in dftb_jobs.items()}
# DFT optimization with Orca
s = templates.geometry
s.functional = 'BP86'
s.basis = 'def2TZVP'
dft_jobs = {
n: orca(s, mol, job_name='orca_{}'.format(n))
for n, mol in opt_mols.items()
}
# TD-DFT ADF with COSMO
s = templates.singlepoint
s.functional = 'camy-b3lyp'
s.basis = 'TZ2P'
s.specific.adf.Solvation.solvent = 'name=Dichloromethane emp=0.0 neql=2.028'
td_dft_jobs = {
n: adf(s, job.molecule, job_name='td_dft_{}'.format(n))
for n, job in dft_jobs.items()
}
energies = [gather(n, j.energy) for n, j in td_dft_jobs.items()]
# coordinates for the new atoms
temp.atoms[47].move_to((0.0, 0.0, 0.0))
temp.atoms[48].move_to((0.0, 0.0, 0.0))
# Replace dummy atoms by new groups, generate coordinates only for new atoms
job_list = []
for mod, smirks in list_of_modifications.items():
print(mod)
temp2, freeze = molkit.apply_reaction_smarts(temp, smirks, complete=True)
# generate job
s = Settings()
s.freeze = freeze
s.specific.dftb.dftb.resourcesdir = 'QUASINANO2015'
partial_geometry = dftb(templates.geometry.overlay(s),
temp2,
job_name="partial_opt_" + mod)
freq_dftb = dftb(templates.freq.overlay(s),
partial_geometry.molecule,
job_name="freq_" + mod)
s = Settings()
s.specific.orca.main = "B97-D"
s.specific.orca.basis.basis = "_6_31G"
s.specific.orca.basis.pol = "_d"
s.inithess = freq_dftb.hessian
ts = orca(templates.ts.overlay(s),
freq_dftb.molecule,
job_name="ts_" + mod)
freq = orca(templates.freq.overlay(s), ts.molecule, job_name="freq" + mod)
job_list.append(freq)
results = run(gather(*job_list), folder="Chris_results", n_processes=1)