def test_freq():
"""Do some constraint optimizations then launch a freq calc."""
mol = Molecule(PATH_MOLECULES / "ethene.xyz", "xyz")
geo_opt = dftb(templates.geometry, mol)
freq_calc = dftb(templates.freq, geo_opt.molecule, job_name="freq")
r = run(freq_calc)
assertion.eq(int(r.frequencies[0]), 831)
assertion.len_eq(r.frequencies, 12)
def test_freq():
"""
Do some constraint optimizations then launch a freq calc.
"""
mol = Molecule("test/test_files/ethene.xyz", "xyz")
geo_opt = dftb(templates.geometry, mol)
freq_calc = dftb(templates.freq, geo_opt.molecule, job_name="freq")
r = run(freq_calc)
assert int(r.frequencies[0]) == 831
assert len(r.frequencies) == 12
def test_freq():
"""
Do some constraint optimizations then launch a freq calc.
"""
mol = Molecule("test/test_files/ethene.xyz", "xyz")
geo_opt = dftb(templates.geometry, mol)
freq_calc = dftb(templates.freq, geo_opt.molecule, job_name="freq")
r = run(freq_calc)
assert int(r.frequencies[0]) == 831
assert len(r.frequencies) == 12
def test_dftb_opt_mock(mocker: MockFixture):
"""Mock a geometry optimization using DFTB."""
jobname = "dftb_geometry"
job = dftb(templates.geometry, WATER, job_name=jobname)
run_mocked = mock_runner(mocker, jobname)
rs = run_mocked(job)
# check the properties
assertion.isfinite(rs.energy)
assertion.len_eq(rs.dipole, 3)
assertion.isinstance(rs.molecule, Molecule)
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
def test_dftb_props():
"""
Get properties from DFTB freq calc
"""
mol = molkit.from_smiles('F[H]')
result = run(dftb(templates.freq, mol, job_name='dftb_FH'))
expected_energy = -4.76
assert abs(result.energy - expected_energy) < 0.01
assert len(result.dipole) == 3
expected_frequency = 3460.92
assert abs(result.frequencies - expected_frequency) < 0.1
assert len(result.charges) == 2
assert abs(result.charges[0] + result.charges[1]) < 1e-6
def test_dftb_props():
"""
Get properties from DFTB freq calc
"""
mol = molkit.from_smiles('F[H]')
result = run(dftb(templates.freq, mol, job_name='dftb_FH'))
expected_energy = -4.76
assert abs(result.energy - expected_energy) < 0.01
assert len(result.dipole) == 3
expected_frequency = 3460.92
assert abs(result.frequencies - expected_frequency) < 0.1
assert len(result.charges) == 2
assert abs(result.charges[0] + result.charges[1]) < 1e-6
def test_dftb_freq_mock(mocker: MockFixture):
"""Mock a geometry optimization using DFTB."""
jobname = "dftb_freq"
job = dftb(templates.geometry, WATER, job_name=jobname)
run_mocked = mock_runner(mocker, jobname)
rs = run_mocked(job)
# Check that hessian is symmetric
hess_list = rs.hessian
dim = int(np.sqrt(len(hess_list)))
hess = np.array(hess_list).reshape(dim, dim)
assertion.isclose(np.sum(hess - hess.T), 0.0)
# enthalpy and Gibbs free energy
assertion.isfinite(rs.enthalpy)
assertion.isfinite(rs.free_energy)
# frequencies
assertion.isfinite(np.sum(rs.frequencies))
def example_freqs():
"""
This examples illustrates the possibility to use different packages interchangeably.
Analytical frequencies are not available for B3LYP in ADF
This workflow captures the resulting error and submits the same job to ORCA.
"""
# Generate water molecule
water = molkit.from_smiles('[OH2]', forcefield='mmff')
# Pre-optimize the water molecule
opt_water = dftb(templates.geometry, water, job_name="dftb_geometry")
jobs = []
# Generate freq jobs for 3 functionals
for functional in ['pbe', 'b3lyp', 'blyp']:
s = Settings()
s.basis = 'DZ'
s.functional = functional
# Try to perform the jobs with adf or orca, take result from first successful calculation
freqjob = find_first_job(is_successful, [adf, orca],
templates.freq.overlay(s),
opt_water.molecule,
job_name=functional)
jobs.append(freqjob)
# Run workflow
results = run(gather(*jobs), n_processes=1)
# extrac results
freqs = [r.frequencies[-3:] for r in results]
functionals = ['pbe', 'b3lyp', 'blyp']
# Print the result
table = [
"{:10s}{:10.3f}{:10.3f}{:10.3f}\n".format(fun, *fs)
for fun, fs in zip(functionals, freqs)
]
print(table)
return freqs
def example_freqs():
"""
This examples illustrates the possibility to use different packages interchangeably.
Analytical frequencies are not available for B3LYP in ADF
This workflow captures the resulting error and submits the same job to ORCA.
"""
# Generate water molecule
water = molkit.from_smiles('[OH2]', forcefield='mmff')
# Pre-optimize the water molecule
opt_water = dftb(templates.geometry, water, job_name="dftb_geometry")
jobs = []
# Generate freq jobs for 3 functionals
for functional in ['pbe', 'b3lyp', 'blyp']:
s = Settings()
s.basis = 'DZ'
s.functional = functional
# Try to perform the jobs with adf or orca, take result from first successful calculation
freqjob = find_first_job(is_successful, [adf, orca], templates.freq.overlay(s),
opt_water.molecule, job_name=functional)
jobs.append(freqjob)
# Run workflow
results = run(gather(*jobs), n_processes=1)
# extrac results
freqs = [r.frequencies[-3:] for r in results]
functionals = ['pbe', 'b3lyp', 'blyp']
# Print the result
table = ["{:10s}{:10.3f}{:10.3f}{:10.3f}\n".format(fun, *fs)
for fun, fs in zip(functionals, freqs)]
print(table)
return freqs
# List of Molecules to simulate
smiles = {
'naphthalene': 'C1=CC2=C(C=C1)C=CC=C2',
'azulene': 'C1=CC2=CC=CC=CC2=C1',
'cycloheptatriene': 'C1=CC=C(C=C1)OC1=CC=CC=C1',
'furaldehyde': 'O=CC1=COC=C1',
'methylthiophene': 'CC1=C(C=CS1)C#C'
}
# transform the string into a format understandable by Qmflows
molecules = {name: from_smiles(smile) for name, smile in smiles.items()}
# Used DFTB to optimize the geometries
dftb_jobs = {
name: dftb(templates.geometry, mol, job_name='dftb_{}'.format(name))
for name, mol in molecules.items()
}
optimized_mols = {name: job.molecule for name, job in dftb_jobs.items()}
# Settings for ADF SAOP single point calculation
s = Settings()
s.basis = 'DZP'
s.specific.adf.basis.core = None
s.specific.adf.xc.model = 'saop'
s.specific.adf.scf.converge = 1e-6
s.specific.adf.symmetry = 'nosym'
# single point calculations using the SAOP functional
singlepoints = [
adf(s, mol, job_name='adf_{}'.format(name))
temp = molkit.modify_atom(temp, 48, '*')
# Put coordinates of dummy atoms to 0.0, this will force generating new
# 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)