def test_selected_atoms_with_adf():
mol = molkit.from_smiles('CO')
s = Settings()
s.selected_atoms = ["H"]
expected_settings = Settings({
'selected_atoms': ['H'],
'specific': {
'adf': {
'constraints': {
'atom 1': '',
'atom 2': ''
},
'geometry': {
'optim': 'cartesian'
}
}
}
})
assert str(adf.generic2specific(s, mol)) == str(expected_settings)
s.selected_atoms = [3, 4, 5, 6]
expected_settings = Settings({
'selected_atoms': [3, 4, 5, 6],
'specific': {
'adf': {
'constraints': {
'atom 1': '',
'atom 2': ''
},
'geometry': {
'optim': 'cartesian'
}
}
}
})
assert str(adf.generic2specific(s, mol)) == str(expected_settings)
def test_selected_atoms_with_orca():
mol = molkit.from_smiles('CO')
s = Settings()
s.selected_atoms = ["H"]
expected_settings = Settings({
'selected_atoms': ['H'],
'specific': {
'orca': {
'geom': {
'Constraints': {
'_end': '{ C 0 C }{ C 1 C }'
}
}
}
}
})
assert str(orca.generic2specific(s, mol)) == str(expected_settings)
s.selected_atoms = [3, 4, 5, 6]
expected_settings = Settings({
'selected_atoms': [3, 4, 5, 6],
'specific': {
'orca': {
'geom': {
'Constraints': {
'_end': '{ C 0 C }{ C 1 C }'
}
}
}
}
})
assert str(orca.generic2specific(s, mol)) == str(expected_settings)
def test_selected_atoms_with_dftb():
mol = molkit.from_smiles('CO')
s = Settings()
s.selected_atoms = ["H"]
expected_settings = Settings(
{'selected_atoms': ['H'], 'specific': dftb_const})
assert dftb.generic2specific(s, mol) == expected_settings
s.selected_atoms = indices
expected_settings = Settings(
{'selected_atoms': indices, 'specific': dftb_const})
assert str(dftb.generic2specific(s, mol)) == str(expected_settings)
def test_selected_atoms_with_dftb():
"""Test the DFTB selection atoms funcionality."""
mol = molkit.from_smiles('CO')
s = Settings()
s.selected_atoms = ["H"]
expected_settings = Settings(
{'selected_atoms': ['H'], 'specific': dftb_const})
assertion.eq(dftb.generic2specific(s, mol), expected_settings)
s.selected_atoms = indices
expected_settings = Settings(
{'selected_atoms': indices, 'specific': dftb_const})
assertion.eq(str(dftb.generic2specific(s, mol)), str(expected_settings))
def test_selected_atoms_with_gamess():
mol = molkit.from_smiles('CO')
s = Settings()
s.selected_atoms = ["H"]
expected_settings = Settings(
{'selected_atoms': ['H'], 'specific': gamess_sett})
assert str(gamess.generic2specific(s, mol)) == str(expected_settings)
s = Settings()
s.selected_atoms = indices
expected_settings = Settings(
{'selected_atoms': indices, 'specific': gamess_sett})
assert str(gamess.generic2specific(s, mol)) == str(expected_settings)
def test_selected_atoms_with_adf():
"""Test the ADF atoms selection features."""
mol = molkit.from_smiles('CO')
s = Settings()
s.selected_atoms = ["H"]
expected_settings = Settings(
{'selected_atoms': ['H'], 'specific': adf_const})
assertion.eq(str(adf.generic2specific(s, mol)), str(expected_settings))
s.selected_atoms = indices
expected_settings = Settings(
{'selected_atoms': indices, 'specific': adf_const})
assertion.eq(str(adf.generic2specific(s, mol)), str(expected_settings))
def test_selected_atoms_with_orca():
"""Test atom selection features for Orca."""
mol = molkit.from_smiles('CO')
s = Settings()
s.selected_atoms = ["H"]
expected_settings = Settings(
{'selected_atoms': ['H'], 'specific': orca_const})
assertion.eq(str(orca.generic2specific(s, mol)), str(expected_settings))
s.selected_atoms = indices
expected_settings = Settings(
{'selected_atoms': indices, 'specific': orca_const})
assertion.eq(str(orca.generic2specific(s, mol)), str(expected_settings))
def test_selected_atoms_with_dftb():
mol = molkit.from_smiles('CO')
s = Settings()
s.selected_atoms = ["H"]
expected_settings = Settings({
'selected_atoms': ['H'],
'specific': dftb_const
})
assert dftb.generic2specific(s, mol) == expected_settings
s.selected_atoms = indices
expected_settings = Settings({
'selected_atoms': indices,
'specific': dftb_const
})
assert str(dftb.generic2specific(s, mol)) == str(expected_settings)
def test_selected_atoms_with_gamess():
mol = molkit.from_smiles('CO')
s = Settings()
s.selected_atoms = ["H"]
expected_settings = Settings({
'selected_atoms': ['H'],
'specific': gamess_sett
})
assert str(gamess.generic2specific(s, mol)) == str(expected_settings)
s = Settings()
s.selected_atoms = indices
expected_settings = Settings({
'selected_atoms': indices,
'specific': gamess_sett
})
assert str(gamess.generic2specific(s, mol)) == str(expected_settings)
def test_selected_atoms_with_gamess():
mol = molkit.from_smiles('CO')
s = Settings()
s.selected_atoms = ["H"]
expected_settings = Settings({
'selected_atoms': ['H'],
'specific': {
'gamess': {
'statpt': 'IFREEZ(1)=1,2,3,4,5,6'
}
}
})
assert str(gamess.generic2specific(s, mol)) == str(expected_settings)
s = Settings()
s.selected_atoms = [3, 4, 5, 6]
expected_settings = Settings({
'selected_atoms': [3, 4, 5, 6],
'specific': {
'gamess': {
'statpt': 'IFREEZ(1)=1,2,3,4,5,6'
}
}
})
assert str(gamess.generic2specific(s, mol)) == str(expected_settings)
def example_partial_geometry_opt():
"""
Performa partial optimization freezing the Hydrogen atoms
"""
methanol = molkit.from_smiles('CO')
# optimize only H atoms
s = Settings()
s.freeze = [1, 2]
geom_job1 = adf(templates.geometry.overlay(s), methanol, job_name='geom_job1').molecule
# optimize only H atoms
s = Settings()
s.selected_atoms = ['H']
geom_job2 = adf(templates.geometry.overlay(s), methanol, job_name='geom_job2').molecule
geom1, geom2 = run(gather(geom_job1, geom_job2), n_processes=1)
return geom1, geom2
def example_partial_geometry_opt():
"""Performa partial optimization freezing the Hydrogen atoms."""
methanol = molkit.from_smiles('CO')
# optimize only H atoms
s = Settings()
s.freeze = [1, 2]
geom_job1 = adf(templates.geometry.overlay(s),
methanol,
job_name='geom_job1').molecule
# optimize only H atoms
s = Settings()
s.selected_atoms = ['H']
geom_job2 = adf(templates.geometry.overlay(s),
methanol,
job_name='geom_job2').molecule
geom1, geom2 = run(gather(geom_job1, geom_job2), n_processes=1)
return geom1, geom2