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