def test_ADFGeometry_Constraint():
"""
Test "freeze" and "selected_atoms" keywords for constrained geometry
optimizations.
"""
an = plams.Molecule('test/test_files/an.xyz', 'xyz')
# optimize only H atoms
s = Settings()
s.freeze = [1, 2, 3]
result1 = adf(templates.geometry.overlay(s), an)
geom1 = result1.molecule
# optimize only H atoms
s = Settings()
s.selected_atoms = ['H']
result2 = adf(templates.geometry.overlay(s), an)
geom2 = result2.molecule
r = run(gather(geom1, geom2), n_processes=1)
assert str(r[0]) == str(r[1])
HH = plams.Molecule("H_Mes2PCBH2_TS3series1.xyz")
HH.guess_bonds()
newmol = rdkitTools.apply_template(HH, template)
# Change the 2 hydrogens to dummy atoms
temp = rdkitTools.modify_atom(newmol, 47, '*')
temp = rdkitTools.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 = rdkitTools.apply_smirks(temp, smirks)[0]
temp2 = rdkitTools.apply_smirks(temp2, smirks)[0]
freeze = rdkitTools.gen_coords(temp2)
# rdkitTools.write_molblock(temp2)
# generate job
s = Settings()
s.freeze = [a + 1 for a in freeze]
partial_geometry = adf(templates.geometry.overlay(s),
temp2,
job_name="partial_opt_" + mod)
job_list.append(
adf(templates.ts, partial_geometry.molecule, job_name="ts_" + mod))
results = run(gather(*job_list), n_processes=1)