def test_linp(self, molecule, control_filepath, delete_tmp_dir):
ms = MoleculeSystem(molecule)
ms.int_def.append(
PerpendicularBendingAngle(indices=[[0, 1, 2, 3]],
value=20,
status="f"))
assert ms.has_inconsistencies()
with temp_dir(delete_tmp_dir) as tmp_dir:
ms.to_file("coord", fmt="coord")
shutil.copy2(control_filepath, "control")
dr = DefineRunner(parameters=dr_parameters)
assert dr.run_update_internal_coords()
ms_new = MoleculeSystem.from_file("coord")
assert not ms_new.has_inconsistencies()
# check that intdef is present and that the value has been updated
assert len(ms_new.int_def) == 1
assert ms_new.int_def[0].value == pytest.approx(
ms.int_def[0].value, abs=1e-4)
# check that there are the same user-defined bonds
assert ms.user_defined_bonds == ms_new.user_defined_bonds
# check that in redundant the coordinate has been taken into account
dg = DataGroups.from_file("coord")
redundant = dg.sdg("redundant", strict=True)
assert re.search(
r"\d+\s+f\s+1\.0+\s+linp\s+1\s+2\s+3\s+4\s+val=\s*20",
redundant)
assert str(ms_new.int_def[0])
def test_distance(self, molecule, control_filepath, delete_tmp_dir):
ms = MoleculeSystem(molecule, frozen_indices={2, 3})
ms.add_distance(0, 1, weights=1.0, value=2.5)
assert ms.has_inconsistencies()
with temp_dir(delete_tmp_dir) as tmp_dir:
ms.to_file("coord", fmt="coord")
shutil.copy2(control_filepath, "control")
dr = DefineRunner(parameters=dr_parameters)
assert dr.run_update_internal_coords()
ms_new = MoleculeSystem.from_file("coord")
assert not ms_new.has_inconsistencies()
# check that intdef is present and that the value has been updated
assert len(ms_new.int_def) == 1
assert ms_new.int_def[0].value == pytest.approx(
ms.int_def[0].value, abs=1e-4)
# check that there are the same user-defined bonds
assert ms.user_defined_bonds == ms_new.user_defined_bonds
# check that in redundant the coordinate has been taken into account
dg = DataGroups.from_file("coord")
redundant = dg.sdg("redundant", strict=True)
assert re.search(r"\d+\s+f\s+1\.0+\s+stre\s+1\s+2\s+val=\s*2.5",
redundant)
# check the presence of the same frozen atoms
assert ms.frozen_indices == ms_new.frozen_indices
assert str(ms_new.int_def[0])
assert_MSONable(ms_new)
def test_distance_linear_combination(self, molecule, control_filepath,
delete_tmp_dir):
ms = MoleculeSystem(molecule)
ms.add_distance([0, 1], [1, 2], weights=[1.0, 1.0], value=None)
assert not ms.has_inconsistencies()
with temp_dir(delete_tmp_dir) as tmp_dir:
ms.to_file("coord", fmt="coord")
shutil.copy2(control_filepath, "control")
dr = DefineRunner(parameters=dr_parameters)
assert dr.run_update_internal_coords()
ms_new = MoleculeSystem.from_file("coord")
assert not ms_new.has_inconsistencies()
# check that intdef is present and that the value has been updated
assert len(ms_new.int_def) == 1
assert ms_new.int_def[0].value == pytest.approx(2.70995, abs=1e-4)
# check that in redundant the coordinate has been taken into account
dg = DataGroups.from_file("coord")
redundant = dg.sdg("redundant", strict=True)
assert re.search(
r"\d+\s+f\s+1\.0+\s+stre\s+1\s+2\s+val=\s*2\.70\d+\s+1\.0+\s+stre\s+2\s+3\s*$",
redundant, re.DOTALL | re.MULTILINE)
def test_to_file(self, molecule, delete_tmp_dir):
ms = MoleculeSystem(molecule)
with temp_dir(delete_tmp_dir) as tmp_dir:
fname = os.path.join(tmp_dir, 'coord_test')
ms.to_file(filepath=fname, fmt="coord")
assert os.path.isfile("coord_test")
dg = DataGroups.from_file("coord_test")
assert dg.show_data_group("coord") is not None
ms.to_file("mol_test.xyz")
assert os.path.isfile("mol_test.xyz")
assert ms.from_file("mol_test.xyz") is not None
def test_dummy_atoms(self, molecule_filepath):
ms = MoleculeSystem.from_file(molecule_filepath, fmt="coord")
mol = ms.molecule
print(mol[-1].specie)
print(mol[-1].specie.__class__)
# Pymatgen's Specie and DummySpecie have been changed to Species and
# DummySpecies in v2020.10.9. We keep testing both for backward compatibility.
assert isinstance(mol[-1].specie, (DummySpecies, DummySpecie))
assert mol[-1].specie.symbol == "Q"
test_value2 = """
0.00000000000000 0.00000000000000 -0.12178983933899 o
1.41713420892173 0.00000000000000 0.96657854674257 h
-1.41713420892173 0.00000000000000 0.96657854674257 h
0.00000000000000 0.00000000000000 0.00000000000000 q
"""
dg = DataGroups(ms.to_coord_string())
assert len(dg.dg_list) == 2
check_dg(dg.sdg("coord", strict=True), test_value2)
assert_MSONable(ms)