def test_random_structure_setup():
struct, forces = get_random_structure(cell=np.eye(3),
unique_species=[1, 2],
noa=2)
assert np.equal(struct.cell, np.eye(3)).all()
assert len(struct.positions) == 2
def test_file_load():
struct1, forces = get_random_structure(cell=np.eye(3),
unique_species=[1, 2],
noa=2)
struct2, forces = get_random_structure(cell=np.eye(3),
unique_species=[1, 2],
noa=2)
with open("test_write.json",'w') as f:
f.write(dumps(struct1.as_dict(),cls=NumpyEncoder))
with pytest.raises(NotImplementedError):
Structure.from_file(file_name='test_write.json', format='xyz')
struct1a = Structure.from_file('test_write.json')
assert dumpcompare(struct1.as_dict() , struct1a.as_dict())
os.remove('test_write.json')
with open("test_write_set.json", 'w') as f:
f.write(dumps(struct1.as_dict(), cls=NumpyEncoder)+'\n')
f.write(dumps(struct2.as_dict(), cls=NumpyEncoder)+'\n')
structs = Structure.from_file('test_write_set.json')
for struc in structs:
assert isinstance(struc, Structure)
assert len(structs) == 2
assert dumpcompare(structs[0].as_dict(), struct1.as_dict())
assert dumpcompare(structs[1].as_dict(), struct2.as_dict())
os.remove('test_write_set.json')
with pytest.raises(FileNotFoundError):
Structure.from_file('fhqwhgads')
vasp_struct = Structure.from_file('./test_files/test_POSCAR')
assert isinstance(vasp_struct, Structure)
assert len(vasp_struct) == 6
def test_file_load():
pmgstruc = pytest.importorskip("pymatgen.core.structure")
struct1, forces = get_random_structure(cell=np.eye(3),
unique_species=[1, 2],
noa=2)
struct2, forces = get_random_structure(cell=np.eye(3),
unique_species=[1, 2],
noa=2)
with open("test_write.json", "w") as f:
f.write(dumps(struct1.as_dict(), cls=NumpyEncoder))
with pytest.raises(NotImplementedError):
Structure.from_file(file_name="test_write.json", format="xyz")
struct1a = Structure.from_file("test_write.json")
assert dumpcompare(struct1.as_dict(), struct1a.as_dict())
os.remove("test_write.json")
with open("test_write_set.json", "w") as f:
f.write(dumps(struct1.as_dict(), cls=NumpyEncoder) + "\n")
f.write(dumps(struct2.as_dict(), cls=NumpyEncoder) + "\n")
structs = Structure.from_file("test_write_set.json")
for struc in structs:
assert isinstance(struc, Structure)
assert len(structs) == 2
assert dumpcompare(structs[0].as_dict(), struct1.as_dict())
assert dumpcompare(structs[1].as_dict(), struct2.as_dict())
os.remove("test_write_set.json")
with pytest.raises(FileNotFoundError):
Structure.from_file("fhqwhgads")
vasp_struct = Structure.from_file("./test_files/test_POSCAR")
assert isinstance(vasp_struct, Structure)
assert len(vasp_struct) == 6
def test_std_in_bound_per_species():
test_structure, _ = get_random_structure(np.eye(3), ['H', 'O'], 3)
test_structure.species_labels = ['H', 'H', 'O']
test_structure.stds = np.array([[1, 0, 0], [2, 0, 0], [3, 0, 0]])
# Test that 'test mode' works
result, target_atoms = \
is_std_in_bound_per_species(rel_std_tolerance=0, abs_std_tolerance=0,
noise=0, structure=test_structure)
assert result is True and target_atoms == [-1]
# Test that high abs tolerance works
result, target_atoms = \
is_std_in_bound_per_species(rel_std_tolerance=0, abs_std_tolerance=4,
noise=0, structure=test_structure)
assert result is True and target_atoms == [-1]
# Test that low abs tolerance works
result, target_atoms = \
is_std_in_bound_per_species(rel_std_tolerance=0, abs_std_tolerance=2.9,
noise=0, structure=test_structure)
assert result is False and target_atoms == [2]
# Test that high rel tolerance works
result, target_atoms = \
is_std_in_bound_per_species(rel_std_tolerance=1, abs_std_tolerance=0,
noise=4, structure=test_structure)
assert result is True and target_atoms == [-1]
# Test that low rel tolerance works
result, target_atoms = \
is_std_in_bound_per_species(rel_std_tolerance=1, abs_std_tolerance=0,
noise=2.9, structure=test_structure)
assert result is False and target_atoms == [2]
# Test that both work
result, target_atoms = \
is_std_in_bound_per_species(rel_std_tolerance=1, abs_std_tolerance=.1,
noise=2.9, structure=test_structure)
assert result is False and target_atoms == [2, 1, 0]
# Test that the max atoms added works
result, target_atoms = \
is_std_in_bound_per_species(rel_std_tolerance=1, abs_std_tolerance=.1,
noise=2.9, structure=test_structure,
max_atoms_added=2)
assert result is False and target_atoms == [2, 1]
result, target_atoms = \
is_std_in_bound_per_species(rel_std_tolerance=1, abs_std_tolerance=.1,
noise=2.9, structure=test_structure,
max_atoms_added=1)
assert result is False and target_atoms == [2]
# Test that max by species works
result, target_atoms = \
is_std_in_bound_per_species(rel_std_tolerance=1, abs_std_tolerance=.1,
noise=2.9, structure=test_structure,
max_atoms_added=1, max_by_species={'H': 1,
'O': 0})
assert result is False and target_atoms == [1]
result, target_atoms = \
is_std_in_bound_per_species(rel_std_tolerance=1, abs_std_tolerance=.1,
noise=2.9, structure=test_structure,
max_atoms_added=1, max_by_species={'H': 0,
'O': 1})
assert result is False and target_atoms == [2]
result, target_atoms = \
is_std_in_bound_per_species(rel_std_tolerance=1, abs_std_tolerance=.1,
noise=2.9, structure=test_structure,
max_atoms_added=1, max_by_species={'H': 2,
'O': 0})
assert result is False and target_atoms == [1]
result, target_atoms = \
is_std_in_bound_per_species(rel_std_tolerance=1, abs_std_tolerance=.1,
noise=2.9, structure=test_structure,
max_atoms_added=3, max_by_species={'H': 2,
'O': 0})
assert result is False and target_atoms == [1, 0]
def test_force_in_bound_per_species():
test_structure, _ = get_random_structure(np.eye(3), ['H', 'O'], 3)
test_structure.species_labels = ['H', 'H', 'O']
test_structure.forces = np.array([[0, 0, 0], [2, 0, 0], [3, 0, 0]])
true_forces = np.array([[.001, 0, 0], [1, 0, 0], [5, 0, 0]])
# Test that 'test mode' works
result, target_atoms = \
is_force_in_bound_per_species(abs_force_tolerance=0,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure)
assert result is True and target_atoms == [-1]
# Test that high abs tolerance works
result, target_atoms = \
is_force_in_bound_per_species(abs_force_tolerance=10,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure)
assert result is True and target_atoms == [-1]
# Test that low abs tolerance works
result, target_atoms = \
is_force_in_bound_per_species(abs_force_tolerance=1.5,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure)
assert result is False and target_atoms == [2]
# Test that the max atoms added works
result, target_atoms = \
is_force_in_bound_per_species(abs_force_tolerance=.01,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
max_atoms_added=2)
assert result is False and target_atoms == [2, 1]
result, target_atoms = \
is_force_in_bound_per_species(abs_force_tolerance=.00001,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
max_atoms_added=1)
assert result is False and target_atoms == [2]
# Test that max by species works
result, target_atoms = \
is_force_in_bound_per_species(abs_force_tolerance=.00001,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
max_atoms_added=1,
max_by_species={'H': 1, 'O': 0})
assert result is False and target_atoms == [1]
result, target_atoms = \
is_force_in_bound_per_species(abs_force_tolerance=.00001,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
max_atoms_added=1,
max_by_species={'H': 0, 'O': 1})
assert result is False and target_atoms == [2]
# Test max force error feature
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=.9,
max_force_error=.00000000001,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
)
assert result is True and target_atoms == [-1]
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=.9,
max_force_error=1.5,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
)
assert result is False and target_atoms == [1]
def test_std_in_bound_per_species():
test_structure, _ = get_random_structure(np.eye(3), ["H", "O"], 3)
test_structure.species_labels = ["H", "H", "O"]
test_structure.stds = np.array([[1, 0, 0], [2, 0, 0], [3, 0, 0]])
# Test that 'test mode' works
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=0, abs_std_tolerance=0, noise=0, structure=test_structure
)
assert result is True and target_atoms == [-1]
# Test that high abs tolerance works
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=0, abs_std_tolerance=4, noise=0, structure=test_structure
)
assert result is True and target_atoms == [-1]
# Test that low abs tolerance works
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=0, abs_std_tolerance=2.9, noise=0, structure=test_structure
)
assert result is False and target_atoms == [2]
# Test that high rel tolerance works
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=1, abs_std_tolerance=0, noise=4, structure=test_structure
)
assert result is True and target_atoms == [-1]
# Test that low rel tolerance works
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=1, abs_std_tolerance=0, noise=2.9, structure=test_structure
)
assert result is False and target_atoms == [2]
# Test that both work
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=1, abs_std_tolerance=0.1, noise=2.9, structure=test_structure
)
assert result is False and target_atoms == [2, 1, 0]
# Test that the max atoms added works
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=1,
abs_std_tolerance=0.1,
noise=2.9,
structure=test_structure,
max_atoms_added=2,
)
assert result is False and target_atoms == [2, 1]
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=1,
abs_std_tolerance=0.1,
noise=2.9,
structure=test_structure,
max_atoms_added=1,
)
assert result is False and target_atoms == [2]
# Test that max by species works
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=1,
abs_std_tolerance=0.1,
noise=2.9,
structure=test_structure,
max_atoms_added=1,
max_by_species={"H": 1, "O": 0},
)
assert result is False and target_atoms == [1]
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=1,
abs_std_tolerance=0.1,
noise=2.9,
structure=test_structure,
max_atoms_added=1,
max_by_species={"H": 0, "O": 1},
)
assert result is False and target_atoms == [2]
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=1,
abs_std_tolerance=0.1,
noise=2.9,
structure=test_structure,
max_atoms_added=1,
max_by_species={"H": 2, "O": 0},
)
assert result is False and target_atoms == [1]
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=1,
abs_std_tolerance=0.1,
noise=2.9,
structure=test_structure,
max_atoms_added=3,
max_by_species={"H": 2, "O": 0},
)
assert result is False and target_atoms == [1, 0]
# Ensure NANS can be handled
test_structure.stds = np.array([[np.nan, np.nan, np.nan], [2, 0, 0], [3, 0, 0]])
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=1,
abs_std_tolerance=0.1,
noise=2.9,
structure=test_structure,
max_atoms_added=3,
max_by_species={"H": 2, "O": 0},
)
assert result is False and target_atoms == [1]
test_structure.stds = np.array(
[[np.nan, np.nan, np.nan], [np.nan, np.nan, np.nan], [3, 0, 0]]
)
result, target_atoms = is_std_in_bound_per_species(
rel_std_tolerance=1,
abs_std_tolerance=0.1,
noise=2.9,
structure=test_structure,
max_atoms_added=3,
max_by_species={"H": 2, "O": 0},
)
assert result is True and target_atoms == [-1]
def test_force_in_bound_per_species():
test_structure, _ = get_random_structure(np.eye(3), ["H", "O"], 3)
test_structure.species_labels = ["H", "H", "O"]
test_structure.forces = np.array([[0, 0, 0], [2, 0, 0], [3, 0, 0]])
true_forces = np.array([[0.001, 0, 0], [1, 0, 0], [5, 0, 0]])
# Test that 'test mode' works
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=0,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
)
assert result is True and target_atoms == [-1]
# Test that high abs tolerance works
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=10,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
)
assert result is True and target_atoms == [-1]
# Test that low abs tolerance works
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=1.5,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
)
assert result is False and target_atoms == [2]
# Test that the max atoms added works
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=0.01,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
max_atoms_added=2,
)
assert result is False and target_atoms == [2, 1]
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=0.00001,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
max_atoms_added=1,
)
assert result is False and target_atoms == [2]
# Test that max by species works
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=0.00001,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
max_atoms_added=1,
max_by_species={"H": 1, "O": 0},
)
assert result is False and target_atoms == [1]
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=0.00001,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
max_atoms_added=1,
max_by_species={"H": 0, "O": 1},
)
assert result is False and target_atoms == [2]
# Test max force error feature
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=0.9,
max_force_error=0.00000000001,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
)
assert result is True and target_atoms == [-1]
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=0.9,
max_force_error=1.5,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
)
assert result is False and target_atoms == [1]
# Ensure that nans can be handled
test_structure.forces = np.array([[np.nan, np.nan, np.nan], [2, 0, 0], [3, 0, 0]])
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=1,
max_force_error=1.5,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
)
assert result is False and target_atoms == [1]
result, target_atoms = is_force_in_bound_per_species(
abs_force_tolerance=0.9,
max_force_error=500,
predicted_forces=test_structure.forces,
label_forces=true_forces,
structure=test_structure,
)
assert result is False and set(target_atoms) == set([1, 2])