def test_env_methods(structure, mask, cutoff, result):
if mask is True:
mask = generate_mask(cutoff)
else:
mask = None
env_test = AtomicEnvironment(structure,
atom=0,
cutoffs=cutoff,
cutoffs_mask=mask)
assert str(env_test) == \
f'Atomic Env. of Type 1 surrounded by {result[0]} atoms' \
' of Types [1, 2, 3]'
the_dict = env_test.as_dict()
assert isinstance(the_dict, dict)
for key in ['positions', 'cell', 'atom', 'cutoffs', 'species']:
assert key in the_dict.keys()
remade_env = AtomicEnvironment.from_dict(the_dict)
assert isinstance(remade_env, AtomicEnvironment)
assert np.array_equal(remade_env.bond_array_2, env_test.bond_array_2)
if len(cutoff) > 1:
assert np.array_equal(remade_env.bond_array_3, env_test.bond_array_3)
if len(cutoff) > 2:
assert np.array_equal(remade_env.q_array, env_test.q_array)
def test_env_methods(structure, mask, cutoff, result):
if mask is True:
mask = generate_mask(cutoff)
else:
mask = None
structure = deepcopy(structure)
structure.forces = np.random.random(size=(len(structure), 3))
env_test = AtomicEnvironment(structure,
atom=0,
cutoffs=cutoff,
cutoffs_mask=mask)
assert np.array_equal(structure.forces[0], env_test.force)
assert (
str(env_test) ==
f"Atomic Env. of Type 1 surrounded by {result[0]} atoms of Types [1, 2, 3]"
)
the_dict = env_test.as_dict()
assert isinstance(the_dict, dict)
the_str = env_test.as_str()
assert dumps(the_dict, cls=NumpyEncoder) == the_str
for key in ["positions", "cell", "atom", "cutoffs", "species"]:
assert key in the_dict.keys()
# This saves a few seconds, the masked envs take longer to read/write
if not mask:
with open("test_environment.json", "w") as f:
f.write(env_test.as_str())
remade_env = AtomicEnvironment.from_file("test_environment.json")
else:
remade_env = AtomicEnvironment.from_dict(the_dict)
assert isinstance(remade_env, AtomicEnvironment)
assert np.array_equal(remade_env.bond_array_2, env_test.bond_array_2)
if len(cutoff) > 1:
assert np.array_equal(remade_env.bond_array_3, env_test.bond_array_3)
if len(cutoff) > 2:
assert np.array_equal(remade_env.q_array, env_test.q_array)
if not mask:
remove("test_environment.json")
def test_env_methods(cutoff):
cell = np.eye(3)
species = [1, 2, 3]
positions = np.array([[0, 0, 0], [0.5, 0.5, 0.5], [0.1, 0.1, 0.1]])
struc_test = Structure(cell, species, positions)
env_test = AtomicEnvironment(struc_test, 0, np.array([1, 1]))
assert str(env_test) == 'Atomic Env. of Type 1 surrounded by 12 atoms' \
' of Types [2, 3]'
the_dict = env_test.as_dict()
assert isinstance(the_dict, dict)
for key in ['positions', 'cell', 'atom', 'cutoffs', 'species']:
assert key in the_dict.keys()
remade_env = AtomicEnvironment.from_dict(the_dict)
assert isinstance(remade_env, AtomicEnvironment)
assert np.array_equal(remade_env.bond_array_2, env_test.bond_array_2)
assert np.array_equal(remade_env.bond_array_3, env_test.bond_array_3)
assert np.array_equal(remade_env.bond_array_mb, env_test.bond_array_mb)
