def test_cif_triclinic_box_properties(self):
lattice_cif = load_cif(file_or_path=get_fn("ETV_triclinic.cif"))
periodic_boxed_molecule = lattice_cif.populate(x=1, y=1, z=1)
periodic_box = periodic_boxed_molecule.box
manual_num_atoms = 42
manual_angles = [105.72, 100.19, 97.02]
manual_lengths = [0.87503, 0.96479, 1.02719]
assert np.all(np.isclose(manual_lengths, list(periodic_box.lengths)))
assert np.all(np.isclose(manual_angles, list(periodic_box.angles)))
assert len(periodic_boxed_molecule.children) == manual_num_atoms
def test_cif_vs_manual_triclinic(self):
spacing = [0.641910000, 0.652305930, 0.704466251]
angles = [91.77954616, 103.97424201, 118.83663410]
points_dict = {
"Re": [
[0.94176500, 0.68947700, 0.50807400],
[0.05823500, 0.31052300, 0.49192600],
[0.51250400, 0.71441700, 0.50209100],
[0.48749600, 0.28558300, 0.49790900],
],
"S": [
[0.74798600, 0.13254800, 0.67588400],
[0.73127300, 0.34781000, 0.26679600],
[0.21989400, 0.10784400, 0.70096800],
[0.25920200, 0.38690600, 0.24012300],
[0.74079800, 0.61309400, 0.75987700],
[0.78010600, 0.89215600, 0.29903200],
[0.25201400, 0.86745200, 0.32411600],
[0.26872700, 0.65219000, 0.73320400],
],
}
lattice_manual = mb.Lattice(
lattice_spacing=spacing, lattice_points=points_dict, angles=angles
)
lattice_cif = load_cif(file_or_path=get_fn("ReS2.cif"))
assert np.all(
np.isclose(
lattice_manual.lattice_spacing, lattice_cif.lattice_spacing
)
)
assert np.all(np.isclose(lattice_manual.angles, lattice_cif.angles))
# sort dicts first (not necessary once we support py 3.7+ only)
# dict sorted by keys
dict_manual = OrderedDict(
sorted(lattice_manual.lattice_points.items(), key=lambda t: t[0])
)
dict_cif = OrderedDict(
sorted(lattice_cif.lattice_points.items(), key=lambda t: t[0])
)
keys_m = dict_manual.keys()
keys_c = dict_cif.keys()
for k_man, k_cif in zip(keys_m, keys_c):
# sort the lists of lists
points_man = dict_manual[k_man]
points_cif = dict_cif[k_cif]
points_man.sort()
points_cif.sort()
points_man = np.asarray(points_man)
points_cif = np.asarray(points_cif)
assert np.all(np.isclose(points_man, points_cif))
def test_cif_monoclinic_box_properties(self):
lattice_cif = load_cif(file_or_path=get_fn("ITG_monoclinic.cif"))
periodic_boxed_molecule = lattice_cif.populate(x=1, y=1, z=1)
periodic_box = periodic_boxed_molecule.box
manual_num_atoms = 168
# manual_num_atoms was found using VESTA: https://gist.github.com/ramanishsingh/d712f57b8101eb073cfe010fc3b4edc3
# xyz file used: https://gist.github.com/ramanishsingh/154cf03d12e25f3d608e526500453e2e
# cif file used: https://gist.github.com/ramanishsingh/2db4ff2a266390242a6a05913d31414a
manual_angles = [90.0, 96.29, 90]
manual_lengths = [1.27411, 1.26989, 2.09991]
assert np.all(np.isclose(manual_lengths, list(periodic_box.lengths)))
assert np.all(np.isclose(manual_angles, list(periodic_box.angles)))
assert len(periodic_boxed_molecule.children) == manual_num_atoms
def test_cif_vs_manual(self):
spacing = [0.760296570, 0.760296570, 0.437540800]
points_dict = {
"La": [[1 / 3, 2 / 3, 1 / 4], [2 / 3, 1 / 3, 3 / 4]],
"Cl": [
[0.69490400, 0.08690400, 1 / 4],
[0.60800000, 0.69490400, 3 / 4],
[0.30509600, 0.91309600, 3 / 4],
[0.39200000, 0.30509600, 1 / 4],
[0.91309600, 0.60800000, 1 / 4],
[0.08690400, 0.39200000, 3 / 4],
],
}
lattice_manual = mb.Lattice(
lattice_spacing=spacing,
lattice_points=points_dict,
angles=[90, 90, 120],
)
lattice_cif = load_cif(file_or_path=get_fn("LaCl3.cif"))
assert np.all(
np.isclose(
lattice_manual.lattice_spacing, lattice_cif.lattice_spacing
)
)
assert np.all(np.isclose(lattice_manual.angles, lattice_cif.angles))
# sort dicts first (not necessary once we support py 3.7+ only)
# dict sorted by keys
dict_manual = OrderedDict(
sorted(lattice_manual.lattice_points.items(), key=lambda t: t[0])
)
dict_cif = OrderedDict(
sorted(lattice_cif.lattice_points.items(), key=lambda t: t[0])
)
keys_m = dict_manual.keys()
keys_c = dict_cif.keys()
for k_man, k_cif in zip(keys_m, keys_c):
# sort the lists of lists
points_man = dict_manual[k_man]
points_cif = dict_cif[k_cif]
points_man.sort()
points_cif.sort()
points_man = np.asarray(points_man)
points_cif = np.asarray(points_cif)
assert np.all(np.isclose(points_man, points_cif))
def test_wrap_true(self):
assert load_cif(
file_or_path=get_fn("needs_to_be_wrapped.cif"), wrap_coords=True
)
def test_wrap_false(self):
with pytest.raises(ValueError):
load_cif(
file_or_path=get_fn("needs_to_be_wrapped.cif"),
wrap_coords=False,
)
def test_malformed_cif(self):
with pytest.raises(Exception):
load_cif(file_or_path=get_fn("extra_blank_field.cif"))
