class TestSphinxStructure(unittest.TestCase):
"""
Testing routines in the sphinx/structure module.
"""
def setUp(self):
self.file_location = os.path.dirname(os.path.abspath(__file__))
structure_directory = "../static/sphinx/sphinx_test_files"
file_list = ["structure_1.sx", "structure_2.sx"]
self.file_list = [
posixpath.join(self.file_location, structure_directory, f)
for f in file_list
]
atom_numbers = np.random.randint(low=1, high=99, size=(1, 3)).flatten()
cell = 10.0 * np.eye(3)
pos = 0.5 * np.ones((3, 3)) - 0.5 * np.eye(3)
self.structure = Atoms(numbers=atom_numbers, cell=cell, positions=pos)
self.assertIsInstance(self.structure, Atoms)
self.structure.repeat([2, 2, 2])
self.element_list = self.structure.get_chemical_elements()
def test_read_atoms(self):
for i, f in enumerate(self.file_list):
atoms = read_atoms(filename=f)
self.assertIsInstance(atoms, Atoms)
if i == 0:
self.assertEqual(atoms.get_chemical_formula(), "Mg5")
self.assertTrue(
np.allclose(
atoms.cell / BOHR_TO_ANGSTROM,
[
[18.0936435257, 0.0, 0.0],
[-12.0624290171, 20.8927399203, 0.0],
[0.0, 0.0, 39.1932378013],
],
))
if i == 1:
self.assertEqual(atoms.get_chemical_formula(), "C2Mg5")
self.assertTrue(
np.allclose(
atoms.cell / BOHR_TO_ANGSTROM,
[
[18.09364353, 0.00000000, 0.00000000],
[-6.03121451, 20.89273992, -0.00000000],
[0.00000000, 0.00000000, 39.19323780],
],
))
def tearDown(self):
pass
class TestVaspStructure(unittest.TestCase):
"""
Testing routines in the vasp/structure module.
"""
def setUp(self):
self.file_location = os.path.dirname(os.path.abspath(__file__))
poscar_directory = os.path.join(
self.file_location, "../static/vasp_test_files/poscar_samples")
file_list = os.listdir(poscar_directory)
self.file_list = [
posixpath.join(poscar_directory, f) for f in file_list
]
atom_numbers = np.random.randint(low=1, high=99, size=(1, 3)).flatten()
cell = 10.0 * np.eye(3)
pos = 0.5 * np.ones((3, 3)) - 0.5 * np.eye(3)
self.structure = Atoms(numbers=atom_numbers, cell=cell, positions=pos)
self.assertIsInstance(self.structure, Atoms)
self.structure.repeat([2, 2, 2])
self.element_list = self.structure.get_chemical_elements()
def test_atoms_from_string(self):
for poscar_file in self.file_list:
with open(poscar_file, "r") as f:
lines = f.readlines()
atoms = atoms_from_string(string=lines)
self.assertIsInstance(atoms, Atoms)
def test_read_atoms(self):
for f in self.file_list:
atoms = read_atoms(filename=f)
self.assertIsInstance(atoms, Atoms)
if f.split("/")[-1] == "POSCAR_1":
self.assertEqual(len(atoms), 744)
self.assertEqual(len(atoms.select_index("H")), 432)
self.assertEqual(len(atoms.select_index("O")), 216)
self.assertEqual(len(atoms.select_index("Mg")), 96)
if f.split("/")[-1] == "POSCAR_scaled":
self.assertEqual(len(atoms), 256)
self.assertEqual(len(atoms.select_index("Cu")), 256)
cell = np.eye(3) * 4. * 3.63
self.assertTrue(np.array_equal(atoms.cell, cell))
self.assertEqual(atoms.get_spacegroup()["Number"], 225)
if f.split("/")[-1] == "POSCAR_volume_scaled":
self.assertEqual(len(atoms), 256)
self.assertEqual(len(atoms.select_index("Cu")), 256)
cell = np.eye(3) * 4. * 3.63
self.assertTrue(np.array_equal(atoms.cell, cell))
self.assertEqual(atoms.get_spacegroup()["Number"], 225)
if f.split("/")[-1] == "POSCAR_random":
self.assertEqual(len(atoms), 33)
self.assertEqual(len(atoms.selective_dynamics), 33)
self.assertEqual(len(atoms.select_index("Zn")), 1)
self.assertFalse(
np.array_equal(atoms.selective_dynamics[0],
[True, True, True]))
self.assertTrue(
np.array_equal(atoms.selective_dynamics[0],
[False, False, False]))
self.assertTrue(
np.array_equal(atoms.selective_dynamics[-5],
[True, True, True]))
self.assertTrue(
np.array_equal(atoms.selective_dynamics[-4],
[False, False, False]))
def test_write_poscar(self):
write_poscar(structure=self.structure,
filename=posixpath.join(self.file_location,
"POSCAR_test"))
test_atoms = read_atoms(
posixpath.join(self.file_location, "POSCAR_test"))
self.assertEqual(self.structure.get_chemical_formula(),
test_atoms.get_chemical_formula())
struct = self.structure.copy()
struct.add_tag(selective_dynamics=[True, True, True])
write_poscar(structure=struct,
filename=posixpath.join(self.file_location,
"POSCAR_test"))
test_atoms = read_atoms(
posixpath.join(self.file_location, "POSCAR_test"))
truth_array = np.empty_like(struct.positions, dtype=bool)
truth_array[:] = [True, True, True]
self.assertTrue(
np.array_equal(np.array(test_atoms.selective_dynamics),
truth_array))
os.remove(posixpath.join(self.file_location, "POSCAR_test"))
def test_vasp_sorter(self):
write_poscar(structure=self.structure,
filename=posixpath.join(self.file_location,
"POSCAR_test"))
test_atoms = read_atoms(
posixpath.join(self.file_location, "POSCAR_test"))
vasp_order = vasp_sorter(self.structure)
self.assertEqual(len(self.structure), len(test_atoms))
self.assertEqual(self.structure[vasp_order], test_atoms)
os.remove(posixpath.join(self.file_location, "POSCAR_test"))
def tearDown(self):
pass