def test_num_atoms(self, copper_cell):
write_poscar(copper_cell, "test.poscar", lattice_constant=0.4123)
with open("test.poscar", "r") as f:
for i, line in enumerate(f):
pass
assert i + 1 == 44
def test_lattice_constant(self, copper_cell):
write_poscar(copper_cell, "test.poscar", lattice_constant=0.4123)
with open("test.poscar", "r") as f:
for i, line in enumerate(f):
if i == 1:
lattice_constant = np.genfromtxt(line.splitlines(True))
assert lattice_constant == 0.4123
def test_num_elements(self, cscl_crystal):
write_poscar(cscl_crystal, "test.poscar", lattice_constant=0.4123)
with open("test.poscar", "r") as f:
for i, line in enumerate(f):
if i == 5:
elements = line.split()
assert len(elements) == 2
def test_coordinate_header(self, gilmerite, coord_type):
write_poscar(gilmerite, "test.poscar", coord_style=coord_type)
with open("test.poscar", "r") as f:
for i, line in enumerate(f):
if i == 7:
coord = line.strip()
assert coord == coord_type
def test_coordinate_header(self, copper_cell, coord_type):
write_poscar(copper_cell,
'test.poscar',
lattice_constant=0.4123,
coord=coord_type)
with open('test.poscar', 'r') as f:
for i, line in enumerate(f):
if i == 7:
coord = line.strip()
assert coord == coord_type
def test_bravais(self, copper_cell):
"""Test that compound with no box has a lattice that is diagonal."""
write_poscar(copper_cell, "test.poscar")
with open("test.poscar", "r") as f:
lines = f.readlines()
bravais = np.stack(
[np.fromstring(line, sep=" ") for line in lines[2:5]])
# zero the diagonal
for i in range(3):
bravais[i, i] = 0
assert np.array_equal(bravais, np.zeros((3, 3)))
def test_bravais(self, copper_cell):
write_poscar(copper_cell, 'test.poscar', lattice_constant=.4123)
with open('test.poscar', 'r') as f:
bravais = list()
for i, line in enumerate(f):
if i in [2, 3, 4]:
bravais.append(np.genfromtxt(line.splitlines(True)))
assert all([
a.all() == b.all() for a, b in zip(bravais, [
np.array([1, 0, 0]),
np.array([0, 1, 0]),
np.array([0, 0, 1])
])
])
def test_write_direct(self, copper_cell):
write_poscar(copper_cell,
"test.poscar",
lattice_constant=0.4123,
coord="direct")
def test_write(self, copper_cell):
write_poscar(copper_cell, "test.poscar", lattice_constant=0.4123)
def test_error_raised(self, copper_cell):
with pytest.raises(ValueError):
write_poscar(copper_cell, "test.poscar", coord_style="heck")
def test_warning_raised(self, copper_cell):
copper_cell.box = None
with pytest.warns(UserWarning):
write_poscar(copper_cell, "test.poscar", coord_style="direct")
def test_read_write_direct(self, gilmerite):
write_poscar(gilmerite, "test.poscar", coord_style="direct")
new_gilmerite = read_poscar("test.poscar")
assert np.allclose(gilmerite.box.lengths, new_gilmerite.box.lengths)
assert np.allclose(gilmerite.box.angles, new_gilmerite.box.angles)
assert np.allclose(gilmerite.xyz, new_gilmerite.xyz)
def test_write_direct(self, copper_cell):
write_poscar(copper_cell,
'test.poscar',
lattice_constant=.4123,
coord='direct')
def test_write(self, copper_cell):
write_poscar(copper_cell, 'test.poscar', lattice_constant=.4123)