def test_supercell_nobonds():
cellpar = 2.867*angstrom
sys111 = System(
numbers=np.array([26, 26]),
pos=np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])*cellpar,
ffatypes=['Fe', 'Fe'],
rvecs=np.identity(3)*cellpar,
)
sys333 = sys111.supercell(3,3,3)
def test_supercell_nobonds():
cellpar = 2.867 * angstrom
sys111 = System(
numbers=np.array([26, 26]),
pos=np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]) * cellpar,
ffatypes=['Fe', 'Fe'],
rvecs=np.identity(3) * cellpar,
)
sys333 = sys111.supercell(3, 3, 3)
def test_supercell_dipoles():
cellpar = 2.867*angstrom
sys111 = System(
numbers=np.array([26, 26]),
pos=np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])*cellpar,
ffatypes=['Fe', 'Fe'],
dipoles=np.array([[0.1,1.0,2.0],[0.5,0.7,0.9]]),
radii2=np.array([0.0,2.0]),
rvecs=np.identity(3)*cellpar,
)
sys333 = sys111.supercell(3,3,3)
assert (sys333.dipoles == np.tile(np.array([[0.1,1.0,2.0],[0.5,0.7,0.9]]), (27,1))).all()
assert (sys333.radii2 == np.tile(np.array([0.0,2.0]), 27)).all()
def test_supercell_charges():
cellpar = 2.867 * angstrom
sys111 = System(
numbers=np.array([26, 26]),
pos=np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]) * cellpar,
ffatypes=['Fe', 'Fe'],
charges=np.array([0.1, 1.0]),
radii=np.array([0.0, 2.0]),
rvecs=np.identity(3) * cellpar,
)
sys333 = sys111.supercell(3, 3, 3)
assert (sys333.charges == np.tile(np.array([0.1, 1.0]), 27)).all()
assert (sys333.radii == np.tile(np.array([0.0, 2.0]), 27)).all()
def test_remove_duplicate_dipoles():
cellpar = 2.867*angstrom
system1 = System(
numbers=np.array([26, 27]),
pos=np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])*cellpar,
ffatypes=['A', 'B'],
dipoles=np.array([[0.1,1.0,2.0],[0.5,0.7,0.9]]),
radii2=np.array([0.0,2.0]),
rvecs=np.identity(3)*cellpar,
)
system2 = system1.supercell(1, 2, 1)
system2.cell = system1.cell
system3 = system2.remove_duplicate()
for j, number in enumerate([26, 27]):
#By removing duplicates, atoms might be reordered
i = np.where( system3.numbers == number)[0]
assert system1.radii2[j] == system3.radii2[i]
assert np.all( system1.dipoles[j] == system3.dipoles[i] )
def test_remove_duplicate_dipoles():
cellpar = 2.867 * angstrom
system1 = System(
numbers=np.array([26, 27]),
pos=np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]) * cellpar,
ffatypes=['A', 'B'],
dipoles=np.array([[0.1, 1.0, 2.0], [0.5, 0.7, 0.9]]),
radii2=np.array([0.0, 2.0]),
rvecs=np.identity(3) * cellpar,
)
system2 = system1.supercell(1, 2, 1)
system2.cell = system1.cell
system3 = system2.remove_duplicate()
for j, number in enumerate([26, 27]):
#By removing duplicates, atoms might be reordered
i = np.where(system3.numbers == number)[0]
assert system1.radii2[j] == system3.radii2[i]
assert np.all(system1.dipoles[j] == system3.dipoles[i])