def test_periodic_images(self):
"""Tests the periodic images seen by the descriptor"""
desc = SOAP(
species=[1, 6, 8], rcut=10.0, nmax=2, lmax=0, periodic=False, crossover=True
)
molecule = H2O.copy()
# Non-periodic for comparison
molecule.set_cell([[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]])
nocell = desc.create(molecule, positions=[[0, 0, 0]])
# Make periodic
desc = SOAP(
species=[1, 6, 8], rcut=10.0, nmax=2, lmax=0, periodic=True, crossover=True
)
molecule.set_pbc(True)
# Cubic
molecule.set_cell([[3.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 3.0]])
cubic_cell = desc.create(molecule, positions=[[0, 0, 0]])
suce = molecule * (2, 1, 1)
cubic_suce = desc.create(suce, positions=[[0, 0, 0]])
# Triclinic
molecule.set_cell([[0.0, 2.0, 2.0], [2.0, 0.0, 2.0], [2.0, 2.0, 0.0]])
triclinic_cell = desc.create(molecule, positions=[[0, 0, 0]])
suce = molecule * (2, 1, 1)
triclinic_suce = desc.create(suce, positions=[[0, 0, 0]])
self.assertTrue(np.sum(np.abs((nocell[:3] - cubic_suce[:3]))) > 0.1)
self.assertAlmostEqual(np.sum(cubic_cell[:3] - cubic_suce[:3]), 0)
self.assertAlmostEqual(np.sum(triclinic_cell[:3] - triclinic_suce[:3]), 0)
def test_unit_cells(self):
"""Tests if arbitrary unit cells are accepted"""
desc = SOAP(species=[1, 6, 8], rcut=10.0, nmax=2, lmax=0, periodic=False, crossover=True)
molecule = H2O.copy()
molecule.set_cell([
[0.0, 0.0, 0.0],
[0.0, 0.0, 0.0],
[0.0, 0.0, 0.0]
])
nocell = desc.create(molecule, positions=[[0, 0, 0]])
desc = SOAP(species=[1, 6, 8], rcut=10.0, nmax=2, lmax=0, periodic=True, crossover=True,)
# Invalid unit cell
molecule.set_cell([
[0.0, 0.0, 0.0],
[0.0, 0.0, 0.0],
[0.0, 0.0, 0.0]
])
with self.assertRaises(ValueError):
desc.create(molecule, positions=[[0, 0, 0]])
molecule.set_pbc(True)
molecule.set_cell([
[20.0, 0.0, 0.0],
[0.0, 30.0, 0.0],
[0.0, 0.0, 40.0],
])
largecell = desc.create(molecule, positions=[[0, 0, 0]])
molecule.set_cell([
[2.0, 0.0, 0.0],
[0.0, 2.0, 0.0],
[0.0, 0.0, 2.0]
])
cubic_cell = desc.create(molecule, positions=[[0, 0, 0]])
molecule.set_cell([
[0.0, 2.0, 2.0],
[2.0, 0.0, 2.0],
[2.0, 2.0, 0.0]
])
triclinic_smallcell = desc.create(molecule, positions=[[0, 0, 0]])
def test_unit_cells(self):
"""Tests if arbitrary unit cells are accepted.
"""
# No cell
molecule = H2O.copy()
molecule.set_cell([[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]])
nocell = default_desc.create(molecule)
# Large cell
molecule.set_pbc(True)
molecule.set_cell([[20.0, 0.0, 0.0], [0.0, 30.0, 0.0],
[0.0, 0.0, 40.0]])
largecell = default_desc.create(molecule)
# Cubic cell
molecule.set_cell([[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]])
cubic_cell = default_desc.create(molecule)
# Triclinic cell
molecule.set_cell([[0.0, 2.0, 2.0], [2.0, 0.0, 2.0], [2.0, 2.0, 0.0]])
triclinic_smallcell = default_desc.create(molecule)