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_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 that arbitrary unit cells are accepted.
"""
desc = copy.deepcopy(default_desc_k1_k2_k3)
desc.periodic = False
desc.species = ["H", "O"]
molecule = H2O.copy()
# No cell needed for finite systems
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)
# Different periodic cells
desc.periodic = True
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)
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)
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)
def test_periodic_images(self):
"""Tests that periodic images are handled correctly.
"""
decay = 1
desc = MBTR(
species=[1],
periodic=True,
k1={
"geometry": {"function": "atomic_number"},
"grid": {"min": 0, "max": 2, "sigma": 0.1, "n": 21}
},
k2={
"geometry": {"function": "inverse_distance"},
"grid": {"min": 0, "max": 1.0, "sigma": 0.02, "n": 21},
"weighting": {"function": "exp", "scale": decay, "cutoff": 1e-4}
},
k3={
"geometry": {"function": "cosine"},
"grid": {"min": -1.0, "max": 1.0, "sigma": 0.02, "n": 21},
"weighting": {"function": "exp", "scale": decay, "cutoff": 1e-4},
},
normalization="l2_each", # This normalizes the spectrum
flatten=True
)
# Tests that a system has the same spectrum as the supercell of
# the same system.
molecule = H.copy()
a = 1.5
molecule.set_cell([
[a, 0.0, 0.0],
[0.0, a, 0.0],
[0.0, 0.0, a]
])
cubic_cell = desc.create(molecule)
suce = molecule * (2, 1, 1)
cubic_suce = desc.create(suce)
diff = abs(np.sum(cubic_cell[0, :] - cubic_suce[0, :]))
cubic_sum = abs(np.sum(cubic_cell[0, :]))
self.assertTrue(diff/cubic_sum < 0.05) # A 5% error is tolerated
# Same test but for triclinic cell
molecule.set_cell([
[0.0, 2.0, 1.0],
[1.0, 0.0, 1.0],
[1.0, 2.0, 0.0]
])
triclinic_cell = desc.create(molecule)
suce = molecule * (2, 1, 1)
triclinic_suce = desc.create(suce)
diff = abs(np.sum(triclinic_cell[0, :] - triclinic_suce[0, :]))
tricl_sum = abs(np.sum(triclinic_cell[0, :]))
self.assertTrue(diff/tricl_sum < 0.05)
# Testing that the same crystal, but different unit cells will have a
# similar spectrum when they are normalized. There will be small
# differences in the shape (due to not double counting distances)
a1 = bulk('H', 'fcc', a=2.0)
a2 = bulk('H', 'fcc', a=2.0, orthorhombic=True)
a3 = bulk('H', 'fcc', a=2.0, cubic=True)
triclinic_cell = desc.create(a1)
orthorhombic_cell = desc.create(a2)
cubic_cell = desc.create(a3)
diff1 = abs(np.sum(triclinic_cell[0, :] - orthorhombic_cell[0, :]))
diff2 = abs(np.sum(triclinic_cell[0, :] - cubic_cell[0, :]))
tricl_sum = abs(np.sum(triclinic_cell[0, :]))
self.assertTrue(diff1/tricl_sum < 0.05)
self.assertTrue(diff2/tricl_sum < 0.05)
# Tests that the correct peak locations are present in a cubic periodic
desc = MBTR(
species=["H"],
periodic=True,
k3={
"geometry": {"function": "cosine"},
"grid": {"min": -1.1, "max": 1.1, "sigma": 0.010, "n": 600},
"weighting": {"function": "exp", "scale": decay, "cutoff": 1e-4}
},
normalization="l2_each", # This normalizes the spectrum
flatten=True
)
a = 2.2
system = Atoms(
cell=[
[a, 0.0, 0.0],
[0.0, a, 0.0],
[0.0, 0.0, a]
],
positions=[
[0, 0, 0],
],
symbols=["H"],
)
cubic_spectrum = desc.create(system)[0, :]
x3 = desc.get_k3_axis()
peak_ids = find_peaks_cwt(cubic_spectrum, [2])
peak_locs = x3[peak_ids]
assumed_peaks = np.cos(np.array(
[
180,
90,
np.arctan(np.sqrt(2))*180/np.pi,
45,
np.arctan(np.sqrt(2)/2)*180/np.pi,
0
])*np.pi/180
)
self.assertTrue(np.allclose(peak_locs, assumed_peaks, rtol=0, atol=5*np.pi/180))
# Tests that the correct peak locations are present in a system with a
# non-cubic basis
desc = MBTR(
species=["H"],
periodic=True,
k3={
"geometry": {"function": "cosine"},
"grid": {"min": -1.0, "max": 1.0, "sigma": 0.030, "n": 200},
"weighting": {"function": "exp", "scale": 1.5, "cutoff": 1e-4}
},
normalization="l2_each", # This normalizes the spectrum
flatten=True,
sparse=False
)
a = 2.2
system = Atoms(
cell=[
[a, 0.0, 0.0],
[0.0, a, 0.0],
[0.0, 0.0, a]
],
positions=[
[0, 0, 0],
],
symbols=["H"],
)
angle = 30
system = Atoms(
cell=ase.geometry.cellpar_to_cell([3*a, a, a, angle, 90, 90]),
positions=[
[0, 0, 0],
],
symbols=["H"],
)
tricl_spectrum = desc.create(system)
x3 = desc.get_k3_axis()
peak_ids = find_peaks_cwt(tricl_spectrum[0, :], [3])
peak_locs = x3[peak_ids]
angle = (6)/(np.sqrt(5)*np.sqrt(8))
assumed_peaks = np.cos(np.array([180, 105, 75, 51.2, 30, 0])*np.pi/180)
self.assertTrue(np.allclose(peak_locs, assumed_peaks, rtol=0, atol=5*np.pi/180))