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"""Tests of FCBasisSetO3."""
from pathlib import Path
import numpy as np
import pytest
from symfc.basis_sets import FCBasisSetO2, FCBasisSetO3
from symfc.solvers import FCSolverO2O3
from symfc.utils.utils import SymfcAtoms
from symfc.utils.utils_O3 import get_lat_trans_compr_matrix_O3
cwd = Path(__file__).parent
def test_fc_basis_set_o3():
"""Test symmetry adapted basis sets of FCBasisSetO3."""
a = 5.4335600299999998
lattice = np.array([[a, 0, 0], [0, a, 0], [0, 0, a]])
positions = np.array(
[
[0.875, 0.875, 0.875],
[0.875, 0.375, 0.375],
[0.375, 0.875, 0.375],
[0.375, 0.375, 0.875],
[0.125, 0.125, 0.125],
[0.125, 0.625, 0.625],
[0.625, 0.125, 0.625],
[0.625, 0.625, 0.125],
]
)
numbers = [1, 1, 1, 1, 1, 1, 1, 1]
supercell = SymfcAtoms(cell=lattice, scaled_positions=positions, numbers=numbers)
sbs = FCBasisSetO3(supercell, log_level=1).run()
basis_ref = [
0.671875,
0.656250,
0.765625,
1.000000,
0.750000,
0.875000,
0.562500,
0.765625,
0.718750,
0.671875,
1.000000,
0.875000,
0.875000,
0.625000,
0.750000,
0.562500,
0.875000,
]
np.testing.assert_allclose(
np.sort([v @ v for v in sbs.basis_set]), np.sort(basis_ref)
)
assert np.linalg.norm(sbs.basis_set) ** 2 == pytest.approx(13.0)
np.testing.assert_array_equal(
sbs.compact_compression_matrix.tocoo().row[[0, 6, 9]], [5, 32, 42]
)
norm = sbs.compression_matrix.data[[0, 6, 9]] @ [
-0.1443375672974064,
0.058925565098878946,
0.0833333333333333,
]
norm /= np.linalg.norm(sbs.compression_matrix.data[[0, 6, 9]])
norm /= np.linalg.norm(
[-0.1443375672974064, 0.058925565098878946, 0.0833333333333333]
)
assert norm == pytest.approx(1.0) or norm == pytest.approx(-1.0)
np.testing.assert_array_equal(
sbs.compression_matrix.tocoo().row[[0, 6, 9]], [5, 32, 42]
)
norm = sbs.compression_matrix.data[[0, 6, 9]] @ [
-0.1443375672974064,
0.058925565098878946,
0.0833333333333333,
]
norm /= np.linalg.norm(sbs.compression_matrix.data[[0, 6, 9]])
norm /= np.linalg.norm(
[-0.1443375672974064, 0.058925565098878946, 0.0833333333333333]
)
assert norm == pytest.approx(1.0) or norm == pytest.approx(-1.0)
lat_trans_compr_matrix_O3 = get_lat_trans_compr_matrix_O3(
sbs.translation_permutations
)
np.testing.assert_allclose(lat_trans_compr_matrix_O3.data, [0.5] * 13824)
assert lat_trans_compr_matrix_O3.indices[-1] == 2726
def test_si_111_fc3(ph3_si_111_fc3: tuple[SymfcAtoms, np.ndarray, np.ndarray]):
"""Test fc2 and fc3 by Si-111-222 supercells and compared with ALM.
This test with ALM is skipped when ALM is not installed.
"""
supercell, displacements, forces = ph3_si_111_fc3
basis_set_o2 = FCBasisSetO2(supercell, log_level=1).run()
basis_set_o3 = FCBasisSetO3(supercell, log_level=1).run()
fc_solver = FCSolverO2O3([basis_set_o2, basis_set_o3], log_level=1).solve(
displacements, forces
)
fc2, fc3 = fc_solver.compact_fc
fc2_ref = np.loadtxt(cwd / ".." / "compact_fc_Si_111_fc3_2.xz").reshape(fc2.shape)
fc3_ref = np.loadtxt(cwd / ".." / "compact_fc_Si_111_fc3_3.xz").reshape(fc3.shape)
np.testing.assert_allclose(fc2_ref, fc2, atol=1e-6)
np.testing.assert_allclose(fc3_ref, fc3, atol=1e-6)
def test_fc_basis_set_o3_wurtzite():
"""Test symmetry adapted basis sets of FCBasisSetO3."""
lattice = np.array(
[
[3.786186160293827, 0, 0],
[-1.893093080146913, 3.278933398271515, 0],
[0, 0, 6.212678269409001],
]
)
positions = np.array(
[
[0.333333333333333, 0.666666666666667, 0.002126465711614],
[0.666666666666667, 0.333333333333333, 0.502126465711614],
[0.333333333333333, 0.666666666666667, 0.376316514288389],
[0.666666666666667, 0.333333333333333, 0.876316514288389],
]
)
numbers = [1, 1, 2, 2]
supercell = SymfcAtoms(cell=lattice, scaled_positions=positions, numbers=numbers)
sbs = FCBasisSetO3(supercell, log_level=1).run()
assert sbs.basis_set.shape[0] == 40
assert sbs.basis_set.shape[1] == 18
compact_basis = sbs.compact_compression_matrix @ sbs.basis_set
assert np.linalg.norm(compact_basis) ** 2 == pytest.approx(18.0)
sbs = FCBasisSetO3(supercell, cutoff=3.0, log_level=1).run()
assert sbs.basis_set.shape[0] == 22
assert sbs.basis_set.shape[1] == 6
compact_basis = sbs.compact_compression_matrix @ sbs.basis_set
assert np.linalg.norm(compact_basis) ** 2 == pytest.approx(6.0)
def test_fc_basis_set_o3_diamond():
"""Test symmetry adapted basis sets of FCBasisSetO4."""
a = 5.4335600299999998
lattice = np.array([[a, 0, 0], [0, a, 0], [0, 0, a]])
positions = np.array(
[
[0.875, 0.875, 0.875],
[0.875, 0.375, 0.375],
[0.375, 0.875, 0.375],
[0.375, 0.375, 0.875],
[0.125, 0.125, 0.125],
[0.125, 0.625, 0.625],
[0.625, 0.125, 0.625],
[0.625, 0.625, 0.125],
]
)
numbers = [1, 1, 1, 1, 1, 1, 1, 1]
supercell = SymfcAtoms(cell=lattice, scaled_positions=positions, numbers=numbers)
sbs = FCBasisSetO3(supercell, log_level=1).run()
assert sbs.basis_set.shape[0] == 17
assert sbs.basis_set.shape[1] == 13
compact_basis = sbs.compact_compression_matrix @ sbs.basis_set
assert np.linalg.norm(compact_basis) ** 2 == pytest.approx(3.25)
sbs = FCBasisSetO3(supercell, cutoff=3.5, log_level=1).run()
assert sbs.basis_set.shape[0] == 5
assert sbs.basis_set.shape[1] == 3
compact_basis = sbs.compact_compression_matrix @ sbs.basis_set
assert np.linalg.norm(compact_basis) ** 2 == pytest.approx(0.75)
def test_fc_basis_set_o3_wurtzite_332(cell_wurtzite_332: SymfcAtoms):
"""Test symmetry adapted basis sets of FCBasisSetO3."""
supercell = cell_wurtzite_332
"""
sbs = FCBasisSetO3(supercell, cutoff=6.0, log_level=1).run()
assert sbs.basis_set.shape[0] == 2162
assert sbs.basis_set.shape[1] == 1950
"""
sbs = FCBasisSetO3(supercell, cutoff=5.0, log_level=1).run()
assert sbs.basis_set.shape[0] == 698
assert sbs.basis_set.shape[1] == 569
sbs = FCBasisSetO3(supercell, cutoff=4.0, log_level=1).run()
assert sbs.basis_set.shape[0] == 306
assert sbs.basis_set.shape[1] == 218
sbs = FCBasisSetO3(supercell, cutoff=3.8, log_level=1).run()
assert sbs.basis_set.shape[0] == 270
assert sbs.basis_set.shape[1] == 187
sbs = FCBasisSetO3(supercell, cutoff=3.0, log_level=1).run()
assert sbs.basis_set.shape[0] == 34
assert sbs.basis_set.shape[1] == 9
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