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"""Tests of Symfc."""
from __future__ import annotations
from pathlib import Path
import numpy as np
import pytest
from symfc import Symfc
from symfc.utils.cutoff_tools import FCCutoff
from symfc.utils.utils import SymfcAtoms
cwd = Path(__file__).parent
def test_api_NaCl_222(ph_nacl_222: tuple[SymfcAtoms, np.ndarray, np.ndarray]):
"""Test Symfc class."""
supercell, displacements, forces = ph_nacl_222
symfc = Symfc(supercell)
symfc.compute_basis_set(2)
symfc.displacements = displacements
assert symfc.displacements is not None
np.testing.assert_array_almost_equal(symfc.displacements, displacements) # type: ignore
symfc.forces = forces
assert symfc.forces is not None
np.testing.assert_array_almost_equal(symfc.forces, forces) # type: ignore
symfc.solve(2)
fc = symfc.force_constants[2]
fc_ref = np.loadtxt(cwd / "compact_fc_NaCl_222.xz").reshape(fc.shape)
np.testing.assert_allclose(fc, fc_ref)
def test_api_NaCl_222_with_dataset(
ph_nacl_222: tuple[SymfcAtoms, np.ndarray, np.ndarray],
):
"""Test Symfc class with displacements and forces as input.
1. symfc.run()
2. basis_set = symfc.basis_set.
3. new_symfc.basis_set
4. new_symfc.solve()
"""
supercell, displacements, forces = ph_nacl_222
symfc = Symfc(supercell)
symfc.displacements = displacements
symfc.forces = forces
symfc.run(max_order=2)
fc = symfc.force_constants[2]
fc_ref = np.loadtxt(cwd / "compact_fc_NaCl_222.xz").reshape(fc.shape)
np.testing.assert_allclose(fc, fc_ref)
new_symfc = Symfc(
supercell,
)
new_symfc.displacements = displacements
new_symfc.forces = forces
new_symfc.basis_set = symfc.basis_set
new_symfc.solve(max_order=2)
np.testing.assert_allclose(new_symfc.force_constants[2], fc_ref)
def test_api_NaCl_222_exception(ph_nacl_222: tuple[SymfcAtoms, np.ndarray, np.ndarray]):
"""Test Symfc class with displacements and forces as input."""
supercell, _, _ = ph_nacl_222
symfc = Symfc(supercell)
symfc.compute_basis_set(2)
with pytest.raises(RuntimeError):
symfc.solve(2)
@pytest.mark.parametrize("is_compact_fc", [True, False])
def test_api_si_111_fc3(
ph3_si_111_fc3: tuple[SymfcAtoms, np.ndarray, np.ndarray], is_compact_fc: bool
):
"""Test Symfc class with displacements and forces as input."""
supercell, displacements, forces = ph3_si_111_fc3
symfc = Symfc(supercell)
symfc.displacements = displacements
symfc.forces = forces
symfc.run(max_order=3, is_compact_fc=is_compact_fc)
fc2 = symfc.force_constants[2]
fc3 = symfc.force_constants[3]
if is_compact_fc:
# np.savetxt(cwd / "compact_fc_Si_111_fc3_2.xz", fc2.ravel())
# np.savetxt(cwd / "compact_fc_Si_111_fc3_3.xz", fc3.ravel())
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)
else:
# np.savetxt(cwd / "full_fc_Si_111_fc3_2.xz", fc2.ravel())
# np.savetxt(cwd / "full_fc_Si_111_fc3_3.xz", fc3.ravel())
fc2_ref = np.loadtxt(cwd / "full_fc_Si_111_fc3_2.xz").reshape(fc2.shape)
fc3_ref = np.loadtxt(cwd / "full_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)
@pytest.mark.parametrize("is_compact_fc", [True, False])
def test_api_si_111_fc4(
ph3_si_111_fc3: tuple[SymfcAtoms, np.ndarray, np.ndarray], is_compact_fc: bool
):
"""Test Symfc class with displacements and forces as input."""
supercell, displacements, forces = ph3_si_111_fc3
symfc = Symfc(supercell)
symfc.displacements = displacements
symfc.forces = forces
symfc.run(orders=[2, 3, 4], is_compact_fc=is_compact_fc)
fc2 = symfc.force_constants[2]
fc3 = symfc.force_constants[3]
fc4 = symfc.force_constants[4]
if is_compact_fc:
# np.savetxt(cwd / "compact_fc_Si_111_fc4_2.xz", fc2.ravel())
# np.savetxt(cwd / "compact_fc_Si_111_fc4_3.xz", fc3.ravel())
# np.savetxt(cwd / "compact_fc_Si_111_fc4_4.xz", fc4.ravel())
fc2_ref = np.loadtxt(cwd / "compact_fc_Si_111_fc4_2.xz").reshape(fc2.shape)
fc3_ref = np.loadtxt(cwd / "compact_fc_Si_111_fc4_3.xz").reshape(fc3.shape)
fc4_ref = np.loadtxt(cwd / "compact_fc_Si_111_fc4_4.xz").reshape(fc4.shape)
else:
# np.savetxt(cwd / "full_fc_Si_111_fc4_2.xz", fc2.ravel())
# np.savetxt(cwd / "full_fc_Si_111_fc4_3.xz", fc3.ravel())
# np.savetxt(cwd / "full_fc_Si_111_fc4_4.xz", fc4.ravel())
fc2_ref = np.loadtxt(cwd / "full_fc_Si_111_fc4_2.xz").reshape(fc2.shape)
fc3_ref = np.loadtxt(cwd / "full_fc_Si_111_fc4_3.xz").reshape(fc3.shape)
fc4_ref = np.loadtxt(cwd / "full_fc_Si_111_fc4_4.xz").reshape(fc4.shape)
np.testing.assert_allclose(fc2_ref, fc2, atol=1e-6)
np.testing.assert_allclose(fc3_ref, fc3, atol=1e-6)
np.testing.assert_allclose(fc4_ref, fc4, atol=1e-6)
@pytest.mark.parametrize("is_compact_fc", [False])
def test_api_si_111_fc4_step(
ph3_si_111_fc3: tuple[SymfcAtoms, np.ndarray, np.ndarray], is_compact_fc: bool
):
"""Test Symfc class with displacements and forces as input."""
supercell, displacements, forces = ph3_si_111_fc3
symfc = Symfc(supercell)
symfc.displacements = displacements
symfc.forces = forces
symfc.run(orders=[2], is_compact_fc=is_compact_fc)
fc2 = symfc.force_constants[2]
natom = fc2.shape[0]
N3 = natom * 3
fc2_mat = fc2.transpose((0, 2, 1, 3)).reshape((N3, N3))
displacements_mat = displacements.reshape((-1, N3))
forces_mat = forces.reshape((-1, N3))
forces_mat -= -displacements_mat @ fc2_mat
forces = forces_mat.reshape((-1, natom, 3))
symfc = Symfc(supercell)
symfc.displacements = displacements
symfc.forces = forces
symfc.run(orders=[3, 4], is_compact_fc=is_compact_fc)
fc3 = symfc.force_constants[3]
fc4 = symfc.force_constants[4]
fc2_ref = np.loadtxt(cwd / "full_fc_Si_111_fc4_2.xz").reshape(fc2.shape)
fc3_ref = np.loadtxt(cwd / "full_fc_Si_111_fc4_3.xz").reshape(fc3.shape)
np.testing.assert_allclose(fc2_ref, fc2, atol=1e-1)
np.testing.assert_allclose(fc3_ref, fc3, atol=1e-1)
# np.savetxt(cwd / "full_fc_Si_111_fc4_step_2.xz", fc2.ravel())
# np.savetxt(cwd / "full_fc_Si_111_fc4_step_3.xz", fc3.ravel())
# np.savetxt(cwd / "full_fc_Si_111_fc4_step_4.xz", fc4.ravel())
fc2_ref = np.loadtxt(cwd / "full_fc_Si_111_fc4_step_2.xz").reshape(fc2.shape)
fc3_ref = np.loadtxt(cwd / "full_fc_Si_111_fc4_step_3.xz").reshape(fc3.shape)
fc4_ref = np.loadtxt(cwd / "full_fc_Si_111_fc4_step_4.xz").reshape(fc4.shape)
np.testing.assert_allclose(fc2_ref, fc2, atol=1e-6)
np.testing.assert_allclose(fc3_ref, fc3, atol=1e-6)
np.testing.assert_allclose(fc4_ref, fc4, atol=1e-6)
def test_api_estimate_basis_size_NaCl_222(
cell_nacl_222: SymfcAtoms,
):
"""Test Symfc class."""
symfc = Symfc(cell_nacl_222)
ref_estimates = {
2: 12,
3: 768,
4: 36864,
}
assert symfc.estimate_basis_size(orders=[2, 3, 4]) == ref_estimates
assert symfc.estimate_basis_size(max_order=4) == ref_estimates
def test_api_NaCl_222_cutoff_attribute(cell_nacl_222: SymfcAtoms):
"""Test accessing FCCutoff via Symfc class."""
symfc = Symfc(cell_nacl_222, cutoff={3: 4.0})
symfc.compute_basis_set(3)
fc_cutoff = symfc.basis_set[3].fc_cutoff
assert isinstance(fc_cutoff, FCCutoff)
assert fc_cutoff.nonzero_atomic_indices_fc3().shape[0] == len(cell_nacl_222) ** 3
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