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Increase mergin for an isotope-test

This commit is contained in:
Atsushi Togo 2024-11-12 11:11:49 +09:00
parent 8973ca2090
commit 64bc1d9511
3 changed files with 7 additions and 5 deletions
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2
doc/random-displacements.md
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@ -1,5 +1,5 @@
(random-displacements)=
# Force constants calculation with randan displacements of atoms
# Force constants calculation with random displacements of atoms
Random displacements and corresponding forces in supercells can be employed as a
displacement-force dataset for computing force constants. This requires an

2
test/other/test_isotope.py
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@ -114,7 +114,7 @@ def test_Phono3pyIsotope_grg(si_pbesol_grg, lang):
iso.grid.grid_matrix, [[-15, 15, 15], [15, -15, 15], [15, 15, -15]]
)
iso.run([23, 103], lang=lang)
np.testing.assert_allclose(si_pbesol_grg_iso, iso.gamma[0], atol=2e-3)
np.testing.assert_allclose(si_pbesol_grg_iso, iso.gamma[0], atol=3e-3)
@pytest.mark.parametrize("lang", ["C", "Py"])

8
test/sscha/test_sscha.py
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@ -57,15 +57,17 @@ def get_supercell_phonon(ph3):
return SupercellPhonon(supercell, fc2, frequency_factor_to_THz=factor)
def mass_sand(matrix, mass):
def mass_sand(matrix: np.ndarray, mass: np.ndarray) -> np.ndarray:
"""Calculate mass sandwich."""
return ((matrix * mass).T * mass).T
def mass_inv(matrix, mass):
def mass_inv(matrix: np.ndarray, mass: np.ndarray, tol: float = 1e-5) -> np.ndarray:
"""Calculate inverse mass sandwich."""
bare = mass_sand(matrix, mass)
inv_bare = np.linalg.pinv(bare)
eigvals, eigvecs = np.linalg.eigh(bare)
inv_eigvals = [1 / x if x > tol else 0 for x in eigvals]
inv_bare = (eigvecs * inv_eigvals) @ eigvecs.T
return mass_sand(inv_bare, mass)