Merge pull request #293 from phonopy/test-tolerance

Increase margin for an isotope-test

doc/random-displacements.md

@@ -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

test/other/test_isotope.py

@@ -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"])

test/sscha/test_sscha.py

@@ -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)