Merge branch 'develop' into publish-gh-pages

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
     exclude: ^example/AlN-LDA/
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.7.0
+  rev: v0.7.3
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

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

phono3py/api_phono3py.py

@@ -47,7 +47,6 @@
     get_random_displacements_dataset,
 )
 from phonopy.harmonic.dynamical_matrix import DynamicalMatrix
-from phonopy.harmonic.force_constants import get_fc2 as get_phonopy_fc2
 from phonopy.harmonic.force_constants import (
     set_permutation_symmetry,
     set_translational_invariance,
@@ -74,7 +73,6 @@
     guess_primitive_matrix,
     shape_supercell_matrix,
 )
-from phonopy.structure.dataset import get_displacements_and_forces
 from phonopy.structure.symmetry import Symmetry
 from phonopy.units import VaspToTHz
 
@@ -1540,30 +1538,19 @@ def produce_fc2(
         else:
             p2s_map = None
 
-        if fc_calculator is not None:
-            disps, forces = get_displacements_and_forces(disp_dataset)
-            self._fc2 = get_fc2(
-                self._phonon_supercell,
-                self._phonon_primitive,
-                disps,
-                forces,
-                fc_calculator=fc_calculator,
-                fc_calculator_options=fc_calculator_options,
-                atom_list=p2s_map,
-                symmetry=self._phonon_supercell_symmetry,
-                symprec=self._symprec,
-                log_level=self._log_level,
-            )
-        else:
-            if "displacements" in disp_dataset:
-                msg = "fc_calculator to solve fc2 has to be set."
-                raise RuntimeError(msg)
-            self._fc2 = get_phonopy_fc2(
-                self._phonon_supercell,
-                self._phonon_supercell_symmetry,
-                disp_dataset,
-                atom_list=p2s_map,
-            )
+        self._fc2 = get_fc2(
+            self._phonon_supercell,
+            self._phonon_primitive,
+            disp_dataset,
+            fc_calculator=fc_calculator,
+            fc_calculator_options=fc_calculator_options,
+            atom_list=p2s_map,
+            symmetry=self._phonon_supercell_symmetry,
+            symprec=self._symprec,
+            log_level=self._log_level,
+        )
+
+        if fc_calculator is None or fc_calculator == "traditional":
             if symmetrize_fc2:
                 if is_compact_fc:
                     symmetrize_compact_force_constants(

pyproject.toml

@@ -8,15 +8,15 @@ dynamic = ["version"]
 readme = { file = "README.md", content-type = "text/markdown" }
 description = "This is the phono3py module."
 authors = [{ name = "Atsushi Togo", email = "[email protected]" }]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dependencies = [
     "numpy>=1.17.0",
     "scipy",
     "PyYAML>=5.3",
     "matplotlib>=2.2.2",
     "h5py>=3.0",
     "spglib>=2.3",
-    "phonopy>=2.29,<2.30",
+    "phonopy>=2.30,<2.31",
 ]
 license = { file = "LICENSE" }
 

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)