Merge branch 'develop' into rc

.github/workflows/phono3py-pytest-conda.yml

@@ -12,7 +12,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/publish-gh-pages.yml

@@ -12,7 +12,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.11"]
+        python-version: ["3.12"]
 
     steps:
     - uses: actions/checkout@v4

.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/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Nov-13-2024: Version 3.7.0
+
+- Update to follow the change of phonopy's internal functions
+
 ## Nov-3-2024: Version 3.6.0
 
 - Maintenance release.

doc/command-options.md

@@ -58,7 +58,7 @@ When using `phono3py-load` (see also {ref}`phono3py_load_command`)
 This specifies input unit cell filename.
 
 ```bash
-% phono3py -c POSCAR-unitcell ... (options)
+% phono3py -c POSCAR-unitcell [OPTIONS]
 ```
 
 ## Calculator interface
@@ -193,7 +193,7 @@ created from `FORCES_FC2` and `phono3py_disp.yaml` instead of `FORCES_FC3` and
 `phono3py_disp.yaml`.
 
 ```bash
-% phono3py --cfs --dim-fc2="x x x"
+% phono3py --cfs --dim-fc2 4 4 4
 ```
 
 (sp_option)=
@@ -283,7 +283,7 @@ order force constants with larger supercell size. The filename is the same as
 that created in the usual phono3py run without `--dim-fc2` option.
 
 ```bash
-% phono3py --dim="2 2 2" --dim_fc2="4 4 4" -c POSCAR-unitcell ... (many options)
+% phono3py --dim 2 2 2 --dim_fc2 4 4 4 -c POSCAR-unitcell [OPTIONS]
 ```
 
 (pa_option)=

doc/conf.py

@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "3.6"
+version = "3.7"
 # The full version, including alpha/beta/rc tags.
-release = "3.6.0"
+release = "3.7.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/cutoff-pair.md

@@ -2,9 +2,9 @@
 
 # Force constants calculation with cutoff pair-distance
 ```{note}
-Since usage of this calculation is complicated. It is recommended to try
-{ref}`random-displacements` with `--fc-calc-opt "cutoff = VAL"` before trying
-this option.
+To reduce the computational demands of force constants or lattice thermal
+conductivity calculations, it is recommended to try {ref}`pypolymlp-interface`
+instead of using the `--cutoff-pair` option.
 ```
 
 Here the detail of the command option {ref}`--cutoff-pair <cutoff_pair_option>`

doc/pypolymlp.md

@@ -48,10 +48,6 @@ in the distribution from GitHub or PyPI.
   conda-forge (recommended). Otherwise, pypolymlp can be installed from
   source-code.
 
-- [symfc](https://github.com/symfc/symfc)
-
-  Installed via pip, conda-forge, or source code.
-
 ## How to calculate
 
 ### Workflow
@@ -357,14 +353,6 @@ an additional 200 supercells. In total, 400 supercells are created. The forces
 for these supercells are then evaluated. Finally, the force constants are
 calculated using symfc.
 
-## Convergence with respect to dataset size
-
-In general, increasing the amount of data improves the accuracy of representing
-force constants. Therefore, it is recommended to check the convergence of the
-target property with respect to the number of supercells in the training
-dataset. Lattice thermal conductivity may be a convenient property to monitor
-when assessing convergence.
-
 ## Parameters for developing MLPs
 
 A few parameters can be specified using the `--mlp-params` option for the
@@ -401,3 +389,30 @@ For parameter adjustments, it is recommended to consult the
 This method provides a straightforward dataset split: the first `ntrain`
 supercells from the list are used for training, while the last `ntest`
 supercells are reserved for testing.
+
+## Convergence with respect to dataset size
+
+In general, increasing the amount of data improves the accuracy of representing
+force constants. Therefore, it is recommended to check the convergence of the
+target property with respect to the number of supercells in the training
+dataset. Lattice thermal conductivity may be a convenient property to monitor
+when assessing convergence.
+
+For example, by preparing an initial set with 100 supercell data, calculations
+can then be performed by varying the size of the training dataset while keeping
+the test dataset unchanged as follows:
+
+```bash
+% phono3py-load --pypolymlp --mlp-params="ntrain=20, ntest=20" --br --mesh 40 phono3py_params.yaml | tee log-20
+% phono3py-load --pypolymlp --mlp-params="ntrain=40, ntest=20" --br --mesh 40 phono3py_params.yaml | tee log-40
+% phono3py-load --pypolymlp --mlp-params="ntrain=60, ntest=20" --br --mesh 40 phono3py_params.yaml | tee log-60
+% phono3py-load --pypolymlp --mlp-params="ntrain=80, ntest=20" --br --mesh 40 phono3py_params.yaml | tee log-80
+```
+
+The computed lattice thermal conductivities (LTCs) are plotted against the size
+of the training dataset to observe LTC convergence. If the LTC has not
+converged, an additional set of supercell data (e.g., forces and energies in
+the next 100 supercells) will be computed and included. With this procedure in
+mind, it may be convenient to generate a sufficiently large number of supercells
+with random displacements in advance, such as 1000 supercells, before starting
+the LTC calculation with pypolymlp.

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(

phono3py/version.py

@@ -34,4 +34,4 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-__version__ = "3.6.0"
+__version__ = "3.7.0"

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)