Merge branch 'develop'

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
   - id: check-added-large-files
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.6.1
+  rev: v0.6.4
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Sep-12-2024: Version 2.28.0
+
+- Maintenance release including minor fixes and updates.
+
 ## Aug-23-2024: Version 2.27.0
 
 - Update for new `SpglibDataset` in spglib v.2.5 (PR #413 by @janosh, #414).

doc/conf.py

@@ -53,9 +53,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "2.27"
+version = "2.28"
 # The full version, including alpha/beta/rc tags.
-release = "2.27.0"
+release = "2.28.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/examples.md

@@ -21,7 +21,7 @@ be different.
 
 ### `FORCE_SETS` file creation for VASP
 
-~~~bash
+~~~
 % phonopy -f vasprun.xml
         _
   _ __ | |__   ___  _ __   ___   _ __  _   _
@@ -48,7 +48,7 @@ where `vasprun.xml` is the VASP output.
 
 ### DOS
 
-~~~bash
+~~~
 % phonopy-load --mesh 31 31 31 -p
         _
   _ __ | |__   ___  _ __   ___   _ __  _   _
@@ -101,7 +101,7 @@ Summary of calculation was written in "phonopy.yaml".
 
 ### Thermal properties
 
-~~~bash
+~~~
 % phonopy-load --mesh 31 31 31 -t -p
         _
   _ __ | |__   ___  _ __   ___   _ __  _   _
@@ -166,7 +166,7 @@ Number of phonon frequencies less than cutoff frequency: 1/178746
 
 This requires to prepare `BORN` file.
 
-~~~bash
+~~~
 % phonopy-load --band "0.0 0.0 0.0  0.5 0.0 0.0  0.5 0.5 0.0  0.0 0.0 0.0  0.5 0.5 0.5" -p
         _
   _ __ | |__   ___  _ __   ___   _ __  _   _
@@ -222,7 +222,7 @@ Summary of calculation was written in "phonopy.yaml".
 
 ### PDOS
 
-~~~bash
+~~~
 % phonopy-load --mesh 41 41 41 --pdos "1, 2" -p
         _
   _ __ | |__   ___  _ __   ___   _ __  _   _
@@ -278,7 +278,7 @@ Summary of calculation was written in "phonopy.yaml".
 
 Band structure and DOS or PDOS can be plotted on one figure together by
 
-~~~bash
+~~~
 % phonopy-load --band "0.0 0.0 0.0  0.5 0.0 0.0  0.5 0.5 0.0  0.0 0.0 0.0  0.5 0.5 0.5" --mesh 41 41 41 --pdos "1, 2" -p
         _
   _ __ | |__   ___  _ __   ___   _ __  _   _

doc/formulation.md

@@ -1,5 +1,4 @@
 (formulations)=
-
 # Formulations
 
 ## Second-order force constants
@@ -43,7 +42,6 @@ a finite displacement {math}`\Delta r_\alpha{(jl)}` and usually
 {math}`F_\beta(j'l') \equiv 0`.
 
 (force_constants_solver_theory)=
-
 ## Modified Parlinski-Li-Kawazoe method
 
 The following is a modified and simplified version of the Parlinski-Li-Kawazoe
@@ -118,7 +116,6 @@ where the superscript with parenthesis gives the index of site-symmetry
 operations. This is solved by pseudo inverse.
 
 (dynacmial_matrix_theory)=
-
 ## Dynamical matrix
 
 In phonopy, a phase convention of dynamical matrix is used as follows:
@@ -162,7 +159,6 @@ annihilation operators of phonon, {math}`\hbar` is the reduced Planck constant,
 and {math}`t` is the time.
 
 (non_analytical_term_correction_theory)=
-
 ## Non-analytical term correction
 
 To treat long range interaction of macroscopic electric field induced by
@@ -180,12 +176,12 @@ D_{\alpha\beta}(jj',\mathbf{q}=\mathbf{0}) + \frac{1}{\sqrt{m_j m_{j'}}}
 {\sum_{\alpha\beta}q_{\alpha}\epsilon_{\alpha\beta}^{\infty} q_{\beta}}.
 ```
 
-Phonon frequencies at general **q**-points with long-range dipole-dipole
-interaction are calculated by the method of Gonze _et al._
-({ref}`reference_dp_dp_NAC`).
+where {math}`\Omega_0` is the unit cell volume. See more details about the
+physical units at {ref}`physical_unit_conversion`. Phonon frequencies at general
+**q**-points with long-range dipole-dipole interaction are calculated by the
+method of Gonze _et al._ ({ref}`reference_dp_dp_NAC`).
 
 (thermal_properties_expressions)=
-
 ## Thermodynamic properties
 
 ### Phonon number
@@ -399,7 +395,6 @@ difference is employed, and {math}`+\Delta q_\alpha` and
 `GV_DELTA_Q` tag.
 
 (physical_unit_conversion)=
-
 ## Physical unit conversion
 
 Phonopy calculates phonon frequencies based on input values from users. In the
@@ -449,8 +444,6 @@ In the default case of the Wien2k interface, the conversion factor is
 the conversion factors are similarly calculated following the unit systems
 employed in phonopy ({ref}`calculator_interfaces`).
 
-(definition_of_commensurate_points)=
-
 ## Crystal structure
 
 ### Coordinates in direct and reciprocal spaces
@@ -502,6 +495,7 @@ written at {ref}`primitive_axes_tag`, therefore
 those calculated following Eq. {eq}`eq_rec_basis_vectors` with this
 {math}`( \mathbf{a} \; \mathbf{b} \; \mathbf{c})`.
 
+(definition_of_commensurate_points)=
 ### Commensurate points
 
 In phonopy, so-called commensurate points mean the q-points whose waves are

doc/output-files.md

@@ -162,7 +162,7 @@ with open("band.yaml") as f:
   - Phonon frequency in a specified unit at each phonon mode
 * - eigenvector
   - Eigenvector at each phonon mode.
-    Each eigenvector :math:`\mathbf{e}` of
+    Each eigenvector {math}`\mathbf{e}` of
     {ref}`dynamical matrix <dynacmial_matrix_theory>`
     is shown as sets of three
     complex values of each atom along the Cartesian axes in

doc/phonopy-module.md

@@ -381,7 +381,7 @@ phonon.run_mesh([20, 20, 20], with_group_velocities=True)
 ```
 
 The first argument of `run_mesh()` can be a float value, which is a length
-measure as explained at {ref}`mehs_tag`, for example:
+measure as explained at {ref}`mesh_tag`, for example:
 
 ```python
 phonon.run_mesh(100.0)

doc/qe.md

@@ -16,6 +16,16 @@ More tags may be supported on request.
 nat, ntyp, celldm(1), ATOMIC_SPECIES, ATOMIC_POSITIONS, CELL_PARAMETERS
 ```
 
+Chemical symbols with natural number for `ATOMIC_SPECIES` like `Xn` (`n>0`),
+e.g.. `Fe1`, can be used. The formats of `X_*` and `X-*` are not supported. When
+this extended symbol is used, masses of all atoms including usual chemical
+symbols are read from QE structure file. Otherwise, masses of respective
+chemical symbols implemented in phonopy are used. Note that when using the
+extended symbol, if the unit cell of QE structure file is not a primitive cell,
+and the primitive cell is defined by the transformation matrix (`PRIMITIVE_AXES`
+tag or `--pa` option), atoms with the extended symbols in the unit cell have to
+be mapped properly to those in the primitive cell.
+
 ## How to run
 
 The procedure of QE-phonopy calculation is shown below using the
@@ -331,7 +341,7 @@ Saving this script as `make_born_q2r.py`,
 #### NaCl example
 
 NaCl example is found at
-https://github.com/phonopy/phonopy/tree/master/example/NaCl-QE-q2r.
+<https://github.com/phonopy/phonopy/tree/master/example/NaCl-QE-q2r>.
 
 ```bash
 % phonopy --qe -c NaCl.in --dim="8 8 8" --band="0 0 0  1/2 0 0  1/2 1/2 0  0 0 0  1/2 1/2 1/2" --readfc --readfc-format=hdf5 --fc-symmetry --nac -p

doc/vasp-dfpt.md

@@ -76,7 +76,7 @@ procedure to calculate phonon properties may be as follows:
 
 6) Run phonopy
 
-   ~~~bash
+   ~~~
    % phonopy-load --readfc --band "0.0 0.0 0.0  0.5 0.0 0.0  0.5 0.5 0.0  0.0 0.0 0.0  0.5 0.5 0.5" -p
 
            _

phonopy/api_phonopy.py

@@ -69,10 +69,10 @@
 from phonopy.interface.fc_calculator import get_fc2
 from phonopy.interface.phonopy_yaml import PhonopyYaml
 from phonopy.interface.pypolymlp import (
-    PypolymlpData,
     PypolymlpParams,
-    develop_polymlp,
+    develop_mlp_by_pypolymlp,
     evalulate_polymlp,
+    load_polymlp,
 )
 from phonopy.phonon.animation import write_animation
 from phonopy.phonon.band_structure import BandStructure, get_band_qpoints_by_seekpath
@@ -189,7 +189,7 @@ def __init__(
         self._log_level = log_level
 
         # Create supercell and primitive cell
-        self._unitcell = PhonopyAtoms(atoms=unitcell)
+        self._unitcell = unitcell.copy()
         self._supercell_matrix = self._shape_supercell_matrix(supercell_matrix)
         if isinstance(primitive_matrix, str):
             self._primitive_matrix = self._set_primitive_matrix(primitive_matrix)
@@ -1242,44 +1242,41 @@ def symmetrize_force_constants_by_space_group(self, show_drift=True) -> None:
         if self._primitive.masses is not None:
             self._set_dynamical_matrix()
 
-    def develop_mlp(self, params: Optional[Union[PypolymlpParams, dict]] = None):
+    def develop_mlp(
+        self,
+        params: Optional[Union[PypolymlpParams, dict, str]] = None,
+        test_size: float = 0.1,
+    ):
         """Develop MLP of pypolymlp.
 
         Parameters
         ----------
         params : PypolymlpParams or dict, optional
             Parameters for developing MLP. Default is None. When dict is given,
             PypolymlpParams instance is created from the dict.
+        test_size : float, optional
+            Training and test data are splitted by this ratio. test_size=0.1
+            means the first 90% of the data is used for training and the rest
+            is used for test. Default is 0.1.
 
         """
         if self._mlp_dataset is None:
             raise RuntimeError("MLP dataset is not set.")
 
-        if isinstance(params, dict):
-            _params = PypolymlpParams(**params)
-        else:
-            _params = params
-
-        disps = self._mlp_dataset["displacements"]
-        forces = self._mlp_dataset["forces"]
-        energies = self._mlp_dataset["supercell_energies"]
-        n = int(len(disps) * 0.9)
-        train_data = PypolymlpData(
-            displacements=disps[:n], forces=forces[:n], supercell_energies=energies[:n]
-        )
-        test_data = PypolymlpData(
-            displacements=disps[n:], forces=forces[n:], supercell_energies=energies[n:]
-        )
-        self._mlp = develop_polymlp(
+        self._mlp = develop_mlp_by_pypolymlp(
+            self._mlp_dataset,
             self._supercell,
-            train_data,
-            test_data,
-            params=_params,
-            verbose=self._log_level - 1 > 0,
+            params=params,
+            test_size=test_size,
+            log_level=self._log_level,
         )
 
+    def load_mlp(self, filename: str = "phonopy.pmlp"):
+        """Load machine learning potential of pypolymlp."""
+        self._mlp = load_polymlp(filename=filename)
+
     def evaluate_mlp(self):
-        """Evaluate the machine learning potential of pypolymlp.
+        """Evaluate machine learning potential of pypolymlp.
 
         This method calculates the supercell energies and forces from the MLP
         for the displacements in self._dataset of type 2. The results are stored
@@ -4002,7 +3999,7 @@ def _build_supercells_with_displacements(self) -> None:
         for positions in all_positions:
             supercells.append(
                 PhonopyAtoms(
-                    numbers=self._supercell.numbers,
+                    symbols=self._supercell.symbols,
                     masses=self._supercell.masses,
                     magnetic_moments=self._supercell.magnetic_moments,
                     positions=positions,

phonopy/cui/collect_cell_info.py

@@ -55,7 +55,7 @@ def collect_cell_info(
     enforce_primitive_matrix_auto=False,
     phonopy_yaml_cls: type[PhonopyYaml] = PhonopyYaml,
     load_phonopy_yaml: bool = False,
-):
+) -> dict:
     """Collect crystal structure information from input file and parameters.
 
     This function returns crystal structure information obtained from an input