Bump phonopy from 2.43.2 to 2.43.6 (#573)

* Bump phonopy from 2.43.2 to 2.43.6

Bumps [phonopy](https://github.com/phonopy/phonopy) from 2.43.2 to 2.43.6.
- [Changelog](https://github.com/phonopy/phonopy/blob/develop/doc/changelog.md)
- [Commits](phonopy/phonopy@v2.43.2...v2.43.6)

---
updated-dependencies:
- dependency-name: phonopy
  dependency-version: 2.43.6
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* [dependabot skip] Update environment

* phonopy fix

* fix chemical symbols

* Update environment-docs.yml

* Update environment.yml

* Update environment.yml

* Update pyproject.toml

* more fixes

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Jan Janßen <janssen@mpie.de>
Co-authored-by: Jan Janssen <jan-janssen@users.noreply.github.com>

Author: 3 people

.ci_support/environment-docs.yml

@@ -11,8 +11,8 @@ dependencies:
 - numpy =2.3.4
 - scipy =1.16.3
 - spglib =2.6.0
-- phonopy =2.43.2
-- structuretoolkit =0.0.36
+- phonopy =2.43.6
+- structuretoolkit =0.0.37
 - seekpath =2.1.0
 - lammps =2024.08.29
 - pandas =2.3.3

.ci_support/environment.yml

@@ -7,12 +7,12 @@ dependencies:
 - mendeleev =1.1.0
 - numpy =2.3.4
 - pandas =2.3.3
-- phonopy =2.43.2
+- phonopy =2.43.6
 - requests =2.32.5
 - scipy =1.16.3
 - seekpath =2.1.0
 - spglib =2.6.0
-- structuretoolkit =0.0.36
+- structuretoolkit =0.0.37
 - sphinx_parser =0.1.3
 - tqdm =4.67.1
 - pyiron_vasp =0.2.15

atomistics/calculators/lammps/phonon.py

@@ -113,9 +113,9 @@ def calc_molecular_dynamics_phonons_with_lammpslib(
     if supercell is None:
         supercell = [2, 2, 2]
     dp_structure = Structure(
-        cell=phonopy_unitcell.get_cell(),
-        scaled_positions=phonopy_unitcell.get_scaled_positions(),
-        atomic_elements=phonopy_unitcell.get_chemical_symbols(),
+        cell=phonopy_unitcell.cell,
+        scaled_positions=phonopy_unitcell.scaled_positions,
+        atomic_elements=phonopy_unitcell.symbols,
         primitive_matrix=phonopy_primitive_matrix,
         force_constants=ForceConstants(
             force_constants,

atomistics/workflows/phonons/helper.py

@@ -220,7 +220,7 @@ def volumes(self) -> np.ndarray:
             np.ndarray: The volumes.
         """
         return np.array(
-            [self._phonopy.unitcell.get_volume()]
+            [self._phonopy.unitcell.volume]
             * len(self._thermal_properties["temperatures"])
         )
 
@@ -287,7 +287,7 @@ def get_tasks_for_harmonic_approximation(
         unitcell=unitcell,
         supercell_matrix=get_supercell_matrix(
             interaction_range=interaction_range,
-            cell=unitcell.get_cell(),
+            cell=unitcell.cell,
         ),
         primitive_matrix=primitive_matrix,
         factor=factor,
@@ -301,7 +301,7 @@ def get_tasks_for_harmonic_approximation(
             structure_with_magmoms=structure,
             structure=structuretoolkit.common.phonopy_to_atoms(sc),
             interaction_range=interaction_range,
-            cell=unitcell.get_cell(),
+            cell=unitcell.cell,
         )
         for ind, sc in enumerate(phonopy_obj.supercells_with_displacements)
     }

binder/environment.yml

@@ -5,8 +5,8 @@ dependencies:
 - numpy =2.3.4
 - scipy =1.16.3
 - spglib =2.6.0
-- phonopy =2.43.2
-- structuretoolkit =0.0.36
+- phonopy =2.43.6
+- structuretoolkit =0.0.37
 - seekpath =2.1.0
 - gpaw =25.7.0
 - lammps =2024.08.29

pyproject.toml

@@ -39,9 +39,9 @@ Repository = "https://github.com/pyiron/atomistics"
 
 [project.optional-dependencies]
 phonopy = [
-    "phonopy==2.43.2",
+    "phonopy==2.43.6",
     "seekpath==2.1.0",
-    "structuretoolkit==0.0.36",
+    "structuretoolkit==0.0.37",
 ]
 gpaw = [
     "gpaw==25.7.0",