Implementation to adjust get_supercell_size to also generate orthorhombic supercells (#923)

* starting with implementation to adjust get_supercell_size

* adding orthorhombic supercells

* add unit test

* fixed the reason for the failing unit tests

* adjust pymatgen version

* adjust pymatgen version

* fix linting

* fix missing max_length in unit test

* adjusted pymatgen version

* add step_size to common_kwds

* put max_atoms to common_kwds

* adjustments to make unit tests pass

* fixing ase unit test

* Update test_jobs.py

---------

Co-authored-by: J. George <[email protected]>

Author: QuantumChemist

src/atomate2/common/flows/phonons.py

@@ -132,7 +132,9 @@ class BasePhononMaker(Maker, ABC):
     symprec: float = SETTINGS.PHONON_SYMPREC
     displacement: float = 0.01
     min_length: float | None = 20.0
+    max_length: float | None = None
     prefer_90_degrees: bool = True
+    allow_orthorhombic: bool = False
     get_supercell_size_kwargs: dict = field(default_factory=dict)
     use_symmetrized_structure: Literal["primitive", "conventional"] | None = None
     bulk_relax_maker: ForceFieldRelaxMaker | BaseVaspMaker | BaseAimsMaker | None = None
@@ -252,9 +254,11 @@ def make(
         # maker to ensure that cell lengths are really larger than threshold
         if supercell_matrix is None:
             supercell_job = get_supercell_size(
-                structure,
-                self.min_length,
-                self.prefer_90_degrees,
+                structure=structure,
+                min_length=self.min_length,
+                max_length=self.max_length,
+                prefer_90_degrees=self.prefer_90_degrees,
+                allow_orthorhombic=self.allow_orthorhombic,
                 **self.get_supercell_size_kwargs,
             )
             jobs.append(supercell_job)

src/atomate2/common/jobs/phonons.py

@@ -57,47 +57,64 @@ def get_total_energy_per_cell(
 
 @job
 def get_supercell_size(
-    structure: Structure, min_length: float, prefer_90_degrees: bool, **kwargs
+    structure: Structure,
+    min_length: float,
+    max_length: float,
+    prefer_90_degrees: bool,
+    allow_orthorhombic: bool = False,
+    **kwargs,
 ) -> list[list[float]]:
     """
-    Determine supercell size with given min_length.
+    Determine supercell size with given min_length and max_length.
 
     Parameters
     ----------
     structure: Structure Object
         Input structure that will be used to determine supercell
     min_length: float
         minimum length of cell in Angstrom
+    max_length: float
+        maximum length of cell in Angstrom
     prefer_90_degrees: bool
         if True, the algorithm will try to find a cell with 90 degree angles first
+    allow_orthorhombic: bool
+        if True, orthorhombic supercells are allowed
     **kwargs:
         Additional parameters that can be set.
     """
     kwargs.setdefault("force_diagonal", False)
-    common_kwds = {
-        "min_length": min_length,
-        "min_atoms": kwargs.get("min_atoms"),
-        "force_diagonal": kwargs["force_diagonal"],
-    }
+    common_kwds = dict(
+        min_length=min_length,
+        max_length=max_length,
+        min_atoms=kwargs.get("min_atoms"),
+        max_atoms=kwargs.get("max_atoms"),
+        step_size=kwargs.get("step_size", 0.1),
+        force_diagonal=kwargs["force_diagonal"],
+    )
 
     if not prefer_90_degrees:
         transformation = CubicSupercellTransformation(
-            **common_kwds, max_atoms=kwargs.get("max_atoms"), force_90_degrees=False
+            **common_kwds,
+            force_90_degrees=False,
+            allow_orthorhombic=allow_orthorhombic,
         )
         transformation.apply_transformation(structure=structure)
     else:
         try:
+            common_kwds.update({"max_atoms": kwargs.get("max_atoms", 1200)})
             transformation = CubicSupercellTransformation(
                 **common_kwds,
-                max_atoms=kwargs.get("max_atoms", 1200),
                 force_90_degrees=True,
                 angle_tolerance=kwargs.get("angle_tolerance", 1e-2),
+                allow_orthorhombic=allow_orthorhombic,
             )
             transformation.apply_transformation(structure=structure)
 
         except AttributeError:
             transformation = CubicSupercellTransformation(
-                **common_kwds, max_atoms=kwargs.get("max_atoms"), force_90_degrees=False
+                **common_kwds,
+                force_90_degrees=False,
+                allow_orthorhombic=allow_orthorhombic,
             )
             transformation.apply_transformation(structure=structure)
 

tests/forcefields/test_phonon.py

@@ -12,14 +12,48 @@
 
 
 def test_phonon_get_supercell_size(clean_dir, si_structure: Structure):
-    job = get_supercell_size(si_structure, min_length=18, prefer_90_degrees=True)
+    job = get_supercell_size(
+        si_structure, min_length=18, max_length=25, prefer_90_degrees=True
+    )
 
     # run the flow or job and ensure that it finished running successfully
     responses = run_locally(job, create_folders=True, ensure_success=True)
 
     assert_allclose(responses[job.uuid][1].output, [[6, -2, 0], [0, 6, 0], [-3, -2, 5]])
 
 
+def test_supercell_orthorhombic(clean_dir, si_structure: Structure):
+    job1 = get_supercell_size(
+        si_structure,
+        min_length=5,
+        max_length=10,
+        prefer_90_degrees=False,
+        allow_orhtorhombic=True,
+    )
+
+    # run the flow or job and ensure that it finished running successfully
+    responses = run_locally(job1, create_folders=True, ensure_success=True)
+
+    assert_allclose(
+        responses[job1.uuid][1].output, [[2, -1, 0], [0, 2, 0], [-1, -1, 2]]
+    )
+
+    job2 = get_supercell_size(
+        si_structure,
+        min_length=5,
+        max_length=10,
+        prefer_90_degrees=True,
+        allow_orhtorhombic=True,
+    )
+
+    # run the flow or job and ensure that it finished running successfully
+    responses = run_locally(job2, create_folders=True, ensure_success=True)
+
+    assert_allclose(
+        responses[job2.uuid][1].output, [[2, -1, 0], [0, 3, 0], [-1, -1, 2]]
+    )
+
+
 def test_phonon_maker_initialization_with_all_mlff(
     si_structure: Structure, test_dir: Path
 ):