Merge pull request #390 from phonopy/fc3-cutoff-in-fdf5

Add fc3_cutoff entry in fc3.hdf5

phono3py/api_phono3py.py

@@ -301,6 +301,7 @@ class Phono3py:
         self._fc2 = None
         self._fc3 = None
         self._fc3_nonzero_indices = None  # available only symfc
+        self._fc3_cutoff = None  # available only symfc
 
         # MLP
         self._mlp = None
@@ -365,6 +366,11 @@ class Phono3py:
     def fc3_nonzero_indices(self, fc3_nonzero_indices):
         self._fc3_nonzero_indices = fc3_nonzero_indices
 
+    @property
+    def fc3_cutoff(self) -> float | None:
+        """Return cutoff value of fc3."""
+        return self._fc3_cutoff
+
     @property
     def fc2(self) -> NDArray | None:
         """Setter and getter of second order force constants (fc2).
@@ -1537,6 +1543,9 @@ class Phono3py:
         if fc_calculator == "symfc":
             symfc_solver = cast(SymfcFCSolver, fc_solver.fc_solver)
             fc3_nonzero_elems = symfc_solver.get_nonzero_atomic_indices_fc3()
+            options = symfc_solver.options
+            if options is not None and "cutoff" in options:
+                self._fc3_cutoff = options["cutoff"].get(3, None)
             if fc3_nonzero_elems is not None:
                 if is_compact_fc:
                     self._fc3_nonzero_indices = np.array(

phono3py/cui/create_force_constants.py

@@ -164,6 +164,7 @@ def create_phono3py_force_constants(
                 fc3_nonzero_indices=phono3py.fc3_nonzero_indices,
                 filename=filename,
                 p2s_map=phono3py.primitive.p2s_map,
+                fc3_cutoff=phono3py.fc3_cutoff,
                 compression=settings.hdf5_compression,
             )
 

phono3py/cui/phono3py_script.py

@@ -681,6 +681,7 @@ def _store_force_constants(ph3py: Phono3py, settings: Phono3pySettings, log_leve
             ph3py.fc3,
             fc3_nonzero_indices=ph3py.fc3_nonzero_indices,
             p2s_map=ph3py.primitive.p2s_map,
+            fc3_cutoff=ph3py.fc3_cutoff,
             compression=settings.hdf5_compression,
         )
         if log_level:

phono3py/file_IO.py

@@ -307,6 +307,7 @@ def write_fc3_to_hdf5(
     fc3_nonzero_indices: NDArray | None = None,
     filename: str = "fc3.hdf5",
     p2s_map: NDArray | None = None,
+    fc3_cutoff: float | None = None,
     compression: str = "gzip",
 ):
     """Write fc3 in fc3.hdf5.
@@ -325,6 +326,8 @@ def write_fc3_to_hdf5(
     p2s_map : ndarray, optional
         Primitive atom indices in supercell index system shape=(n_patom,),
         dtype=intc
+    fc3_cutoff : float, optional
+        Cutoff distance for fc3.
     compression : str or int, optional
         h5py's lossless compression filters (e.g., "gzip", "lzf"). None gives no
         compression. See the detail at docstring of h5py.Group.create_dataset.
@@ -338,6 +341,8 @@ def write_fc3_to_hdf5(
             w.create_dataset(
                 "fc3_nonzero_indices", data=fc3_nonzero_indices, compression=compression
             )
+            if fc3_cutoff is not None:
+                w.create_dataset("fc3_cutoff", data=fc3_cutoff)
         if p2s_map is not None:
             w.create_dataset("p2s_map", data=p2s_map)
 

test/cui/test_phono3py_load_script.py

@@ -128,6 +128,8 @@ def test_phono3py_load_with_typeII_dataset(
                         assert "fc3_nonzero_indices" not in f
                     else:
                         assert "fc3_nonzero_indices" in f
+                        assert "fc3_cutoff" in f
+                        assert f["fc3_cutoff"][()] == pytest.approx(4.0)
             file_path.unlink()