Add tests for supercell_energies and forces attributes of API

phono3py/api_phono3py.py

@@ -34,6 +34,7 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
+import copy
 from collections.abc import Sequence
 from typing import Literal, Optional, Union
 
@@ -610,7 +611,20 @@ def dataset(self):
 
     @dataset.setter
     def dataset(self, dataset):
-        self._dataset = dataset
+        if dataset is None:
+            self._dataset = None
+        elif "first_atoms" in dataset:
+            self._dataset = copy.deepcopy(dataset)
+        elif "displacements" in dataset:
+            self._dataset = {}
+            self.displacements = dataset["displacements"]
+            if "forces" in dataset:
+                self.forces = dataset["forces"]
+            if "supercell_energies" in dataset:
+                self.supercell_energies = dataset["supercell_energies"]
+        else:
+            raise RuntimeError("Data format of dataset is wrong.")
+
         self._supercells_with_displacements = None
         self._phonon_supercells_with_displacements = None
 
@@ -643,7 +657,21 @@ def phonon_dataset(self):
 
     @phonon_dataset.setter
     def phonon_dataset(self, dataset):
-        self._phonon_dataset = dataset
+        if dataset is None:
+            self._phonon_dataset = None
+        elif "first_atoms" in dataset:
+            self._phonon_dataset = copy.deepcopy(dataset)
+        elif "displacements" in dataset:
+            self._phonon_dataset = {}
+            self.phonon_displacements = dataset["displacements"]
+            if "forces" in dataset:
+                self.phonon_forces = dataset["forces"]
+            if "supercell_energies" in dataset:
+                self.phonon_supercell_energies = dataset["supercell_energies"]
+        else:
+            raise RuntimeError("Data format of dataset is wrong.")
+
+        self._phonon_supercells_with_displacements = None
 
     @property
     def band_indices(self):
@@ -929,7 +957,7 @@ def phonon_forces(self):
             be the same order of phonon_supercells_with_displacements.
 
         """
-        self._get_phonon_forces_energies(target="forces")
+        return self._get_phonon_forces_energies(target="forces")
 
     @phonon_forces.setter
     def phonon_forces(self, values):
@@ -948,7 +976,7 @@ def phonon_supercell_energies(self):
             to be the same order of phonon_supercells_with_displacements.
 
         """
-        self._get_phonon_forces_energies(target="supercell_energies")
+        return self._get_phonon_forces_energies(target="supercell_energies")
 
     @phonon_supercell_energies.setter
     def phonon_supercell_energies(self, values):
@@ -2261,10 +2289,15 @@ def _extract_fc2_fc3_calculators(self, fc_calculator, fc_calculator_options, ord
 
     def _get_forces_energies(
         self, target: Literal["forces", "supercell_energies"]
-    ) -> np.ndarray:
-        if target in self._dataset:
+    ) -> Optional[np.ndarray]:
+        """Return fc3 forces and supercell energies.
+
+        Return None if tagert data is not found rather than raising exception.
+
+        """
+        if target in self._dataset:  # type-2
             return self._dataset[target]
-        elif "first_atoms" in self._dataset:
+        elif "first_atoms" in self._dataset:  # type-1
             num_scells = len(self._dataset["first_atoms"])
             for disp1 in self._dataset["first_atoms"]:
                 num_scells += len(disp1["second_atoms"])
@@ -2274,30 +2307,31 @@ def _get_forces_energies(
                     dtype="double",
                     order="C",
                 )
+                type1_target = "forces"
             elif target == "supercell_energies":
                 values = np.zeros(num_scells, dtype="double")
+                type1_target = "supercell_energy"
             count = 0
             for disp1 in self._dataset["first_atoms"]:
-                values[count] = disp1[target]
+                values[count] = disp1[type1_target]
                 count += 1
             for disp1 in self._dataset["first_atoms"]:
                 for disp2 in disp1["second_atoms"]:
-                    values[count] = disp2[target]
+                    values[count] = disp2[type1_target]
                     count += 1
             return values
-        else:
-            raise RuntimeError("FC3 displacement dataset is in wrong format.")
+        return None
 
     def _set_forces_energies(
         self, values, target: Literal["forces", "supercell_energies"]
     ):
-        if "first_atoms" in self._dataset:
+        if "first_atoms" in self._dataset:  # type-1
             count = 0
             for disp1 in self._dataset["first_atoms"]:
                 if target == "forces":
                     disp1[target] = np.array(values[count], dtype="double", order="C")
                 elif target == "supercell_energies":
-                    disp1[target] = float(values[count])
+                    disp1["supercell_energy"] = float(values[count])
                 count += 1
             for disp1 in self._dataset["first_atoms"]:
                 for disp2 in disp1["second_atoms"]:
@@ -2306,22 +2340,27 @@ def _set_forces_energies(
                             values[count], dtype="double", order="C"
                         )
                     elif target == "supercell_energies":
-                        disp2[target] = float(values[count])
+                        disp2["supercell_energy"] = float(values[count])
                     count += 1
-        elif "displacements" in self._dataset or "forces" in self._dataset:
+        elif "displacements" in self._dataset or "forces" in self._dataset:  # type-2
             self._dataset[target] = np.array(values, dtype="double", order="C")
         else:
             raise RuntimeError("Set of FC3 displacements is not available.")
 
     def _get_phonon_forces_energies(
         self, target: Literal["forces", "supercell_energies"]
-    ):
+    ) -> Optional[np.ndarray]:
+        """Return fc2 forces and supercell energies.
+
+        Return None if tagert data is not found rather than raising exception.
+
+        """
         if self._phonon_dataset is None:
             raise RuntimeError("Dataset for fc2does not exist.")
 
-        if target in self._phonon_dataset:
+        if target in self._phonon_dataset:  # type-2
             return self._phonon_dataset[target]
-        elif "first_atoms" in self._phonon_dataset:
+        elif "first_atoms" in self._phonon_dataset:  # type-1
             values = []
             for disp in self._phonon_dataset["first_atoms"]:
                 if target == "forces":
@@ -2332,10 +2371,7 @@ def _get_phonon_forces_energies(
                         values.append(disp["supercell_energy"])
             if values:
                 return np.array(values, dtype="double", order="C")
-            else:
-                None
-        else:
-            raise RuntimeError("FC2 displacement dataset is in wrong format.")
+        return None
 
     def _set_phonon_forces_energies(
         self, values, target: Literal["forces", "supercell_energies"]
@@ -2351,7 +2387,7 @@ def _set_phonon_forces_energies(
                     disp["supercell_energy"] = float(v)
         elif "displacements" in self._phonon_dataset:
             _values = np.array(values, dtype="double", order="C")
-            natom = len(self._supercell)
+            natom = len(self._phonon_supercell)
             ndisps = len(self._phonon_dataset["displacements"])
             if target == "forces" and (
                 _values.ndim != 3 or _values.shape != (ndisps, natom, 3)

test/api/test_api_phono3py.py

@@ -1,7 +1,11 @@
 """Tests of Phono3py API."""
 
+from __future__ import annotations
+
 from pathlib import Path
 
+import numpy as np
+
 from phono3py import Phono3py
 
 cwd = Path(__file__).parent
@@ -40,3 +44,125 @@ def test_displacements_setter_Si(si_pbesol_111_222_fd: Phono3py):
     )
     ph3.displacements = displacements
     ph3.phonon_displacements = phonon_displacements
+
+
+def test_type1_forces_energies_setter_Si(si_111_222_fd: Phono3py):
+    """Test type1 supercell_energies, phonon_supercell_energies attributes."""
+    ph3_in = si_111_222_fd
+    ref_ph_supercell_energies = [-346.85204143]
+    ref_supercell_energies = [
+        -43.3509760,
+        -43.33608775,
+        -43.35352904,
+        -43.34370672,
+        -43.34590849,
+        -43.34540162,
+        -43.34421408,
+        -43.34481089,
+        -43.34703607,
+        -43.34241924,
+        -43.34786243,
+        -43.34168203,
+        -43.34274245,
+        -43.34703607,
+        -43.34786243,
+        -43.34184454,
+    ]
+    np.testing.assert_allclose(ph3_in.supercell_energies, ref_supercell_energies)
+    np.testing.assert_allclose(
+        ph3_in.phonon_supercell_energies, ref_ph_supercell_energies
+    )
+
+    ref_force00 = [-0.4109520800000000, 0.0000000100000000, 0.0000000300000000]
+    ref_force_last = [0.1521426300000000, 0.0715600600000000, -0.0715600700000000]
+    ref_ph_force00 = [-0.4027479600000000, 0.0000000200000000, 0.0000001000000000]
+    np.testing.assert_allclose(ph3_in.forces[0, 0], ref_force00)
+    np.testing.assert_allclose(ph3_in.forces[-1, -1], ref_force_last)
+    np.testing.assert_allclose(ph3_in.phonon_forces[0, 0], ref_ph_force00)
+
+    ph3 = Phono3py(
+        ph3_in.unitcell,
+        supercell_matrix=ph3_in.supercell_matrix,
+        phonon_supercell_matrix=ph3_in.phonon_supercell_matrix,
+        primitive_matrix=ph3_in.primitive_matrix,
+    )
+    ph3.dataset = ph3_in.dataset
+    ph3.phonon_dataset = ph3_in.phonon_dataset
+
+    ph3.supercell_energies = ph3_in.supercell_energies + 1
+    ph3.phonon_supercell_energies = ph3_in.phonon_supercell_energies + 1
+    np.testing.assert_allclose(ph3_in.supercell_energies + 1, ph3.supercell_energies)
+    np.testing.assert_allclose(
+        ph3_in.phonon_supercell_energies + 1, ph3.phonon_supercell_energies
+    )
+
+    ph3.forces = ph3_in.forces + 1
+    ph3.phonon_forces = ph3_in.phonon_forces + 1
+    np.testing.assert_allclose(ph3_in.forces + 1, ph3.forces)
+    np.testing.assert_allclose(ph3_in.phonon_forces + 1, ph3.phonon_forces)
+
+
+def test_type2_forces_energies_setter_Si(si_111_222_rd: Phono3py):
+    """Test type2 supercell_energies, phonon_supercell_energies attributes."""
+    ph3_in = si_111_222_rd
+    ref_ph_supercell_energies = [
+        -346.81061270,  # 1
+        -346.81263617,  # 2
+    ]
+    ref_supercell_energies = [
+        -43.35270268,  # 1
+        -43.35211687,  # 2
+        -43.35122776,  # 3
+        -43.35226673,  # 4
+        -43.35146358,  # 5
+        -43.35133209,  # 6
+        -43.35042212,  # 7
+        -43.35008442,  # 8
+        -43.34968796,  # 9
+        -43.35348999,  # 10
+        -43.35134937,  # 11
+        -43.35335251,  # 12
+        -43.35160892,  # 13
+        -43.35009115,  # 14
+        -43.35202797,  # 15
+        -43.35076370,  # 16
+        -43.35174477,  # 17
+        -43.35107001,  # 18
+        -43.35037949,  # 19
+        -43.35126123,  # 20
+    ]
+    np.testing.assert_allclose(ph3_in.supercell_energies, ref_supercell_energies)
+    np.testing.assert_allclose(
+        ph3_in.phonon_supercell_energies, ref_ph_supercell_energies
+    )
+
+    ref_force00 = [0.0445647800000000, 0.1702929900000000, 0.0913398200000000]
+    ref_force_last = [-0.1749668700000000, 0.0146997300000000, -0.1336066300000000]
+    ref_ph_force00 = [-0.0161598900000000, -0.1161657500000000, 0.1399128100000000]
+    ref_ph_force_last = [0.1049486700000000, 0.0795870900000000, 0.1062164600000000]
+
+    np.testing.assert_allclose(ph3_in.forces[0, 0], ref_force00)
+    np.testing.assert_allclose(ph3_in.forces[-1, -1], ref_force_last)
+    np.testing.assert_allclose(ph3_in.phonon_forces[0, 0], ref_ph_force00)
+    np.testing.assert_allclose(ph3_in.phonon_forces[-1, -1], ref_ph_force_last)
+
+    ph3 = Phono3py(
+        ph3_in.unitcell,
+        supercell_matrix=ph3_in.supercell_matrix,
+        phonon_supercell_matrix=ph3_in.phonon_supercell_matrix,
+        primitive_matrix=ph3_in.primitive_matrix,
+    )
+    ph3.dataset = ph3_in.dataset
+    ph3.phonon_dataset = ph3_in.phonon_dataset
+    ph3.supercell_energies = ph3_in.supercell_energies + 1
+    ph3.phonon_supercell_energies = ph3_in.phonon_supercell_energies + 1
+
+    np.testing.assert_allclose(ph3_in.supercell_energies + 1, ph3.supercell_energies)
+    np.testing.assert_allclose(
+        ph3_in.phonon_supercell_energies + 1, ph3.phonon_supercell_energies
+    )
+
+    ph3.forces = ph3_in.forces + 1
+    ph3.phonon_forces = ph3_in.phonon_forces + 1
+    np.testing.assert_allclose(ph3_in.forces + 1, ph3.forces)
+    np.testing.assert_allclose(ph3_in.phonon_forces + 1, ph3.phonon_forces)

test/conftest.py

@@ -483,6 +483,20 @@ def aln_lda(request) -> Phono3py:
     )
 
 
+@pytest.fixture(scope="session")
+def si_111_222_fd() -> Phono3py:
+    """Return Phono3py class instance of Si-1x1x1-2x2x2 FD."""
+    yaml_filename = cwd / "phono3py_params_Si-111-222-fd.yaml.xz"
+    return phono3py.load(yaml_filename, produce_fc=False, log_level=1)
+
+
+@pytest.fixture(scope="session")
+def si_111_222_rd() -> Phono3py:
+    """Return Phono3py class instance of Si-1x1x1-2x2x2 RD."""
+    yaml_filename = cwd / "phono3py_params_Si-111-222-rd.yaml.xz"
+    return phono3py.load(yaml_filename, produce_fc=False, log_level=1)
+
+
 @pytest.fixture(scope="session")
 def ph_nacl() -> Phonopy:
     """Return Phonopy class instance of NaCl 2x2x2."""
@@ -512,7 +526,7 @@ def ph_si() -> Phonopy:
 
 
 @pytest.fixture(scope="session")
-def si_111_222_fd() -> tarfile.TarFile:
+def si_111_222_fd_raw_data() -> tarfile.TarFile:
     """Return Si fc3 111 fc2 222 vasp inputs.
 
     tar.getnames()
@@ -546,7 +560,7 @@ def si_111_222_fd() -> tarfile.TarFile:
 
 
 @pytest.fixture(scope="session")
-def si_111_222_rd() -> tarfile.TarFile:
+def si_111_222_rd_raw_data() -> tarfile.TarFile:
     """Return Si fc3 111 fc2 222 vasp inputs.
 
     tar.getnames()