Merge branch 'rc'

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
     - "--ignore=E203,W503"
 
 - repo: https://github.com/psf/black
-  rev: 24.4.0
+  rev: 24.4.2
   hooks:
   - id: black
     args:

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## May-4-2024: Version 3.0.3
+
+- Release to follow the update of phonopy.
+
 ## Apr-21-2024: Version 3.0.2
 
 - New way of ph-ph interaction calculation (see {ref}`changelog_v290`) is used as

doc/conf.py

@@ -60,7 +60,7 @@
 # The short X.Y version.
 version = "3.0"
 # The full version, including alpha/beta/rc tags.
-release = "3.0.2"
+release = "3.0.3"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

phono3py/api_phono3py.py

@@ -34,8 +34,9 @@
 # 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 Optional, Union
+from typing import Literal, Optional, Union
 
 import numpy as np
 from phonopy.exception import ForceCalculatorRequiredError
@@ -582,6 +583,7 @@ def dataset(self):
                       {'number': atom index of second displaced atom,
                        'displacement': displacement in Cartesian coordinates},
                        'forces': forces on atoms in supercell,
+                       'supercell_energy': energy of supercell,
                        'pair_distance': distance between paired atoms,
                        'included': with cutoff pair distance in displacement
                                    pair generation, this indicates if this
@@ -591,9 +593,11 @@ def dataset(self):
                       ... ] }, ... ] }
             Type 2. All atomic displacements in each supercell:
                 {'displacements': ndarray, dtype='double', order='C',
-                                  shape=(supercells, atoms in supercell, 3)
+                                  shape=(supercells, atoms in supercell, 3),
                  'forces': ndarray, dtype='double',, order='C',
-                                  shape=(supercells, atoms in supercell, 3)}
+                                  shape=(supercells, atoms in supercell, 3),
+                 'supercell_energies': ndarray, dtype='double',
+                                  shape=(supercells,)}
             In type 2, displacements and forces can be given by numpy array
             with different shape but that can be reshaped to
             (supercells, natom, 3).
@@ -607,7 +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
 
@@ -622,12 +639,15 @@ def phonon_dataset(self):
                  'first_atoms': [
                    {'number': atom index of first displaced atom,
                     'displacement': displacement in Cartesian coordinates,
-                    'forces': forces on atoms in supercell} ... ]}
+                    'forces': forces on atoms in supercell,
+                    'supercell_energy': energy of supercell}, ... ]}
             Type 2. All atomic displacements in each supercell:
                 {'displacements': ndarray, dtype='double', order='C',
-                                  shape=(supercells, atoms in supercell, 3)
+                                  shape=(supercells, atoms in supercell, 3),
                  'forces': ndarray, dtype='double',, order='C',
-                                  shape=(supercells, atoms in supercell, 3)}
+                                  shape=(supercells, atoms in supercell, 3),
+                 'supercell_energies': ndarray, dtype='double',
+                                  shape=(supercells,)}
             In type 2, displacements and forces can be given by numpy array
             with different shape but that can be reshaped to
             (supercells, natom, 3).
@@ -637,7 +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):
@@ -816,45 +850,32 @@ def forces(self):
             be the same order of supercells_with_displacements.
 
         """
-        dataset = self._dataset
-        if "forces" in dataset:
-            return dataset["forces"]
-        elif "first_atoms" in dataset:
-            num_scells = len(dataset["first_atoms"])
-            for disp1 in dataset["first_atoms"]:
-                num_scells += len(disp1["second_atoms"])
-            forces = np.zeros(
-                (num_scells, self._supercell.get_number_of_atoms(), 3),
-                dtype="double",
-                order="C",
-            )
-            i = 0
-            for disp1 in dataset["first_atoms"]:
-                forces[i] = disp1["forces"]
-                i += 1
-            for disp1 in dataset["first_atoms"]:
-                for disp2 in disp1["second_atoms"]:
-                    forces[i] = disp2["forces"]
-                    i += 1
-            return forces
-        else:
-            raise RuntimeError("displacement dataset has wrong format.")
+        return self._get_forces_energies(target="forces")
 
     @forces.setter
-    def forces(self, forces_fc3):
-        forces = np.array(forces_fc3, dtype="double", order="C")
-        dataset = self._dataset
-        if "first_atoms" in dataset:
-            i = 0
-            for disp1 in dataset["first_atoms"]:
-                disp1["forces"] = forces[i]
-                i += 1
-            for disp1 in dataset["first_atoms"]:
-                for disp2 in disp1["second_atoms"]:
-                    disp2["forces"] = forces[i]
-                    i += 1
-        elif "displacements" in dataset or "forces" in dataset:
-            dataset["forces"] = forces
+    def forces(self, values):
+        self._set_forces_energies(values, target="forces")
+
+    @property
+    def supercell_energies(self):
+        """Setter and getter of supercell energies in displacement dataset.
+
+        A set of supercell energies of displaced supercells. The order of
+        displaced supercells has to match with that in displacement dataset.
+        shape=(displaced supercells,)
+
+        getter : ndarray
+
+        setter : array_like
+            The order of supercells used for calculating supercell energies has
+            to be the same order of supercells_with_displacements.
+
+        """
+        return self._get_forces_energies(target="supercell_energies")
+
+    @supercell_energies.setter
+    def supercell_energies(self, values):
+        self._set_forces_energies(values, target="supercell_energies")
 
     @property
     def phonon_displacements(self):
@@ -922,7 +943,7 @@ def phonon_displacements(self, displacements):
 
     @property
     def phonon_forces(self):
-        """Setter and getter of forces in displacement dataset for fc2.
+        """Setter and getter of forces in fc2 displacement dataset.
 
         A set of atomic forces in displaced supercells. The order of
         displaced supercells has to match with that in phonon displacement
@@ -936,39 +957,30 @@ def phonon_forces(self):
             be the same order of phonon_supercells_with_displacements.
 
         """
-        if self._phonon_dataset is None:
-            raise RuntimeError("phonon_displacement_dataset does not exist.")
-
-        dataset = self._phonon_dataset
-        if "forces" in dataset:
-            return dataset["forces"]
-        elif "first_atoms" in dataset:
-            num_scells = len(dataset["first_atoms"])
-            forces = np.zeros(
-                (num_scells, self._phonon_supercell.get_number_of_atoms(), 3),
-                dtype="double",
-                order="C",
-            )
-            for i, disp1 in enumerate(dataset["first_atoms"]):
-                forces[i] = disp1["forces"]
-            return forces
-        else:
-            raise RuntimeError("displacement dataset has wrong format.")
+        return self._get_phonon_forces_energies(target="forces")
 
     @phonon_forces.setter
-    def phonon_forces(self, forces_fc2):
-        if self._phonon_dataset is None:
-            raise RuntimeError("phonon_displacement_dataset does not exist.")
+    def phonon_forces(self, values):
+        self._set_phonon_forces_energies(values, target="forces")
 
-        forces = np.array(forces_fc2, dtype="double", order="C")
-        dataset = self._phonon_dataset
-        if "first_atoms" in dataset:
-            i = 0
-            for i, disp1 in enumerate(dataset["first_atoms"]):
-                disp1["forces"] = forces[i]
-                i += 1
-        elif "displacements" in dataset or "forces" in dataset:
-            dataset["forces"] = forces
+    @property
+    def phonon_supercell_energies(self):
+        """Setter and getter of supercell energies in fc2 displacement dataset.
+
+        shape=(displaced supercells,)
+
+        getter : ndarray
+
+        setter : array_like
+            The order of supercells used for calculating supercell energies has
+            to be the same order of phonon_supercells_with_displacements.
+
+        """
+        return self._get_phonon_forces_energies(target="supercell_energies")
+
+    @phonon_supercell_energies.setter
+    def phonon_supercell_energies(self, values):
+        self._set_phonon_forces_energies(values, target="supercell_energies")
 
     @property
     def phph_interaction(self):
@@ -2274,3 +2286,116 @@ def _extract_fc2_fc3_calculators(self, fc_calculator, fc_calculator_options, ord
             _fc_calculator_options = None
 
         return _fc_calculator, _fc_calculator_options
+
+    def _get_forces_energies(
+        self, target: Literal["forces", "supercell_energies"]
+    ) -> 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:  # type-1
+            num_scells = len(self._dataset["first_atoms"])
+            for disp1 in self._dataset["first_atoms"]:
+                num_scells += len(disp1["second_atoms"])
+            if target == "forces":
+                values = np.zeros(
+                    (num_scells, len(self._supercell), 3),
+                    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[type1_target]
+                count += 1
+            for disp1 in self._dataset["first_atoms"]:
+                for disp2 in disp1["second_atoms"]:
+                    values[count] = disp2[type1_target]
+                    count += 1
+            return values
+        return None
+
+    def _set_forces_energies(
+        self, values, target: Literal["forces", "supercell_energies"]
+    ):
+        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["supercell_energy"] = float(values[count])
+                count += 1
+            for disp1 in self._dataset["first_atoms"]:
+                for disp2 in disp1["second_atoms"]:
+                    if target == "forces":
+                        disp2[target] = np.array(
+                            values[count], dtype="double", order="C"
+                        )
+                    elif target == "supercell_energies":
+                        disp2["supercell_energy"] = float(values[count])
+                    count += 1
+        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:  # type-2
+            return self._phonon_dataset[target]
+        elif "first_atoms" in self._phonon_dataset:  # type-1
+            values = []
+            for disp in self._phonon_dataset["first_atoms"]:
+                if target == "forces":
+                    if target in disp:
+                        values.append(disp[target])
+                elif target == "supercell_energies":
+                    if "supercell_energy" in disp:
+                        values.append(disp["supercell_energy"])
+            if values:
+                return np.array(values, dtype="double", order="C")
+        return None
+
+    def _set_phonon_forces_energies(
+        self, values, target: Literal["forces", "supercell_energies"]
+    ):
+        if self._phonon_dataset is None:
+            raise RuntimeError("Dataset for fc2 does not exist.")
+
+        if "first_atoms" in self._phonon_dataset:
+            for disp, v in zip(self._phonon_dataset["first_atoms"], values):
+                if target == "forces":
+                    disp[target] = np.array(v, dtype="double", order="C")
+                elif target == "supercell_energies":
+                    disp["supercell_energy"] = float(v)
+        elif "displacements" in self._phonon_dataset:
+            _values = np.array(values, dtype="double", order="C")
+            natom = len(self._phonon_supercell)
+            ndisps = len(self._phonon_dataset["displacements"])
+            if target == "forces" and (
+                _values.ndim != 3 or _values.shape != (ndisps, natom, 3)
+            ):
+                raise RuntimeError(f"Array shape of input {target} is incorrect.")
+            elif target == "supercell_energies":
+                if _values.ndim != 1 or _values.shape != (ndisps,):
+                    raise RuntimeError(f"Array shape of input {target} is incorrect.")
+            self._phonon_dataset[target] = _values
+        else:
+            raise RuntimeError("Set of FC2 displacements is not available.")