Refactoring around API

src/phelel/api_phelel.py

@@ -16,19 +16,20 @@
 
 from phelel.base.Dij_qij import DDijQij
 from phelel.base.local_potential import DLocalPotential
-from phelel.file_IO import write_dDijdu_hdf5, write_dVdu_hdf5, write_phelel_params_hdf5
+from phelel.file_IO import write_phelel_params_hdf5
 from phelel.version import __version__
 
 
 @dataclass
-class PhelelInput:
+class PhelelDataset:
     """Data structure of input data to run derivatives."""
 
-    local_potentials: list
-    Dijs: list
-    qijs: list
+    local_potentials: list[np.ndarray]
+    Dijs: list[np.ndarray]
+    qijs: list[np.ndarray]
     lm_channels: list[dict]
     dataset: Optional[dict] = None
+    phonon_dataset: Optional[dict] = None
     forces: Optional[np.ndarray] = None
 
 
@@ -79,6 +80,8 @@ def __init__(
         symprec: float = 1e-5,
         is_symmetry: bool = True,
         calculator: Optional[str] = None,
+        nufft: Optional[str] = None,
+        finufft_eps: Optional[float] = None,
         log_level: int = 0,
     ):
         """Init method.
@@ -115,18 +118,21 @@ def __init__(
             Use crystal symmetry or not. Default is True.
         calculator :
             A dummy parameter.
+        nufft : str or None, optional
+            'finufft' only. Default is None, which corresponds to 'finufft'.
+        finufft_eps : float or None, optional
+            Accuracy of finufft interpolation. Default is None, which
+            corresponds to 1e-6.
         log_level : int, optional
             Log level. 0 is most quiet. Default is 0.
 
         """
         self._unitcell = unitcell
-        if fft_mesh is None:
-            self._fft_mesh = None
-        else:
-            self.fft_mesh = fft_mesh
         self._symprec = symprec
         self._is_symmetry = is_symmetry
         self._calculator = calculator
+        self._nufft = nufft
+        self._finufft_eps = finufft_eps
         self._log_level = log_level
 
         ph = self._get_phonopy(supercell_matrix, primitive_matrix)
@@ -156,7 +162,17 @@ def __init__(
         self._dVdu = None
         self._dDijdu = None
 
-        self._raw_data = None
+        if fft_mesh is None:
+            self._fft_mesh = None
+        else:
+            self.fft_mesh = fft_mesh
+
+        self._dDijdu = DDijQij(
+            self._supercell,
+            symmetry=self._symmetry,
+            atom_indices=self._atom_indices_in_derivatives,
+            verbose=self._log_level > 0,
+        )
 
     @property
     def version(self) -> str:
@@ -306,12 +322,22 @@ def phonon(self) -> Phonopy:
 
     @property
     def fft_mesh(self) -> np.ndarray:
-        """Return FFT mesh numbers."""
+        """Setter and getter of FFT mesh numbers."""
         return self._fft_mesh
 
     @fft_mesh.setter
-    def fft_mesh(self, fft_mesh):
+    def fft_mesh(self, fft_mesh: Union[Sequence, np.ndarray]):
         self._fft_mesh = np.array(fft_mesh, dtype="int_")
+        self._dVdu = DLocalPotential(
+            self._fft_mesh,
+            self._p2s_matrix,
+            self._supercell,
+            symmetry=self._symmetry,
+            atom_indices=self._atom_indices_in_derivatives,
+            nufft=self._nufft,
+            finufft_eps=self._finufft_eps,
+            verbose=self._log_level > 0,
+        )
 
     @property
     def dVdu(self) -> Optional[DLocalPotential]:
@@ -323,7 +349,7 @@ def dVdu(self, dVdu: DLocalPotential):
         self._dVdu = dVdu
 
     @property
-    def dDijdu(self) -> Optional[DDijQij]:
+    def dDijdu(self) -> DDijQij:
         """Return DDijQij class instance."""
         return self._dDijdu
 
@@ -368,7 +394,7 @@ def generate_displacements(
         )
         self._dataset = ph.dataset
 
-    def run_derivatives(self, phe_input: PhelelInput, nufft=None, finufft_eps=None):
+    def run_derivatives(self, phe_input: PhelelDataset):
         """Run displacement derivatives calculations from temporary raw data.
 
         Note
@@ -383,20 +409,27 @@ def run_derivatives(self, phe_input: PhelelInput, nufft=None, finufft_eps=None):
             )
             raise RuntimeError(msg)
 
-        self.prepare_phonon(dataset=phe_input.dataset, forces=phe_input.forces)
-        self.run_dVdu(
-            phe_input.local_potentials,
-            dataset=phe_input.dataset,
-            nufft=nufft,
-            finufft_eps=finufft_eps,
-        )
-        self.run_dDijdu(
-            phe_input.Dijs,
-            phe_input.qijs,
+        if phe_input.dataset is not None:
+            self._dataset = phe_input.dataset
+        loc_pots = phe_input.local_potentials
+        Dijs = phe_input.Dijs
+        qijs = phe_input.qijs
+
+        if phe_input.phonon_dataset is not None:
+            self._prepare_phonon(
+                dataset=phe_input.phonon_dataset, forces=phe_input.forces
+            )
+        else:
+            self._prepare_phonon(dataset=self._dataset, forces=phe_input.forces)
+        self._dVdu.run(loc_pots[0], loc_pots[1:], self._dataset["first_atoms"])
+        self._dDijdu.run(
+            Dijs[0],
+            Dijs[1:],
+            qijs[0],
+            qijs[1:],
+            self._dataset["first_atoms"],
             phe_input.lm_channels,
-            dataset=phe_input.dataset,
         )
-        self._raw_data = None
 
     def save_hdf5(
         self, filename: Union[str, bytes, os.PathLike, io.IOBase] = "phelel_params.hdf5"
@@ -421,71 +454,7 @@ def save_hdf5(
             filename=filename,
         )
 
-    def run_dVdu(
-        self,
-        loc_pots,
-        dataset=None,
-        nufft=None,
-        finufft_eps=None,
-        write_hdf5=False,
-    ):
-        """Calculate dV/du.
-
-        Parameters
-        ----------
-        nufft : str or None, optional
-            'finufft' only. Default is None, which corresponds to 'finufft'.
-        finufft_eps : float or None, optional
-            Accuracy of finufft interpolation. Default is None, which
-            corresponds to 1e-6.
-
-        """
-        dVdu = DLocalPotential(
-            self._fft_mesh,
-            self._p2s_matrix,
-            self._supercell,
-            symmetry=self._symmetry,
-            atom_indices=self._atom_indices_in_derivatives,
-            nufft=nufft,
-            finufft_eps=finufft_eps,
-            verbose=True,
-        )
-        if dataset is not None:
-            self._dataset = dataset
-        displacements = self._dataset["first_atoms"]
-        dVdu.run(loc_pots[0], loc_pots[1:], displacements)
-
-        if write_hdf5:
-            write_dVdu_hdf5(
-                dVdu,
-                self._supercell_matrix,
-                self._primitive_matrix,
-                self._primitive,
-                self._unitcell,
-                self._supercell,
-                filename="dVdu.hdf5",
-            )
-        self._dVdu = dVdu
-
-    def run_dDijdu(self, Dijs, qijs, lm_channels, dataset=None, write_hdf5=False):
-        """Calculate dDij/du."""
-        dDijdu = DDijQij(
-            self._supercell,
-            symmetry=self._symmetry,
-            atom_indices=self._atom_indices_in_derivatives,
-            verbose=True,
-        )
-        if dataset is not None:
-            self._dataset = dataset
-        displacements = self._dataset["first_atoms"]
-        dDijdu.run(Dijs[0], Dijs[1:], qijs[0], qijs[1:], displacements, lm_channels)
-
-        if write_hdf5:
-            write_dDijdu_hdf5(dDijdu)
-
-        self._dDijdu = dDijdu
-
-    def prepare_phonon(
+    def _prepare_phonon(
         self,
         dataset: Optional[dict] = None,
         forces: Optional[

src/phelel/cui/phelel_argparse.py

@@ -56,7 +56,6 @@ def get_parser():
         "--dim-phonon",
         nargs="+",
         dest="phonon_supercell_dimension",
-        metavar="INT",
         default=None,
         help=(
             "Supercell dimensions for phonon with three integers or "
@@ -65,9 +64,8 @@ def get_parser():
     )
     parser.add_argument(
         "--fft-mesh",
-        nargs=3,
+        nargs="+",
         dest="fft_mesh_numbers",
-        metavar="INT",
         default=None,
         help="FFT mesh numbers used in primitive cell",
     )

src/phelel/cui/phelel_script.py

@@ -134,6 +134,21 @@ def main(**argparse_control):
         cell_info["phonon_supercell_matrix"] = ph_smat
     phonon_supercell_matrix = cell_info["phonon_supercell_matrix"]
 
+    if settings.create_displacements:
+        phelel = create_phelel_supercells(
+            cell_info,
+            settings,
+            symprec,
+            log_level=log_level,
+        )
+        finalize_phelel(
+            phelel,
+            confs=phelel_conf.confs,
+            log_level=log_level,
+            displacements_mode=True,
+            filename="phelel_disp.yaml",
+        )
+
     fft_mesh = settings.fft_mesh_numbers
     phelel = Phelel(
         unitcell,
@@ -143,6 +158,7 @@ def main(**argparse_control):
         fft_mesh=fft_mesh,
         symprec=symprec,
         is_symmetry=settings.is_symmetry,
+        finufft_eps=settings.finufft_eps,
     )
 
     if log_level > 0:
@@ -179,20 +195,6 @@ def main(**argparse_control):
             print_cell(phelel.phonon.supercell)
         print("-" * 76)
 
-    if settings.create_displacements:
-        phelel = create_phelel_supercells(
-            cell_info,
-            settings,
-            symprec,
-            log_level=log_level,
-        )
-        finalize_phelel(
-            phelel,
-            confs=phelel_conf.confs,
-            log_level=log_level,
-            displacements_mode=True,
-            filename="phelel_disp.yaml",
-        )
     ##################################
     # Create dV/du, dDij/du, dqij/du #
     ##################################
@@ -229,13 +231,13 @@ def main(**argparse_control):
             create_derivatives(
                 phelel,
                 settings.create_derivatives,
-                finufft_eps=settings.finufft_eps,
                 subtract_rfs=settings.subtract_rfs,
                 log_level=log_level,
             )
-            phelel.save_hdf5(filename="phelel_params.hdf5")
-            if log_level > 0:
-                print('"phelel_params.hdf5" has been created.')
+            if phelel.fft_mesh is not None:
+                phelel.save_hdf5(filename="phelel_params.hdf5")
+                if log_level > 0:
+                    print('"phelel_params.hdf5" has been created.')
             print_end()
             sys.exit(0)
 

src/phelel/cui/settings.py

@@ -77,10 +77,7 @@ def _read_options(self):
                 self._confs["create_derivatives"] = " ".join(dir_names)
         if "fft_mesh_numbers" in self._args:
             if self._args.fft_mesh_numbers:
-                if len(self._args.fft_mesh_numbers) == 1:
-                    self._confs["fft_mesh"] = self._args.fft_mesh_numbers[0]
-                elif len(self._args.fft_mesh_numbers) == 3:
-                    self._confs["fft_mesh"] = " ".join(self._args.fft_mesh_numbers)
+                self._confs["fft_mesh"] = " ".join(self._args.fft_mesh_numbers)
         if "finufft_eps" in self._args:
             if self._args.finufft_eps is not None:
                 self._confs["finufft_eps"] = self._args.finufft_eps