Merge branch 'develop' into publish-gh-pages

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Jan-8-2025: Version 0.8.1
+
+- Fix minor bugs in velph command
+
 ## Jan-5-2025: Version 0.8.0
 
 - Refactoring of `Phelel` class

doc/conf.py

@@ -11,7 +11,7 @@
 author = "Atsushi Togo"
 
 version = "0.8"
-release = "0.8.0"
+release = "0.8.1"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

doc/reference.md

@@ -0,0 +1,12 @@
+(references)=
+# References
+
+This page presents the methodologies and software packages that the phelel code relies on.
+
+(reference_finufft)=
+## finufft
+
+The local potentials from VASP calculation results are interpolated using
+[finufft](https://finufft.readthedocs.io/). For more information and references
+on finufft, visit
+[https://finufft.readthedocs.io/en/latest/refs.html](https://finufft.readthedocs.io/en/latest/refs.html).

doc/velph-subcommands.md

@@ -66,6 +66,14 @@ This subcommand calculates the derivatives of local potentials and PAW strengths
 with respect to displacement, performing similar operations as steps 1 and 3
 carried out by the `phelel` command in the {ref}`workflow <workflow_minimal>`.
 
+The subcommands below should be executed in the following order:
+
+1. {ref}`velph_phelel_init_subcommand`
+2. {ref}`velph_phelel_generate_subcommand`
+3. {ref}`velph_phelel_differentiate_subcommand`
+4. {ref}`velph_phelel_phonopy_subcommand` (optional)
+
+(velph_phelel_init_subcommand)=
 ### `velph phelel init`
 
 This subcommand generates the `phelel_disp.yaml` file, which contains
@@ -82,8 +90,11 @@ Found "nac" directory. Read NAC params.
 VASP input files will be generated by "velph phelel generate".
 ```
 
+(velph_phelel_generate_subcommand)=
 ### `velph phelel generate`
 
+VASP input files and job scripts are generated.
+
 ```bash
 % velph phelel generate
 VASP input files were generated in "phelel/disp-000".
@@ -93,10 +104,33 @@ VASP input files were generated in "phelel/disp-003".
 VASP input files were generated in "phelel/disp-004".
 ```
 
+(velph_phelel_differentiate_subcommand)=
 ### `velph phelel differentiate`
 
+The derivatives of local potentials and PAW strengths with respect to
+displacement are calculated and stored in `phelel_params.hdf5`.
+
+```bash
+% velph phelel differentiate
+FFT mesh: [30 30 30].
+Running finufft (eps=1.000e-06)...
+Running finufft (eps=1.000e-06)...
+"phelel/phelel_params.hdf5" has been made.
+```
+
+(velph_phelel_phonopy_subcommand)=
 ### `velph phelel phonopy`
 
+`phonopy_params.yaml` that contains information necessary for phonon calculation
+by the phonopy code is generated from `phelel_disp.yaml` and the results of the
+VASP inputs generated by `velph phelel generate`.
+
+```bash
+% velph phelel phonopy
+"phelel/phonopy_params.yaml" has been made.
+% phonopy-load phelel/phonopy_params.yaml --band auto -p
+```
+
 ## `velph transport`
 
 ### `velph transport generate`

src/phelel/api_phelel.py

@@ -349,11 +349,6 @@ def unit_conversion_factor(self) -> float:
         else:
             return self._phonon.unit_conversion_factor
 
-    @property
-    def phonon(self) -> Optional[Phonopy]:
-        """Return Phonopy class instance."""
-        return self._phonon
-
     @property
     def fft_mesh(self) -> np.ndarray:
         """Setter and getter of FFT mesh numbers."""
@@ -427,6 +422,20 @@ def generate_displacements(
             distance=distance, is_plusminus=is_plusminus, is_diagonal=is_diagonal
         )
 
+    def generate_phonon_displacements(
+        self,
+        distance=0.01,
+        is_plusminus="auto",
+        is_diagonal=True,
+    ):
+        """Generate displacement dataset."""
+        if self._phonon is None:
+            msg = "Phonon instance has to be initialized."
+            raise RuntimeError(msg)
+        self._phonon.generate_displacements(
+            distance=distance, is_plusminus=is_plusminus, is_diagonal=is_diagonal
+        )
+
     def run_derivatives(self, phe_input: PhelelDataset):
         """Run displacement derivatives calculations from temporary raw data.
 
@@ -488,6 +497,7 @@ def save_hdf5(
             "atom_indices_in_derivatives": self._atom_indices_in_derivatives,
             "disp_dataset": self._phelel_phonon.dataset,
             "nac_params": self._phelel_phonon.nac_params,
+            "filename": filename,
         }
         if self._phonon is not None:
             params.update(
@@ -497,11 +507,29 @@ def save_hdf5(
                     "phonon_primitive": self._phonon.primitive,
                     "phonon_supercell": self._phonon.supercell,
                     "symmetry_dataset": self._phonon.primitive_symmetry.dataset,
-                    "filename": filename,
                 }
             )
         write_phelel_params_hdf5(**params)
 
+    def save_phonon(
+        self,
+        filename="phonopy_params.yaml",
+        settings=None,
+        hdf5_settings=None,
+        compression: Union[str, bool] = False,
+    ):
+        """Save phonon in yaml format."""
+        if self._phonon is None:
+            ph = self._phelel_phonon
+        else:
+            ph = self._phonon
+        ph.save(
+            filename=filename,
+            settings=settings,
+            hdf5_settings=hdf5_settings,
+            compression=compression,
+        )
+
     def _prepare_phonon(
         self,
         dataset: Optional[dict] = None,

src/phelel/cui/create_supercells.py

@@ -78,14 +78,14 @@ def create_phelel_supercells(
         additional_info=additional_info,
     )
 
-    if phelel.phonon is not None:
+    if phelel.phonon_supercell_matrix is not None:
         additional_info = get_additional_info_to_write_fc2_supercells(
             interface_mode, phelel.phonon_supercell_matrix, suffix="PH"
         )
         write_supercells_with_displacements(
-            phelel.phonon.calculator,
-            phelel.phonon.supercell,
-            phelel.phonon.supercells_with_displacements,
+            phelel.calculator,
+            phelel.phonon_supercell,
+            phelel.phonon_supercells_with_displacements,
             optional_structure_info=optional_structure_info,
             additional_info=additional_info,
         )
@@ -115,12 +115,12 @@ def generate_phelel_supercells(
         print("Displacement distance: %s" % _distance)
         print("Number of displacements: %d" % len(phelel.supercells_with_displacements))
 
-    if phelel.phonon is not None:
-        phelel.phonon.generate_displacements(
+    if phelel.phonon_supercell_matrix is not None:
+        phelel.generate_phonon_displacements(
             distance=distance, is_plusminus=is_plusminus, is_diagonal=is_diagonal
         )
         if log_level:
             print(
                 "Number of displacements for phonon: %d"
-                % len(phelel.phonon.supercells_with_displacements)
+                % len(phelel.phonon_supercells_with_displacements)
             )

src/phelel/cui/phelel_script.py

@@ -219,7 +219,7 @@ def main(**argparse_control):
         print_cell(phelel.supercell)
         if phelel.phonon_supercell_matrix is not None:
             print("-" * 28 + " phonon super cell " + "-" * 29)
-            print_cell(phelel.phonon.supercell)
+            print_cell(phelel.phonon_supercell)
         print("-" * 76)
 
     ##################################

src/phelel/interface/vasp/derivatives.py

@@ -78,10 +78,7 @@ def read_files(
             "atoms in the vasprun.xml file."
         )
 
-    if phelel.phonon_supercell_matrix is None:
-        phelel.forces = forces
-    else:
-        phelel.phonon.forces = forces
+    phelel.forces = forces
 
     nac_params = _read_born(
         phelel.primitive, phelel.primitive_symmetry, log_level=log_level

src/phelel/velph/cli/phelel/phonopy.py

@@ -63,12 +63,16 @@ def create_phonopy_yaml(
 
     # NAC params should be contained phelel_disp.yaml.
     # Therefore nac_params is not set to phe here.
+    if phe.phonon_supercell_matrix is None:
+        supercell = phe.supercell
+    else:
+        supercell = phe.phonon_supercell
     forces = read_forces_from_vasprunxmls(
         [d / "vasprun.xml" for d in dir_names],
-        phe.phonon,
+        supercell,
         subtract_rfs=subtract_residual_forces,
         log_level=0,
     )
-    phe.phonon.forces = forces
-    phe.phonon.save(filename=phonopy_yaml_filename)
+    phe.forces = forces
+    phe.save_phonon(filename=phonopy_yaml_filename)
     click.echo(f'"{phonopy_yaml_filename}" has been made.')

src/phelel/version.py

@@ -1,3 +1,3 @@
 """Version number."""
 
-__version__ = "0.8.0"
+__version__ = "0.8.1"