Merge pull request #32 from phonopy/phelel-script-read-nac

Read NAC params in phelel command

src/phelel/api_phelel.py

@@ -509,5 +509,6 @@ def _get_phonopy(
             symprec=self._symprec,
             is_symmetry=self._is_symmetry,
             store_dense_svecs=False,
+            calculator=self._calculator,
             log_level=self._log_level,
         )

src/phelel/cui/create_supercells.py

@@ -1,12 +1,14 @@
 """Utilities of main CUI script."""
 
+import pathlib
 from typing import Optional, Union
 
 from phono3py.interface.calculator import (
     get_additional_info_to_write_fc2_supercells,
     get_additional_info_to_write_supercells,
     get_default_displacement_distance,
 )
+from phonopy.cui.phonopy_script import store_nac_params
 from phonopy.interface.calculator import write_supercells_with_displacements
 
 from phelel.api_phelel import Phelel
@@ -17,6 +19,7 @@ def create_phelel_supercells(
     settings,
     symprec,
     interface_mode="vasp",
+    load_phelel_yaml=False,
     log_level=1,
 ):
     """Create displacements and supercells.
@@ -26,6 +29,8 @@ def create_phelel_supercells(
 
     """
     optional_structure_info = cell_info["optional_structure_info"]
+    unitcell_filename = cell_info["optional_structure_info"][0]
+    phe_yml = cell_info["phonopy_yaml"]
 
     phelel = Phelel(
         cell_info["unitcell"],
@@ -39,7 +44,7 @@ def create_phelel_supercells(
 
     if log_level:
         print("")
-        print('Unit cell was read from "%s".' % optional_structure_info[0])
+        print(f'Unit cell was read from "{unitcell_filename}".')
 
     generate_phelel_supercells(
         phelel,
@@ -50,6 +55,16 @@ def create_phelel_supercells(
         log_level=log_level,
     )
 
+    if pathlib.Path("BORN").exists() or (phe_yml and phe_yml.nac_params):
+        store_nac_params(
+            phelel.phonon,
+            settings,
+            phe_yml,
+            unitcell_filename,
+            log_level,
+            load_phonopy_yaml=load_phelel_yaml,
+        )
+
     additional_info = get_additional_info_to_write_supercells(
         interface_mode, phelel.supercell_matrix
     )

src/phelel/cui/phelel_script.py

@@ -13,6 +13,7 @@
     print_error,
     print_error_message,
     print_version,
+    store_nac_params,
 )
 from phonopy.interface.calculator import get_default_physical_units
 from phonopy.structure.cells import print_cell
@@ -47,22 +48,22 @@ def finalize_phelel(
     filename: Union[str, pathlib.Path] = "phelel.yaml",
     sys_exit_after_finalize: bool = True,
 ) -> None:
-    """Write phono3py.yaml and then exit.
+    """Write phelel.yaml and then exit.
 
     Parameters
     ----------
-    phono3py : Phono3py
-        Phono3py instance.
+    phelel : Phelel
+        Phelel instance.
     confs : dict
         This contains the settings and command options that the user set.
     log_level : int
         Log level. 0 means quiet.
     displacements_mode : Bool
         When True, crystal structure is written in the length unit of
-        calculator interface in phono3py_disp.yaml. Otherwise, the
+        calculator interface in phelel_disp.yaml. Otherwise, the
         default unit (angstrom) is used.
     filename : str, optional
-        phono3py.yaml is written in this filename.
+        phelel.yaml is written in this filename.
 
     """
     if displacements_mode:
@@ -165,6 +166,7 @@ def main(**argparse_control):
             cell_info,
             settings,
             symprec,
+            load_phelel_yaml=load_phelel_yaml,
             log_level=log_level,
         )
         finalize_phelel(
@@ -189,7 +191,7 @@ def main(**argparse_control):
 
     if log_level > 0:
         print("")
-        print('Crystal structure was read from "%s".' % unitcell_filename)
+        print(f'Crystal structure was read from "{unitcell_filename}".')
         print("Settings:")
         if (np.diag(np.diag(supercell_matrix)) - supercell_matrix).any():
             print("  Supercell matrix:")
@@ -246,12 +248,23 @@ def main(**argparse_control):
                     print(f'Read displacement datasets from "{filename}".')
                 phe_yml = PhelelYaml()
                 phe_yml.read(filename)
+
             phelel.dataset = phe_yml.dataset
             if phe_yml.phonon_dataset is None:
                 phelel.phonon_dataset = phe_yml.dataset
             else:
                 phelel.phonon_dataset = phe_yml.phonon_dataset
 
+            if pathlib.Path("BORN").exists() or phe_yml.nac_params:
+                store_nac_params(
+                    phelel.phonon,
+                    settings,
+                    cell_info["phonopy_yaml"],
+                    unitcell_filename,
+                    log_level,
+                    load_phonopy_yaml=load_phelel_yaml,
+                )
+
         if settings.create_derivatives:
             create_derivatives(
                 phelel,

src/phelel/interface/vasp/derivatives.py

@@ -242,5 +242,5 @@ def _read_PAW_strength_and_overlap(
             Dijs.append(dij)
             qijs.append(qij)
             if log_level:
-                print('"{Dij_qij_path}" was read.')
+                print(f'"{Dij_qij_path}" was read.')
     return Dijs, qijs

test/cui/test_phelel_cui.py

@@ -39,7 +39,7 @@ def __contains__(self, item):
 
 
 def test_phelel_script():
-    """Test phonopy-load command."""
+    """Test phelel command."""
     # Check sys.exit(0)
     cell_filename = str(cwd / ".." / "phelel_disp_C111.yaml")
     argparse_control = _get_phelel_load_args(cell_filename=cell_filename)