Transition to pymatgen VASP input sets

.github/workflows/testing.yml

@@ -61,15 +61,16 @@ jobs:
           python -m pip install --upgrade pip
           mkdir -p ~/.abinit/pseudos
           cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
+          pip install git+https://github.com/materialsproject/pymatgen
           # ase needed to get FrechetCellFilter used by ML force fields
           pip install git+https://gitlab.com/ase/ase
           pip install .[strict,tests,abinit]
           pip install torch-runstats
           pip install --no-deps nequip==0.5.6
 
-      - name: Install pymatgen from master if triggered by pymatgen repo dispatch
-        if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
-        run: pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'
+      #- name: Install pymatgen from master if triggered by pymatgen repo dispatch
+      #  if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
+      #  run: pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'
 
       - name: Test
         env:

src/atomate2/abinit/sets/base.py

@@ -325,12 +325,11 @@ def get_input_set(
         ----------
         structure : Structure
             Pymatgen Structure object.
-        restart_from : str or Path or list or tuple
-            Directory (as a str or Path) or list/tuple of 1 directory (as a str
-            or Path) to restart from.
-        prev_outputs : str or Path or list or tuple
-            Directory (as a str or Path) or list/tuple of directories (as a str
-            or Path) needed as dependencies for the AbinitInputSet generated.
+        restart_from : str | Path | list | tuple
+            Directory or list/tuple of 1 directory to restart from.
+        prev_outputs : str | Path | list | tuple
+            Directory or list/tuple of directories needed as dependencies for the
+                AbinitInputSet generated.
         """
         # Get the pseudos as a PseudoTable
         pseudos = as_pseudo_table(self.pseudos) if self.pseudos else None

src/atomate2/abinit/utils/history.py

@@ -195,7 +195,7 @@ def get_total_run_time(self) -> Any:
         """Get the total run time based summing the abinit stop event run times."""
         total_run_time = 0
         for te in self.get_events_by_types(JobEvent.ABINIT_STOP):
-            run_time = te.details.get("run_time", None)
+            run_time = te.details.get("run_time")
             if run_time:
                 total_run_time += run_time
 

src/atomate2/common/files.py

@@ -35,11 +35,11 @@ def copy_files(
         either "usernamehost" or just "host" in which case the username
         will be inferred from the current user. If ``None``, the local filesystem will
         be used as the source.
-    include_files : None or list of (str or .Path)
+    include_files : None | list[str | Path]
         Filenames to include as a list of str or Path objects given relative to
         ``src_dir``. Glob file paths are supported, e.g. "\*.dat". If ``None``, all
         files in the source directory will be copied.
-    exclude_files : None or list of (str or .Path)
+    exclude_files : None | list[str | Path]
         Filenames to exclude. Supports glob file matching, e.g., "\*.dat".
     suffix : str
         A suffix to add to copied files. For example ".original".
@@ -97,11 +97,11 @@ def delete_files(
         The hostname used to specify a remote filesystem. Can be given as either
         "username@host" or just "host" in which case the username will be
         inferred from the current user. If ``None``, the local filesystem will be used.
-    include_files : None or list of (str or Path)
+    include_files : None or list of (str | Path)
         Filenames to include as a list of str or Path objects given relative to
         directory. Glob file paths are supported, e.g. "\*.dat". If ``None``, all files
         in the directory will be deleted.
-    exclude_files : None or list of (str or Path)
+    exclude_files : None or list of (str | Path)
         Filenames to exclude. Supports glob file matching, e.g., "\*.dat".
     allow_missing : bool
         Whether to error if a file in ``include_files`` is not present in the directory.
@@ -188,11 +188,11 @@ def gzip_files(
         The hostname used to specify a remote filesystem. Can be given as either
         "username@host" or just "host" in which case the username will be
         inferred from the current user. If ``None``, the local filesystem will be used.
-    include_files : None or list of (str or Path)
+    include_files : None or list of (str | Path)
         Filenames to include as a list of str or Path objects given relative to
         directory. Glob file paths are supported, e.g. "\*.dat". If ``None``, all files
         in the directory will be gzipped.
-    exclude_files : None or list of (str or Path)
+    exclude_files : None or list of (str | Path)
         Filenames to exclude. Supports glob file matching, e.g., "\*.dat".
     allow_missing : bool
         Whether to error if a file in ``include_files`` is not present in the directory.
@@ -241,11 +241,11 @@ def gunzip_files(
         The hostname used to specify a remote filesystem. Can be given as either
         "username@host" or just "host" in which case the username will be
         inferred from the current user. If ``None``, the local filesystem will be used.
-    include_files : None or list of (str or Path)
+    include_files : None or list of (str | Path)
         Filenames to include as a list of str or Path objects given relative to
         directory. Glob file paths are supported, e.g. "\*.dat". If ``None``, all
         gzipped files in the directory will be gunzipped.
-    exclude_files : None or list of (str or Path)
+    exclude_files : None or list of (str | Path)
         Filenames to exclude. Supports glob file matching, e.g., "\*.dat".
     allow_missing : bool
         Whether to error if a file in ``include_files`` is not present in the directory.
@@ -287,11 +287,11 @@ def find_and_filter_files(
         A file client.
     directory : str or Path
         A directory in which to find files.
-    include_files : None or list of (str or Path)
+    include_files : None or list of (str | Path)
         Filenames to include as a list of str or Path objects given relative to
         directory. Glob file paths are supported, e.g. "\*.dat". If ``None``, all files
         in the source directory will be returned.
-    exclude_files : None or list of (str or Path)
+    exclude_files : None or list of (str | Path)
         Filenames to exclude. Supports glob file matching, e.g., "\*.dat".
     host : str or None
         A hostname used to specify a remote filesystem. Can be given as either

src/atomate2/common/jobs/defect.py

@@ -459,7 +459,7 @@ def get_defect_entry(charge_state_summary: dict, bulk_summary: dict) -> list[dic
                 "bulk_dir_name": bulk_dir_name,
                 "bulk_locpot": bulk_locpot,
                 "bulk_uuid": bulk_summary.get("uuid"),
-                "defect_uuid": qq_summary.get("uuid", None),
+                "defect_uuid": qq_summary.get("uuid"),
             }
         )
     return defect_ent_res

src/atomate2/cp2k/jobs/base.py

@@ -92,7 +92,7 @@ class BaseCp2kMaker(Maker):
     ----------
     name : str
         The job name.
-    input_set_generator : .VaspInputGenerator
+    input_set_generator : .Cp2kInputGenerator
         A generator used to make the input set.
     write_input_set_kwargs : dict
         Keyword arguments that will get passed to :obj:`.write_cp2k_input_set`.

src/atomate2/vasp/files.py

@@ -201,4 +201,4 @@ def write_vasp_input_set(
                 Path(filename).unlink()
 
     logger.info("Writing VASP input set.")
-    vis.write_input(directory, potcar_spec=potcar_spec, **kwargs)
+    vis.write_input(directory, **kwargs)

src/atomate2/vasp/flows/defect.py

@@ -207,8 +207,8 @@ def check_defect_relax_maker(relax_maker: RelaxMaker) -> RelaxMaker:
             input_gen = relax_maker.input_set_generator
             if input_gen.use_structure_charge is False:
                 raise ValueError("use_structure_charge should be set to True")
-            isif_ = input_gen.get_incar_updates(None).get("ISIF", None)
-            isif = input_gen.user_incar_settings.get("ISIF", isif_)
+            default_isif = input_gen.incar_updates.get("ISIF")
+            isif = input_gen.user_incar_settings.get("ISIF", default_isif)
             if isif != 2:
                 raise ValueError("ISIF should be set to 2")
             return relax_maker

src/atomate2/vasp/jobs/lobster.py

@@ -103,14 +103,11 @@ def get_basis_infos(
     """
     # this logic enables handling of a flow or a simple maker
     try:
-        potcar_symbols = vasp_maker.static_maker.input_set_generator._get_potcar(
-            structure=structure, potcar_spec=True
-        )
-
+        vis = vasp_maker.static_maker.input_set_generator
     except AttributeError:
-        potcar_symbols = vasp_maker.input_set_generator._get_potcar(
-            structure=structure, potcar_spec=True
-        )
+        vis = vasp_maker.input_set_generator
+    vis.structure = structure
+    potcar_symbols = vis.potcar_symbols
 
     # get data from LobsterInput
     list_basis_dict = Lobsterin.get_all_possible_basis_functions(