Merge branch 'main' into pydantic2

docs/about/contributors.md

@@ -24,7 +24,7 @@ Lawrence Livermore National Laboratory
 [jmmshn]: https://github.com/jmmshn
 [0000-0002-2743-7531]: https://orcid.org/0000-0002-2743-7531
 
-**Janosh Riebesell** [![gh]][janosh] [![orc]][0000-0001-5233-3462]\
+**Janosh Riebesell** [![gh]][janosh] [![orc]][0000-0001-5233-3462] \
 PhD Student \
 Cambridge University
 
@@ -68,16 +68,30 @@ Microsoft Research
 [0000-0001-7777-8871]: https://orcid.org/0000-0001-7777-8871
 
 **Zhuoying Zhu** [![gh]][zhuoying] [![orc]][0000-0003-1775-7651] \
-Postdoctoral researcher\
+Postdoctoral Researcher \
 Lawrence Berkeley National Laboratory
 
 [zhuoying]: https://github.com/zhuoying
 [0000-0003-1775-7651]: https://orcid.org/0000-0003-1775-7651
 
 **Aakash Ashok Naik** [![gh]][naik-aakash] [![orc]][0000-0002-6071-6786] \
-PhD student\
+PhD student \
 Federal Institute for Materials Research and Testing (Berlin) \
 Friedrich Schiller University Jena
 
 [naik-aakash]: https://github.com/naik-aakash
 [0000-0002-6071-6786]: https://orcid.org/0000-0002-6071-6786
+
+**Aaron Kaplan** [![gh]][esoteric-ephemera] [![orc]][0000-0003-3439-4856] \
+Postdoctoral Researcher \
+Lawrence Berkeley National Laboratory
+
+[esoteric-ephemera]: https://github.com/esoteric-ephemera
+[0000-0003-3439-4856]: https://orcid.org/0000-0003-3439-4856
+
+**Matthew McDermott** [![gh]][mattmcdermott] [![orc]][0000-0002-4071-3000] \
+PhD student \
+University of California, Berkeley
+
+[mattmcdermott]: https://github.com/mattmcdermott
+[0000-0002-4071-3000]: https://orcid.org/0000-0002-4071-3000

docs/user/atomate-1-vs-2.md

@@ -0,0 +1,25 @@
+# Atomate 1 vs 2
+
+This document contains introductory context for people coming from atomate 1.
+One of atomate2's core ideas is to allow scaling from a single material, to 100 materials, or 100,000 materials. Therefore, both local submission options and a connection to workflow managers such as FireWorks exist. We plan to support more workflow managers in the future to further ease job submission.
+## Relation between managers running the actual jobs and the workflow as written in `atomate2`
+
+There is no leakage between job manager and the workflow definition in `atomate2`. For example, Fireworks is not a required dependency of `atomate2` or `jobflow`. Any `atomate2` workflow can be run using the local manager or an extensible set of external providers, Fireworks just one among them. E.g. all tests are run with mocked calls to the executables using the local manager.
+
+## Do I need to write separate codes for different managers?
+
+If you are adding a new manager option beyond local or FireWorks, you'll need to write a new converter in `jobflow` that takes a job or flow and converts it to the analogous object(s) for the manager you wish to use. This does not impact the `atomate2` code in any way.
+
+Typically, the workflow is as follows:
+
+1. Write a workflow in `atomate2` that represents a job or flow.
+2. Import the job or flow in your script/notebook from `atomate2`.
+3. Convert the job or flow to manager-compatible objects using a convenience function in `jobflow`.
+4. Define the specs for the new object type based on your desired resources.
+5. Dispatch the jobs.
+
+## What if a workflow manager stops being maintained?
+
+`atomate2` and `jobflow` remain unaffected in such a case. The user can choose a different manager to suit their needs. This ensures that workflow definition and dispatch are fully decoupled.
+
+In an ideal world, `jobflow` would offer multiple manager options, allowing users to run `atomate2` codes as per their preference. This full decoupling is one of the most powerful features of this stack.

src/atomate2/amset/schemas.py

@@ -165,7 +165,7 @@ def from_directory(
         from amset.io import load_mesh
         from amset.util import cast_dict_list
 
-        additional_fields = {} if additional_fields is None else additional_fields
+        additional_fields = additional_fields or {}
         dir_name = Path(dir_name)
 
         settings = loadfn("settings.yaml")

src/atomate2/common/schemas/cclib.py

@@ -120,7 +120,7 @@ def from_logfile(
 
         logger.info(f"Getting task doc from {logfile}")
 
-        additional_fields = {} if additional_fields is None else additional_fields
+        additional_fields = additional_fields or {}
 
         # Let's parse the log file with cclib
         cclib_obj = ccread(logfile, logging.ERROR)

src/atomate2/cp2k/run.py

@@ -94,8 +94,8 @@ def run_cp2k(
     custodian_kwargs : dict
         Keyword arguments that are passed to :obj:`.Custodian`.
     """
-    cp2k_job_kwargs = {} if cp2k_job_kwargs is None else cp2k_job_kwargs
-    custodian_kwargs = {} if custodian_kwargs is None else custodian_kwargs
+    cp2k_job_kwargs = cp2k_job_kwargs or {}
+    custodian_kwargs = custodian_kwargs or {}
 
     cp2k_cmd = expandvars(cp2k_cmd)
     split_cp2k_cmd = shlex.split(cp2k_cmd)

src/atomate2/cp2k/schemas/task.py

@@ -336,7 +336,7 @@ def from_directory(
         """
         logger.info(f"Getting task doc in: {dir_name}")
 
-        additional_fields = {} if additional_fields is None else additional_fields
+        additional_fields = additional_fields or {}
         dir_name = Path(dir_name)
         task_files = _find_cp2k_files(dir_name, volumetric_files=volumetric_files)
 

src/atomate2/cp2k/sets/base.py

@@ -77,7 +77,7 @@ def __init__(
 
         """
         self.cp2k_input = cp2k_input
-        self.optional_files = {} if optional_files is None else optional_files
+        self.optional_files = optional_files or {}
 
     def write_input(
         self,
@@ -98,8 +98,8 @@ def write_input(
             Whether to overwrite an input file if it already exists.
         """
         directory = Path(directory)
-        if make_dir and not directory.exists():
-            os.makedirs(directory)
+        if make_dir:
+            os.makedirs(directory, exist_ok=True)
 
         inputs = {
             "input": {"filename": "cp2k.inp", "object": self.cp2k_input},
@@ -270,9 +270,7 @@ def get_input_updates(self, structure, prev_input) -> dict:
         raise NotImplementedError
 
     def get_kpoints_updates(
-        self,
-        structure: Structure,
-        prev_input: Cp2kInput = None,
+        self, structure: Structure, prev_input: Cp2kInput = None
     ) -> dict:
         """
         Get updates to the kpoints configuration for this calculation type.
@@ -329,8 +327,8 @@ def _get_input(
         input_updates: dict = None,
     ):
         """Get the input."""
-        previous_input = {} if previous_input is None else previous_input
-        input_updates = {} if input_updates is None else input_updates
+        previous_input = previous_input or {}
+        input_updates = input_updates or {}
         input_settings = dict(self.config_dict["cp2k_input"])
 
         # Generate base input but override with user input settings
@@ -349,9 +347,9 @@ def _get_input(
                 and input_settings[setting]
                 and callable(getattr(cp2k_input, setting))
             ):
-                subsettings = input_settings.get(setting)
+                sub_settings = input_settings.get(setting)
                 getattr(cp2k_input, setting)(
-                    **subsettings if isinstance(subsettings, dict) else {}
+                    **sub_settings if isinstance(sub_settings, dict) else {}
                 )
 
         cp2k_input.update(overrides)
@@ -399,7 +397,7 @@ def _get_kpoints(
         kpoints_updates: dict[str, Any] | None,
     ) -> Kpoints | None:
         """Get the kpoints object."""
-        kpoints_updates = {} if kpoints_updates is None else kpoints_updates
+        kpoints_updates = kpoints_updates or {}
 
         # use user setting if set otherwise default to base config settings
         if self.user_kpoints_settings != {}:

src/atomate2/lobster/run.py

@@ -68,8 +68,8 @@ def run_lobster(
     custodian_kwargs : dict
          Keyword arguments that are passed to :obj:`.Custodian`.
     """
-    lobster_job_kwargs = {} if lobster_job_kwargs is None else lobster_job_kwargs
-    custodian_kwargs = {} if custodian_kwargs is None else custodian_kwargs
+    lobster_job_kwargs = lobster_job_kwargs or {}
+    custodian_kwargs = custodian_kwargs or {}
 
     lobster_cmd = expandvars(lobster_cmd)
     split_lobster_cmd = shlex.split(lobster_cmd)

src/atomate2/lobster/schemas.py

@@ -211,7 +211,7 @@ def from_directory(
         which_bonds: str
             mode for condensed bonding analysis: "cation-anion" and "all".
         """
-        plot_kwargs = {} if plot_kwargs is None else plot_kwargs
+        plot_kwargs = plot_kwargs or {}
         dir_name = Path(dir_name)
         cohpcar_path = dir_name / "COHPCAR.lobster.gz"
         charge_path = dir_name / "CHARGE.lobster.gz"
@@ -451,7 +451,7 @@ def from_directory(
         LobsterTaskDocument
             A task document for the lobster calculation.
         """
-        additional_fields = {} if additional_fields is None else additional_fields
+        additional_fields = additional_fields or {}
         dir_name = Path(dir_name)
 
         # Read in lobsterout and lobsterin

src/atomate2/vasp/files.py

@@ -82,7 +82,7 @@ def copy_vasp_outputs(
 
     # check at least one type of POTCAR file is included
     if len([f for f in optional_files if "POTCAR" in f.name]) == 0:
-        raise FileNotFoundError("Could not find POTCAR file to copy.")
+        raise FileNotFoundError(f"Could not find a POTCAR file in {src_dir!r} to copy")
 
     copy_files(
         src_dir,

src/atomate2/vasp/jobs/defect.py

@@ -51,7 +51,7 @@ def calculate_finite_diff(
         previous calculations).
     """
     ref_calc_dir = distorted_calc_dirs[ref_calc_index]
-    run_vasp_kwargs = {} if run_vasp_kwargs is None else run_vasp_kwargs
+    run_vasp_kwargs = run_vasp_kwargs or {}
     fc = FileClient()
     copy_vasp_outputs(ref_calc_dir, additional_vasp_files=["WAVECAR"], file_client=fc)
 

src/atomate2/vasp/jobs/mp.py

@@ -138,6 +138,7 @@ class MPPreRelaxMaker(BaseVaspMaker):
                 "GGA": "PS",
                 "LWAVE": True,
                 "LCHARG": True,
+                "METAGGA": None,
             },
         )
     )

src/atomate2/vasp/run.py

@@ -118,8 +118,8 @@ def run_vasp(
     custodian_kwargs : dict
         Keyword arguments that are passed to :obj:`.Custodian`.
     """
-    vasp_job_kwargs = {} if vasp_job_kwargs is None else vasp_job_kwargs
-    custodian_kwargs = {} if custodian_kwargs is None else custodian_kwargs
+    vasp_job_kwargs = vasp_job_kwargs or {}
+    custodian_kwargs = custodian_kwargs or {}
 
     vasp_cmd = expandvars(vasp_cmd)
     vasp_gamma_cmd = expandvars(vasp_gamma_cmd)

src/atomate2/vasp/sets/base.py

@@ -67,7 +67,7 @@ def __init__(
         self.poscar = poscar
         self.potcar = potcar
         self.kpoints = kpoints
-        self.optional_files = {} if optional_files is None else optional_files
+        self.optional_files = optional_files or {}
 
     def write_input(
         self,
@@ -89,8 +89,8 @@ def write_input(
             Whether to overwrite an input file if it already exists.
         """
         directory = Path(directory)
-        if make_dir and not directory.exists():
-            os.makedirs(directory)
+        if make_dir:
+            os.makedirs(directory, exist_ok=True)
 
         inputs = {
             "INCAR": self.incar,
@@ -620,8 +620,8 @@ def _get_incar(
         ispin: int = None,
     ):
         """Get the INCAR."""
-        previous_incar = {} if previous_incar is None else previous_incar
-        incar_updates = {} if incar_updates is None else incar_updates
+        previous_incar = previous_incar or {}
+        incar_updates = incar_updates or {}
         incar_settings = dict(self.config_dict["INCAR"])
         config_magmoms = incar_settings.get("MAGMOM", {})
         auto_updates = {}
@@ -717,7 +717,7 @@ def _get_kpoints(
         bandgap: float | None,
     ) -> Kpoints | None:
         """Get the kpoints file."""
-        kpoints_updates = {} if kpoints_updates is None else kpoints_updates
+        kpoints_updates = kpoints_updates or {}
 
         # use user setting if set otherwise default to base config settings
         if self.user_kpoints_settings != {}:

tests/forcefields/test_jobs.py

@@ -1,4 +1,6 @@
-from pytest import approx
+from pytest import approx, importorskip
+
+importorskip("quippy")
 
 
 def test_chgnet_static_maker(si_structure):

tests/test_data/vasp/Si_hse_optics/hse_optics/inputs/INCAR

@@ -1,4 +1,4 @@
-ALGO = All
+ALGO = Normal
 EDIFF = 1e-05
 ENAUG = 1360.0
 ENCUT = 680.0
@@ -20,10 +20,12 @@ LVTOT = True
 LWAVE = False
 NBANDS = 11
 NCORE = 4
-NEDOS = 5062
+NEDOS = 1265
 NELM = 200
 NELMIN = 5
 NSW = 0
 PREC = Accurate
 PRECFOCK = Fast
 SIGMA = 0.05
+CSHIFT = 1e-5
+LDAU = False

tests/test_data/vasp/Si_hse_optics/hse_static/inputs/INCAR

@@ -1,4 +1,4 @@
-ALGO = All
+ALGO = Normal
 EDIFF = 1e-05
 ENAUG = 1360
 ENCUT = 680
@@ -10,10 +10,11 @@ KSPACING = 0.5
 LAECHG = True
 LASPH = True
 LCHARG = True
-LELF = True
+LELF = False
 LHFCALC = True
 LMIXTAU = True
 LORBIT = 11
+LDAU = False
 LREAL = False
 LVTOT = True
 LWAVE = False
@@ -23,4 +24,4 @@ NELM = 200
 NSW = 0
 PREC = Accurate
 PRECFOCK = Fast
-SIGMA = 0.05
+SIGMA = 0.2

tests/test_data/vasp/Si_mp_meta_gga_relax/pbesol_pre_relax/inputs/INCAR

@@ -19,7 +19,6 @@ LREAL = Auto
 LVTOT = True
 LWAVE = True
 MAGMOM = 2*0.0
-METAGGA = R2scan
 NELM = 200
 NSW = 99
 PREC = Accurate

tests/test_data/vasp/Si_mp_meta_gga_relax/r2scan_final_static/inputs/INCAR

@@ -2,7 +2,6 @@ ALGO = Fast
 EDIFF = 1e-05
 ENAUG = 1360.0
 ENCUT = 680.0
-GGA = Ps
 ISMEAR = -5
 ISPIN = 2
 KSPACING = 0.29539340980039036

tests/test_data/vasp/Si_mp_meta_gga_relax/r2scan_relax/inputs/INCAR

@@ -3,10 +3,9 @@ EDIFF = 1e-05
 EDIFFG = -0.05
 ENAUG = 1360.0
 ENCUT = 680.0
-GGA = Ps
 IBRION = 2
 ISIF = 3
-ISMEAR = 0
+ISMEAR = -5
 ISPIN = 2
 KSPACING = 0.28253269576667883
 LAECHG = True