Merge branch 'main' into patch_prv

.github/workflows/deploy.yml

@@ -80,7 +80,7 @@ jobs:
 
       - name: Write release info
         run: |
-          awk 'BEGIN {p = 0} {a = 0 }; /^v\d*.\d*.\d*./ { p += 1; a = 1}; p + a == 1 { print } ' CHANGELOG.md | sed -e '1,1d' | sed  -e '/./,$!d' -e :a -e '/^\n*$/{$d;N;ba' -e '}' > release_info.txt
+          awk 'BEGIN {p = 0} {a = 0 }; /^\#\#\ v\d*.\d*.\d*./ { p += 1; a = 1}; p + a == 1 { print } ' CHANGELOG.md | sed -e '1,1d' | sed  -e '/./,$!d' -e :a -e '/^\n*$/{$d;N;ba' -e '}' > release_info.txt
           echo "" >> release_info.txt
           awk '/CONTRIBUTOR SECTION/{f=1; c=0} f' CHANGELOG.md >> release_info.txt
 

.pre-commit-config.yaml

@@ -2,10 +2,11 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.1.1
+  rev: v0.1.3
   hooks:
   - id: ruff
     args: [--fix]
+  - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.5.0
   hooks:
@@ -14,10 +15,6 @@ repos:
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/psf/black
-  rev: 23.10.0
-  hooks:
-  - id: black
 - repo: https://github.com/asottile/blacken-docs
   rev: 1.16.0
   hooks:

CHANGELOG.md

@@ -1,5 +1,55 @@
 # Change log
 
+## v0.0.12
+
+* Breaking: default `Atomate2Settings.VASP_INHERIT_INCAR` to `False` by @janosh in https://github.com/materialsproject/atomate2/pull/594
+
+### Bug Fixes 🐛
+* Enforce magmom precedence in INCAR creation by @mattmcdermott in https://github.com/materialsproject/atomate2/pull/506
+* Warn on empty config by @janosh in https://github.com/materialsproject/atomate2/pull/522
+* CP2K use `calcs_reversed[0]` instead of `calcs_reversed[-1]` to not reverse again by @janosh in https://github.com/materialsproject/atomate2/pull/534
+* Fix wrong INCAR values in MP workflows by @janosh in https://github.com/materialsproject/atomate2/pull/550
+* Fix failing tests from Pydantic v2 migration by @hrushikesh-s in https://github.com/materialsproject/atomate2/pull/558
+* fixing pydantic v2 test errors by @hrushikesh-s in https://github.com/materialsproject/atomate2/pull/565
+* `parse_additional_json()` ignore `FW.json.gz` in output directories by @janosh in https://github.com/materialsproject/atomate2/pull/574
+* Fix `bandgap_tol` and delete `bandgap_override` on `MPMetaGGARelaxSetGenerator` by @janosh in https://github.com/materialsproject/atomate2/pull/553
+* Fix `VaspInputGenerator`'s `_set_kspacing` not respecting `auto_ismear = False` nor `auto_kspacing = False` by @janosh in https://github.com/materialsproject/atomate2/pull/576
+* Clean up VASP powerups, correct params in MP flows, test for `_set_u_params`, test for `_set_kspacing`, fix `_get_incar` method of `VaspInputSet` by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/561
+* Fix Lobster workflow by @JaGeo in https://github.com/materialsproject/atomate2/pull/583
+* Change `MatPesGGAPlusMetaGGAStaticMaker.output` to dict containing both statics by @janosh in https://github.com/materialsproject/atomate2/pull/586
+* Test MP + MatPES set generators by @janosh in https://github.com/materialsproject/atomate2/pull/596
+### Enhancements 🛠
+* Add StructureMetadata as baseclass for output documents by @gpetretto in https://github.com/materialsproject/atomate2/pull/514
+* Materials Project GGA and meta-GGA workflows by @janosh in https://github.com/materialsproject/atomate2/pull/504
+* [WIP] MP-compatible r2SCAN workflow (and a few general INCAR improvements) by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/362
+* Update to Pydantic v2 by @hrushikesh-s in https://github.com/materialsproject/atomate2/pull/567
+* Add MatPES GGA and r2SCAN static makers by @janosh in https://github.com/materialsproject/atomate2/pull/532
+* Move elastic workflow to common and build force-field elastic workflow by @JaGeo in https://github.com/materialsproject/atomate2/pull/581
+### Documentation 📖
+* Update @arosen93 to @Andrew-S-Rosen by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/516
+* Add Aaron Kaplan and Matthew McDermott to `contributors.md` by @janosh in https://github.com/materialsproject/atomate2/pull/560
+* Document architectural difference between atomate 1 and 2 by @janosh in https://github.com/materialsproject/atomate2/pull/381
+* Add Thomas Purcell to `contributors.md` by @tpurcell90 in https://github.com/materialsproject/atomate2/pull/568
+* Add Alex Bonkowski to contributors list by @JaGeo in https://github.com/materialsproject/atomate2/pull/573
+* Add @matthewkuner to contributors by @matthewkuner in https://github.com/materialsproject/atomate2/pull/575
+* Update contributors.md by @utf in https://github.com/materialsproject/atomate2/pull/579
+### House-Keeping 🧹
+* Remove `__all__` from all modules by @janosh in https://github.com/materialsproject/atomate2/pull/540
+* removed py38 support, and add py 3.11 support by @naik-aakash in https://github.com/materialsproject/atomate2/pull/537
+* Check full INCAR by default in `mock_vasp` fixture by @janosh in https://github.com/materialsproject/atomate2/pull/551
+* skip validate charge test by @jmmshn in https://github.com/materialsproject/atomate2/pull/563
+* Add some type annotations by @ab5424 in https://github.com/materialsproject/atomate2/pull/578
+* Future type annotations by @janosh in https://github.com/materialsproject/atomate2/pull/580
+* Use `numpy.testing.assert_allclose` over assert `np.(all|is)close` by @janosh in https://github.com/materialsproject/atomate2/pull/582
+
+## New Contributors
+* @mattmcdermott made their first contribution in https://github.com/materialsproject/atomate2/pull/506
+* @tpurcell90 made their first contribution in https://github.com/materialsproject/atomate2/pull/568
+* @esoteric-ephemera made their first contribution in https://github.com/materialsproject/atomate2/pull/561
+* @ab5424 made their first contribution in https://github.com/materialsproject/atomate2/pull/578
+
+**Full Changelog**: https://github.com/materialsproject/atomate2/compare/v0.0.11...v0.0.12
+
 ## v0.0.11
 
 ### Task Document Changes

pyproject.toml

@@ -49,7 +49,7 @@ docs = [
     "FireWorks==2.0.3",
     "autodoc_pydantic==2.0.1",
     "furo==2023.9.10",
-    "ipython==8.16.1",
+    "ipython==8.17.2",
     "jsonschema[format]",
     "myst_parser==2.0.0",
     "numpydoc==1.6.0",
@@ -58,15 +58,15 @@ docs = [
     "sphinx_design==0.5.0",
 ]
 dev = ["pre-commit>=2.12.1"]
-tests = ["FireWorks==2.0.3", "pytest-cov==4.1.0", "pytest==7.4.2"]
+tests = ["FireWorks==2.0.3", "pytest-cov==4.1.0", "pytest==7.4.3"]
 strict = [
     "PyYAML==6.0.1",
     "cclib==1.8",
-    "chgnet==0.2.2",
+    "chgnet==0.3.1",
     "click==8.1.7",
     "custodian==2023.10.9",
     "dscribe==2.1.0",
-    "emmet-core==0.71.2",
+    "emmet-core==0.72.8",
     "jobflow==0.1.14",
     "lobsterpy==0.3.2",
     "matgl==0.8.3",

src/atomate2/amset/jobs.py

@@ -42,7 +42,7 @@ class AmsetMaker(Maker):
     def make(
         self,
         settings: dict,
-        prev_amset_dir: str | Path = None,
+        prev_dir: str | Path = None,
         wavefunction_dir: str | Path = None,
         deformation_dir: str | Path = None,
         bandstructure_dir: str | Path = None,
@@ -54,7 +54,7 @@ def make(
         ----------
         settings : dict
             Amset settings.
-        prev_amset_dir : str or Path
+        prev_dir : str or Path
             A previous AMSET calculation directory to copy output files from. The
             previous directory is also used to check for transport convergence.
         wavefunction_dir : str or Path
@@ -66,14 +66,12 @@ def make(
             band_structure_data.json).
         """
         # copy previous inputs
-        from_prev = prev_amset_dir is not None
-        if prev_amset_dir is not None:
-            copy_amset_files(prev_amset_dir)
+        from_prev = prev_dir is not None
+        if prev_dir is not None:
+            copy_amset_files(prev_dir)
         else:
             if bandstructure_dir is None:
-                raise ValueError(
-                    "Either prev_amset_dir or bandstructure_dir must be set"
-                )
+                raise ValueError("Either prev_dir or bandstructure_dir must be set")
 
             copy_amset_files(bandstructure_dir)
 
@@ -116,7 +114,7 @@ def make(
         if self.resubmit and not converged:
             replace = self.make(
                 {"interpolation_factor": settings.get("interpolation_factor", 10) + 5},
-                prev_amset_dir=task_doc.dir_name,
+                prev_dir=task_doc.dir_name,
             )
 
         return Response(output=task_doc, replace=replace)

src/atomate2/common/flows/defect.py

@@ -112,7 +112,7 @@ def make(
             struct2,
             distortions=self.distortions,
             static_maker=self.static_maker,
-            prev_vasp_dir=dir1,
+            prev_dir=dir1,
             add_name="q1",
             add_info={"relaxed_uuid": relax1.uuid, "distorted_uuid": relax2.uuid},
         )
@@ -122,7 +122,7 @@ def make(
             struct1,
             distortions=self.distortions,
             static_maker=self.static_maker,
-            prev_vasp_dir=dir2,
+            prev_dir=dir2,
             add_name="q2",
             add_info={"relaxed_uuid": relax2.uuid, "distorted_uuid": relax1.uuid},
         )

src/atomate2/common/flows/elastic.py

@@ -94,7 +94,7 @@ def make(
         ----------
         structure : .Structure
             A pymatgen structure.
-        prev_vasp_dir : str or Path or None
+        prev_dir : str or Path or None
             A previous vasp calculation directory to use for copying outputs.
         equilibrium_stress : tuple of tuple of float
             The equilibrium stress of the (relaxed) structure, if known.

src/atomate2/common/jobs/defect.py

@@ -71,7 +71,7 @@ def spawn_energy_curve_calcs(
     distorted_structure: Structure,
     distortions: Iterable[float],
     static_maker: StaticMaker,
-    prev_vasp_dir: str | Path | None = None,
+    prev_dir: str | Path | None = None,
     add_name: str = "",
     add_info: dict | None = None,
 ) -> Response:
@@ -109,7 +109,7 @@ def spawn_energy_curve_calcs(
     )
     # add all the distorted structures
     for i, d_struct in enumerate(distorted_structures):
-        static_job = static_maker.make(d_struct, prev_vasp_dir=prev_vasp_dir)
+        static_job = static_maker.make(d_struct, prev_dir=prev_dir)
         suffix = f" {i}" if add_name == "" else f" {add_name} {i}"
 
         # write some provenances data in info.json file

src/atomate2/common/jobs/phonons.py

@@ -252,7 +252,7 @@ def run_phonon_displacements(
     structure: Structure,
     supercell_matrix,
     phonon_maker: BaseVaspMaker | ForceFieldStaticMaker = None,
-    prev_vasp_dir: str | Path = None,
+    prev_dir: str | Path = None,
 ) -> Flow:
     """
     Run phonon displacements.
@@ -268,7 +268,7 @@ def run_phonon_displacements(
         supercell matrix for meta data
     phonon_maker : .BaseVaspMaker
         A VaspMaker to use to generate the elastic relaxation jobs.
-    prev_vasp_dir : str or Path or None
+    prev_dir : str or Path or None
         A previous vasp calculation directory to use for copying outputs.
     """
     if phonon_maker is None:
@@ -282,8 +282,8 @@ def run_phonon_displacements(
     }
 
     for i, displacement in enumerate(displacements):
-        if prev_vasp_dir is not None:
-            phonon_job = phonon_maker.make(displacement, prev_vasp_dir=prev_vasp_dir)
+        if prev_dir is not None:
+            phonon_job = phonon_maker.make(displacement, prev_dir=prev_dir)
         else:
             phonon_job = phonon_maker.make(displacement)
         phonon_job.append_name(f" {i + 1}/{len(displacements)}")

src/atomate2/common/schemas/phonons.py

@@ -410,19 +410,16 @@ def from_forces_born(
                 kwargs.get("tmax_thermal_displacements", 500),
                 kwargs.get("tstep_thermal_displacements", 100),
             )
-            for i, temp in enumerate(temperature_range_thermal_displacements):
+            for idx, temp in enumerate(temperature_range_thermal_displacements):
                 phonon.thermal_displacement_matrices.write_cif(
                     phonon.primitive,
-                    i,
-                    filename="tdispmat_" + str(temp) + "K.cif",
+                    idx,
+                    filename=f"tdispmat_{temp}K.cif",
                 )
-            tdisp_mat = (
-                phonon._thermal_displacement_matrices.thermal_displacement_matrices.tolist()
-            )
+            _disp_mat = phonon._thermal_displacement_matrices
+            tdisp_mat = _disp_mat.thermal_displacement_matrices.tolist()
 
-            tdisp_mat_cif = (
-                phonon._thermal_displacement_matrices.thermal_displacement_matrices_cif.tolist()
-            )
+            tdisp_mat_cif = _disp_mat.thermal_displacement_matrices_cif.tolist()
 
         else:
             tdisp_mat = None

src/atomate2/common/utils.py

@@ -116,7 +116,7 @@ def parse_additional_json(dir_name: Path) -> dict[str, Any]:
     additional_json = {}
     for filename in dir_name.glob("*.json*"):
         key = filename.name.split(".")[0]
-        # ignore FW.json(.gz) so jobflow doesn't try to parse prev_vasp_dir
+        # ignore FW.json(.gz) so jobflow doesn't try to parse prev_dir
         # OutputReferences was causing atomate2 MP workflows to fail with ValueError:
         # Could not resolve reference 7f5a7f14-464c-4a5b-85f9-8d11b595be3b not in store
         # or cache contact @janosh in case of questions