Update LobsterTaskDoc (#723)

* decouple file pymatgen file parsing and post-processing (lobsterpy) * attempt temp fix to by pass pydantic error * revert allow_arbitrary type * update pymatgen version * update schema, lobster job and tests * update monty version * Update pyproject.toml * Update pyproject.toml * removed redundant are_cobis/are_coops in strongestbonds, add lobsterpy kwargs to taskdoc * Update pyproject.toml * move typically small objects like charge, madelung back to mongostore * restructure strongest bonds field * fix vasp/flows/test_electrode.py::test_electrode_makers - TypeError: Lattice.get_all_distances() got an unexpected keyword argument 'fcoords1' https://github.com/materialsproject/pymatgen-analysis-defects/releases/tag/v2024.5.11 * pin nequip==0.5.6 mir-group/nequip#431 --------- Co-authored-by: J. George <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>
materialsproject · May 11, 2024 · ae3d0d6 · ae3d0d6
1 parent 6b9d8bb
commit ae3d0d6
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Showing 6 changed files with 293 additions and 286 deletions.
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -57,7 +57,7 @@ jobs:
           pip install git+https://gitlab.com/ase/ase
           pip install .[strict,tests,abinit]
           pip install torch-runstats
-          pip install --no-deps nequip
+          pip install --no-deps nequip==0.5.6
 
       - name: Test
         env:

diff --git a/pyproject.toml b/pyproject.toml
@@ -34,7 +34,7 @@ dependencies = [
     "numpy",
     "pydantic-settings>=2.0.3",
     "pydantic>=2.0.1",
-    "pymatgen>=2024.3.1",
+    "pymatgen>=2024.4.13",
 ]
 
 [project.optional-dependencies]
@@ -43,10 +43,10 @@ amset = ["amset>=0.4.15", "pydash"]
 cclib = ["cclib"]
 mp = ["mp-api>=0.37.5"]
 phonons = ["phonopy>=1.10.8", "seekpath"]
-lobster = ["ijson>=3.2.2", "lobsterpy>=0.3.7"]
+lobster = ["ijson>=3.2.2", "lobsterpy>=0.3.8"]
 defects = [
     "dscribe>=1.2.0",
-    "pymatgen-analysis-defects>=2022.11.30",
+    "pymatgen-analysis-defects>=2024.5.11",
     "python-ulid",
 ]
 forcefields = [
@@ -89,7 +89,7 @@ strict = [
     "emmet-core==0.82.2",
     "ijson==3.2.3",
     "jobflow==0.1.17",
-    "lobsterpy==0.3.8",
+    "lobsterpy==0.4.0",
     "mace-torch>=0.3.3",
     "matgl==1.1.1",
     "monty==2024.3.31",
@@ -98,8 +98,8 @@ strict = [
     "phonopy==2.22.1",
     "pydantic-settings==2.2.1",
     "pydantic==2.7.1",
-    "pymatgen-analysis-defects==2024.4.23",
-    "pymatgen==2024.3.1",
+    "pymatgen-analysis-defects==2024.5.11",
+    "pymatgen==2024.5.1",
     "python-ulid==2.5.0",
     "quippy-ase==0.9.14",
     "seekpath==2.1.0",

diff --git a/src/atomate2/lobster/jobs.py b/src/atomate2/lobster/jobs.py
@@ -9,7 +9,7 @@
 from jobflow import Maker, job
 from pymatgen.electronic_structure.cohp import CompleteCohp
 from pymatgen.electronic_structure.dos import LobsterCompleteDos
-from pymatgen.io.lobster import Lobsterin
+from pymatgen.io.lobster import Bandoverlaps, Icohplist, Lobsterin
 
 from atomate2 import SETTINGS
 from atomate2.common.files import gzip_output_folder
@@ -56,7 +56,15 @@ class LobsterMaker(Maker):
     run_lobster_kwargs: dict = field(default_factory=dict)
     calculation_type: str = "standard"
 
-    @job(output_schema=LobsterTaskDocument, data=[CompleteCohp, LobsterCompleteDos])
+    @job(
+        output_schema=LobsterTaskDocument,
+        data=[
+            CompleteCohp,
+            LobsterCompleteDos,
+            Bandoverlaps,
+            Icohplist,
+        ],
+    )
     def make(
         self,
         wavefunction_dir: str | Path = None,