Merge pull request materialsproject#404 from naik-aakash/main

update lobstertask schema: add bandoverlaps,grosspop and sitepotentials fields

src/atomate2/lobster/schemas.py

@@ -12,12 +12,15 @@
 from pymatgen.electronic_structure.cohp import CompleteCohp
 from pymatgen.electronic_structure.dos import LobsterCompleteDos
 from pymatgen.io.lobster import (
+    Bandoverlaps,
     Charge,
     Doscar,
+    Grosspop,
     Icohplist,
     Lobsterin,
     Lobsterout,
     MadelungEnergies,
+    SitePotential,
 )
 
 from atomate2 import __version__
@@ -79,19 +82,20 @@ class LobsteroutModel(BaseModel):
     )
     has_charge: bool = Field(None, description="Bool indicating if CHARGE is present.")
     has_madelung: bool = Field(
-        None, description="Bool indicating if Madelung file is present."
+        None,
+        description="Bool indicating if Site Potentials and Madelung file is present.",
     )
     has_projection: bool = Field(
         None, description="Bool indicating if projection file is present."
     )
     has_bandoverlaps: bool = Field(
-        None, description="Bool indicating if BANDOVERLAPS file is presetn"
+        None, description="Bool indicating if BANDOVERLAPS file is present"
     )
     has_fatbands: bool = Field(
         None, description="Bool indicating if Fatbands are present."
     )
     has_grosspopulation: bool = Field(
-        None, description="Bool indicating if GrossPopulations file is present."
+        None, description="Bool indicating if GROSSPOP file is present."
     )
     has_density_of_energies: bool = Field(
         None, description="Bool indicating if DensityofEnergies is present"
@@ -399,6 +403,24 @@ class LobsterTaskDocument(BaseModel):
         description="Madelung energies dict from"
         " LOBSTER based on Mulliken and Loewdin charges",
     )
+    site_potentials: dict = Field(
+        None,
+        description="Site potentials dict from"
+        " LOBSTER based on Mulliken and Loewdin charges",
+    )
+
+    gross_populations: dict = Field(
+        None,
+        description="Gross populations dict from"
+        " LOBSTER based on Mulliken and Loewdin charges with"
+        "each site as a key and the gross population as a value.",
+    )
+
+    band_overlaps: dict = Field(
+        None,
+        description="Band overlaps data for each k-point from"
+        " bandOverlaps.lobster file if it exists",
+    )
 
     _schema: str = Field(
         __version__,
@@ -454,6 +476,9 @@ def from_directory(
         doscar_path = dir_name / "DOSCAR.lobster.gz"
         structure_path = dir_name / "POSCAR.gz"
         madelung_energies_path = dir_name / "MadelungEnergies.lobster.gz"
+        site_potentials_path = dir_name / "SitePotentials.lobster.gz"
+        gross_populations_path = dir_name / "GROSSPOP.lobster.gz"
+        band_overlaps_path = dir_name / "bandOverlaps.lobster.gz"
 
         # Do automatic bonding analysis with LobsterPy
         condensed_bonding_analysis = None
@@ -553,6 +578,37 @@ def from_directory(
                 "Ewald_splitting": madelung_obj.ewald_splitting,
             }
 
+        # Read in Site Potentials
+        site_potentials = None
+        if site_potentials_path.exists():
+            site_potentials_obj = SitePotential(filename=site_potentials_path)
+
+            site_potentials = {
+                "Mulliken": site_potentials_obj.sitepotentials_Mulliken,
+                "Loewdin": site_potentials_obj.sitepotentials_Loewdin,
+                "Ewald_splitting": site_potentials_obj.ewald_splitting,
+            }
+
+        # Read in Gross Populations
+        gross_populations = None
+        if gross_populations_path.exists():
+            gross_populations_obj = Grosspop(filename=gross_populations_path)
+
+            gross_populations = {}
+            for atom_index, gross_pop in enumerate(
+                gross_populations_obj.list_dict_grosspop
+            ):
+                gross_populations[atom_index] = gross_pop
+
+        # Read in Band overlaps
+        band_overlaps = None
+        if band_overlaps_path.exists():
+            band_overlaps_obj = Bandoverlaps(filename=band_overlaps_path)
+
+            band_overlaps = {}
+            for spin, value in band_overlaps_obj.bandoverlapsdict.items():
+                band_overlaps[str(spin.value)] = value
+
         doc = cls(
             structure=struct,
             dir_name=dir_name,
@@ -579,6 +635,9 @@ def from_directory(
             lso_dos=lso_dos,
             charges=charges,
             madelung_energies=madelung_energies,
+            site_potentials=site_potentials,
+            gross_populations=gross_populations,
+            band_overlaps=band_overlaps,
         )
         return doc.copy(update=additional_fields)
 

tests/vasp/lobster/flows/test_lobster.py

@@ -96,7 +96,7 @@ def test_lobsteruniformmaker(mock_vasp, mock_lobster, clean_dir, memory_jobstore
         .dict()
         .items()
     ):
-        if key == "lso_dos":
+        if key == "lso_dos" or key == "band_overlaps":
             assert value is None
         else:
             assert value is not None
@@ -170,7 +170,7 @@ def test_lobstermaker(mock_vasp, mock_lobster, clean_dir, memory_jobstore):
         .dict()
         .items()
     ):
-        if key == "lso_dos":
+        if key == "lso_dos" or key == "band_overlaps":
             assert value is None
         else:
             assert value is not None

tests/vasp/lobster/schemas/test_lobster.py

@@ -89,11 +89,29 @@ def test_LobsterTaskDocument(lobster_test_dir):
     assert isinstance(doc.coop_data, CompleteCohp)
     assert isinstance(doc.dos, LobsterCompleteDos)
     assert np.isclose(doc.madelung_energies["Mulliken"], -0.68)
+    assert np.allclose(
+        doc.site_potentials["Mulliken"],
+        [-1.26, -1.27, -1.26, -1.27, 1.27, 1.27, 1.26, 1.26],
+        rtol=1e-2,
+    )
+    assert np.isclose(doc.site_potentials["Ewald_splitting"], 3.14)
+    assert len(doc.gross_populations) == 8
+    assert doc.gross_populations[5]["element"] == "As"
+    expected_gross_popp = {
+        "4s": 1.38,
+        "4p_y": 1.18,
+        "4p_z": 1.18,
+        "4p_x": 1.18,
+        "total": 4.93,
+    }
+    gross_popp_here = doc.gross_populations[5]["Loewdin GP"]
+    assert expected_gross_popp == gross_popp_here
     assert np.allclose(
         doc.charges["Mulliken"],
         [0.13, 0.13, 0.13, 0.13, -0.13, -0.13, -0.13, -0.13],
         rtol=1e-2,
     )
+    assert len(doc.band_overlaps["1"]) + len(doc.band_overlaps["-1"]) == 12
 
     doc2 = LobsterTaskDocument.from_directory(
         dir_name=lobster_test_dir / "lobsteroutputs/mp-754354", save_cohp_plots=False
@@ -104,3 +122,44 @@ def test_LobsterTaskDocument(lobster_test_dir):
     assert np.isclose(
         doc2.strongest_bonds_icohp.strongest_bonds["Ba-F"]["ICOHP"], -0.44806
     )
+    assert len(doc2.band_overlaps["1"]) + len(doc2.band_overlaps["-1"]) == 2
+    assert np.allclose(
+        doc2.site_potentials["Loewdin"],
+        [
+            -15.09,
+            -15.09,
+            -15.09,
+            -15.09,
+            -15.09,
+            -15.09,
+            -15.09,
+            -15.09,
+            14.78,
+            14.78,
+            8.14,
+            8.14,
+            8.48,
+            8.48,
+            8.14,
+            8.14,
+            8.14,
+            8.14,
+            8.48,
+            8.48,
+            8.14,
+            8.14,
+        ],
+        rtol=1e-2,
+    )
+    assert np.isclose(doc2.site_potentials["Ewald_splitting"], 3.14)
+    assert len(doc2.gross_populations) == 22
+    assert doc2.gross_populations[10]["element"] == "F"
+    expected_gross_popp = {
+        "2s": 1.98,
+        "2p_y": 1.97,
+        "2p_z": 1.97,
+        "2p_x": 1.97,
+        "total": 7.88,
+    }
+    gross_popp_here = doc2.gross_populations[10]["Mulliken GP"]
+    assert expected_gross_popp == gross_popp_here