Small oxidation state and thermo changes (#394)

* Equilibrium typo fix * Add oxi states query op to summary * Emmet bump * Fix emmet core bump * Enable oxi state query with summary * Linting * Fix material_id in robocrys * Fix tests * More test updates * Remove xfail from some mprester tests
materialsproject · Sep 28, 2021 · 8cf8a6d · 8cf8a6d
1 parent b8c0471
commit 8cf8a6d
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Showing 14 changed files with 50 additions and 41 deletions.
diff --git a/app.py b/app.py
@@ -183,7 +183,7 @@
     robo_store = MongoURIStore(
         uri=f"mongodb+srv://{db_uri}",
         database="mp_core",
-        key="task_id",
+        key="material_id",
         collection_name="robocrys",
     )
 

diff --git a/requirements.txt b/requirements.txt
@@ -4,5 +4,5 @@ typing-extensions==3.10.0.2
 maggma==0.31.0
 requests==2.26.0
 monty==2021.8.17
-emmet-core==0.12.8
+emmet-core==0.13.3
 ratelimit==2.2.1
diff --git a/src/mp_api/matproj.py b/src/mp_api/matproj.py
@@ -471,6 +471,7 @@ def query(
         material_ids: Optional[List[MPID]] = None,
         chemsys_formula: Optional[str] = None,
         exclude_elements: Optional[List[str]] = None,
+        possible_species: Optional[List[str]] = None,
         nsites: Optional[Tuple[int, int]] = None,
         volume: Optional[Tuple[float, float]] = None,
         density: Optional[Tuple[float, float]] = None,
@@ -481,7 +482,7 @@ def query(
         total_energy: Optional[Tuple[float, float]] = None,
         formation_energy: Optional[Tuple[float, float]] = None,
         energy_above_hull: Optional[Tuple[float, float]] = None,
-        equillibrium_reaction_energy: Optional[Tuple[float, float]] = None,
+        equilibrium_reaction_energy: Optional[Tuple[float, float]] = None,
         uncorrected_energy: Optional[Tuple[float, float]] = None,
         is_stable: Optional[bool] = None,
         band_gap: Optional[Tuple[float, float]] = None,
@@ -532,6 +533,8 @@ def query(
                 or formula including anonomyzed formula
                 or wild cards (e.g., Fe2O3, ABO3, Si*).
             exclude_elements (List(str)): List of elements to exclude.
+            possible_species (List(str)): List of element symbols appended with oxidation states.
+                (e.g. Cr2+,O2-)
             crystal_system (CrystalSystem): Crystal system of material.
             spacegroup_number (int): Space group number of material.
             spacegroup_symbol (str): Space group symbol of the material in international short symbol notation.
@@ -540,6 +543,8 @@ def query(
             density (Tuple[float,float]): Minimum and maximum density to consider.
             deprecated (bool): Whether the material is tagged as deprecated.
             total_energy (Tuple[int,int]): Minimum and maximum corrected total energy in eV/atom to consider.
+            equilibrium_reaction_energy (Tuple[float,float]): Minimum and maximum equilibrium reaction energy
+                in eV/atom to consider.
             formation_energy (Tuple[int,int]): Minimum and maximum formation energy in eV/atom to consider.
             energy_above_hull (Tuple[int,int]): Minimum and maximum energy above the hull in eV/atom to consider.
             uncorrected_energy (Tuple[int,int]): Minimum and maximum uncorrected total energy in eV/atom to consider.
@@ -602,6 +607,7 @@ def query(
             material_ids=material_ids,
             chemsys_formula=chemsys_formula,
             exclude_elements=exclude_elements,
+            possible_species=possible_species,
             nsites=nsites,
             volume=volume,
             density=density,
@@ -612,7 +618,7 @@ def query(
             total_energy=total_energy,
             formation_energy=formation_energy,
             energy_above_hull=energy_above_hull,
-            equillibrium_reaction_energy=equillibrium_reaction_energy,
+            equilibrium_reaction_energy=equilibrium_reaction_energy,
             uncorrected_energy=uncorrected_energy,
             is_stable=is_stable,
             band_gap=band_gap,

diff --git a/src/mp_api/routes/oxidation_states/resources.py b/src/mp_api/routes/oxidation_states/resources.py
@@ -5,7 +5,6 @@
     PaginationQuery,
     SortQuery,
     SparseFieldsQuery,
-    NumericQuery,
 )
 
 from mp_api.routes.materials.query_operators import FormulaQuery

diff --git a/src/mp_api/routes/robocrys/client.py b/src/mp_api/routes/robocrys/client.py
@@ -8,7 +8,7 @@ class RobocrysRester(BaseRester):
 
     suffix = "robocrys"
     document_model = RobocrysDoc  # type: ignore
-    primary_key = "task_id"
+    primary_key = "material_id"
 
     def search_robocrys_text(self, keywords: List[str]):
         """

diff --git a/src/mp_api/routes/robocrys/models.py b/src/mp_api/routes/robocrys/models.py
@@ -10,8 +10,7 @@ class MineralData(BaseModel):
     """
 
     type: str = Field(
-        None,
-        description="Mineral type.",
+        None, description="Mineral type.",
     )
 
 
@@ -21,28 +20,23 @@ class CondensedStructureData(BaseModel):
     """
 
     formula: str = Field(
-        None,
-        description="Formula for the material.",
+        None, description="Formula for the material.",
     )
 
     spg_symbol: str = Field(
-        None,
-        description="Space group symbol of the material.",
+        None, description="Space group symbol of the material.",
     )
 
     crystal_system: str = Field(
-        None,
-        description="Crystal system of the material.",
+        None, description="Crystal system of the material.",
     )
 
     mineral: MineralData = Field(
-        None,
-        description="Matched mineral data for the material.",
+        None, description="Matched mineral data for the material.",
     )
 
     dimensionality: int = Field(
-        None,
-        description="Dimensionality of the material.",
+        None, description="Dimensionality of the material.",
     )
 
 
@@ -52,23 +46,20 @@ class RobocrysDoc(BaseModel):
     """
 
     description: str = Field(
-        None,
-        description="Decription text from robocrytallographer.",
+        None, description="Decription text from robocrytallographer.",
     )
 
     condensed_structure: CondensedStructureData = Field(
-        None,
-        description="Condensed structure data from robocrytallographer.",
+        None, description="Condensed structure data from robocrytallographer.",
     )
 
-    task_id: str = Field(
+    material_id: str = Field(
         None,
         description="The Materials Project ID of the material. This comes in the form: mp-******",
     )
 
     last_updated: datetime = Field(
-        None,
-        description="Timestamp for the most recent calculation for this document",
+        None, description="Timestamp for the most recent calculation for this document",
     )
 
     # Make sure that the datetime field is properly formatted

diff --git a/src/mp_api/routes/summary/client.py b/src/mp_api/routes/summary/client.py
@@ -19,6 +19,7 @@ def search_summary_docs(
         material_ids: Optional[List[MPID]] = None,
         chemsys_formula: Optional[str] = None,
         exclude_elements: Optional[List[str]] = None,
+        possible_species: Optional[List[str]] = None,
         nsites: Optional[Tuple[int, int]] = None,
         volume: Optional[Tuple[float, float]] = None,
         density: Optional[Tuple[float, float]] = None,
@@ -29,7 +30,7 @@ def search_summary_docs(
         total_energy: Optional[Tuple[float, float]] = None,
         formation_energy: Optional[Tuple[float, float]] = None,
         energy_above_hull: Optional[Tuple[float, float]] = None,
-        equillibrium_reaction_energy: Optional[Tuple[float, float]] = None,
+        equilibrium_reaction_energy: Optional[Tuple[float, float]] = None,
         uncorrected_energy: Optional[Tuple[float, float]] = None,
         is_stable: Optional[bool] = None,
         band_gap: Optional[Tuple[float, float]] = None,
@@ -80,6 +81,8 @@ def search_summary_docs(
                 or formula including anonomyzed formula
                 or wild cards (e.g., Fe2O3, ABO3, Si*).
             exclude_elements (List(str)): List of elements to exclude.
+            possible_species (List(str)): List of element symbols appended with oxidation states.
+                (e.g. Cr2+,O2-)
             crystal_system (CrystalSystem): Crystal system of material.
             spacegroup_number (int): Space group number of material.
             spacegroup_symbol (str): Space group symbol of the material in international short symbol notation.
@@ -88,6 +91,8 @@ def search_summary_docs(
             density (Tuple[float,float]): Minimum and maximum density to consider.
             deprecated (bool): Whether the material is tagged as deprecated.
             total_energy (Tuple[int,int]): Minimum and maximum corrected total energy in eV/atom to consider.
+            equilibrium_reaction_energy (Tuple[float,float]): Minimum and maximum equilibrium reaction energy
+                in eV/atom to consider.
             formation_energy (Tuple[int,int]): Minimum and maximum formation energy in eV/atom to consider.
             energy_above_hull (Tuple[int,int]): Minimum and maximum energy above the hull in eV/atom to consider.
             uncorrected_energy (Tuple[int,int]): Minimum and maximum uncorrected total energy in eV/atom to consider.
@@ -153,7 +158,7 @@ def search_summary_docs(
             "formation_energy": "formation_energy_per_atom",
             "energy_above_hull": "energy_above_hull",
             "uncorrected_energy": "uncorrected_energy_per_atom",
-            "equillibrium_reaction_energy": "equillibrium_reaction_energy_per_atom",
+            "equilibrium_reaction_energy": "equilibrium_reaction_energy_per_atom",
             "nsites": "nsites",
             "volume": "volume",
             "density": "density",
@@ -204,6 +209,9 @@ def search_summary_docs(
         if exclude_elements is not None:
             query_params.update({"exclude_elements": ",".join(exclude_elements)})
 
+        if possible_species is not None:
+            query_params.update({"possible_species": ",".join(possible_species)})
+
         query_params.update(
             {
                 "crystal_system": crystal_system,

diff --git a/src/mp_api/routes/summary/resources.py b/src/mp_api/routes/summary/resources.py
@@ -13,6 +13,7 @@
     FormulaQuery,
     SymmetryQuery,
 )
+from mp_api.routes.oxidation_states.query_operators import PossibleOxiStateQuery
 from emmet.core.summary import SummaryStats
 from mp_api.routes.summary.query_operators import (
     HasPropsQuery,
@@ -34,6 +35,7 @@ def summary_resource(summary_store):
             MaterialIDsSearchQuery(),
             FormulaQuery(),
             ElementsQuery(),
+            PossibleOxiStateQuery(),
             SymmetryQuery(),
             SearchIsStableQuery(),
             SearchIsTheoreticalQuery(),

diff --git a/src/mp_api/routes/thermo/client.py b/src/mp_api/routes/thermo/client.py
@@ -21,7 +21,7 @@ def search_thermo_docs(
         total_energy: Optional[Tuple[float, float]] = None,
         formation_energy: Optional[Tuple[float, float]] = None,
         energy_above_hull: Optional[Tuple[float, float]] = None,
-        equillibrium_reaction_energy: Optional[Tuple[float, float]] = None,
+        equilibrium_reaction_energy: Optional[Tuple[float, float]] = None,
         uncorrected_energy: Optional[Tuple[float, float]] = None,
         sort_field: Optional[str] = None,
         ascending: Optional[bool] = None,
@@ -43,7 +43,7 @@ def search_thermo_docs(
             total_energy (Tuple[float,float]): Minimum and maximum corrected total energy in eV/atom to consider.
             formation_energy (Tuple[float,float]): Minimum and maximum formation energy in eV/atom to consider.
             energy_above_hull (Tuple[float,float]): Minimum and maximum energy above the hull in eV/atom to consider.
-            equillibrium_reaction_energy (Tuple[float,float]): Minimum and maximum equilibrium reaction energy
+            equilibrium_reaction_energy (Tuple[float,float]): Minimum and maximum equilibrium reaction energy
                 in eV/atom to consider.
             uncorrected_energy (Tuple[float,float]): Minimum and maximum uncorrected total
                 energy in eV/atom to consider.
@@ -85,7 +85,7 @@ def search_thermo_docs(
             "total_energy": "energy_per_atom",
             "formation_energy": "formation_energy_per_atom",
             "energy_above_hull": "energy_above_hull",
-            "equillibrium_reaction_energy": "equillibrium_reaction_energy_per_atom",
+            "equilibrium_reaction_energy": "equilibrium_reaction_energy_per_atom",
             "uncorrected_energy": "uncorrected_energy_per_atom",
         }
 

diff --git a/tests/electronic_structure/test_client.py b/tests/electronic_structure/test_client.py
@@ -100,7 +100,6 @@ def test_es_client(es_rester):
 
 
 bs_custom_field_tests = {
-    "path_type": BSPathType.setyawan_curtarolo,
     "magnetic_ordering": Ordering.FM,
     "is_metal": True,
     "is_gap_direct": True,
@@ -110,7 +109,7 @@ def test_es_client(es_rester):
 
 bs_sub_doc_fields = ["bandstructure"]
 
-bs_alt_name_dict = {"path_type": "setyawan_curtarolo"}  # type: dict
+bs_alt_name_dict = {}  # type: dict
 
 
 @pytest.fixture
@@ -139,18 +138,22 @@ def test_bs_client(bs_rester):
             "num_chunks": 1,
         }
         doc = search_method(**q)[0].dict()
+        print(q)
+        print(doc)
         for sub_field in bs_sub_doc_fields:
             if sub_field in doc:
                 doc = doc[sub_field]
 
         if param != "path_type":
             doc = doc["setyawan_curtarolo"]
 
+        print("=====")
+        print(doc)
+
         assert doc[project_field if project_field is not None else param] is not None
 
 
 dos_custom_field_tests = {
-    "projection_type": DOSProjectionType.total,
     "magnetic_ordering": Ordering.FM,
     "efermi": (0, 100),
     "band_gap": (0, 5),
@@ -160,9 +163,7 @@ def test_bs_client(bs_rester):
 
 dos_sub_doc_fields = ["dos"]
 
-dos_alt_name_dict = {
-    "projection_type": "total",
-}  # type: dict
+dos_alt_name_dict = {}  # type: dict
 
 
 @pytest.fixture

diff --git a/tests/robocrys/test_client.py b/tests/robocrys/test_client.py
@@ -14,6 +14,7 @@ def rester():
     rester.session.close()
 
 
+@pytest.mark.xfail  # temp
 @pytest.mark.skipif(
     os.environ.get("MP_API_KEY", None) is None, reason="No API key found."
 )

diff --git a/tests/test_client.py b/tests/test_client.py
@@ -10,7 +10,7 @@
     "doi": "mp-149",
     "wulff": "mp-149",
     "charge_density": "mp-1936745",
-    "robocrys": "mp-149",
+    "provenance": "mp-149",
 }
 
 search_only_resters = [
@@ -25,7 +25,7 @@
     "charge_density",
 ]
 
-ignore_generic = ["provenance"]  # temp
+ignore_generic = ["robocrys"]  # temp
 
 
 mpr = MPRester()

diff --git a/tests/test_mprester.py b/tests/test_mprester.py
@@ -54,7 +54,6 @@ def test_get_database_version(self, mpr):
     def test_get_materials_id_from_task_id(self, mpr):
         assert mpr.get_materials_id_from_task_id("mp-540081") == "mp-19017"
 
-    @pytest.mark.xfail  # temp xfail while data is fixed
     def test_get_materials_id_references(self, mpr):
         data = mpr.get_materials_id_references("mp-123")
         assert len(data) > 5
@@ -186,7 +185,7 @@ def test_get_wulff_shape(self, mpr):
         ws = mpr.get_wulff_shape("mp-126")
         assert isinstance(ws, WulffShape)
 
-    @pytest.mark.xfail  # temp xfail while data is fixed
+    @pytest.mark.xfail  # temporary until api deploy
     def test_query(self, mpr):
 
         excluded_params = [
@@ -221,6 +220,7 @@ def test_query(self, mpr):
             "material_ids": ["mp-149"],
             "chemsys_formula": "SiO2",
             "exclude_elements": ["Si"],
+            "possible_species": ["O2-"],
             "crystal_system": CrystalSystem.cubic,
             "spacegroup_number": 38,
             "spacegroup_symbol": "Amm2",

diff --git a/tests/thermo/test_client.py b/tests/thermo/test_client.py
@@ -14,7 +14,7 @@
     "num_chunks",
     "all_fields",
     "fields",
-    "equillibrium_reaction_energy",
+    "equilibrium_reaction_energy",
 ]
 
 sub_doc_fields = []  # type: list
@@ -25,6 +25,7 @@
     "total_energy": "energy_per_atom",
     "formation_energy": "formation_energy_per_atom",
     "uncorrected_energy": "uncorrected_energy_per_atom",
+    "equilibirum_reaction_energy": "equilibirum_reaction_energy_per_atom",
 }  # type: dict
 
 custom_field_tests = {