Add FEFF schema

aimmdb/adapters/feff.py

@@ -0,0 +1,6 @@
+from tiled.adapters.dataframe import DataFrameAdapter
+
+
+# dataframe adapter representing FEFF data
+class FEFFAdapter(DataFrameAdapter):
+    specs = ["FEFF"]

aimmdb/schemas.py

@@ -145,3 +145,66 @@ class BatteryChargeMetadataInternal(pydantic.BaseModel):
 
 class BatteryChargeMetadata(pydantic.BaseModel, extra=pydantic.Extra.allow):
     charge: BatteryChargeMetadataInternal
+
+class FEFFpotentials(pydantic.BaseModel, extra=pydantic.Extra.allow):
+    x: Optional[str]
+    ipot: int
+    Z: str
+    element: int
+    l_scmt: int
+    l_fms: int
+    #FEFFpotentials = (x, ipot, Z, element, l_scmt, l_fms)
+    #converted_potentials = str(FEFFpotentials)
+    #smiles = string
+
+class FEFFcards(pydantic.BaseModel, extra=pydantic.Extra.allow):
+    atoms: float
+    control: int
+    exchange: float
+    title: Optional[str]
+    rpath: int
+    potentials: FEFFpotentials
+    xanes: float
+    edge: str
+    scf: float
+    fms: float
+    S02: float
+    corehole: str
+    #smiles = string
+
+#class FEFFDataFrame(DataFrameStructure):
+    #file_input = "xmu.dat"
+    #omega: float
+    #e: float
+    #k: float
+    #mu: float
+    #mu0: float
+    #chi: float
+    #FEFFDataFrame_inputs = (omega, e, k, mu, mu0, chi)
+    #smiles = string
+
+   #need to write validation for the Dataframe
+
+#class ExperimentalFEFFMetadata(pydantic.BaseModel, extra=pydantic.Extra.allow):
+    #FileType = "feff.out"; "feff.inp"
+    #measurement_type: MeasurementEnum = pydantic.Field("feff", const=True)
+    #title = measurement_type(pydantic.field("title"))
+    #absorbing_atom = measurement_type(pydantic.field("edge"))
+    #cards = measurement_type(FEFFcards)
+    #smiles = string
+
+class FEFFInputMetadata(pydantic.BaseModel, extra=pydantic.Extra.allow):
+    element: XDIElement
+    measurement_type: MeasurementEnum = pydantic.Field("FEFF", const=True)
+    dataset: str
+    sample_id: str
+    input_script: str
+
+class FEFFOutputMetadata(pydantic.BaseModel, extra=pydantic.Extra.allow):
+    element: XDIElement
+    measurement_type: MeasurementEnum = pydantic.Field("FEFF", const=True)
+    dataset: str
+    sample_id: str
+    #change to output log
+    output_script: str
+

aimmdb/validation.py

@@ -1,7 +1,7 @@
 import pydantic
 from tiled.validation_registration import ValidationError
 
-from .schemas import BatteryChargeMetadata, ExperimentalXASMetadata
+from .schemas import BatteryChargeMetadata, ExperimentalXASMetadata, ExperimentalFEFFMetadata
 
 
 def validate_xas_metadata(metadata, structure_family, structure, spec):
@@ -45,3 +45,14 @@ def validate_battery_charge_data(metadata, structure_family, structure, spec):
         metadata = BatteryChargeMetadata.parse_obj(metadata)
     except pydantic.ValidationError as e:
         raise ValidationError(str(e))
+
+def validate_feff(metadata, structure_family, structure, spec):
+    #validate_xas_metadata(metadata, structure_family, structure, spec)
+
+    columns = set(structure.macro.columns)
+
+    required_columns = {"omega", "e", "k", "mu", "mu0", "chi"}
+
+
+    if not required_columns.issubset(columns):
+        raise ValidationError(f"columns {columns} must contain {required_columns}")