clean up add generator function

emmet-core/emmet/core/thermo.py

@@ -1,14 +1,15 @@
 """ Core definition of a Thermo Document """
 from datetime import datetime
-from typing import ClassVar, Dict, List
 from enum import Enum
+from typing import ClassVar, Dict, List
 
 from pydantic import BaseModel, Field
+from pymatgen.analysis.phase_diagram import PhaseDiagram, PhaseDiagramError
 from pymatgen.core.periodic_table import Element
 
 from emmet.core.material import PropertyDoc
 from emmet.core.structure import StructureMetadata
-from emmet.stubs import ComputedEntry, Composition
+from emmet.stubs import Composition, ComputedEntry
 
 
 class DecompositionProduct(BaseModel):
@@ -29,7 +30,7 @@ class DecompositionProduct(BaseModel):
     )
 
 
-class Thermo(PropertyDoc):
+class ThermoDoc(PropertyDoc):
     """
     A thermo entry document
     """
@@ -39,11 +40,11 @@ class Thermo(PropertyDoc):
     )
 
     uncorrected_energy_per_atom: float = Field(
-        None, description="The total DFT energy of this material per atom in eV/atom"
+        ..., description="The total DFT energy of this material per atom in eV/atom"
     )
 
     energy_per_atom: float = Field(
-        None,
+        ...,
         description="The total corrected DFT energy of this material per atom in eV/atom",
     )
 
@@ -54,14 +55,15 @@ class Thermo(PropertyDoc):
     formation_energy_per_atom: float = Field(
         None, description="The formation energy per atom in eV/atom"
     )
-    e_above_hull: float = Field(
-        None, description="The energy above the hull in eV/Atom"
+
+    energy_above_hull: float = Field(
+        ..., description="The energy above the hull in eV/Atom"
     )
     is_stable: bool = Field(
-        None,
+        False,
         description="Flag for whether this material is on the hull and therefore stable",
     )
-    equillibrium_reaction_energy_per_atmo: float = Field(
+    equillibrium_reaction_energy_per_atom: float = Field(
         None,
         description="The reaction energy of a stable entry from the neighboring equilibrium stable materials in eV."
         " Also known as the inverse distance to hull.",
@@ -73,7 +75,7 @@ class Thermo(PropertyDoc):
     )
 
     energy_type: str = Field(
-        None,
+        ...,
         description="The type of calculation this energy evaluation comes from. TODO: Convert to enum?",
     )
 
@@ -86,3 +88,54 @@ class Thermo(PropertyDoc):
         description="List of all entries that are valid for this material."
         " The keys for this dictionary are names of various calculation types",
     )
+
+    @classmethod
+    def from_entries(cls, entries: List[ComputedEntry], sandboxes=None):
+
+        pd = PhaseDiagram(entries)
+
+        docs = []
+
+        for e in entries:
+            (decomp, ehull) = pd.get_decomp_and_e_above_hull(e)
+
+            d = {
+                "material_id": e.entry_id,
+                "uncorrected_energy_per_atom": e.uncorrected_energy
+                / e.composition.num_atoms,
+                "energy_per_atom": e.uncorrected_energy / e.composition.num_atoms,
+                "formation_energy_per_atom": pd.get_form_energy_per_atom(e),
+                "energy_above_hull": ehull,
+                "is_stable": e in pd.stable_entries,
+                "sandboxes": sandboxes,
+            }
+
+            if "last_updated" in e.data:
+                d["last_updated"] = e.data["last_updated"]
+
+            # Store different info if stable vs decomposes
+            if d["is_stable"]:
+                d[
+                    "equillibrium_reaction_energy_per_atom"
+                ] = pd.get_equilibrium_reaction_energy(e)
+            else:
+                d["decomposes_to"] = [
+                    {
+                        "material_id": de.entry_id,
+                        "formula": de.composition.formula,
+                        "amount": amt,
+                    }
+                    for de, amt in decomp.items()
+                ]
+
+            d["energy_type"] = e.parameters["run_type"]
+
+            elsyms = sorted(set([el.symbol for el in e.composition.elements]))
+            d["chemsys"] = "-".join(elsyms)
+            d["nelements"] = len(elsyms)
+            d["elements"] = list(elsyms)
+            d["last_updated"] = e.data["last_updated"]
+
+            docs.append(ThermoDoc(**d))
+
+        return docs