Fix use of PatchedPhaseDiagram in ThermoBuilder (#566)

* FIx default value of pd_docs * Fix patched phase diagram build issue * Fix setup.py files * Flake8 linting * More linting
materialsproject · Oct 22, 2022 · d564566 · d564566
1 parent f79b390
commit d564566
Show file tree

Hide file tree

Showing 5 changed files with 45 additions and 80 deletions.
diff --git a/emmet-api/setup.py b/emmet-api/setup.py
@@ -8,9 +8,9 @@
 setup(
     name="emmet-api",
     use_scm_version={
-        "root": ".",
+        "root": "..",
         "relative_to": __file__,
-        "write_to": "emmet/api/_version.py",
+        "write_to": "emmet-api/emmet/api/_version.py",
         "write_to_template": '__version__ = "{version}"',
         "fallback_version": fallback_version,
     },
@@ -20,14 +20,7 @@
     author_email="feedback@materialsproject.org",
     url="https://github.com/materialsproject/emmet",
     packages=find_namespace_packages(include=["emmet.*"]),
-    install_requires=[
-        "emmet-core[all]",
-        "fastapi",
-        "uvicorn",
-        "gunicorn",
-        "boto3",
-        "maggma",
-    ],
+    install_requires=["emmet-core[all]", "fastapi", "uvicorn", "gunicorn", "boto3", "maggma"],
     python_requires=">=3.8",
     license="modified BSD",
     zip_safe=False,

diff --git a/emmet-builders/emmet/builders/vasp/thermo.py b/emmet-builders/emmet/builders/vasp/thermo.py
@@ -153,11 +153,7 @@ def get_items(self) -> Iterator[List[Dict]]:
         # Remove overlapping chemical systems
         processed = set()
         to_process_chemsys = []
-        for chemsys in sorted(
-            updated_chemsys | new_chemsys | affected_chemsys,
-            key=lambda x: len(x),
-            reverse=True,
-        ):
+        for chemsys in sorted(updated_chemsys | new_chemsys | affected_chemsys, key=lambda x: len(x), reverse=True,):
             if chemsys not in processed:
                 processed |= chemsys_permutations(chemsys)
                 to_process_chemsys.append(chemsys)
@@ -236,20 +232,17 @@ def _produce_pair(self, pd_entries, thermo_type, elements):
         try:
             docs, pds = ThermoDoc.from_entries(pd_entries, thermo_type, deprecated=False)
 
-            pd_data = None
+            pd_docs = [None]
 
             if self.phase_diagram:
                 if self.num_phase_diagram_eles is None or len(elements) <= self.num_phase_diagram_eles:
                     pd_docs = []
 
                     for pd in pds:
-                        chemsys = '-'.join(sorted(set([e.symbol for e in pd.elements])))
+                        chemsys = "-".join(sorted(set([e.symbol for e in pd.elements])))
                         pd_id = "{}_{}".format(chemsys, str(thermo_type))
                         pd_doc = PhaseDiagramDoc(
-                            phase_diagram_id=pd_id,
-                            chemsys=chemsys,
-                            phase_diagram=pd,
-                            thermo_type=thermo_type,
+                            phase_diagram_id=pd_id, chemsys=chemsys, phase_diagram=pd, thermo_type=thermo_type,
                         )
 
                         pd_data = jsanitize(pd_doc.dict(), allow_bson=True)
@@ -337,10 +330,7 @@ def get_entries(self, chemsys: str) -> List[Dict]:
                 d["material_id"]: d.get("average_oxidation_states", {})
                 for d in self.oxidation_states.query(
                     properties=["material_id", "average_oxidation_states"],
-                    criteria={
-                        "material_id": {"$in": material_ids},
-                        "state": "successful",
-                    },
+                    criteria={"material_id": {"$in": material_ids}, "state": "successful"},
                 )
             }
 
@@ -361,9 +351,7 @@ def get_entries(self, chemsys: str) -> List[Dict]:
 
         return all_entries
 
-    def get_updated_chemsys(
-        self,
-    ) -> Set:
+    def get_updated_chemsys(self,) -> Set:
         """Gets updated chemical system as defined by the updating of an existing material"""
 
         updated_mats = self.thermo.newer_in(self.materials, criteria=self.query)

diff --git a/emmet-builders/setup.py b/emmet-builders/setup.py
@@ -8,9 +8,9 @@
 setup(
     name="emmet-builders",
     use_scm_version={
-        "root": ".",
+        "root": "..",
         "relative_to": __file__,
-        "write_to": "emmet/builders/_version.py",
+        "write_to": "emmet-builders/emmet/builders/_version.py",
         "write_to_template": '__version__ = "{version}"',
         "fallback_version": fallback_version,
     },

diff --git a/emmet-core/emmet/core/thermo.py b/emmet-core/emmet/core/thermo.py
@@ -20,16 +20,13 @@ class DecompositionProduct(BaseModel):
     """
 
     material_id: MPID = Field(
-        None,
-        description="The Materials Project ID for the material this decomposition points to.",
+        None, description="The Materials Project ID for the material this decomposition points to.",
     )
     formula: str = Field(
-        None,
-        description="The formula of the decomposed material this material decomposes to.",
+        None, description="The formula of the decomposed material this material decomposes to.",
     )
     amount: float = Field(
-        None,
-        description="The amount of the decomposed material by formula units this this material decomposes to.",
+        None, description="The amount of the decomposed material by formula units this this material decomposes to.",
     )
 
 
@@ -48,22 +45,19 @@ class ThermoDoc(PropertyDoc):
     property_name = "thermo"
 
     thermo_type: Union[ThermoType, RunType] = Field(
-        ...,
-        description="Functional types of calculations involved in the energy mixing scheme.",
+        ..., description="Functional types of calculations involved in the energy mixing scheme.",
     )
 
     thermo_id: str = Field(
-        ...,
-        description="Unique document ID which is composed of the Material ID and thermo data type.",
+        ..., description="Unique document ID which is composed of the Material ID and thermo data type.",
     )
 
     uncorrected_energy_per_atom: float = Field(
         ..., description="The total DFT energy of this material per atom in eV/atom."
     )
 
     energy_per_atom: float = Field(
-        ...,
-        description="The total corrected DFT energy of this material per atom in eV/atom.",
+        ..., description="The total corrected DFT energy of this material per atom in eV/atom.",
     )
 
     energy_uncertainy_per_atom: float = Field(None, description="")
@@ -73,8 +67,7 @@ class ThermoDoc(PropertyDoc):
     energy_above_hull: float = Field(..., description="The energy above the hull in eV/Atom.")
 
     is_stable: bool = Field(
-        False,
-        description="Flag for whether this material is on the hull and therefore stable.",
+        False, description="Flag for whether this material is on the hull and therefore stable.",
     )
 
     equilibrium_reaction_energy_per_atom: float = Field(
@@ -89,18 +82,15 @@ class ThermoDoc(PropertyDoc):
     )
 
     decomposition_enthalpy: float = Field(
-        None,
-        description="Decomposition enthalpy as defined by `get_decomp_and_phase_separation_energy` in pymatgen.",
+        None, description="Decomposition enthalpy as defined by `get_decomp_and_phase_separation_energy` in pymatgen.",
     )
 
     decomposition_enthalpy_decomposes_to: List[DecompositionProduct] = Field(
-        None,
-        description="List of decomposition data associated with the decomposition_enthalpy quantity.",
+        None, description="List of decomposition data associated with the decomposition_enthalpy quantity.",
     )
 
     energy_type: str = Field(
-        ...,
-        description="The type of calculation this energy evaluation comes from.",
+        ..., description="The type of calculation this energy evaluation comes from.",
     )
 
     entry_types: List[str] = Field(description="List of available energy types computed for this material.")
@@ -122,7 +112,20 @@ def from_entries(
         # lowest energy entries.
         patched_pd = PatchedPhaseDiagram(entries, keep_all_spaces=True)
 
-        pd = patched_pd.pds[frozenset(patched_pd.elements)]  # Main PD of parent chemsys
+        # Main PD of parent chemsys
+        try:
+            pd = patched_pd.pds[frozenset(patched_pd.elements)]
+        except KeyError:
+            entries_by_comp = defaultdict(list)
+            for e in entries:
+                entries_by_comp[e.composition.reduced_formula].append(e)
+
+            # Only use lowest entry per composition to speed up QHull in Phase Diagram
+            reduced_entries = [
+                sorted(comp_entries, key=lambda e: e.energy_per_atom)[0] for comp_entries in entries_by_comp.values()
+            ]
+            pd = PhaseDiagram(reduced_entries)
+            patched_pd.pds = {frozenset(patched_pd.elements): pd}
 
         docs = []
 
@@ -173,23 +176,15 @@ def _energy_eval(entry: ComputedStructureEntry):
                 d["equilibrium_reaction_energy_per_atom"] = pd.get_equilibrium_reaction_energy(blessed_entry)
             else:
                 d["decomposes_to"] = [
-                    {
-                        "material_id": de.data["material_id"],
-                        "formula": de.composition.formula,
-                        "amount": amt,
-                    }
+                    {"material_id": de.data["material_id"], "formula": de.composition.formula, "amount": amt}
                     for de, amt in decomp.items()
                 ]
 
             try:
                 decomp, energy = pd.get_decomp_and_phase_separation_energy(blessed_entry)
                 d["decomposition_enthalpy"] = energy
                 d["decomposition_enthalpy_decomposes_to"] = [
-                    {
-                        "material_id": de.data["material_id"],
-                        "formula": de.composition.formula,
-                        "amount": amt,
-                    }
+                    {"material_id": de.data["material_id"], "formula": de.composition.formula, "amount": amt}
                     for de, amt in decomp.items()
                 ]
             except ValueError:
@@ -242,23 +237,19 @@ class PhaseDiagramDoc(BaseModel):
     property_name = "phase_diagram"
 
     phase_diagram_id: str = Field(
-        ...,
-        description="Phase diagram ID consisting of the chemical system and thermo type",
+        ..., description="Phase diagram ID consisting of the chemical system and thermo type",
     )
 
     chemsys: str = Field(
-        ...,
-        description="Dash-delimited string of elements in the material",
+        ..., description="Dash-delimited string of elements in the material",
     )
 
     thermo_type: Union[ThermoType, RunType] = Field(
-        ...,
-        description="Functional types of calculations involved in the energy mixing scheme.",
+        ..., description="Functional types of calculations involved in the energy mixing scheme.",
     )
 
     phase_diagram: PhaseDiagram = Field(
-        ...,
-        description="Phase diagram for the chemical system.",
+        ..., description="Phase diagram for the chemical system.",
     )
 
     last_updated: datetime = Field(

diff --git a/emmet-core/setup.py b/emmet-core/setup.py
@@ -9,9 +9,9 @@
 setup(
     name="emmet-core",
     use_scm_version={
-        "root": ".",
+        "root": "..",
         "relative_to": __file__,
-        "write_to": "emmet/core/_version.py",
+        "write_to": "emmet-core/emmet/core/_version.py",
         "write_to_template": '__version__ = "{version}"',
         "fallback_version": fallback_version,
     },
@@ -21,10 +21,7 @@
     author_email="feedback@materialsproject.org",
     url="https://github.com/materialsproject/emmet",
     packages=find_namespace_packages(include=["emmet.*"]),
-    package_data={
-        "emmet.core.vasp.calc_types": ["*.yaml"],
-        "emmet.core.subtrates": ["*.json"],
-    },
+    package_data={"emmet.core.vasp.calc_types": ["*.yaml"], "emmet.core.subtrates": ["*.json"]},
     include_package_data=True,
     install_requires=[
         "pymatgen>=2021.3,<2023.0",
@@ -35,11 +32,7 @@
         "spglib<2.0.0",
     ],
     extras_require={
-        "all": [
-            "robocrys>=0.2.7",
-            "pymatgen-analysis-diffusion>=2022.1.15",
-            "pymatgen-analysis-alloys>=0.0.3",
-        ],
+        "all": ["robocrys>=0.2.7", "pymatgen-analysis-diffusion>=2022.1.15", "pymatgen-analysis-alloys>=0.0.3"],
     },
     python_requires=">=3.8",
     license="modified BSD",