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Fix use of PatchedPhaseDiagram in ThermoBuilder #566

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merged 6 commits into from
Oct 22, 2022
Merged

Fix use of PatchedPhaseDiagram in ThermoBuilder #566

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84e1e15
FIx default value of pd_docs
munrojm Oct 22, 2022
34c417d
Fix patched phase diagram build issue
munrojm Oct 22, 2022
11bea9b
Merge branch 'main' into bugfix/thermo_patched_pd
munrojm Oct 22, 2022
a04e078
Fix setup.py files
munrojm Oct 22, 2022
ba30dc9
Flake8 linting
munrojm Oct 22, 2022
7faec93
More linting
munrojm Oct 22, 2022
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13 changes: 3 additions & 10 deletions emmet-api/setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,9 @@
setup(
name="emmet-api",
use_scm_version={
"root": ".",
"root": "..",
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This basically reverts #565

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Yes, I had to revert as the git information wasn't properly being accessed by setuptools when root is set to .

I will try and find another solution, but in the mean time this change needed to happen so our deployment pipelines don't break.

"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,
},
Expand All @@ -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,
Expand Down
24 changes: 6 additions & 18 deletions emmet-builders/emmet/builders/vasp/thermo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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"},
)
}

Expand All @@ -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)
Expand Down
4 changes: 2 additions & 2 deletions emmet-builders/setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
},
Expand Down
69 changes: 30 additions & 39 deletions emmet-core/emmet/core/thermo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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.",
)


Expand All @@ -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="")
Expand All @@ -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(
Expand All @@ -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.")
Expand All @@ -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 = []

Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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(
Expand Down
15 changes: 4 additions & 11 deletions emmet-core/setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,
},
Expand All @@ -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",
Expand All @@ -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",
Expand Down