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""" Core definition of a Materials Document """
from typing import Dict, List, Mapping, Optional
from pydantic import BaseModel, Field
from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer
from pymatgen.analysis.structure_matcher import StructureMatcher
from pymatgen.entries.computed_entries import ComputedStructureEntry
from emmet.core.base import EmmetMeta
from emmet.core.material import MaterialsDoc as CoreMaterialsDoc
from emmet.core.material import PropertyOrigin
from emmet.core.settings import EmmetSettings
from emmet.core.structure import StructureMetadata
from emmet.core.tasks import TaskDoc
from emmet.core.vasp.calc_types import CalcType, RunType, TaskType
SETTINGS = EmmetSettings()
class BlessedCalcs(BaseModel):
GGA: Optional[ComputedStructureEntry] = None
GGA_U: Optional[ComputedStructureEntry] = Field(None, alias="GGA+U")
PBESol: Optional[ComputedStructureEntry] = None
SCAN: Optional[ComputedStructureEntry] = None
R2SCAN: Optional[ComputedStructureEntry] = None
HSE: Optional[ComputedStructureEntry] = None
class MaterialsDoc(CoreMaterialsDoc, StructureMetadata):
calc_types: Optional[Mapping[str, CalcType]] = Field( # type: ignore
None,
description="Calculation types for all the calculations that make up this material",
)
task_types: Optional[Mapping[str, TaskType]] = Field(
None,
description="Task types for all the calculations that make up this material",
)
run_types: Optional[Mapping[str, RunType]] = Field(
None,
description="Run types for all the calculations that make up this material",
)
origins: Optional[List[PropertyOrigin]] = Field(
None, description="Mappingionary for tracking the provenance of properties"
)
entries: Optional[BlessedCalcs] = Field(
None, description="Dictionary for tracking entries for VASP calculations"
)
@classmethod
def from_tasks(
cls,
task_group: List[TaskDoc],
structure_quality_scores: Dict[
str, int
] = SETTINGS.VASP_STRUCTURE_QUALITY_SCORES,
use_statics: bool = SETTINGS.VASP_USE_STATICS,
commercial_license: bool = True,
) -> "MaterialsDoc":
"""
Converts a group of tasks into one material
Args:
task_group: List of task document
structure_quality_scores: quality scores for various calculation types
use_statics: Use statics to define a material
commercial_license: Whether the data should be licensed with BY-C (otherwise BY-NC).
"""
if len(task_group) == 0:
raise Exception("Must have more than one task in the group.")
# Metadata
last_updated = max(task.last_updated for task in task_group)
created_at = min(task.completed_at for task in task_group)
task_ids = list({task.task_id for task in task_group})
deprecated_tasks = {task.task_id for task in task_group if not task.is_valid}
run_types = {task.task_id: task.run_type for task in task_group}
task_types = {task.task_id: task.task_type for task in task_group}
calc_types = {task.task_id: task.calc_type for task in task_group}
structure_optimizations = [
task for task in task_group if task.task_type == TaskType.Structure_Optimization # type: ignore
]
statics = [task for task in task_group if task.task_type == TaskType.Static] # type: ignore
structure_calcs = (
structure_optimizations + statics
if use_statics
else structure_optimizations
)
validity_check = [doc for doc in structure_calcs if doc.is_valid]
if not validity_check:
raise ValueError("Group must contain at least one valid task")
# Material ID
possible_mat_ids = [task.task_id for task in structure_optimizations]
if use_statics:
possible_mat_ids += [task.task_id for task in statics]
material_id = min(possible_mat_ids)
# Always prefer a static over a structure opt
structure_task_quality_scores = {"Structure Optimization": 1, "Static": 2}
def _structure_eval(task: TaskDoc):
"""
Helper function to order structures optimization and statics calcs by
- Functional Type
- Spin polarization
- Special Tags
- Energy
"""
task_run_type = task.run_type
_SPECIAL_TAGS = ["LASPH", "ISPIN"]
special_tags = sum(
(
task.input.parameters.get(tag, False)
if task.input.parameters
else False
)
for tag in _SPECIAL_TAGS
)
return (
-1 * int(task.is_valid),
-1 * structure_quality_scores.get(task_run_type.value, 0),
-1 * structure_task_quality_scores.get(task.task_type.value, 0),
-1 * special_tags,
task.output.energy_per_atom,
)
best_structure_calc = sorted(structure_calcs, key=_structure_eval)[0]
structure = best_structure_calc.output.structure
# Initial Structures
initial_structures = [task.input.structure for task in task_group]
sm = StructureMatcher(
ltol=0.1, stol=0.1, angle_tol=0.1, scale=False, attempt_supercell=False
)
initial_structures = [
group[0] for group in sm.group_structures(initial_structures)
]
# Deprecated
deprecated = all(task.task_id in deprecated_tasks for task in structure_calcs)
deprecated = deprecated or best_structure_calc.task_id in deprecated_tasks
# Origins
origins = [
PropertyOrigin(
name="structure",
task_id=best_structure_calc.task_id,
last_updated=best_structure_calc.last_updated,
)
]
# Entries
# **current materials docs must contain at last one GGA or GGA+U entry
# Always prefer a static over a structure opt
entry_task_quality_scores = {"Structure Optimization": 1, "Static": 2}
def _entry_eval(task: TaskDoc):
"""
Helper function to order entries and statics calcs by
- Spin polarization
- Special Tags
- Energy
"""
_SPECIAL_TAGS = ["LASPH", "ISPIN"]
special_tags = sum(
(
task.input.parameters.get(tag, False)
if task.input.parameters
else False
)
for tag in _SPECIAL_TAGS
)
return (
-1 * int(task.is_valid),
-1 * entry_task_quality_scores.get(task.task_type.value, 0),
-1 * special_tags,
task.output.energy_per_atom,
)
# Entries
# **current materials docs must contain at last one GGA or GGA+U entry
entries = {}
all_run_types = set(run_types.values())
for rt in all_run_types:
relevant_calcs = sorted(
[doc for doc in structure_calcs if doc.run_type == rt and doc.is_valid],
key=_entry_eval,
)
if len(relevant_calcs) > 0:
best_task_doc = relevant_calcs[0]
entry = best_task_doc.structure_entry
entry.data["task_id"] = entry.entry_id
entry.data["material_id"] = material_id
entry.entry_id = "{}-{}".format(material_id, rt.value)
entry.parameters["is_hubbard"] = best_task_doc.input.is_hubbard
entry.parameters["hubbards"] = best_task_doc.input.hubbards
entries[rt] = entry
if RunType.GGA not in entries and RunType.GGA_U not in entries:
raise ValueError(
"Individual material entry must contain at least one GGA or GGA+U calculation"
)
# Builder meta and license
builder_meta = EmmetMeta(license="BY-C" if commercial_license else "BY-NC")
return cls.from_structure(
structure=structure,
material_id=material_id,
last_updated=last_updated,
created_at=created_at,
task_ids=task_ids,
calc_types=calc_types,
run_types=run_types,
task_types=task_types,
initial_structures=initial_structures,
deprecated=deprecated,
deprecated_tasks=deprecated_tasks,
origins=origins,
entries=entries,
builder_meta=builder_meta,
)
@classmethod
def construct_deprecated_material(
cls,
task_group: List[TaskDoc],
commercial_license: bool = True,
) -> "MaterialsDoc":
"""
Converts a group of tasks into a deprecated material
Args:
task_group: List of task document
commercial_license: Whether the data should be licensed with BY-C (otherwise BY-NC).
"""
if len(task_group) == 0:
raise Exception("Must have more than one task in the group.")
# Metadata
last_updated = max(task.last_updated for task in task_group)
created_at = min(task.completed_at for task in task_group)
task_ids = list({task.task_id for task in task_group})
deprecated_tasks = {task.task_id for task in task_group}
run_types = {task.task_id: task.run_type for task in task_group}
task_types = {task.task_id: task.task_type for task in task_group}
calc_types = {task.task_id: task.calc_type for task in task_group}
# Material ID
material_id = min([task.task_id for task in task_group])
# Choose any random structure for metadata
structure = SpacegroupAnalyzer(
task_group[0].output.structure, symprec=0.1
).get_conventional_standard_structure()
# Deprecated
deprecated = True
# Builder meta and license
builder_meta = EmmetMeta(license="BY-C" if commercial_license else "BY-NC")
return cls.from_structure(
structure=structure,
material_id=material_id,
last_updated=last_updated,
created_at=created_at,
task_ids=task_ids,
calc_types=calc_types,
run_types=run_types,
task_types=task_types,
deprecated=deprecated,
deprecated_tasks=deprecated_tasks,
builder_meta=builder_meta,
)
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