emmet-builders 0.84.9rc0__py3-none-any.whl → 0.84.10__py3-none-any.whl
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- emmet/builders/abinit/phonon.py +5 -1
- emmet/builders/abinit/sound_velocity.py +5 -1
- emmet/builders/materials/absorption_spectrum.py +6 -1
- emmet/builders/materials/corrected_entries.py +7 -1
- emmet/builders/materials/dielectric.py +7 -1
- emmet/builders/materials/elasticity.py +11 -3
- emmet/builders/materials/electrodes.py +6 -1
- emmet/builders/materials/magnetism.py +7 -1
- emmet/builders/materials/optimade.py +5 -1
- emmet/builders/materials/provenance.py +5 -1
- emmet/builders/materials/substrates.py +2 -2
- emmet/builders/materials/summary.py +2 -2
- emmet/builders/materials/thermo.py +8 -2
- emmet/builders/matscholar/missing_compositions.py +5 -1
- emmet/builders/molecules/atomic.py +7 -1
- emmet/builders/molecules/bonds.py +7 -1
- emmet/builders/molecules/electric.py +7 -1
- emmet/builders/molecules/metal_binding.py +6 -1
- emmet/builders/molecules/orbitals.py +6 -1
- emmet/builders/molecules/redox.py +8 -1
- emmet/builders/molecules/summary.py +9 -1
- emmet/builders/molecules/thermo.py +8 -1
- emmet/builders/molecules/trajectory.py +7 -1
- emmet/builders/molecules/vibration.py +6 -1
- emmet/builders/qchem/molecules.py +13 -6
- emmet/builders/utils.py +7 -3
- emmet/builders/vasp/materials.py +7 -1
- emmet/builders/vasp/task_validator.py +2 -1
- {emmet_builders-0.84.9rc0.dist-info → emmet_builders-0.84.10.dist-info}/METADATA +2 -1
- emmet_builders-0.84.10.dist-info/RECORD +54 -0
- emmet_builders-0.84.9rc0.dist-info/RECORD +0 -54
- {emmet_builders-0.84.9rc0.dist-info → emmet_builders-0.84.10.dist-info}/WHEEL +0 -0
- {emmet_builders-0.84.9rc0.dist-info → emmet_builders-0.84.10.dist-info}/top_level.txt +0 -0
emmet/builders/abinit/phonon.py
CHANGED
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import os
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import tempfile
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from math import ceil
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from typing import Iterator
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import numpy as np
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from abipy.abio.inputs import AnaddbInput
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@@ -36,6 +35,11 @@ from emmet.core.phonon import (
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from emmet.core.polar import BornEffectiveCharges, DielectricDoc, IRDielectric
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from emmet.core.utils import jsanitize
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from typing import TYPE_CHECKING
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from collections.abc import Iterator
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SETTINGS = EmmetBuildSettings()
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import tempfile
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import traceback
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from math import ceil
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from typing import Iterator
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from abipy.dfpt.ddb import DdbFile
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from abipy.dfpt.vsound import SoundVelocity as AbiSoundVelocity
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from emmet.core.phonon import SoundVelocity
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from emmet.core.utils import jsanitize
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from typing import TYPE_CHECKING
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from collections.abc import Iterator
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class SoundVelocityBuilder(Builder):
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def __init__(
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from __future__ import annotations
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import numpy as np
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from maggma.builders import Builder
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from emmet.core.absorption import AbsorptionDoc
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class AbsorptionBuilder(Builder):
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def __init__(
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from __future__ import annotations
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import copy
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from maggma.core import Builder, Store
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from maggma.utils import grouper
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from emmet.core.thermo import ThermoType
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class CorrectedEntriesBuilder(Builder):
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def __init__(
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from emmet.core.polar import DielectricDoc
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class DielectricBuilder(Builder):
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def __init__(
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7. Fit the elastic tensor.
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"""
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from maggma.core import Builder, Store
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from pymatgen.core.tensors import TensorMapping
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from emmet.core.elasticity import ElasticityDoc
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from emmet.core.mpid import MPID
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from emmet.core.vasp.calc_types import CalcType
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from emmet.core.mpid import AlphaID, MPID
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class ElasticityBuilder(Builder):
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"""
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Process all tasks belong to the same material into an elasticity doc.
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__author__ = "Shyam Dwaraknath <shyamd@lbl.gov>, Matthew Horton <mkhorton@lbl.gov>"
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from emmet.core.utils import confirm_molecule, get_graph_hash, jsanitize
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SETTINGS = EmmetBuildSettings()
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@@ -11,6 +12,13 @@ from emmet.builders.settings import EmmetBuildSettings
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from emmet.core.molecules.summary import MoleculeSummaryDoc
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# from monty.serialization import loadfn, dumpfn
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@@ -17,6 +18,12 @@ from emmet.core.qchem.molecule import MoleculeDoc, evaluate_lot
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__author__ = "Evan Spotte-Smith"
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SETTINGS = EmmetBuildSettings()
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from __future__ import annotations
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@@ -14,6 +15,11 @@ from emmet.core.qchem.molecule import MoleculeDoc, evaluate_lot
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__author__ = "Evan Spotte-Smith"
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SETTINGS = EmmetBuildSettings()
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@@ -1,8 +1,10 @@
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1
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from __future__ import annotations
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2
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from collections import defaultdict
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@@ -14,6 +16,9 @@ from emmet.core.qchem.molecule import MoleculeDoc, evaluate_lot
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from emmet.core.qchem.task import TaskDocument
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__author__ = "Evan Spotte-Smith"
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SETTINGS = EmmetBuildSettings()
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from __future__ import annotations
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|
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from typing import Any, Iterable, Iterator, Set
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import networkx as nx
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from maggma.builders import Builder
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@@ -19,6 +20,12 @@ from emmet.core.qchem.molecule import (
|
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20
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from emmet.core.qchem.task import TaskDocument
|
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from emmet.core.utils import get_molecule_id, group_molecules, jsanitize, make_mol_graph
|
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|
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|
__author__ = "Evan Spotte-Smith <ewcspottesmith@lbl.gov>"
|
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24
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@@ -554,11 +561,11 @@ class MoleculesBuilder(Builder):
|
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554
561
|
levels_of_theory = dict()
|
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555
562
|
solvents = dict()
|
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556
563
|
lot_solvents = dict()
|
|
557
|
-
unique_calc_types:
|
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558
|
-
unique_task_types:
|
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559
|
-
unique_levels_of_theory:
|
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560
|
-
unique_solvents:
|
|
561
|
-
unique_lot_solvents:
|
|
564
|
+
unique_calc_types: set[str | CalcType] = set()
|
|
565
|
+
unique_task_types: set[str | TaskType] = set()
|
|
566
|
+
unique_levels_of_theory: set[str | LevelOfTheory] = set()
|
|
567
|
+
unique_solvents: set[str] = set()
|
|
568
|
+
unique_lot_solvents: set[str] = set()
|
|
562
569
|
origins = list()
|
|
563
570
|
entries = list()
|
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564
571
|
best_entries: dict[str, Any] = dict()
|
emmet/builders/utils.py
CHANGED
|
@@ -7,7 +7,6 @@ from gzip import GzipFile
|
|
|
7
7
|
from io import BytesIO
|
|
8
8
|
from itertools import chain, combinations
|
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9
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from pathlib import Path
|
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10
|
-
from typing import Any, Literal, Set
|
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11
10
|
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12
11
|
import orjson
|
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13
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|
from botocore.exceptions import ClientError
|
|
@@ -18,8 +17,13 @@ from pymatgen.io.vasp.inputs import PotcarSingle
|
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18
17
|
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19
18
|
from emmet.builders.settings import EmmetBuildSettings
|
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20
19
|
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20
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+
from typing import TYPE_CHECKING
|
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21
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|
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-
|
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+
if TYPE_CHECKING:
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from typing import Any, Literal
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24
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|
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25
|
+
|
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26
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+
def maximal_spanning_non_intersecting_subsets(sets) -> set[set[Any]]:
|
|
23
27
|
"""
|
|
24
28
|
Finds the maximal spanning non intersecting subsets of a group of sets
|
|
25
29
|
This is usefull for parsing out the sandboxes and figuring out how to group
|
|
@@ -47,7 +51,7 @@ def maximal_spanning_non_intersecting_subsets(sets) -> Set[Set]:
|
|
|
47
51
|
return set(to_return_subsets)
|
|
48
52
|
|
|
49
53
|
|
|
50
|
-
def chemsys_permutations(chemsys) ->
|
|
54
|
+
def chemsys_permutations(chemsys) -> set[str]:
|
|
51
55
|
# Function to get all relevant chemical subsystems
|
|
52
56
|
# e.g. for Li-Mn-O returns Li, Li-Mn, Li-Mn-O, Li-O, Mn, Mn-O, O
|
|
53
57
|
elements = chemsys.split("-")
|
emmet/builders/vasp/materials.py
CHANGED
|
@@ -1,7 +1,8 @@
|
|
|
1
|
+
from __future__ import annotations
|
|
2
|
+
|
|
1
3
|
from datetime import datetime
|
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2
4
|
from itertools import chain
|
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3
5
|
from math import ceil
|
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4
|
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from typing import Iterable, Iterator
|
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5
6
|
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6
7
|
from maggma.builders import Builder
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7
8
|
from maggma.stores import Store
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@@ -13,6 +14,11 @@ from emmet.core.utils import group_structures, jsanitize, undeform_structure
|
|
|
13
14
|
from emmet.core.vasp.calc_types import TaskType
|
|
14
15
|
from emmet.core.vasp.material import MaterialsDoc
|
|
15
16
|
|
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17
|
+
from typing import TYPE_CHECKING
|
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18
|
+
|
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|
+
if TYPE_CHECKING:
|
|
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|
+
from collections.abc import Iterable, Iterator
|
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21
|
+
|
|
16
22
|
__author__ = "Shyam Dwaraknath <shyamd@lbl.gov>"
|
|
17
23
|
|
|
18
24
|
SETTINGS = EmmetBuildSettings()
|
|
@@ -5,7 +5,8 @@ from emmet.builders.settings import EmmetBuildSettings
|
|
|
5
5
|
from emmet.builders.utils import get_potcar_stats
|
|
6
6
|
from emmet.core.tasks import TaskDoc
|
|
7
7
|
from emmet.core.vasp.calc_types.enums import CalcType
|
|
8
|
-
from emmet.core.vasp.validation import DeprecationMessage
|
|
8
|
+
from emmet.core.vasp.validation import DeprecationMessage
|
|
9
|
+
from emmet.core.vasp.validation_legacy import ValidationDoc
|
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9
10
|
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10
11
|
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|
11
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|
class TaskValidator(MapBuilder):
|
|
@@ -1,6 +1,6 @@
|
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1
1
|
Metadata-Version: 2.4
|
|
2
2
|
Name: emmet-builders
|
|
3
|
-
Version: 0.84.
|
|
3
|
+
Version: 0.84.10
|
|
4
4
|
Summary: Builders for the Emmet Library
|
|
5
5
|
Home-page: https://github.com/materialsproject/emmet
|
|
6
6
|
Author: The Materials Project
|
|
@@ -13,6 +13,7 @@ Requires-Dist: maggma>=0.57.6
|
|
|
13
13
|
Requires-Dist: matminer>=0.9.1
|
|
14
14
|
Requires-Dist: solvation-analysis>=0.4.0
|
|
15
15
|
Requires-Dist: MDAnalysis>=2.7.0
|
|
16
|
+
Requires-Dist: pymatgen-io-validation>=0.1.0
|
|
16
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|
Provides-Extra: test
|
|
17
18
|
Requires-Dist: pre-commit; extra == "test"
|
|
18
19
|
Requires-Dist: pytest; extra == "test"
|
|
@@ -0,0 +1,54 @@
|
|
|
1
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