Merge remote-tracking branch 'materialsproject/master' into s_group

.github/workflows/release.yml

@@ -15,7 +15,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2.3.4
 
-    - uses: actions/setup-python@v2.1.4
+    - uses: actions/setup-python@v2.2.1
       with:
         python-version: 3.7
 
@@ -43,7 +43,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2.3.4
 
-    - uses: actions/setup-python@v2.1.4
+    - uses: actions/setup-python@v2.2.1
       with:
         python-version: 3.7
 

.github/workflows/testing.yml

@@ -21,7 +21,7 @@ jobs:
       - uses: actions/checkout@v2.3.4
 
       - name: Set up Python 3.7
-        uses: actions/setup-python@v2.1.4
+        uses: actions/setup-python@v2.2.1
         with:
           python-version: 3.7
 
@@ -52,7 +52,7 @@ jobs:
       - uses: actions/checkout@v2.3.4
 
       - name: Set up Python 3.7
-        uses: actions/setup-python@v2.1.4
+        uses: actions/setup-python@v2.2.1
         with:
           python-version: 3.7
 
@@ -85,7 +85,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2.3.4
 
-    - uses: actions/setup-python@v2.1.4
+    - uses: actions/setup-python@v2.2.1
       with:
         python-version: 3.8
 

emmet-builders/setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name="emmet-builders",
-    use_scm_version={"relative_to": Path(__file__).parent},
+    use_scm_version={"root": "..", "relative_to": __file__},
     setup_requires=["setuptools_scm"],
     description="Builders for the Emmet Library",
     author="The Materials Project",

emmet-core/emmet/core/thermo.py

@@ -1,15 +1,15 @@
 """ Core definition of a Thermo Document """
 from datetime import datetime
 from enum import Enum
-from typing import ClassVar, Dict, List
+from typing import ClassVar, Dict, List, Union
 
 from pydantic import BaseModel, Field
 from pymatgen.analysis.phase_diagram import PhaseDiagram, PhaseDiagramError
 from pymatgen.core.periodic_table import Element
 
 from emmet.core.material_property import PropertyDoc
 from emmet.core.structure import StructureMetadata
-from emmet.stubs import Composition, ComputedEntry
+from emmet.stubs import Composition, ComputedEntry, ComputedStructureEntry
 
 
 class DecompositionProduct(BaseModel):
@@ -83,14 +83,14 @@ class ThermoDoc(PropertyDoc):
         description="List of available energy types computed for this material"
     )
 
-    entries: Dict[str, ComputedEntry] = Field(
-        None,
+    entries: Dict[str, Union[ComputedEntry, ComputedStructureEntry]] = Field(
+        ...,
         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]):
+    def from_entries(cls, entries: List[Union[ComputedEntry, ComputedStructureEntry]]):
 
         pd = PhaseDiagram(entries)
 

emmet-core/emmet/core/vasp/material.py

@@ -12,7 +12,7 @@
 from emmet.core.structure import StructureMetadata
 from emmet.core.vasp.calc_types import CalcType, RunType, TaskType
 from emmet.core.vasp.task import TaskDocument
-from emmet.stubs import ComputedEntry, Structure
+from emmet.stubs import ComputedStructureEntry, Structure
 
 
 class MaterialsDoc(CoreMaterialsDoc, StructureMetadata):
@@ -34,7 +34,7 @@ class MaterialsDoc(CoreMaterialsDoc, StructureMetadata):
         None, description="Mappingionary for tracking the provenance of properties"
     )
 
-    entries: Mapping[RunType, ComputedEntry] = Field(
+    entries: Mapping[RunType, ComputedStructureEntry] = Field(
         None, description="Dictionary for tracking entries for VASP calculations"
     )
 
@@ -136,7 +136,7 @@ def _structure_eval(task: TaskDocument):
 
             if len(relevant_calcs) > 0:
                 best_task_doc = relevant_calcs[0]
-                entry = best_task_doc.entry
+                entry = best_task_doc.structure_entry
                 entry.data["task_id"] = entry.entry_id
                 entry.entry_id = material_id
                 entries[rt] = entry

emmet-core/emmet/core/vasp/task.py

@@ -18,7 +18,13 @@
     run_type,
     task_type,
 )
-from emmet.stubs import ComputedEntry, Matrix3D, Structure, Vector3D
+from emmet.stubs import (
+    ComputedEntry,
+    ComputedStructureEntry,
+    Matrix3D,
+    Structure,
+    Vector3D,
+)
 
 
 class Status(ValueEnum):
@@ -153,3 +159,11 @@ def entry(self):
         }
 
         return ComputedEntry.from_dict(entry_dict)
+
+    @property
+    def structure_entry(self):
+        """ Turns a Task Doc into a ComputedStructureEntry"""
+        entry_dict = self.entry.as_dict()
+        entry_dict["structure"] = self.output.structure
+
+        return ComputedStructureEntry.from_dict(entry_dict)

emmet-core/emmet/core/vasp/validation.py

@@ -2,7 +2,7 @@
 from typing import Dict, List, Union
 
 import numpy as np
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, PyObject
 
 from emmet.core import SETTINGS
 from emmet.core.utils import DocEnum
@@ -11,11 +11,12 @@
 
 
 class DeprecationMessage(DocEnum):
-
-    kpoints = "kpoints", "Too few Kpoints"
-    encut = "encut", "ENCUT too low"
-    ldau = "ldau", "LDAU parameters don't match"
-    manual = "manual", "Manually deprecated"
+    MANUAL = "M", "manual deprecation"
+    KPTS = "C001", "Too few KPoints"
+    ENCUT = "C002", "ENCUT too low"
+    FORCES = "C003", "Forces too large"
+    CONVERGENCE = "E001", "Calculation did not converge"
+    LDAU = "I001", "LDAU Parameters don't match the inputset"
 
 
 class ValidationDoc(BaseModel):
@@ -30,7 +31,10 @@ class ValidationDoc(BaseModel):
         default_factory=datetime.utcnow,
     )
     reasons: List[Union[DeprecationMessage, str]] = Field(
-        [], description="List of deprecation tags detailing why this task isn't valid"
+        None, description="List of deprecation tags detailing why this task isn't valid"
+    )
+    warnings: List[str] = Field(
+        [], description="List of potential warnings about this calculation"
     )
 
     class Config:
@@ -41,7 +45,7 @@ def from_task_doc(
         cls,
         task_doc: TaskDocument,
         kpts_tolerance: float = SETTINGS.VASP_KPTS_TOLERANCE,
-        input_sets: Dict[str, type] = SETTINGS.VASP_DEFAULT_INPUT_SETS,
+        input_sets: Dict[str, PyObject] = SETTINGS.VASP_DEFAULT_INPUT_SETS,
         LDAU_fields: List[str] = SETTINGS.VASP_CHECKED_LDAU_FIELDS,
     ) -> "ValidationDoc":
         """
@@ -58,7 +62,6 @@ def from_task_doc(
         task_type = task_doc.task_type
         inputs = task_doc.orig_inputs
 
-        is_valid = True
         reasons = []
         data = {}
 
@@ -74,16 +77,14 @@ def from_task_doc(
             )
             data["kpts_ratio"] = num_kpts / valid_num_kpts
             if data["kpts_ratio"] < kpts_tolerance:
-                is_valid = False
-                reasons.append(DeprecationMessage.kpoints)
+                reasons.append(DeprecationMessage.KPTS)
 
             # Checking ENCUT
             encut = inputs.get("incar", {}).get("ENCUT")
             valid_encut = valid_input_set.incar["ENCUT"]
             data["encut_ratio"] = float(encut) / valid_encut  # type: ignore
             if data["encut_ratio"] < 1:
-                is_valid = False
-                reasons.append(DeprecationMessage.encut)
+                reasons.append(DeprecationMessage.ENCUT)
 
             # Checking U-values
             if valid_input_set.incar.get("LDAU"):
@@ -108,14 +109,13 @@ def from_task_doc(
                     input_set_ldau_params[el] != input_params
                     for el, input_params in input_ldau_params.items()
                 ):
-                    is_valid = False
-                    reasons.append(DeprecationMessage.ldau)
+                    reasons.append(DeprecationMessage.LDAU)
 
         doc = ValidationDoc(
             task_id=task_doc.task_id,
             task_type=task_doc.task_type,
             run_type=task_doc.run_type,
-            valid=is_valid,
+            valid=len(reasons) == 0,
             reasons=reasons,
             **data
         )

emmet-core/emmet/core/xrd.py

@@ -54,7 +54,7 @@ def get_target_and_edge(cls, values: Dict):
         return values
 
     @classmethod
-    def from_structure(
+    def from_structure(  # type: ignore[override]
         cls,
         material_id: str,
         spectrum_id: str,

emmet-core/emmet/stubs/__init__.py

@@ -1,3 +1,4 @@
+# isort: off
 """
 This module stubs in pydantic models for common MSONable classes, particularly those in Pymatgen
 Use pymatgen classes in pydantic models by importing them from there when you need schema
@@ -7,14 +8,15 @@
 from pymatgen.analysis.diffraction.xrd import DiffractionPattern
 from pymatgen.analysis.xas.spectrum import XAS
 from pymatgen.core.structure import Composition, Lattice, Structure
-from pymatgen.entries.computed_entries import ComputedEntry
+from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 
+from emmet.stubs.utils import patch_msonable, use_model
 from emmet.stubs.math import Matrix3D, Vector3D
-from emmet.stubs.misc import Composition as StubComposition
-from emmet.stubs.misc import ComputedEntry as StubComputedEntry
 from emmet.stubs.structure import Lattice as StubLattice
 from emmet.stubs.structure import Structure as StubStructure
-from emmet.stubs.utils import patch_msonable, use_model
+from emmet.stubs.entries import Composition as StubComposition
+from emmet.stubs.entries import ComputedEntry as StubComputedEntry
+from emmet.stubs.entries import ComputedStructureEntry as StubComputedStructureEntry
 from emmet.stubs.xrd import XRDPattern as StubXRDPattern
 
 """
@@ -27,6 +29,7 @@
 use_model(Composition, StubComposition, add_monty=False)
 use_model(ComputedEntry, StubComputedEntry)
 use_model(DiffractionPattern, StubXRDPattern)
+use_model(ComputedStructureEntry, StubComputedStructureEntry)
 
 # This is after the main block since it depends on that
 from emmet.stubs.xas import XASSpectrum  # noqa

emmet-core/emmet/stubs/misc.py → emmet-core/emmet/stubs/entries.py

@@ -3,6 +3,8 @@
 from pydantic import BaseModel, Field
 from pymatgen.core.periodic_table import Element
 
+from emmet.stubs.structure import Structure
+
 
 class Composition(BaseModel):
     """A dictionary mapping element to total quantity"""
@@ -32,3 +34,11 @@ class ComputedEntry(BaseModel):
     )
     data: Dict = Field(None, description="Dictionary of extra data")
     entry_id: str = Field(None, description="Entry ID")
+
+
+class ComputedStructureEntry(ComputedEntry):
+    """
+    A entry of thermodynamic information for a particular structure
+    """
+
+    structure: Structure

emmet-core/requirements.txt

@@ -1,4 +1,4 @@
-pymatgen==2020.4.29
+pymatgen==2020.12.31
 monty==4.0.2
 pydantic==1.7.3
 pybtex==0.23.0

tests/emmet-core/test_thermo.py

@@ -68,6 +68,7 @@ def entries():
     )
 
 
+@pytest.mark.xfail
 def test_from_entries(entries):
     docs = ThermoDoc.from_entries(entries)