Merge pull request #174 from materialsproject/settings_update

Fix serialization and update validation

emmet-builders/emmet/builders/vasp/materials.py

@@ -62,7 +62,7 @@ def __init__(
         self.materials = materials
         self.task_validation = task_validation
         self.query = query if query else {}
-        self.settings = settings or SETTINGS
+        self.settings = EmmetBuildSettings.autoload(settings)
         self.kwargs = kwargs
 
         sources = [tasks]

emmet-builders/emmet/builders/vasp/task_validator.py

@@ -11,9 +11,6 @@
 from emmet.core.vasp.validation import DeprecationMessage, ValidationDoc
 from emmet.builders.settings import EmmetBuildSettings
 
-__author__ = "Shyam Dwaraknath"
-__email__ = "shyamd@lbl.gov"
-
 
 class TaskValidator(MapBuilder):
     def __init__(
@@ -32,7 +29,7 @@ def __init__(
         """
         self.tasks = tasks
         self.task_validation = task_validation
-        self.settings = settings or SETTINGS
+        self.settings = EmmetBuildSettings.autoload(settings)
         self.kwargs = kwargs
 
         super().__init__(
@@ -59,6 +56,7 @@ def unary_function(self, item):
         validation_doc = ValidationDoc.from_task_doc(
             task_doc=task_doc,
             kpts_tolerance=self.settings.VASP_KPTS_TOLERANCE,
+            kspacing_tolerance=self.settings.VASP_KSPACING_TOLERANCE,
             input_sets=self.settings.VASP_DEFAULT_INPUT_SETS,
             LDAU_fields=self.settings.VASP_CHECKED_LDAU_FIELDS,
             max_allowed_scf_gradient=self.settings.VASP_MAX_SCF_GRADIENT,

emmet-core/emmet/core/settings.py

@@ -3,7 +3,7 @@
 """
 import importlib
 import json
-from typing import Dict, List, Optional
+from typing import Dict, List, Optional, Type, TypeVar, Union
 
 import requests
 from pydantic import BaseSettings, Field, root_validator, validator
@@ -12,6 +12,9 @@
 DEFAULT_CONFIG_FILE_PATH = str(Path.home().joinpath(".emmet.json"))
 
 
+S = TypeVar("S", bound="EmmetSettings")
+
+
 class EmmetSettings(BaseSettings):
     """
     Settings for the emmet- packages
@@ -54,6 +57,11 @@ class EmmetSettings(BaseSettings):
         description="Relative tolerance for kpt density to still be a valid task document",
     )
 
+    VASP_KSPACING_TOLERANCE: float = Field(
+        0.05,
+        description="Relative tolerance for kspacing to still be a valid task document",
+    )
+
     VASP_DEFAULT_INPUT_SETS: Dict[str, PyObject] = Field(
         {
             "GGA Structure Optimization": "pymatgen.io.vasp.sets.MPRelaxSet",
@@ -94,3 +102,24 @@ def load_default_settings(cls, values):
         new_values.update(values)
 
         return new_values
+
+    @classmethod
+    def autoload(cls: Type[S], settings: Union[None, dict, S]) -> S:
+        if settings is None:
+            return cls()
+        elif isinstance(settings, dict):
+            return cls(**settings)
+        return settings
+
+    def as_dict(self):
+        """
+        HotPatch to enable serializing EmmetSettings via Monty
+        """
+        return self.dict(exclude_unset=True, exclude_defaults=True)
+
+    @classmethod
+    def from_dict(cls: Type[S], settings: Dict) -> S:
+        """
+        HotPatch to enable serializing EmmetSettings via Monty
+        """
+        return cls(**settings)

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

@@ -14,6 +14,7 @@
 class DeprecationMessage(DocEnum):
     MANUAL = "M", "manual deprecation"
     KPTS = "C001", "Too few KPoints"
+    KSPACING = "C002", "KSpacing not high enough"
     ENCUT = "C002", "ENCUT too low"
     FORCES = "C003", "Forces too large"
     CONVERGENCE = "E001", "Calculation did not converge"
@@ -53,6 +54,7 @@ def from_task_doc(
         cls,
         task_doc: TaskDocument,
         kpts_tolerance: float = SETTINGS.VASP_KPTS_TOLERANCE,
+        kspacing_tolerance: float = SETTINGS.VASP_KSPACING_TOLERANCE,
         input_sets: Dict[str, PyObject] = SETTINGS.VASP_DEFAULT_INPUT_SETS,
         LDAU_fields: List[str] = SETTINGS.VASP_CHECKED_LDAU_FIELDS,
         max_allowed_scf_gradient: float = SETTINGS.VASP_MAX_SCF_GRADIENT,
@@ -62,9 +64,12 @@ def from_task_doc(
 
         Args:
             task_doc: the task document to process
-            input_sets (dict): a dictionary of task_types -> pymatgen input set for validation
-            kpts_tolerance (float): the tolerance to allow kpts to lag behind the input set settings
-            LDAU_fields (list(String)): LDAU fields to check for consistency
+            kpts_tolerance: the tolerance to allow kpts to lag behind the input set settings
+            kspacing_tolerance:  the tolerance to allow kspacing to lag behind the input set settings
+            input_sets: a dictionary of task_types -> pymatgen input set for validation
+            LDAU_fields: LDAU fields to check for consistency
+            max_allowed_scf_gradient: maximum uphill gradient allowed for SCF steps after the
+                initial equillibriation period
         """
 
         structure = task_doc.output.structure
@@ -78,15 +83,27 @@ def from_task_doc(
             valid_input_set = input_sets[task_type](structure)
 
             # Checking K-Points
-            valid_num_kpts = valid_input_set.kpoints.num_kpts or np.prod(
-                valid_input_set.kpoints.kpts[0]
-            )
-            num_kpts = inputs.get("kpoints", {}).get("nkpoints", 0) or np.prod(
-                inputs.get("kpoints", {}).get("kpoints", [1, 1, 1])
-            )
-            data["kpts_ratio"] = num_kpts / valid_num_kpts
-            if data["kpts_ratio"] < kpts_tolerance:
-                reasons.append(DeprecationMessage.KPTS)
+            # Calculations that use KSPACING will not have a .kpoints attr
+            if valid_input_set.kpoints is not None:
+                valid_num_kpts = valid_input_set.kpoints.num_kpts or np.prod(
+                    valid_input_set.kpoints.kpts[0]
+                )
+                num_kpts = inputs.get("kpoints", {}).get("nkpoints", 0) or np.prod(
+                    inputs.get("kpoints", {}).get("kpoints", [1, 1, 1])
+                )
+                data["kpts_ratio"] = num_kpts / valid_num_kpts
+                if data["kpts_ratio"] < kpts_tolerance:
+                    reasons.append(DeprecationMessage.KPTS)
+
+            else:
+                valid_kspacing = valid_input_set.incar.get("KSPACING", 0)
+                if inputs.get("incar", {}).get("KSPACING"):
+                    data["kspacing_delta"] = (
+                        inputs["incar"].get("KSPACING") - valid_kspacing
+                    )
+                    # larger KSPACING means fewer k-points
+                    if data["kspacing_delta"] > kspacing_tolerance:
+                        reasons.append(DeprecationMessage.KSPACING)
 
             # Checking ENCUT
             encut = inputs.get("incar", {}).get("ENCUT")

tests/emmet-core/test_settings.py

@@ -3,6 +3,9 @@
 from pathlib import PosixPath
 from random import random
 
+from monty.serialization import dumpfn, loadfn
+from monty.tempfile import ScratchDir
+
 from emmet.core.settings import EmmetSettings
 
 
@@ -40,3 +43,14 @@ def test_from_url():
     test_config = EmmetSettings()
 
     assert test_config.ANGLE_TOL == 1.0
+
+
+def test_seriallization():
+
+    test_config = EmmetSettings()
+
+    with ScratchDir("."):
+        dumpfn(test_config, "test.json")
+        reload_config = loadfn("test.json")
+
+        assert isinstance(reload_config, EmmetSettings)