Merge branch 'hackingmaterials:main' into main

Author: rdguha1995

.pre-commit-config.yaml

@@ -9,16 +9,10 @@ default_install_hook_types: [pre-commit, commit-msg]
 exclude: ^(docs/|.*test_files/|.*tests/)
 
 repos:
-  - repo: https://github.com/myint/autoflake
+  - repo: https://github.com/PyCQA/autoflake
     rev: v1.4
     hooks:
       - id: autoflake
-        args:
-          - --in-place
-          - --remove-unused-variables
-          - --remove-all-unused-imports
-          - --expand-star-imports
-          - --ignore-init-module-imports
 
   - repo: https://github.com/psf/black
     rev: 22.6.0
@@ -29,6 +23,7 @@ repos:
     rev: 5.0.4
     hooks:
       - id: flake8
+        additional_dependencies: [flake8-bugbear]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v0.971

atomate/qchem/drones.py

@@ -232,7 +232,8 @@ def generate_doc(self, dir_name, qcinput_files, qcoutput_files, multirun):
                     ]
             if d["output"]["job_type"] in ["freq", "frequency"]:
                 d["output"]["frequencies"] = d_calc_final["frequencies"]
-                d["output"]["frequency_modes"] = d_calc_final["frequency_mode_vectors"]
+                # Note: for single-atom freq calcs, this key may not exist
+                d["output"]["frequency_modes"] = d_calc_final.get("frequency_mode_vectors", [])
                 d["output"]["enthalpy"] = d_calc_final["total_enthalpy"]
                 d["output"]["entropy"] = d_calc_final["total_entropy"]
                 if d["input"]["job_type"] in ["opt", "optimization", "ts"]:
@@ -507,7 +508,7 @@ def validate_doc(self, d):
         to pass validation is unfortunately unlikely to be noticed by a user.
         """
         for k, v in self.schema.items():
-            diff = v.difference(set(d.get(k, d).keys()))
+            diff = v - set(d.get(k, d).keys())
             if diff:
                 logger.warning(f"The keys {diff} in {k} not set")
 

atomate/utils/database.py

@@ -35,7 +35,7 @@ def __init__(
         **kwargs,
     ):
         """
-        Obeject to handle storing calculation data to MongoDB databases.
+        Object to handle storing calculation data to MongoDB databases.
         The results of calculations will be parsed by a Drone and
         CalcDb is only responsible for putting that data into the database
 
@@ -50,7 +50,7 @@ def __init__(
                         other authentication information will be ignored
             maggma_store_kwargs: additional kwargs for mongodb login.
                 Currently supports:
-                    S3 store kwarges:
+                    S3 store kwargs:
                         "bucket" : the S3 bucket where the data is stored
                         "s3_profile" : the S3 profile that contains the login information
                                         typically found at ~/.aws/credentials
@@ -255,7 +255,7 @@ def _get_s3_store(self, store_name):
         and the store_name will double as the sub_dir name.
 
         Args:
-            store_name: correspond to the the key within calcs_reversed.0 that will be stored
+            store_name: correspond to the key within calcs_reversed.0 that will be stored
         """
         if self.host_uri is not None:
             index_store_ = MongoURIStore(

atomate/vasp/drones.py

@@ -828,9 +828,9 @@ def validate_doc(self, d):
         # notice if the validation fails? -computron
         for k, v in self.schema.items():
             if k == "calcs_reversed":
-                diff = v.difference(set(d.get(k, d)[0].keys()))
+                diff = v - set(d.get(k, d)[0].keys())
             else:
-                diff = v.difference(set(d.get(k, d).keys()))
+                diff = v - set(d.get(k, d).keys())
             if diff:
                 logger.warning(f"The keys {diff} in {k} not set")
 

atomate/vasp/firetasks/electrode_tasks.py

@@ -10,15 +10,7 @@
 from atomate.vasp.database import VaspCalcDb
 from atomate.vasp.firetasks import pass_vasp_result
 from atomate.vasp.fireworks.core import OptimizeFW, StaticFW
-
-try:
-    from pymatgen.analysis.defects import ChargeInsertionAnalyzer
-except ImportError:
-    print(
-        "Failed to import ChargeInsertionAnalyzer. This is likely due to converting the pymatgen defects module "
-        "to a namespace package. See https://github.com/materialsproject/pymatgen/pull/2582#issuecomment-1198318101 "
-        "for updates."
-    )
+from pymatgen.analysis.defects.utils import ChargeInsertionAnalyzer
 
 __author__ = "Jimmy Shen"
 __email__ = "[email protected]"

atomate/vasp/firetasks/write_inputs.py

@@ -630,7 +630,6 @@ def run_task(self, fw_spec):
             t_cls = None
             for m in [
                 "advanced_transformations",
-                "defect_transformations",
                 "site_transformations",
                 "standard_transformations",
             ]:

atomate/vasp/test_files/setup_test/POSCAR

@@ -1,10 +1,10 @@
 Si2
 1.0
-3.840198 0.000000 0.000000
-1.920099 3.325710 0.000000
-0.000000 -2.217138 3.135509
+   3.8401979336999998    0.0000000000000000    0.0000000000000000
+   1.9200989667999999    3.3257101909000002    0.0000000000000000
+   0.0000000000000000   -2.2171384942999999    3.1355090603000000
 Si
 2
 direct
-0.000000 0.000000 0.000000 Si
-0.750000 0.500000 0.750000 Si
+   0.0000000000000000    0.0000000000000000    0.0000000000000000 Si
+   0.7500000000000000    0.5000000000000000    0.7500000000000000 Si

atomate/vasp/tests/test_setup.py

@@ -1,4 +1,5 @@
 import os
+from turtle import pos
 import unittest
 
 from pymatgen.core import IStructure, Lattice

atomate/vasp/workflows/base/adsorption.py

@@ -30,7 +30,7 @@ def get_slab_fw(
     add_slab_metadata=True,
 ):
     """
-    Function to generate a a slab firework.  Returns a TransmuterFW if
+    Function to generate a slab firework.  Returns a TransmuterFW if
     bulk_structure is specified, constructing the necessary transformations
     from the slab and slab generator parameters, or an OptimizeFW if only a
     slab is specified.

atomate/vasp/workflows/base/neb.py

@@ -83,7 +83,7 @@ def get_wf_neb_from_structure(
                     user_incar_settings is used to determine how many NEB rounds will be. Default
                     is [{}, {}, {}].
         additional_spec (dict): User spec settings to overwrite default_spec.
-        user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at at
+        user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at
                     least three elements, which is similar to user_incar_settings. For example,
                     [{}, {}, {"grid_density": 100}] for the workflow from the parent structure
                     relaxation, then the endpoint relaxation followed by one-round NEB simulation.
@@ -170,7 +170,7 @@ def get_wf_neb_from_structure(
             )
         )
 
-        for i, label in enumerate(["ep0", "ep1"]):
+        for label in ["ep0", "ep1"]:
             fw = NEBRelaxationFW(
                 spec=spec,
                 label=label,
@@ -221,7 +221,7 @@ def get_wf_neb_from_endpoints(
                     user_incar_settings is used to determine how many NEB rounds will be. Default
                     is [{}, {}, {}].
         additional_spec (dict): User spec settings to overwrite default_spec.
-        user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at at
+        user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at
                     least three elements, which is similar to user_incar_settings. For example,
                     [{}, {}, {"grid_density": 100}] for the workflow from the parent structure
                     relaxation, then the endpoint relaxation followed by one-round NEB simulation.
@@ -320,7 +320,7 @@ def get_wf_neb_from_images(
                     user_incar_settings is used to determine how many NEB rounds will be. Default
                     is [{}, {}, {}].
         additional_spec (dict): User spec settings to overwrite default_spec.
-        user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at at
+        user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at
                     least three elements, which is similar to user_incar_settings. For example,
                     [{}, {}, {"grid_density": 100}] for the workflow from the parent structure
                     relaxation, then the endpoint relaxation followed by one-round NEB simulation.