Electronic (#2)

* adding electronic properites workflow

* first commit of new workflow

* introduce new code: automate routine for computing electronic and bader

* update vasp from prev for dos and bader

* update workflow package imports, add new electronic workflow, move functions to logical modules

* create parsers, now in workflow testing phase

* fix workflow run bugs

* update icharg value

* modify run_calc file and workflow to do a double kpoint run for chgcar

* update gridfs for dos

* update parser output

* update electronic workflow

* fix bug in average_z_sep

* fix bug in average_z_sep

* add correct name to 2d-substrate heterostructs based on stacked wyckoff sites

* fix bugs

* update parse output

* update run calc and core to use custom custodian handler

* debugging run_calc and appending cdd analysis to same db entry as dos,bader run

* modify run_calc to set npar. custodian currently does not search for the correct slurm variable to set npar. so i fixed it

* updated ToDb: dos->element projected with 0.05 eV res and default [4,6] eV window around efermi. add user option for window

* update obj_id variable pass

* fix auto_npar

* push obj_id to cdd calculation spec

* add flags to depends to trigger slurm_npar

* remove parent cdd_combined from iso NSCF, clarify error message in workflow, add task_label to additional_fields not tags

* update cdd error message

* fix bug in vasp interface set

* fix logic error for vis_static; structure now updates to the isolated structures

* add logger to CDD parser

* delete random }

* clean up unneeded comments

* include amin. add option to include dipole correction in nscf calculation. fix cmdlrelaxset's ediff value. reformat name for electronicFW if not cdd.

* change out final structure from previous run is obtained.

* remove amin

* fix pushing obj_id for combined system so the cdd analysis can be pushed to that obj_id

* remove conflicting isym tag

* clean up formatting of documents

* change task_name to task_label

* update parser

* fix parse output

* fix parse output

* fix parse output

* fix entry of dos into grid fs

* don't push None to fw spec

* fix brackets for database pushing

* cleaning up store_data for cdd update

* add logger info to processing document clean up debug code, add exception errors

* fix logic error in slurm_npar

* update docs, add get_dos utility, update parser to put completedos into database. machine learning needs that object

* fix Electronic to DB parser. add z proj chg for NSCF structures

* update decompress to describe behaviour of function

* fix stupid error

* add complete dos to import for utils

* add todo

Author: tboland1

hetero2d/firetasks/heteroiface_tasks.py

@@ -10,21 +10,23 @@
 
 from __future__ import division, print_function, unicode_literals, absolute_import
 
-import fnmatch, glob, gzip, json, os, re
-
+import glob, os, re
 from six.moves import range
 from copy import deepcopy
 from importlib import import_module
 
 from monty.json import jsanitize
 from monty.serialization import dumpfn
 
-from atomate.utils.utils import get_logger, env_chk
+from pymatgen import Structure
+
 from fireworks.core.firework import FiretaskBase, FWAction
 from fireworks.utilities.fw_utilities import explicit_serialize
-from pymatgen import Structure
 
-from hetero2d.manipulate.utils import get_mongo_client
+from atomate.utils.utils import get_logger, env_chk
+
+from hetero2d.manipulate.utils import get_mongo_client 
+
 
 __author__ = 'Tara M. Boland'
 __copyright__ = "Copyright 2020, CMD Lab"
@@ -33,44 +35,6 @@
 
 logger = get_logger(__name__)
 
-
-def find(pattern, path):
-    """
-    Finds a file on a given search path that matches the
-    pattern.
-
-    Args:
-        pattern (str): String to match on.
-        path (str): File path to search over.
-
-    Returns:
-        a list of files matching the criteria
-    """
-    result = []
-    for root, dirs, files in os.walk(path):
-        for name in files:
-            if fnmatch.fnmatch(name, pattern):
-                result.append(name)
-    return result
-
-
-def get_FWjson():
-    """
-    Helper function which reads the FW.json file in the
-    local directory and returns the FW.json file.
-    """
-    fw_file = find('FW.json*', '.')[0]
-
-    if fw_file == 'FW.json.gz':
-        with gzip.GzipFile('FW.json.gz', 'r') as p:
-            fw_json_file = json.loads(p.read().decode('utf-8'))
-    elif fw_file == 'FW.json':
-        with open('FW.json', 'rb') as p:
-            fw_json_file = json.load(p)
-
-    return fw_json_file
-
-
 # Helper Functions
 def _update_spec(additional_spec):
     """
@@ -174,7 +138,6 @@ def _update_spec(additional_spec):
                              "_dupefinder": {"_fw_name": "DupeFinderExact"}})
     return default_spec
 
-
 @explicit_serialize
 class TransferSlabTask(FiretaskBase):
     """
@@ -184,8 +147,8 @@ class TransferSlabTask(FiretaskBase):
     Args:
         label (str): The name of the structure in the 
             additional_spec dict - struct_sub.
-            
-    Returns: 
+
+    Returns:
         FWAction updating the spec
     """
     required_params = ['label']
@@ -202,7 +165,6 @@ def run_task(self, fw_spec):
 
         return FWAction(update_spec=update_spec)
 
-
 @explicit_serialize
 class CreateHeterostructureTask(FiretaskBase):
     """