How to use the atomate.utils.utils.get_logger function in atomate

from monty.serialization import dumpfn
from monty.json import jsanitize

from atomate.qchem.database import QChemCalcDb
from atomate.utils.utils import env_chk
from atomate.utils.utils import get_logger

__author__ = "Samuel Blau"
__copyright__ = "Copyright 2018, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Samuel Blau"
__email__ = "samblau1@gmail.com"
__status__ = "Alpha"
__date__ = "11/13/18"

logger = get_logger(__name__)


@explicit_serialize
class GatherGeometries(FiretaskBase):
    """
    """
    required_params = ["prefix", "suffix"]
    optional_params = ["db_file"]

    def run_task(self, fw_spec):

        data = []
        for key in fw_spec:
            if len(key) > len(self["prefix"])+len(self["suffix"]):
                if key[0:len(self["prefix"])] == self["prefix"]:
                    to_add = copy.deepcopy(fw_spec[key])

def _get_images_by_linear_interp(self, nimages, ep0, ep1):
        logger = get_logger(__name__)
        sort_tol = self.get("sort_tol", 0.0)

        try:
            images = ep0.interpolate(ep1, nimages=nimages + 1, autosort_tol=sort_tol)
        except Exception as e:
            if "Unable to reliably match structures " in str(e):
                logger.warning("Auto sorting is turned off because it is unable to match the "
                            "end-point structures!")
                images = ep0.interpolate(ep1, nimages=nimages + 1, autosort_tol=0)
            else:
                raise e

        return images

"""
This module defines the point defects workflow: structure optimization followed by transmuter fireworks.
"""

from fireworks import Workflow

from atomate.utils.utils import get_logger
from atomate.vasp.fireworks.core import OptimizeFW, TransmuterFW, StaticFW

from pymatgen.io.vasp.sets import MPRelaxSet, MPStaticSet

__author__ = 'Kiran Mathew'
__email__ = 'kmathew@lbl.gov'

logger = get_logger(__name__)


def get_wf_point_defects(structure, defect_transformations, defect_transformations_params,
                         charge_states=None, name="point_defects", vasp_input_set=None,
                         lepsilon=False, vasp_cmd="vasp", db_file=None, user_kpoints_settings=None,
                         tag=""):
    """
    Returns a point defects workflow.

    Firework 1 : structural relaxation

    Firework 2 : static

    Firework 3 - : Apply the defect transformations and run static calculation for each charge state.

import os
import yaml
import pymongo

from fireworks import LaunchPad
from pymongo import MongoClient
from atomate.utils.utils import get_logger
from atomate.vasp.database import VaspCalcDb
from atomate.vasp.drones import VaspDrone

logger =get_logger(__name__)

class PostRunInsertion():
    """
    Inserts existing amorphous calculations into MongoDB
    """
    def __init__(self):
        with open("/global/homes/s/sivonxay/.conda/envs/knl_env/config/my_launchpad.yaml", "r") as f:
            t = yaml.load(f)
        client = MongoClient(t['host'])
        db = client.fw_es_vasp
        db.authenticate(t['username'], t['password'])
        self.tasks = db.tasks

        db_file = "/global/homes/s/sivonxay/.conda/envs/knl_env/config/db.json"
        self.mmdb = VaspCalcDb.from_db_file(db_file, admin=True)

# coding: utf-8


from tqdm import tqdm

from atomate.utils.utils import get_database

from pymatgen import MPRester, Structure
from pymatgen.entries.computed_entries import ComputedEntry

from atomate.utils.utils import get_logger
from atomate.vasp.builders.base import AbstractBuilder

logger = get_logger(__name__)

__author__ = 'Anubhav Jain '


class MaterialsEhullBuilder(AbstractBuilder):
    def __init__(self, materials_write, mapi_key=None, update_all=False):
        """
        Starting with an existing materials collection, adds stability information and
        The Materials Project ID.
        Args:
            materials_write: mongodb collection for materials (write access needed)
            mapi_key: (str) Materials API key (if MAPI_KEY env. var. not set)
            update_all: (bool) - if true, updates all docs. If false, only updates
                docs w/o a stability key
        """
        self._materials = materials_write

from atomate.common.firetasks.glue_tasks import get_calc_loc
from atomate.qchem.database import QChemCalcDb
from atomate.utils.utils import env_chk
from atomate.utils.utils import get_logger
from atomate.qchem.drones import QChemDrone

__author__ = "Samuel Blau"
__copyright__ = "Copyright 2018, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Samuel Blau"
__email__ = "samblau1@gmail.com"
__status__ = "Alpha"
__date__ = "4/25/18"
__credits__ = "Brandon Wood, Shyam Dwaraknath, Xiaohui Qu"

logger = get_logger(__name__)


@explicit_serialize
class QChemToDb(FiretaskBase):
    """
    Enter a QChem run into the database. Uses current directory unless you
    specify calc_dir or calc_loc.

    Optional params:
        calc_dir (str): path to dir (on current filesystem) that contains QChem
            input and output files. Default: use current working directory.
        calc_loc (str OR bool): if True will set most recent calc_loc. If str
            search for the most recent calc_loc with the matching name
        input_file (str): name of the QChem input file
        output_file (str): name of the QChem output file
        additional_fields (dict): dict of additional fields to add

from pymatgen.core import Structure
from pymatgen.io.vasp.sets import MPRelaxSet, MVLScanRelaxSet
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.entries.computed_entries import ComputedStructureEntry
from pymatgen.analysis.defects.generators import VacancyGenerator, SubstitutionGenerator, \
    InterstitialGenerator, VoronoiInterstitialGenerator, SimpleChargeGenerator

from fireworks import FiretaskBase, FWAction, explicit_serialize

from atomate.utils.utils import get_logger
from atomate.vasp.fireworks.core import TransmuterFW

from monty.serialization import dumpfn
from monty.json import MontyEncoder

logger = get_logger(__name__)

def optimize_structure_sc_scale(inp_struct, final_site_no):
    """
    A function for finding optimal supercell transformation
    by maximizing the nearest image distance with the number of
    atoms remaining less than final_site_no

    Args:
        inp_struct: input pymatgen Structure object
        final_site_no (float or int): maximum number of atoms
        for final supercell

    Returns:
        3 x 1 array for supercell transformation
    """
    if final_site_no <= len(inp_struct.sites):

add_tags,
    add_additional_fields_to_taskdocs,
    add_wf_metadata,
    add_common_powerups,
)
from atomate.vasp.workflows.base.core import get_wf
from atomate.vasp.firetasks.parse_outputs import (
    MagneticDeformationToDb,
    MagneticOrderingsToDb,
)

from pymatgen.alchemy.materials import TransformedStructure

from atomate.utils.utils import get_logger

logger = get_logger(__name__)

from atomate.vasp.config import VASP_CMD, DB_FILE, ADD_WF_METADATA

from atomate.vasp.workflows.presets.scan import wf_scan_opt
from uuid import uuid4
from pymatgen.io.vasp.sets import MPRelaxSet
from pymatgen.core import Lattice, Structure
from pymatgen.analysis.magnetism.analyzer import (
    CollinearMagneticStructureAnalyzer,
    MagneticStructureEnumerator,
)

__author__ = "Matthew Horton"
__maintainer__ = "Matthew Horton"
__email__ = "mkhorton@lbl.gov"
__status__ = "Production"

# coding: utf-8


from tqdm import tqdm

from atomate.utils.utils import get_database

from pymatgen import Composition

from atomate.vasp.builders.base import AbstractBuilder
from atomate.utils.utils import get_logger

logger = get_logger(__name__)

__author__ = 'Anubhav Jain '


class FileMaterialsBuilder(AbstractBuilder):
    def __init__(self, materials_write, data_file, delimiter=",", header_lines=0):
        """
        Updates the database using a data file. Format of file must be:
        , , 

        Comment lines should *start* with '#'.

        Args:
            materials_write: mongodb collection for materials (write access needed)
            data_file (str): path to data file
            delimiter (str): delimiter for file parsing

from pymatgen.io.vasp.outputs import Chgcar
from pymatgen.apps.borg.hive import AbstractDrone
from pymatgen.command_line.bader_caller import bader_analysis_from_path

from atomate.utils.utils import get_uri

from atomate.utils.utils import get_logger
from atomate import __version__ as atomate_version
from atomate.vasp.config import STORE_VOLUMETRIC_DATA, STORE_ADDITIONAL_JSON

__author__ = 'Kiran Mathew, Shyue Ping Ong, Shyam Dwaraknath, Anubhav Jain'
__email__ = 'kmathew@lbl.gov'
__date__ = 'Mar 27, 2016'
__version__ = "0.1.0"

logger = get_logger(__name__)

bader_exe_exists = which("bader") or which("bader.exe")


class VaspDrone(AbstractDrone):
    """
    pymatgen-db VaspToDbTaskDrone with updated schema and documents processing methods.
    Please refer to matgendb.creator.VaspToDbTaskDrone documentation.
    """

    __version__ = atomate_version  # note: the version is inserted into the task doc

    # Schema def of important keys and sub-keys; used in validation
    schema = {
        "root": {
            "schema", "dir_name", "chemsys", "composition_reduced",