atomate.common.firetasks package

Submodules

atomate.common.firetasks.glue_tasks module

class atomate.common.firetasks.glue_tasks.PassCalcLocs(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Passes information about where the current calculation is located for the next FireWork. This is achieved by passing a key to the fw_spec called “calc_locs” with this information.

Required params:
name (str): descriptive name for this calculation file/dir
Optional params:
filesystem (str or custom user format): name of filesystem. Supports env_chk.
defaults to None
path (str): The path to the directory containing the calculation. defaults to
current working directory.
optional_params = [u'filesystem', u'path']
required_params = [u'name']
run_task(fw_spec)
atomate.common.firetasks.glue_tasks.get_calc_loc(target_name, calc_locs)

This is a helper method that helps you pick out a certain calculation from an array of calc_locs.

There are three modes:
  • If you set target_name to a String, search for most recent calc_loc

    with matching nameget_

  • Otherwise, return most recent calc_loc overall

Args:
target_name: (bool or str) If str, will search for calc_loc with
matching name, else use most recent calc_loc

calc_locs: (dict) The dictionary of all calc_locs

Returns:
(dict) dict with subkeys path, filesystem, and name

atomate.common.firetasks.parse_outputs module

class atomate.common.firetasks.parse_outputs.ToDbTask(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

General task to parse output data via a Drone and either (i) write to JSON file or (ii) insert into a database.

Required params:
drone (AbstractDrone): Drone to convert the data to dict
Optional params:
db_file (str): path to file containing the database credentials. Supports env_chk.
Default is None, which will write data to JSON file.

mmdb (MMDb) (str): If db_file, sets the type of MMDb, e.g. “atomate.vasp.database.MMVaspDb” calc_dir (str): path to dir (on current filesystem) that contains calculation 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

options (dict): dict of options to pass into the Drone additional_fields (dict): dict of additional fields to add

optional_params = [u'mmdb', u'db_file', u'calc_dir', u'calc_loc', u'additional_fields', u'options']
required_params = [u'drone']
run_task(fw_spec)

atomate.common.firetasks.run_calc module

class atomate.common.firetasks.run_calc.RunCommand(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Execute a command directly (no custodian).

Required params:
cmd (str): the name of the full executable to run. Supports env_chk.
Optional params:
expand_vars (str): Set to true to expand variable names in the cmd.
optional_params = ['expand_vars']
required_params = ['cmd']
run_task(fw_spec)
class atomate.common.firetasks.run_calc.RunCustodianFromObjects(*args, **kwargs)

Bases: fireworks.core.firework.FiretaskBase

Run VASP using custodian in a generic manner using built-in custodian objects

Required params:
jobs: ([Job]) - a list of custodian jobs to run handlers: ([ErrorHandler]) - a list of error handlers
Optional params:
validators: ([Validator]) - a list of Validators custodian_params ({}) - dict of all other custodian parameters
optional_params = ['validators', 'custodian_params']
required_params = ['jobs', 'handlers']
run_task(fw_spec)

Module contents