atomate.common.firetasks package¶
Subpackages¶
Submodules¶
atomate.common.firetasks.glue_tasks module¶
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class
atomate.common.firetasks.glue_tasks.
CopyFiles
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Task to copy the given list of files from the given directory to the destination directory. To customize override the setup_copy and copy_files methods.
- Optional params:
- from_dir (str): path to the directory containing the files to be copied. to_dir (str): path to the destination directory filesystem (str) files_to_copy (list): list of file names. exclude_files (list): list of file names to be excluded.
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copy_files
()¶ Defines the copy operation. Override this to customize copying.
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optional_params
= [u'from_dir', u'to_dir', u'filesystem', u'files_to_copy', u'exclude_files']¶
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run_task
(fw_spec)¶
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setup_copy
(from_dir, to_dir=None, filesystem=None, files_to_copy=None, exclude_files=None, from_path_dict=None)¶ setup the copy i.e setup the from directory, filesystem, destination directory etc.
- Args:
from_dir (str) to_dir (str) filesystem (str) files_to_copy (list): if None all the files in the from_dir will be copied exclude_files (list) from_path_dict (dict): dict specification of the path. If specified must contain atleast
the key “path” that specifies the path to the from_dir.
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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.
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optional_params
= [u'filesystem', u'path']¶
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required_params
= [u'name']¶
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run_task
(fw_spec)¶
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class
atomate.common.firetasks.glue_tasks.
PassResult
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Passes properties and corresponding user-specified data resulting from a run from parent to child fireworks. Uses a string syntax similar to Mongo-style queries to designate values of output file dictionaries to retrieve. For example, one could specify a task to pass the stress from the current calculation using:
PassResult(pass_dict={‘stress’: “>>ionic_steps.-1.stress”})
- Required params:
- pass_dict (dict): dictionary designating keys and values to pass
- to child fireworks. If value is a string beginning with ‘>>’, the firework will search the parsed VASP output dictionary for the designated property by following the sequence of keys separated with periods, e. g. “>>ionic_steps.-1.stress” is used to designate the stress from the last ionic_step. If the value is not a string or does not begin with “>>”, it is passed as is.
- parse_class (str): string representation of complete path to a class
- with which to parse the output, e. g. pymatgen.io.vasp.Vasprun or pymatgen.io.feff.LDos.from_file, class must be MSONable
- parse_kwargs (str): dict of kwargs for the parse class,
- e. g. {“filename”: “vasprun.xml”, “parse_dos”: False, “parse_eigen”: False}
- Optional params:
- calc_dir (str): path to dir that contains VASP output files, defaults
- to ‘.’, e. g. current directory
- mod_spec_cmd (str): command to issue for mod_spec, e. g. “_set” or “_push”,
- defaults to “_set”
- mod_spec_key (str): key to pass to mod_spec _set dictmod command, defaults
- to “prev_calc_result”
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optional_params
= [u'calc_dir', u'mod_spec_cmd', u'mod_spec_key']¶
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required_params
= [u'pass_dict', u'parse_class', u'parse_kwargs']¶
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run_task
(fw_spec)¶
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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¶
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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
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optional_params
= [u'mmdb', u'db_file', u'calc_dir', u'calc_loc', u'additional_fields', u'options']¶
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required_params
= [u'drone']¶
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run_task
(fw_spec)¶
atomate.common.firetasks.run_calc module¶
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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.
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optional_params
= [u'expand_vars']¶
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required_params
= [u'cmd']¶
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run_task
(fw_spec)¶
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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
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optional_params
= [u'validators', u'custodian_params']¶
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required_params
= [u'jobs', u'handlers']¶
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run_task
(fw_spec)¶