atomate.feff.firetasks package¶
Subpackages¶
Submodules¶
atomate.feff.firetasks.glue_tasks module¶
-
class
atomate.feff.firetasks.glue_tasks.
CopyFeffOutputs
(*args, **kwargs)¶ Bases:
atomate.common.firetasks.glue_tasks.CopyFiles
Copy files from a previous run directory to the current directory. Note: must specify either “calc_loc” or “calc_dir” to indicate the directory
containing the files to copy.
- Optional params:
- 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.
calc_dir (str): path to dir that contains VASP output files. filesystem (str): remote filesystem. e.g. username@host exclude_files (list): list fo filenames to be excluded when copying.
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optional_params
= ['calc_loc', 'calc_dir', 'filesystem', 'exclude_files']¶
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run_task
(fw_spec)¶ This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
atomate.feff.firetasks.parse_outputs module¶
-
class
atomate.feff.firetasks.parse_outputs.
AddPathsToFilepadTask
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Insert the scattering amplitude outputs(all feffNNNN.dat files) to gridfs using filepad.
- Optional_params:
labels (list): list of labels to tag the inserted files. Useful for querying later. filepad_file (str): path to the filepad connection settings file. compress (bool): wether or not to compress the file contents before insertion. metadata (dict): metadata.
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optional_params
= ['labels', 'filepad_file', 'compress', 'metadata']¶
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run_task
(fw_spec)¶ This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
-
class
atomate.feff.firetasks.parse_outputs.
SpectrumToDbTask
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Parse the output of absorption/core-loss spectrum calculations(xmu.dat, eels.dat) and insert it into the database.
- Required_params:
absorbing_atom (str): absorbing atom symbol structure (Structure): input structure spectrum_type (str): XANES, EXAFS, ELNES, EXELFS output_file (str): the output file name. xmu.dat or eels.dat
- Optional_params:
input_file (str): path to the feff input file. calc_dir (str): path to dir (on current filesystem) that contains FEFF 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
db_file (str): path to the db file. edge (str): absorption edge metadata (dict): meta data
-
optional_params
= ['input_file', 'calc_dir', 'calc_loc', 'db_file', 'edge', 'metadata']¶
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required_params
= ['absorbing_atom', 'structure', 'spectrum_type', 'output_file']¶
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run_task
(fw_spec)¶ This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
atomate.feff.firetasks.run_calc module¶
This module defines tasks to run FEFF.
-
class
atomate.feff.firetasks.run_calc.
RunFeffDirect
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Run FEFF.
- Required params:
feff_cmd (str): the name of the full executable for running FEFF (supports env_chk)
-
required_params
= ['feff_cmd']¶
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run_task
(fw_spec)¶ This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
atomate.feff.firetasks.write_inputs module¶
This module defines tasks for writing FEFF input sets.
-
class
atomate.feff.firetasks.write_inputs.
WriteEXAFSPaths
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Write the scattering paths to paths.dat file.
- Required_params:
feff_input_set: (FeffDictSet subclass) paths (list): list of paths. A path = list of site indices.
- Optional_params:
degeneracies (list): list of path degeneracies.
-
optional_params
= ['degeneracies']¶
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required_params
= ['feff_input_set', 'paths']¶
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run_task
(fw_spec)¶ This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
-
class
atomate.feff.firetasks.write_inputs.
WriteFeffFromIOSet
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Generate FEFF input (feff.inp) from the given InputSet object or InputSet name
- Required_params:
absorbing_atom (str): absorbing atom symbol structure (Structure): input structure feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string
then either the entire path to the class or the spectrum type must be provided e.g. “pymatgen.io.feff.sets.MPXANESSet” or “XANES”
- Optional_params:
radius (float): cluster radius in angstroms other_params (dict): **kwargs to pass into the desired InputSet if using str feff_input_set
-
optional_params
= ['radius', 'other_params']¶
-
required_params
= ['absorbing_atom', 'structure', 'feff_input_set']¶
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run_task
(fw_spec)¶ This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
-
atomate.feff.firetasks.write_inputs.
get_feff_input_set_obj
(fis, *args, **kwargs)¶ returns feff input set object.
- Args:
- fis (str or FeffDictSet subclass): The inputset for setting params. If string then
the entire path to the class or the spectrum type must be provided e.g. “pymatgen.io.feff.sets.MPXANESSet” or “XANES”
args (tuple): feff input set args kwargs (dict): feff input set kwargs
- Returns:
FeffDictSet object