atomate.qchem.firetasks package¶
Subpackages¶
Submodules¶
atomate.qchem.firetasks.geo_transformations module¶
-
class
atomate.qchem.firetasks.geo_transformations.
RotateTorsion
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Writes QChem Input files from input sets. A dictionary is passed to WriteInputFromIOSet where parameters are given as keys in the dictionary.
- required_params:
- atom_indexes (list): This should be a list of the pymatgen molecule indexes of the four atoms in torsion angle to be rotated angle (float): This is the desired torsion angle in degrees (the value should be between -180 and 180)
- optional_params:
- molecule (Molecule): Specify a pymatgen molecule to be rotated. A molecule is optional because molecules can be inherited from previous fireworks
-
optional_params
= ['molecule']¶
-
required_params
= ['atom_indexes', 'angle']¶
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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.qchem.firetasks.parse_outputs module¶
-
class
atomate.qchem.firetasks.parse_outputs.
QChemToDb
(*args, **kwargs)¶ Bases:
fireworks.core.firework.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 db_file (str): path to file containing the database credentials.
Supports env_chk. Default: write data to JSON file.- fw_spec_field (str): if set, will update the task doc with the contents
- of this key in the fw_spec.
- multirun (bool): Whether the job to parse includes multiple
- calculations in one input / output pair.
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optional_params
= ['calc_dir', 'calc_loc', 'input_file', 'output_file', 'additional_fields', 'db_file', 'fw_spec_field', 'multirun']¶
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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.qchem.firetasks.run_calc module¶
atomate.qchem.firetasks.write_inputs module¶
-
class
atomate.qchem.firetasks.write_inputs.
WriteCustomInput
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Writes QChem Input files from custom input sets. This firetask gives the maximum flexibility when trying to define custom input parameters.
- required_params:
- qchem_input_custom (dict): Define custom input parameters to generate a qchem input file. This should be a dictionary of dictionaries (i.e. {{“rem”: {“method”: “b3lyp”, basis”: “6-31*G++”, …} Each QChem section should be a key with its own dictionary as the value. For more details on how the input should be structured look at pymatgen.io.qchem.inputs * *
- optional_params:
- molecule (Molecule): input_file (str): Name of the QChem input file. Defaults to mol.qin write_to_dir (str): Path of the directory where the QChem input file will be written, the default is to write to the current working directory
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optional_params
= ['molecule', 'opt', 'pcm', 'solvent', 'input_file', 'write_to_dir']¶
-
required_params
= ['rem']¶
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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.qchem.firetasks.write_inputs.
WriteInput
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Writes QChem input file from QCInput object.
- required_params:
- qc_input (QCInput): QCInput object
- optional_params:
- input_file (str): Name of the QChem input file. Defaults to mol.qin write_to_dir (str): Path of the directory where the QChem input file will be written, the default is to write to the current working directory
-
optional_params
= ['input_file', 'write_to_dir']¶
-
required_params
= ['qc_input']¶
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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.qchem.firetasks.write_inputs.
WriteInputFromIOSet
(*args, **kwargs)¶ Bases:
fireworks.core.firework.FiretaskBase
Writes QChem Input files from input sets. A dictionary is passed to WriteInputFromIOSet where parameters are given as keys in the dictionary.
- required_params:
- qc_input_set (QChemDictSet or str): Either a QChemDictSet object or a string name for the QChem input set (e.g., “OptSet”). * Note that if the molecule is to be inherited through fw_spec qc_input_set must be a string name for the QChem input set. *
- optional_params:
- qchem_input_params (dict): When using a string name for QChem input set, use this as a dict to specify kwargs for instantiating the input set parameters. For example, if you want to change the DFT_rung, you should provide: {“DFT_rung”: …}. This setting is ignored if you provide the full object representation of a QChemDictSet rather than a String. molecule (Molecule): input_file (str): Name of the QChem input file. Defaults to mol.qin write_to_dir (str): Path of the directory where the QChem input file will be written, the default is to write to the current working directory
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optional_params
= ['molecule', 'qchem_input_params', 'input_file', 'write_to_dir']¶
-
required_params
= ['qchem_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)