atomate.qchem.firetasks package

Submodules

atomate.qchem.firetasks.critic2 module

atomate.qchem.firetasks.fragmenter module

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']
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

atomate.qchem.firetasks.run_calc module

atomate.qchem.firetasks.write_inputs module

Module contents