# catkit.flow package¶

## catkit.flow.fwio module¶

catkit.flow.fwio.array_to_list(data)[source]

A function to covert all arrays in a structure of embeded dictionaries and lists into lists themselves.

catkit.flow.fwio.atoms_to_encode(images)[source]

Converts an list of atoms objects to an encoding from a .traj file.

catkit.flow.fwio.encode_to_atoms(encode, out_file='input.traj')[source]

Dump the encoding to a local traj file.

## Module contents¶

Catalysis WorkFlow.

class catkit.flow.Laminar(host, username=None, name=None, password=None)[source]

Simple submission script helper for CatFlow.

bulk_relaxation(atoms, parameters, spec=None)[source]

Run a relaxation of a given DB entry or atoms object. If a database object is used, the calculation will automatically store the keys and data for later retrieval.

The entries uuid will also be stored and $$data.calculator_parameters$$ will be used as the calculation parameters.

Parameters: images (Atoms object) – Initial atoms to perform workflow on. parameters (dict) – Calculation parameters to use. workflow_name (str) – Name of the fireworks calculation to be used. spec (dict) – Additional fireworks specifications to pass to the database.
submit_relaxation(image, workflow_name, parameters=None, spec=None)[source]

Run a relaxation of a given DB entry or atoms object. If a database object is used, the calculation will automatically store the keys and data for later retrieval.

The entries uuid will also be stored and $$data.calculator_parameters$$ will be used as the calculation parameters.

Parameters: images (Atoms object | AtomsRow object) – ASE database entry or atoms object to relax. workflow_name (str) – Name of the fireworks calculation to be used. parameters (dict) – Calculation parameters to use. Will be pulled from a database entry $$data.calculator_parameters$$. spec (dict) – Additional fireworks specifications to pass to the database.
submit_relaxation_db(database, spec=None)[source]

Submit each entry of an ASE database for relaxation. This requires that the calculation parameters be stored in the data under $$data.calculator_parameters$$.

Parameters: database (str) – Path to ASE database to be looped over for relaxation. spec (dict) – Additional specification to be passed to Fireworks.