catkit.flow package

Submodules

catkit.flow.fwespresso module

catkit.flow.fwio module

catkit.flow.fwio.array_to_list(data)

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

catkit.flow.fwio.atoms_to_encode(images)

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

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

Dump the encoding to a local traj file.

catkit.flow.hpcio module

catkit.flow.qeio module

Module contents

Catalysis WorkFlow.

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

Simple submission script helper for CatFlow.

bulk_relaxation(atoms, parameters, spec=None)

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)

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)

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.