catkit.flow package

Submodules

catkit.flow.fwespresso module

catkit.flow.fwespresso.get_neb(in_file='input.traj')

Performs a ASE NEB optimization with the ase-espresso calculator with the keywords defined inside the atoms object information.

Parameters:in_file (str) – Name of the input file to load from the local directory.

catkit.flow.fwespresso.get_pdos(out_file='dos.msg')

Calculate and save the projected DOS. Requires a previously relaxed calculation.

Parameters:out_file (str) – Name of the output file to save the results to.

catkit.flow.fwespresso.get_potential_energy(in_file='input.traj')

Performs a ASE get_potential_energy() call with the ase-espresso calculator with the keywords defined inside the atoms object information.

This can be a singlepoint calculation or a full relaxation depending on the keywords.

Parameters:in_file (str) – Name of the input file to load from the local directory.

catkit.flow.fwespresso.get_relaxed_calculation(in_file='output.traj')

Attach a stored calculator in the current directory to the provided atoms object.

Then return the atoms object with the calculator attached.

Parameters:in_file (str) – Name of the relaxed trajectroy file to load.

catkit.flow.fwespresso.get_total_potential(out_file='potential.msg')

Calculate and save the total potential. Requires a previously relaxed calculation.

Parameters:out_file (str) – Name of the output file to save the results to.

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.hpcio.get_nnodes()

Get the number of nodes being used in this environment. This is meant to be run on a calculation node.

catkit.flow.hpcio.get_server()

A function for determining which server the job is currently running on. This is meant to be run on a calculation node.

catkit.flow.qeio module

catkit.flow.qeio.attach_results(f, atoms, write_file=True)

Return the TS corrected energy for a scf instance in a log file and attach them to the given atoms obejct.

Will also attach the forces and stress if applicable.

catkit.flow.qeio.cd(*args, **kwds)

Does path management: if the path doesn’t exists, create it otherwise, move into it until the indentation is broken.

e.g.

with cd(‘the/path/is/real’):

‘do things in the new path’

Parameters:path (str) – Directory path to create and change into.

catkit.flow.qeio.geometry_hash(atoms)

A hash based strictly on the geometry features of an atoms object: positions, cell, and symbols.

This is intended for planewave basis set calculations, so pbc is not considered.

Each element is sorted in the algorithem to help prevent new hashs for identical geometries.

catkit.flow.qeio.log_to_atoms(log_file='log', ent=-1, out_file=None)

Parse a QE log file for atoms trajectory and return a list of atoms objects representative of the relaxation path.

NOTE: trajectory information is only returned for calculations run with BFGS internal to QE.

catkit.flow.qeio.write_to_db(path, db_name='master.db', keys={}, traj=False, pdos=False)

This function is used to write an ASE database entry for each atoms image inside a QE directory.

Module contents