pyiron_atomistics.sphinx.base.Output

class pyiron_atomistics.sphinx.base.Output(job)

Bases: object

Handles the output from a SPHInX simulation.

__init__(job)

Methods

__init__(job)
clear()	(Re)set to a clean state.
collect([directory])	The collect function, collects all the output from a SPHInX simulation.
collect_charge_density(file_name, cwd)
collect_electrostatic_potential(file_name, cwd)
collect_energy_dat([file_name, cwd])	param file_name:
collect_energy_struct([file_name, cwd])	param file_name:
collect_eps_dat([file_name, cwd])	param file_name:
collect_relaxed_hist([file_name, cwd])	param file_name:
collect_residue_dat([file_name, cwd])	param file_name:
collect_sphinx_log([file_name, cwd])	param file_name:
collect_spins_dat([file_name, cwd])	param file_name:
from_hdf(hdf)	Load output from an HDF5 file
to_hdf(hdf[, force_update])	Store output in an HDF5 file

clear()

(Re)set to a clean state.

collect(directory=None)

The collect function, collects all the output from a SPHInX simulation.

Parameters:

directory (str) – the directory to collect the output from.

collect_energy_dat(file_name='energy.dat', cwd=None)

Parameters:

• file_name

• cwd

Returns:

collect_energy_struct(file_name='energy-structOpt.dat', cwd=None)

Parameters:

• file_name

• cwd

Returns:

collect_eps_dat(file_name=None, cwd=None)

Parameters:

• file_name

• cwd

Returns:

collect_relaxed_hist(file_name='relaxHist.sx', cwd=None)

Parameters:

• file_name

• cwd

Returns:

collect_residue_dat(file_name='residue.dat', cwd=None)

Parameters:

• file_name

• cwd

Returns:

collect_sphinx_log(file_name='sphinx.log', cwd=None)

Parameters:

• file_name

• cwd

Returns:

collect_spins_dat(file_name='spins.dat', cwd=None)

Parameters:

• file_name

• cwd

Returns:

from_hdf(hdf)

Load output from an HDF5 file

to_hdf(hdf, force_update=False)

Store output in an HDF5 file

Parameters:

• hdf – HDF5 group

• force_update (bool)