pyiron.sphinx.interactive module

class pyiron.sphinx.interactive.SphinxInt2(project, job_name)

Bases: pyiron.sphinx.interactive.SphinxInteractive

class pyiron.sphinx.interactive.SphinxInteractive(project, job_name)

Bases: pyiron.sphinx.base.SphinxBase, pyiron.atomistics.job.interactive.GenericInteractive

calc_minimize(electronic_steps=None, ionic_steps=None, max_iter=None, pressure=None, algorithm=None, retain_charge_density=False, retain_electrostatic_potential=False, ionic_energy=None, ionic_forces=None, volume_only=False)

Setup the hamiltonian to perform ionic relaxations.

The convergence goal can be set using either the ionic_energy as a limit for fluctuations in energy or the ionic_forces.

Loads defaults for all Sphinx input groups, including a ricQN-based main Group.

Parameters

• retain_electrostatic_potential –

• retain_charge_density –

• algorithm –

• pressure –

• max_iter –

• electronic_steps (int) – maximum number of electronic steps per electronic convergence

• ionic_steps (int) – maximum number of ionic steps

• ionic_energy (float) – convergence goal in terms of energy (optional)

• ionic_forces (float) – convergence goal in terms of forces (optional)

calc_static(electronic_steps=400, blockSize=8, dSpinMoment=1e-08, algorithm=None, retain_charge_density=False, retain_electrostatic_potential=False)

Function to setup the hamiltonian to perform static SCF DFT runs

Parameters

• retain_electrostatic_potential –

• retain_charge_density –

• algorithm –

• electronic_steps (int) – maximum number of electronic steps, which can be used to achieve convergence

property coarse_run

collect_output(force_update=False)

Collects the outputs and stores them to the hdf file

get_structure(iteration_step=- 1, wrap_atoms=True)

Gets the structure from a given iteration step of the simulation (MD/ionic relaxation). For static calculations there is only one ionic iteration step :param iteration_step: Step for which the structure is requested :type iteration_step: int :param wrap_atoms: True if the atoms are to be wrapped back into the unit cell :type wrap_atoms: bool

Returns

The required structure

Return type

pyiron.atomistics.structure.atoms.Atoms

interactive_cells_getter()

interactive_close()

For jobs which executables are available as Python library, those can also be executed with a library call instead of calling an external executable. This is usually faster than a single core python job. After the interactive execution, the job can be closed using the interactive_close function.

interactive_energy_pot_getter()

interactive_energy_tot_getter()

interactive_fetch()

For jobs which executables are available as Python library, those can also be executed with a library call instead of calling an external executable. This is usually faster than a single core python job. To access the output data during the execution the interactive_fetch function is used.

interactive_forces_getter()

interactive_initialize_interface()

interactive_magnetic_forces_getter()

interactive_positions_getter()

interactive_positions_setter(positions)

interactive_spin_constraints_getter()

interactive_spin_constraints_setter(spins)

interactive_spins_getter()

load_main_group()

Load the main Group.

The group is populated based on the type of calculation and settings in the GenericParameters (self.input).

run_if_interactive()

For jobs which executables are available as Python library, those can also be executed with a library call instead of calling an external executable. This is usually faster than a single core python job.

run_if_interactive_non_modal()

For jobs which executables are available as Python library, those can also be executed with a library call instead of calling an external executable. This is usually faster than a single core python job.

property structure

Returns:

class pyiron.sphinx.interactive.SphinxOutput(job)

Bases: pyiron.atomistics.job.interactive.GenericInteractiveOutput

check_band_occupancy(plot=True)

Check whether there are still empty bands available.

Parameters

plot (bool) – plots occupancy of the last step

Returns

True if there are still empty bands