pyiron.sphinx.interactive module

class pyiron.sphinx.interactive.SphinxInt2(project, job_name)[source]

Bases: pyiron.sphinx.interactive.SphinxInteractive

class pyiron.sphinx.interactive.SphinxInteractive(project, job_name)[source]

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_tolerance=0.0, ionic_force_tolerance=0.01, ionic_energy=None, ionic_forces=None, volume_only=False)[source]

Setup the hamiltonian to perform ionic relaxations.

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

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_tolerance (float) – convergence goal in terms of energy (optional)

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

calc_static(electronic_steps=100, blockSize=8, dSpinMoment=1e-08, algorithm=None, retain_charge_density=False, retain_electrostatic_potential=False)[source]

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)[source]

Collects the outputs and stores them to the hdf file

get_structure(iteration_step=- 1, wrap_atoms=True)[source]

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()[source]
interactive_close()[source]

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()[source]
interactive_energy_tot_getter()[source]
interactive_fetch()[source]

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()[source]
interactive_initialize_interface()[source]
interactive_magnetic_forces_getter()[source]
interactive_positions_getter()[source]
interactive_positions_setter(positions)[source]
interactive_spin_constraints_getter()[source]
interactive_spin_constraints_setter(spins)[source]
interactive_spins_getter()[source]
load_main_group()[source]

Load the main Group.

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

run_if_interactive()[source]

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()[source]

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)[source]

Bases: pyiron.atomistics.job.interactive.GenericInteractiveOutput

check_band_occupancy(plot=True)[source]

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