pyiron.gpaw.pyiron_ase module

class pyiron.gpaw.pyiron_ase.AseAdapter(ham, fast_mode=False)

Bases: object

property communicator

get_angular_momentum()

Get total angular momentum with respect to the center of mass.

get_center_of_mass(scaled=False)

Get the center of mass.

If scaled=True the center of mass in scaled coordinates is returned.

get_forces(md=True)

get_kinetic_energy()

Get the kinetic energy.

get_masses()

get_momenta()

Get array of momenta.

get_number_of_atoms()

get_positions()

get_velocities()

Get array of velocities.

has(name)

Check for existence of array.

name must be one of: ‘tags’, ‘momenta’, ‘masses’, ‘initial_magmoms’, ‘initial_charges’.

interactive_close()

new_array(name, a, dtype=None, shape=None)

Add new array.

If shape is not None, the shape of a will be checked.

set_array(name, a, dtype=None, shape=None)

Update array.

If shape is not None, the shape of a will be checked. If a is None, then the array is deleted.

set_momenta(momenta, apply_constraint=True)

Set momenta.

set_positions(positions)

set_velocities(velocities)

Set the momenta by specifying the velocities.

class pyiron.gpaw.pyiron_ase.AseJob(project, job_name)

Bases: pyiron.atomistics.job.interactive.GenericInteractive

collect_output()

Collect the output files of the external executable and store the information in the HDF5 file. This method has to be implemented in the individual hamiltonians.

from_hdf(hdf=None, group_name=None)

Recreates instance from the hdf5 file :param hdf: Path to the hdf5 file :type hdf: str :param group_name: Name of the group which contains the object :type group_name: str

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: :type wrap_atoms: bool

Returns

atomistics.structure.atoms.Atoms object

interactive_cells_getter()

interactive_close()

Returns:

interactive_energy_pot_getter()

interactive_energy_tot_getter()

interactive_forces_getter()

interactive_index_organizer()

interactive_indices_getter()

interactive_initialize_interface()

interactive_positions_getter()

interactive_positions_setter(positions)

interactive_pressures_getter()

interactive_steps_getter()

interactive_structure_setter(structure)

interactive_time_getter()

interactive_volume_getter()

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_scheduler()

The run if queue function is called by run if the user decides to submit the job to and queing system. The job is submitted to the queuing system using subprocess.Popen()

Returns

Returns the queue ID for the job.

Return type

int

run_static()

The run static function is called by run to execute the simulation.

set_calculator()

property structure

Returns:

to_hdf(hdf=None, group_name=None)

Store the GenericJob in an HDF5 file

Parameters

• hdf (ProjectHDFio) – HDF5 group object - optional

• group_name (str) – HDF5 subgroup name - optional

write_input()

Write the input files for the external executable. This method has to be implemented in the individual hamiltonians.

pyiron.gpaw.pyiron_ase.ase_calculator_fromdict(class_path, class_dict)

pyiron.gpaw.pyiron_ase.ase_structure_fromdict(atoms_dict)

pyiron.gpaw.pyiron_ase.ase_structure_todict(structure)