pyiron.dft.job.generic module

class pyiron.dft.job.generic.GenericDFTJob(project, job_name)[source]

Bases: pyiron.atomistics.job.atomistic.AtomisticGenericJob

calc_md(temperature=None, n_ionic_steps=1000, n_print=1, time_step=1.0, retain_charge_density=False, retain_electrostatic_potential=False, **kwargs)[source]
calc_minimize(electronic_steps=60, ionic_steps=100, max_iter=None, pressure=None, algorithm=None, retain_charge_density=False, retain_electrostatic_potential=False, ionic_energy_tolerance=None, ionic_force_tolerance=None, ionic_energy=None, ionic_forces=None, volume_only=False)[source]
Parameters

  • ionic_energy_tolerance (float) – Maximum energy difference between 2 steps

  • ionic_force_tolerance (float) – Maximum force magnitude that each of atoms is allowed to have

  • e_tol (float) – same as ionic_energy_tolerance (deprecated)

  • f_tol (float) – same as ionic_force_tolerance (deprecated)

  • max_iter (int) – Maximum number of force evluations

  • pressure (float/list) – Targetpressure values

  • n_print (int) – Print period

Returns:

calc_static(electronic_steps=100, algorithm=None, retain_charge_density=False, retain_electrostatic_potential=False)[source]

Returns:

property encut
property exchange_correlation_functional
property fix_spin_constraint
property fix_symmetry
get_density_of_states(sigma=0.1, shift_by_fermi_energy=True, grid=None)[source]

Get density of states from a fully converged result. A Gaussian smeared histogram is returned

Parameters

  • sigma (float) – Gaussian smearing parameter in energy unit.

  • shift_by_fermi_energy (bool) – Shift the histogram by the Fermi energy value. Setting this to False will return code specific absolute values which have physically no meaning.

  • grid (list/numpy.ndarray) – Energy grid. If None, the interval between maximum and minimum eigenvalues plus 5 x sigma with a step length of sigma will be taken.

Returns

grid and density of states (n_spin x energy_grid)

Return type

(dict)

get_electronic_structure()[source]

Gets the electronic structure instance from the hdf5 file

Returns

pyiron.atomistics.waves.electronic.ElectronicStructure instance

get_encut()[source]
get_k_mesh_by_cell(k_mesh_spacing, cell=None)[source]

Get k-mesh density according to the box size.

Parameters

  • k_mesh_spacing (float) – K-point spacing in units of 2 * pi reciprocal Angstrom. (smaller values result in a denser mesh for a given structure).

  • cell (numpy.ndarray/list) – The cell shape

Returns

Mesh size

Return type

list/numpy.ndarray

get_kpoints()[source]
get_magnetic_moments(iteration_step=- 1)[source]

Gives the magnetic moments of a calculation for each iteration step.

Parameters

iteration_step (int) – Step for which the structure is requested

Returns

array of final magmetic moments or None if no magnetic moment is given

Return type

numpy.ndarray/None

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

property k_mesh_center_shift

Number of unreduced k-points per Angstrom of the lattice vector

Returns

Number of k-points per Angstrom

Return type

float

property k_mesh_spacing

Number of unreduced k-points per Angstrom of the lattice vector

Returns

Number of k-points per Angstrom

Return type

float

property kpoint_mesh
modify_kpoints()[source]
property plane_wave_cutoff
property reduce_kpoint_symmetry

Number of unreduced k-points per Angstrom of the lattice vector

Returns

Number of k-points per Angstrom

Return type

float

restart_for_band_structure_calculations(job_name=None)[source]

Restart a new job created from an existing calculation by reading the charge density for band structure calculations.

Parameters

job_name (str/None) – Job name

Returns

New job

Return type

new_ham (pyiron.dft.job.generic.GenericDFTJob)

save()[source]

Save the object, by writing the content to the HDF5 file and storing an entry in the database.

Returns

Job ID stored in the database

Return type

(int)

set_empty_states(n_empty_states=None)[source]
set_encut(encut)[source]

Sets the plane-wave energy cutoff :param encut: The energy cutoff in eV :type encut: float

set_exchange_correlation_functional(exchange_correlation_functional)[source]
set_kpoints(mesh=None, scheme='MP', center_shift=None, symmetry_reduction=True, manual_kpoints=None, weights=None, reciprocal=True, k_mesh_spacing=None, n_path=None, path_name=None)[source]

Function to setup the k-points

Parameters

  • mesh (list/numpy.ndarray) – Size of the mesh (ignored if scheme is not set to ‘MP’ or kpoints_per_reciprocal_

  • is set) (angstrom) –

  • scheme (str) – Type of k-point generation scheme (MP/GP(gamma point)/Manual/Line)

  • center_shift (list/numpy.ndarray/None) – Shifts the center of the mesh from the gamma point by the given vector in relative coordinates

  • symmetry_reduction (boolean) – Tells if the symmetry reduction is to be applied to the k-points

  • manual_kpoints (list/numpy.ndarray) – Manual list of k-points

  • weights (list/numpy.ndarray) – Manually supplied weights to each k-point in case of the manual mode

  • reciprocal (bool) – Tells if the supplied values are in reciprocal (direct) or cartesian coordinates (in

  • space) (reciprocal) –

  • k_mesh_spacing (float) – K-point spacing in units of 2 * pi reciprocal Angstrom. (smaller values result in a denser mesh for a given structure).

  • n_path (int) – Number of points per trace part for line mode

  • path_name (str) – Name of high symmetry path used for band structure calculations.

set_mixing_parameters(method=None, n_pulay_steps=None, density_mixing_parameter=None, spin_mixing_parameter=None)[source]
property spin_constraints
property xc
class pyiron.dft.job.generic.MapFunctions[source]

Bases: pyiron.atomistics.job.atomistic.MapFunctions

pyiron.dft.job.generic.get_k_mesh_by_density(cell, k_mesh_spacing=0.5)[source]

Get k-mesh density according to the box size.

Parameters

  • cell (numpy.ndarray/list) – The cell shape

  • k_mesh_spacing (float) – K-point spacing in units of 2 * pi reciprocal Angstrom. (smaller values result in a denser mesh for a given structure).

Returns

Mesh size

Return type

list/numpy.ndarray

pyiron.dft.job.generic.set_encut(job, parameter)[source]
pyiron.dft.job.generic.set_kpoints(job, parameter)[source]