pyiron_atomistics.sphinx.interactive.SphinxOutput

pyiron_atomistics.sphinx.interactive.SphinxOutput#

class pyiron_atomistics.sphinx.interactive.SphinxOutput(job)[source]#

Bases: Output, GenericInteractiveOutput

Handles the output from a SPHInX simulation.

__init__(job)#

Methods

__init__(job)

check_band_occupancy([plot])

Check whether there are still empty bands available.

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

get_displacements(structure, positions, cells)

Output for 3-d displacements between successive snapshots, with minimum image convention.

to_hdf(hdf[, force_update])

Store output in an HDF5 file

Attributes

cells

computation_time

displacements

Output for 3-d displacements between successive snapshots, with minimum image convention. For the total displacements from the initial configuration, use total_displacements This algorithm collapses if (if unwrapped_positions is not available in output): - the ID's are not consistent (i.e. you can also not change the number of atoms) - there are atoms which move by more than half a box length in any direction within two snapshots (due to periodic boundary conditions).

energy_pot

energy_tot

force_max

maximum force magnitude of each step which is used for convergence criterion of structure optimizations

forces

indices

positions

pressures

steps

temperature

time

total_displacements

Output for 3-d total displacements from the initial configuration, with minimum image convention. For the displacements for the successive snapshots, use displacements This algorithm collapses if (if unwrapped_positions is not available in the output): - the ID's are not consistent (i.e. you can also not change the number of atoms) - there are atoms which move by more than half a box length in any direction within two snapshots (due to periodic boundary conditions).

unwrapped_positions

volume

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

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:

property displacements#

Output for 3-d displacements between successive snapshots, with minimum image convention. For the total displacements from the initial configuration, use total_displacements This algorithm collapses if (if unwrapped_positions is not available in output):

  • the ID’s are not consistent (i.e. you can also not change the number of atoms)

  • there are atoms which move by more than half a box length in any direction within

    two snapshots (due to periodic boundary conditions)

property force_max#

maximum force magnitude of each step which is used for convergence criterion of structure optimizations

from_hdf(hdf)#

Load output from an HDF5 file

static get_displacements(structure, positions, cells)#

Output for 3-d displacements between successive snapshots, with minimum image convention. For the total displacements from the initial configuration, use total_displacements This algorithm collapses if: - the ID’s are not consistent (i.e. you can also not change the number of atoms) - there are atoms which move by more than half a box length in any direction within two snapshots (due to periodic boundary conditions)

Parameters:

  • structure (pyiron.atomistics.structure.atoms.Atoms) – The initial structure

  • positions (numpy.ndarray/list) – List of positions in cartesian coordinates (N_steps x N_atoms x 3)

  • cells (numpy.ndarray/list) – List of cells (N_steps x 3 x 3)

Returns:

Displacements (N_steps x N_atoms x 3)

Return type:

numpy.ndarray

to_hdf(hdf, force_update=False)#

Store output in an HDF5 file

Parameters:

  • hdf – HDF5 group

  • force_update (bool)

property total_displacements#

Output for 3-d total displacements from the initial configuration, with minimum image convention. For the displacements for the successive snapshots, use displacements This algorithm collapses if (if unwrapped_positions is not available in the output):

  • the ID’s are not consistent (i.e. you can also not change the number of atoms)

  • there are atoms which move by more than half a box length in any direction within

    two snapshots (due to periodic boundary conditions)