pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerOutput

class pyiron_atomistics.interactive.scipy_minimizer.ScipyMinimizerOutput(job)

Bases: GenericInteractiveOutput

__init__(job)

Methods

__init__(job)
get_displacements(structure, positions, cells)	Output for 3-d displacements between successive snapshots, with minimum image convention.
to_hdf(hdf[, group_name])

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

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

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

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)