pyiron.atomistics.job.atomistic module

class pyiron.atomistics.job.atomistic.AtomisticGenericJob(project, job_name)

Bases: pyiron.base.job.generic.GenericJob

Atomistic Generic Job class extends the Generic Job class with all the functionality to run jobs containing atomistic structures. From this class all specific atomistic Hamiltonians are derived. Therefore it should contain the properties/routines common to all atomistic jobs. The functions in this module should be as generic as possible.

Parameters

• project (ProjectHDFio) – ProjectHDFio instance which points to the HDF5 file the job is stored in

• job_name (str) – name of the job, which has to be unique within the project

.. attribute:: job_name

name of the job, which has to be unique within the project

.. attribute:: status

execution status of the job, can be one of the following [initialized, appended, created, submitted, running,

aborted, collect, suspended, refresh, busy, finished]

.. attribute:: job_id

unique id to identify the job in the pyiron database

.. attribute:: parent_id

job id of the predecessor job - the job which was executed before the current one in the current job series

.. attribute:: master_id

job id of the master job - a meta job which groups a series of jobs, which are executed either in parallel or in serial.

.. attribute:: child_ids

list of child job ids - only meta jobs have child jobs - jobs which list the meta job as their master

.. attribute:: project

Project instance the jobs is located in

.. attribute:: project_hdf5

ProjectHDFio instance which points to the HDF5 file the job is stored in

.. attribute:: job_info_str

short string to describe the job by it is job_name and job ID - mainly used for logging

.. attribute:: working_directory

working directory of the job is executed in - outside the HDF5 file

.. attribute:: path

path to the job as a combination of absolute file system path and path within the HDF5 file.

.. attribute:: version

Version of the hamiltonian, which is also the version of the executable unless a custom executable is used.

.. attribute:: executable

Executable used to run the job - usually the path to an external executable.

.. attribute:: library_activated

For job types which offer a Python library pyiron can use the python library instead of an external executable.

.. attribute:: server

Server object to handle the execution environment for the job.

.. attribute:: queue_id

the ID returned from the queuing system - it is most likely not the same as the job ID.

.. attribute:: logger

logger object to monitor the external execution and internal pyiron warnings.

.. attribute:: restart_file_list

list of files which are used to restart the calculation from these files.

.. attribute:: job_type

Job type object with all the available job types: [‘ExampleJob’, ‘SerialMaster’, ‘ParallelMaster’, ‘ScriptJob’,

‘ListMaster’]

animate_structure(spacefill=True, show_cell=True, stride=1, center_of_mass=False, particle_size=0.5)

Animates the job if a trajectory is present

Parameters

• spacefill (bool) –

• show_cell (bool) –

• stride (int) –

  show animation every stride [::stride] use value >1 to make animation faster

  default=1

• center_of_mass (bool) –

Returns

nglview IPython widget

Return type

animation

calc_md(temperature=None, pressure=None, n_ionic_steps=1000, time_step=None, n_print=100, temperature_damping_timescale=100.0, pressure_damping_timescale=None, seed=None, tloop=None, initial_temperature=True, langevin=False)

calc_minimize(e_tol=0, f_tol=0.0001, max_iter=1000, pressure=None, n_print=1)

Parameters

• e_tol –

• f_tol –

• max_iter –

• pressure –

• n_print –

Returns:

calc_static()

Returns:

continue_with_final_structure(job_type=None, job_name=None)

Parameters

• job_type –

• job_name –

Returns:

continue_with_restart_files(job_type=None, job_name=None)

Parameters

• job_type –

• job_name –

Returns:

copy_to(project=None, new_job_name=None, input_only=False, new_database_entry=True)

Parameters

• destination –

• new_job_name –

• input_only –

• new_database_entry –

Returns:

db_entry()

Generate the initial database entry

Returns

db_dict

Return type

(dict)

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_encut()

get_final_structure()

Returns:

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: 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

gui()

Returns:

map(function, parameter_lst)

restart(job_name=None, job_type=None)

Restart a new job created from an existing calculation. :param project: Project instance at which the new job should be created :type project: pyiron.project.Project instance :param job_name: Job name :type job_name: str :param job_type: Job type :type job_type: str

Returns

New job

Return type

new_ham

set_encut(encut)

Parameters

encut –

Returns:

set_input_to_read_only()

This function enforces read-only mode for the input classes, but it has to be implement in the individual classes.

set_kpoints(mesh=None, scheme='MP', center_shift=None, symmetry_reduction=True, manual_kpoints=None, weights=None, reciprocal=True)

Parameters

• mesh –

• scheme –

• center_shift –

• symmetry_reduction –

• manual_kpoints –

• weights –

• reciprocal –

Returns:

store_structure()

Returns:

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

trajectory(stride=1, center_of_mass=False, atom_indices=None, snapshot_indices=None, overwrite_positions=None, overwrite_cells=None)

Parameters

• stride (int) – The trajectories are generated with every ‘stride’ steps

• center_of_mass (list/numpy.ndarray) – The center of mass

• atom_indices (list/numpy.ndarray) – The atom indices for which the trajectory should be generated

• snapshot_indices (list/numpy.ndarray) – The snapshots for which the trajectory should be generated

• overwrite_positions (list/numpy.ndarray) – List of positions that are meant to overwrite the existing trajectory. Useful to wrap coordinates for example

• overwrite_cells (list/numpy.ndarray) – List of cells that are meant to overwrite the existing trajectory. Only used when overwrite_positions is defined. This must have the same length of overwrite_positions

Returns

Trajectory instance

Return type

pyiron.atomistics.job.atomistic.Trajectory

validate_ready_to_run()

Returns:

view_structure(snapshot=- 1, spacefill=True, show_cell=True)

Parameters

• snapshot (int) – Snapshot of the trajectory one wants

• spacefill (bool) –

• show_cell (bool) –

Returns

nglview IPython widget

Return type

view

write_traj(filename, file_format=None, parallel=True, append=False, stride=1, center_of_mass=False, atom_indices=None, snapshot_indices=None, overwrite_positions=None, overwrite_cells=None, **kwargs)

Writes the trajectory in a given file file_format based on the ase.io.write function.

Parameters

• filename (str) – Filename of the output

• file_format (str) – The specific file_format of the output

• parallel (bool) – ase parameter

• append (bool) – ase parameter

• stride (int) – Writes trajectory every stride steps

• center_of_mass (bool) – True if the positions are centered on the COM

• atom_indices (list/numpy.ndarray) – The atom indices for which the trajectory should be generated

• snapshot_indices (list/numpy.ndarray) – The snapshots for which the trajectory should be generated

• overwrite_positions (list/numpy.ndarray) – List of positions that are meant to overwrite the existing trajectory. Useful to wrap coordinates for example

• overwrite_cells (list/numpy.ndarray) – List of cells that are meant to overwrite the existing trajectory. Only used when overwrite_positions is defined. This must have the same length of overwrite_positions

• **kwargs – Additional ase arguments

class pyiron.atomistics.job.atomistic.GenericInput(input_file_name=None, table_name='generic')

Bases: pyiron.base.generic.parameters.GenericParameters

load_default()

Loads the default file content

class pyiron.atomistics.job.atomistic.GenericOutput(job)

Bases: object

property cells

property computation_time

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: - 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 energy_pot

property energy_tot

property force_max

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

property forces

static get_displacements(structure, positions, cells, varying_cell=False)

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)

• varying_cell (bool) – True if the cell shape varies during the trajectory (raises a warning)

Returns

Displacements (N_steps x N_atoms x 3)

Return type

numpy.ndarray

property indices

property positions

property pressures

property steps

property temperature

property total_displacements

Output for 3-d total displacements from the initial configuration, with minimum image convention. For the diplacements for the successive snapshots, use 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)

property unwrapped_positions

property volume

class pyiron.atomistics.job.atomistic.MapFunctions

Bases: object

class pyiron.atomistics.job.atomistic.Trajectory(positions, structure, center_of_mass=False, cells=None, indices=None)

Bases: object

A trajectory instance compatible with the ase.io class

Parameters

• positions (numpy.ndarray) – The array of the trajectory in cartesian coordinates

• structure (pyiron.atomistics.structure.atoms.Atoms) – The initial structure instance from which the species info is derived

• center_of_mass (bool) – False (default) if the specified positions are w.r.t. the origin

• cells (numpy.ndarray) – Optional argument of the cell shape at every time step (Nx3x3 array) when the volume varies

pyiron.atomistics.job.atomistic.set_encut(job, parameter)

pyiron.atomistics.job.atomistic.set_kpoints(job, parameter)

pyiron.atomistics.job.atomistic.set_structure(job, parameter)