pyiron.atomistics.job package

Submodules

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=1e-08, f_tol=1e-08, 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)

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

Returns

The required structure

Return type

pyiron.atomistics.structure.atoms.Atoms

gui()

Returns:

map(function, parameter_lst)

restart(snapshot=-1, 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 snapshot: Snapshot of the calculations which would be the initial structure of the new job :type snapshot: int :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_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:

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)

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

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, **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) –

• append (bool) –

• 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

• **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

cells

computation_time

energy_pot

energy_tot

forces

positions

pressures

steps

temperature

unwrapped_positions

volume

class pyiron.atomistics.job.atomistic.MapFunctions

Bases: object

class pyiron.atomistics.job.atomistic.Trajectory(positions, structure, center_of_mass=False, cells=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)

pyiron.atomistics.job.interactive module

class pyiron.atomistics.job.interactive.GenericInteractive(project, job_name)

Bases: pyiron.atomistics.job.atomistic.AtomisticGenericJob, pyiron.base.job.interactive.InteractiveBase

current_structure

get_structure(iteration_step=-1)

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

Returns

atomistics.structure.atoms.Atoms object

initial_structure

interactive_cells_getter()

interactive_cells_setter(cell)

interactive_collect()

interactive_energy_pot_getter()

interactive_energy_tot_getter()

interactive_enforce_structure_reset

interactive_flush(path='interactive', include_last_step=False)

Parameters

• path –

• include_last_step –

Returns:

interactive_forces_getter()

interactive_indices_getter()

interactive_indices_setter(indices)

interactive_initialize_interface()

interactive_magnetic_forces_getter()

interactive_positions_getter()

interactive_positions_setter(positions)

interactive_pressures_getter()

interactive_spin_constraints_getter()

interactive_spin_constraints_setter(spins)

interactive_spins_getter()

interactive_steps_getter()

interactive_stress_getter()

interactive_structure_setter(structure)

interactive_temperatures_getter()

interactive_time_getter()

interactive_unwrapped_positions_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.

species_from_hdf()

structure

Returns:

class pyiron.atomistics.job.interactive.GenericInteractiveOutput(job)

Bases: pyiron.atomistics.job.atomistic.GenericOutput

cells

energy_pot

energy_tot

forces

indices

positions

pressures

steps

temperature

time

unwrapped_positions

volume

class pyiron.atomistics.job.interactive.InteractiveInterface

Bases: object

get_cell()

get_energy_pot()

get_energy_tot()

get_forces()

get_positions()

get_pressure()

get_temperature()

run_interactive()

set_cell(cell)

set_energy_pot(energy_pot)

set_energy_tot(energy_tot)

set_forces(forces)

set_positions(positions)

set_pressure(pressure)

set_temperature(temperature)

pyiron.atomistics.job.interactivewrapper module

class pyiron.atomistics.job.interactivewrapper.InteractiveWrapper(project, job_name)

Bases: pyiron.base.master.generic.GenericMaster

check_setup()

Checks whether certain parameters (such as plane wave cutoff radius in DFT) are changed from the pyiron standard values to allow for a physically meaningful results. This function is called manually or only when the job is submitted to the queueing system.

collect_logfiles()

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

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.

db_entry()

Generate the initial database entry

Returns

db_dict

Return type

(dict)

from_hdf(hdf=None, group_name=None)

Restore the InteractiveWrapper from an HDF5 file

Parameters

• hdf (ProjectHDFio) – HDF5 group object - optional

• group_name (str) – HDF5 subgroup name - optional

get_final_structure()

Returns:

ref_job

Get the reference job template from which all jobs within the ParallelMaster are generated.

Returns

reference job

Return type

GenericJob

ref_job_initialize()

structure

to_hdf(hdf=None, group_name=None)

Store the InteractiveWrapper in an HDF5 file

Parameters

• hdf (ProjectHDFio) – HDF5 group object - optional

• group_name (str) – HDF5 subgroup name - optional

validate_ready_to_run()

Validate that the calculation is ready to be executed. By default no generic checks are performed, but one could check that the input information is complete or validate the consistency of the input at this point.

class pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput(job)

Bases: object

cells

energy_pot

energy_tot

forces

indices

positions

pressures

steps

temperatures

time

unwrapped_positions

volume

pyiron.atomistics.job.potentials module

An abstract Potential class to provide an easy access for the available potentials. Currently implemented for the OpenKim https://openkim.org database.

class pyiron.atomistics.job.potentials.PotentialAbstract(potential_df, default_df=None, selected_atoms=None)

Bases: object

The PotentialAbstract class loads a list of available potentials and sorts them. Afterwards the potentials can be accessed through:

PotentialAbstract.<Element>.<Element> or PotentialAbstract.find_potentials_set({<Element>, <Element>}

Parameters

• potential_df –

• default_df –

• selected_atoms –

find(element)

Find the potentials

Parameters

element (set, str) – element or set of elements for which you want the possible LAMMPS potentials

Returns

of possible potentials for the element or the combination of elements

Return type

list

find_by_name(potential_name)

list()

List the available potentials

Returns

of possible potentials for the element or the combination of elements

Return type

list

pyiron.atomistics.job.structurecontainer module

class pyiron.atomistics.job.structurecontainer.StructureContainer(project, job_name)

Bases: pyiron.atomistics.job.atomistic.AtomisticGenericJob

append(structure_to_append)

Metajobs like GenericMaster, ParallelMaster, SerialMaser or ListMaster allow other jobs to be appended. In the GenericJob definition this is only a template function.

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

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.

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

Module contents