pyiron_atomistics.vasp.base.VaspBase

class pyiron_atomistics.vasp.base.VaspBase(project, job_name)

Bases: GenericDFTJob

Class to setup and run and analyze VASP simulations which is a derivative of pyiron_atomistics.objects.job.generic.GenericJob. The functions in these modules are written in such the function names and attributes are very generic (get_structure(), molecular_dynamics(), version) but the functions are written to handle VASP specific input/output.

Parameters:

• project (pyiron_atomistics.project.Project instance) – Specifies the project path among other attributes

• job_name (str) – Name of the job

input

Instance which handles the input

Type:

pyiron_atomistics.vasp.vasp.Input

Examples

Let’s say you need to run a vasp simulation where you would like to control the input parameters manually. To set up a static dft run with Gaussian smearing and a k-point MP mesh of [6, 6, 6]. You would have to set it up as shown below:

>>> ham = VaspBase(job_name="trial_job")
>>> ham.input.incar[IBRION] = -1
>>> ham.input.incar[ISMEAR] = 0
>>> ham.input.kpoints.set_kpoints_file(size_of_mesh=[6, 6, 6])

However, the according to pyiron’s philosophy, it is recommended to avoid using code specific tags like IBRION, ISMEAR etc. Therefore the recommended way to set this calculation is as follows:

>>> ham = VaspBase(job_name="trial_job")
>>> ham.calc_static()
>>> ham.set_occupancy_smearing(smearing="gaussian")
>>> ham.set_kpoints(mesh=[6, 6, 6])
The exact same tags as in the first examples are set automatically.

__init__(project, job_name)

Methods

__init__(project, job_name)
animate_structure([spacefill, show_cell, ...])	Animates the job if a trajectory is present
animate_structures([spacefill, show_cell, ...])	Animate a series of atomic structures.
append_charge_density([job_specifier, path])	Append charge density file (CHGCAR)
append_wave_function([job_specifier, path])	Append wave function file (WAVECAR)
calc_md([temperature, n_ionic_steps, ...])	Sets appropriate tags for molecular dynamics in VASP
calc_minimize([electronic_steps, ...])	Function to setup the hamiltonian to perform ionic relaxations using DFT.
calc_static([electronic_steps, algorithm, ...])	Function to setup the hamiltonian to perform static SCF DFT runs.
check_if_job_exists([job_name, project])	Check if a job already exists in an specific project.
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.
cleanup([files_to_remove])	Removes excess files (by default: WAVECAR, CHGCAR, CHG)
clear_job()	Convenience function to clear job info after suspend.
collect_errors()	Collects errors from the VASP run
collect_logfiles()	Collect errors and warnings.
collect_output()	Collect the output files of the external executable and store the information in the HDF5 file.
collect_structures([filter_function])	Collects a copy of all structures in a compact StructureStorage.
collect_warnings()	Collects warnings from the VASP run
compress([files_to_compress])	Compress the output files of a job object.
continue_with_final_structure([job_type, ...])	param job_type:
continue_with_restart_files([job_type, job_name])	param job_type:
convergence_check()	Checks for electronic and ionic convergence according to the user specified tolerance
copy()	Copy the GenericJob object which links to the job and its HDF5 file
copy_file_to_working_directory(file)	Copy a specific file to the working directory before the job is executed.
copy_hamiltonian(job_name)	Copies a job to new one with a different name.
copy_template([project, new_job_name])	Copy the content of the job including the HDF5 file but without the output data to a new location
copy_to([project, new_job_name, input_only, ...])	Copy the content of the job including the HDF5 file to a new location.
create_job(job_type, job_name[, ...])	Create one of the following jobs: - 'StructureContainer’: - ‘StructurePipeline’: - ‘AtomisticExampleJob’: example job just generating random number - ‘ExampleJob’: example job just generating random number - ‘Lammps’: - ‘KMC’: - ‘Sphinx’: - ‘Vasp’: - ‘GenericMaster’: - ‘ParallelMaster’: series of jobs run in parallel - ‘KmcMaster’: - ‘ThermoLambdaMaster’: - ‘RandomSeedMaster’: - ‘MeamFit’: - ‘Murnaghan’: - ‘MinimizeMurnaghan’: - ‘ElasticMatrix’: - ‘ConvergenceEncutParallel’: - ‘ConvergenceKpointParallel’: - ’PhonopyMaster’: - ‘DefectFormationEnergy’: - ‘LammpsASE’: - ‘PipelineMaster’: - ’TransformationPath’: - ‘ThermoIntEamQh’: - ‘ThermoIntDftEam’: - ‘ScriptJob’: Python script or jupyter notebook job container - ‘ListMaster': list of jobs
create_pipeline(step_lst[, delete_existing_job])	Create a job pipeline
db_entry()	Generate the initial database entry
decompress()	Decompress the output files of a compressed job object.
drop_status_to_aborted()	Change the job status to aborted when the job was intercepted.
from_dict(obj_dict)	Populate the object from the serialized object.
from_directory(directory)	The Vasp instance is created by parsing the input and output from the specified directory
from_hdf([hdf, group_name])	Recreates instance from the hdf5 file
from_hdf_args(hdf)	Read arguments for instance creation from HDF5 file
get(name[, default])	Internal wrapper function for __getitem__() - self[name]
get_bader_charges()	Returns the total charge on every atom determined by the Bader charge partitioning scheme.
get_bader_volumes()	Returns the integration volume around every atom from the Bader charge partitioning scheme.
get_calculate_function()	Generate calculate() function
get_charge_density()	Gets the charge density from the hdf5 file.
get_density_of_states([sigma, ...])	Get density of states from a fully converged result.
get_eddrmm_handling()	returns: status of EDDRMM handling
get_electronic_structure()	Gets the electronic structure instance from the hdf5 file
get_electrostatic_potential()	Gets the electrostatic potential from the hdf5 file.
get_encut()
get_final_structure()	Get the final structure calculated from the job.
get_final_structure_from_file(cwd[, filename])	Get the final structure of the simulation usually from the CONTCAR file
get_from_table(path, name)	Get a specific value from a pandas.Dataframe
get_icharg_value([icharg, self_consistent_calc])	Gives the correct ICHARG value for the restart calculation.
get_input_parameter_dict()	Get an hierarchical dictionary of input files.
get_job_id([job_specifier])	get the job_id for job named job_name in the local project path from database
get_k_mesh_by_cell(k_mesh_spacing[, cell])	Get k-mesh density according to the box size.
get_kpoints()
get_magnetic_moments([iteration_step])	Gives the magnetic moments of a calculation for each iteration step.
get_neighbors([start, stop, stride, ...])	Get the neighbors for a given section of the trajectory
get_neighbors_snapshots([snapshot_indices, ...])	Get the neighbors only for the required snapshots from the trajectory
get_nelect()	Returns the number of electrons in the systems
get_output_parameter_dict()
get_rwigs()	Gets the radii of Wigner-Seitz cell.
get_structure([frame, wrap_atoms, ...])	Retrieve structure from object.
get_valence_and_total_charge_density()	Gives the valence and total charge densities
get_workdir_file(filename)	Checks if a given file exists within the job's working directory and returns the absolute path to it.
gui()	Returns:
inspect(job_specifier)	Inspect an existing pyiron object - most commonly a job - from the database
instantiate(obj_dict[, version])	Create a blank instance of this class.
interactive_close()	For jobs which executables are available as Python library, those can also be executed with a library call instead of calling an external executable.
interactive_fetch()	For jobs which executables are available as Python library, those can also be executed with a library call instead of calling an external executable.
interactive_flush([path, include_last_step])	For jobs which executables are available as Python library, those can also be executed with a library call instead of calling an external executable.
is_compressed()	Check if the job is already compressed or not.
is_master_id(job_id)	Check if the job ID job_id is the master ID for any child job
is_self_archived()	Check if the HDF5 file of the Job is compressed as tar-archive
iter_structures([wrap_atoms])	Iterate over all structures in this object.
job_file_name(file_name[, cwd])	combine the file name file_name with the path of the current working directory
kill()	Kill the job.
list_all()	Returns dictionary of :method:`.list_groups()` and :method:`.list_nodes()`.
list_childs()	List child jobs as JobPath objects - not loading the full GenericJob objects for each child
list_files()	List files inside the working directory
list_groups()	Return a list of names of all nested groups.
list_nodes()	Return a list of names of all nested nodes.
list_potentials()	Lists all the possible POTCAR files for the elements in the structure depending on the XC functional
load(job_specifier[, convert_to_object])	Load an existing pyiron object - most commonly a job - from the database
map(function, parameter_lst)	Create MapMaster with the current job as reference job.
modify_kpoints()
move_to(project)	Move the content of the job including the HDF5 file to a new location
nbands_convergence_check()	Function to check if there are a sufficient number of empty bands in the calculation to ensure electronic convergence.
refresh_job_status()	Refresh job status by updating the job status with the status from the database if a job ID is available.
relocate_hdf5([h5_path])	Relocate the hdf file.
remove([_protect_childs])	Remove the job - this removes the HDF5 file, all data stored in the HDF5 file an the corresponding database entry.
remove_and_reset_id([_protect_childs])	Remove the job and reset its ID.
remove_child()	internal function to remove command that removes also child jobs.
rename(new_job_name)	Rename the job - by changing the job name
reset_job_id([job_id])	Reset the job id sets the job_id to None in the GenericJob as well as all connected modules like JobStatus.
reset_output()	Resets the output instance
restart([job_name, job_type])	Creates a "restart" job from an existing Vasp calculation.
restart_for_band_structure_calculations([...])	Restart a new job created from an existing Vasp calculation by reading the charge density for band structure calculations.
restart_from_charge_density([job_name, ...])	Restart a new job created from an existing Vasp calculation by reading the charge density.
restart_from_wave_and_charge([job_name, ...])	Restart a new job created from an existing Vasp calculation by reading the charge density and the wave function.
restart_from_wave_functions([job_name, ...])	Restart a new job created from an existing Vasp calculation by reading the wave functions.
run([delete_existing_job, repair, debug, ...])	This is the main run function, depending on the job status ['initialized', 'created', 'submitted', 'running', 'collect','finished', 'refresh', 'suspended'] the corresponding run mode is chosen.
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.
run_if_interactive_non_modal()	For jobs which executables are available as Python library, those can also be executed with a library call instead of calling an external executable.
run_if_modal()	The run if modal function is called by run to execute the simulation, while waiting for the output.
run_if_refresh()	Internal helper function the run if refresh function is called when the job status is 'refresh'.
run_if_scheduler()	The run if queue function is called by run if the user decides to submit the job to and queing system.
run_static()	The run static function is called by run to execute the simulation.
run_time_to_db()	Internal helper function to store the run_time in the database
save()	Save the object, by writing the content to the HDF5 file and storing an entry in the database.
save_output([output_dict, shell_output])	Internal helper function to store the hierarchical output dictionary in the HDF5 file of the pyiron job object
self_archive()	Compress HDF5 file of the job object to tar-archive
self_unarchive()	Decompress HDF5 file of the job object from tar-archive
set_algorithm([algorithm, ialgo])	Sets the type of electronic minimization algorithm
set_convergence_precision([...])	Sets the electronic and ionic convergence precision.
set_coulomb_interactions([interaction_type, ...])	Write the on-site Coulomb interactions in the INCAR file
set_dipole_correction([direction, dipole_center])	Apply a dipole correction using the dipole layer method proposed by Neugebauer & Scheffler
set_eddrmm_handling([status])	Sets the way, how EDDRMM warning is handled.
set_electric_field([e_field, direction, ...])	Set an external electric field using the dipole layer method proposed by Neugebauer & Scheffler
set_empty_states([n_empty_states])	Sets the number of empty states in the calculation :param n_empty_states: Required number of empty states :type n_empty_states: int
set_encut(encut)	Sets the plane-wave energy cutoff :param encut: The energy cutoff in eV :type encut: float
set_exchange_correlation_functional(...)
set_fft_mesh([nx, ny, nz])	Set the number of points in the respective directions for the 3D FFT mesh used for computing the charge density or electrostatic potentials.
set_for_band_structure_calc(num_points[, ...])	Sets up the input for a non self-consistent bandstructure calculation
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, scheme, center_shift, ...])	Function to setup the k-points
set_mixing_parameters([method, ...])	param method: mixing method 'PULAY' or 'KERKER' (default: PULAY)
set_occupancy_smearing([smearing, width, ...])	Set how the finite temperature smearing is applied in determining partial occupancies
set_rwigs(rwigs_dict)	Sets the radii of Wigner-Seitz cell.
set_spin_constraint(lamb, rwigs_dict[, ...])	Sets spin constrains including 'LAMBDA' and 'RWIGS'.
show_hdf()	Iterating over the HDF5 datastructure and generating a human readable graph.
signal_intercept(sig)	Abort the job and log signal that caused it.
stop_calculation([next_electronic_step])	Call to stop the VASP calculation
store_structure()	Create StructureContainer job with the initial structure of the job and sets that jobs parent_id from this job.
suspend()	Suspend the job by storing the object and its state persistently in HDF5 file and exit it.
to_dict()	Reduce the object to a dictionary.
to_hdf([hdf, group_name])	Stores the instance attributes into the hdf5 file
to_object([object_type])	Load the full pyiron object from an HDF5 file
trajectory([stride, center_of_mass, ...])	Returns a Trajectory instance containing the necessary information to describe the evolution of the atomic structure during the atomistic simulation.
transfer_from_remote()	Transfer the job from a remote location to the local machine.
transform_structures(modify)	Return a modified object by applying a function to each object lazily.
update_master([force_update])	After a job is finished it checks whether it is linked to any metajob - meaning the master ID is pointing to this jobs job ID.
validate_ready_to_run()	Returns:
view_structure([snapshot, spacefill, show_cell])	param snapshot: Snapshot of the trajectory one wants
write_input()	Call routines that generate the code specific input files Returns:
write_magmoms()	Write the magnetic moments in INCAR from that assigned to the species
write_traj(filename[, file_format, ...])	Writes the trajectory in a given file file_format based on the ase.io.write function.

Attributes

calculate_kwargs	Generate keyword arguments for the calculate() function.
child_ids	list of child job ids - only meta jobs have child jobs - jobs which list the meta job as their master
content
database_entry
encut
exchange_correlation_functional	The exchange correlation functional used (LDA or GGA)
exclude_groups_hdf	Get the list of groups which are excluded from storing in the hdf5 file
exclude_nodes_hdf	Get the list of nodes which are excluded from storing in the hdf5 file
executable	Get the executable used to run the job - usually the path to an external executable.
executor_type
files	Allows to browse the files in a job directory.
files_to_compress
files_to_remove
fix_spin_constraint	Tells if the type of constraints the spins have for this calculation
fix_symmetry
id	Unique id to identify the job in the pyiron database - use self.job_id instead
job_id	Unique id to identify the job in the pyiron database
job_info_str	Short string to describe the job by it is job_name and job ID - mainly used for logging
job_name	Get name of the job, which has to be unique within the project
job_type	['ExampleJob', 'ParallelMaster', 'ScriptJob',
k_mesh_center_shift	Number of unreduced k-points per Angstrom of the lattice vector
k_mesh_spacing	Number of unreduced k-points per Angstrom of the lattice vector
kpoint_mesh
logger	Get the logger object to monitor the external execution and internal pyiron warnings.
master_id	Get job id of the master job - a meta job which groups a series of jobs, which are executed either in parallel or in serial.
name	Get name of the job, which has to be unique within the project
number_of_structures	maximum iteration_step + 1 that can be passed to get_structure().
parent_id	Get job id of the predecessor job - the job which was executed before the current one in the current job series
path	Absolute path of the HDF5 group starting from the system root - combination of the absolute system path plus the absolute path inside the HDF5 file starting from the root group.
plane_wave_cutoff	Plane wave energy cutoff in eV
potential
potential_available
potential_list
potential_view
project	Project instance the jobs is located in
project_hdf5	Get the ProjectHDFio instance which points to the HDF5 file the job is stored in
publication
queue_id	Get the queue ID, the ID returned from the queuing system - it is most likely not the same as the job ID.
reduce_kpoint_symmetry	Number of unreduced k-points per Angstrom of the lattice vector
restart_file_dict	A dictionary of the new name of the copied restart files
restart_file_list	Get the list of files which are used to restart the calculation from these files.
server	Get the server object to handle the execution environment for the job.
sorted_indices	How the original atom indices are ordered in the vasp format (species by species)
spin_constraints	Returns True if the calculation is spin constrained
status	Execution status of the job, can be one of the following [initialized, appended, created, submitted, running,
structure	Returns:
version	Get the version of the hamiltonian, which is also the version of the executable unless a custom executable is used.
working_directory	Get the working directory of the job is executed in - outside the HDF5 file. The working directory equals the path but it is represented by the filesystem: /absolute/path/to/the/file.h5/path/inside/the/hdf5/file becomes: /absolute/path/to/the/file_hdf5/path/inside/the/hdf5/file.
write_charge_density	True if the charge density file CHGCAR file is/should be written
write_electrostatic_potential	True if the local potential or electrostatic potential LOCPOT file is/should be written
write_resolved_dos	True if the resolved DOS should be written (in the vasprun.xml file)
write_wave_funct	True if the wave function file WAVECAR file is/should be written
xc

animate_structure(spacefill: bool = True, show_cell: bool = True, stride: int = 1, center_of_mass: bool = False, particle_size: float = 0.5, camera: str = 'orthographic', atom_indices: list | ndarray = None, snapshot_indices: list | ndarray = None, repeat: int | Tuple[int, int, int] = None)

Animates the job if a trajectory is present

Parameters:

• spacefill (bool) – If True, then atoms are visualized in spacefill stype

• show_cell (bool) – True if the cell boundaries of the structure is to be shown

• stride (int) –

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

  default=1

• particle_size (float) – Scaling factor for the spheres representing the atoms. (The radius is determined by the atomic number)

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

• camera (str) – camera perspective, choose from “orthographic” or “perspective”

• 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

• repeat (int/3-tuple of int) – Repeat the structures by this before animating

Returns:

nglview IPython widget

Return type:

animation

animate_structures(spacefill: bool = True, show_cell: bool = True, center_of_mass: bool = False, particle_size: float = 0.5, camera: str = 'orthographic')

Animate a series of atomic structures.

Parameters:

• spacefill (bool) – If True, then atoms are visualized in spacefill stype

• show_cell (bool) – True if the cell boundaries of the structure is to be shown

• particle_size (float) – Scaling factor for the spheres representing the atoms. (The radius is determined by the atomic number)

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

• camera (str) – camera perspective, choose from “orthographic” or “perspective”

Returns:

nglview IPython widget

Return type:

animation

append_charge_density(job_specifier=None, path=None)

Append charge density file (CHGCAR)

Parameters:

• job_specifier (str/int) – name of the job or job ID

• path (str) – path to CHGCAR file

append_wave_function(job_specifier=None, path=None)

Append wave function file (WAVECAR)

Parameters:

• job_specifier (str/int) – name of the job or job ID

• path (str) – path to WAVECAR file

calc_md(temperature=None, n_ionic_steps=1000, n_print=1, time_step=1.0, retain_charge_density=False, retain_electrostatic_potential=False, **kwargs)

Sets appropriate tags for molecular dynamics in VASP

Parameters:

• temperature (int/float/list) – Temperature/ range of temperatures in Kelvin

• n_ionic_steps (int) – Maximum number of ionic steps

• n_print (int) – Prints outputs every n_print steps

• time_step (float) – time step (fs)

• retain_charge_density (bool) – True id the charge density should be written

• retain_electrostatic_potential (bool) – True if the electrostatic potential should be written

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, volume_only=False, cell_only=False)

Function to setup the hamiltonian to perform ionic relaxations using DFT. The ISIF tag has to be supplied separately.

Parameters:

• electronic_steps (int) – Maximum number of electronic steps

• ionic_steps (int) – Maximum number of ionic

• max_iter (int) – Maximum number of iterations

• pressure (float) – External pressure to be applied

• algorithm (str) – Type of VASP algorithm to be used “Fast”/”Accurate”

• retain_charge_density (bool) – True if the charge density should be written

• retain_electrostatic_potential (boolean) – True if the electrostatic potential should be written

• ionic_energy_tolerance (float) – Ionic energy convergence criteria (eV)

• ionic_force_tolerance (float) – Ionic forces convergence criteria (overwrites ionic energy) (ev/A)

• volume_only (bool) – Option to relax only the volume (keeping the relative coordinates fixed)

• cell_only (bool) – Option to relax only the cell parameters (keeping the relative coordinates fixed)

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

Function to setup the hamiltonian to perform static SCF DFT runs.

Parameters:

• electronic_steps (int) – Maximum number of electronic steps

• algorithm (str) – Type of VASP algorithm to be used “Fast”/”Accurate”

• retain_charge_density (bool) – True if

• retain_electrostatic_potential (bool) – True/False

property calculate_kwargs: dict

Generate keyword arguments for the calculate() function. A new simulation code only has to extend the get_input_parameter_dict() function which by default specifies an hierarchical dictionary with files_to_write and files_to_copy.

Example:

>>> calculate_function = job.get_calculate_function()
>>> shell_output, parsed_output, job_crashed = calculate_function(**job.calculate_kwargs)
>>> job.save_output(output_dict=parsed_output, shell_output=shell_output)

Returns:

keyword arguments for the calculate() function

Return type:

dict

check_if_job_exists(job_name: str | None = None, project: ProjectHDFio | pyiron_base.project.generic.Project | None = None)

Check if a job already exists in an specific project.

Parameters:

• job_name (str) – Job name (optional)

• project (ProjectHDFio, Project) – Project path (optional)

Returns:

True / False

Return type:

(bool)

check_setup() → None

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.

property child_ids: list

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

Returns:

list of child job ids

Return type:

list

cleanup(files_to_remove=('WAVECAR', 'CHGCAR', 'CHG', 'vasprun.xml'))

Removes excess files (by default: WAVECAR, CHGCAR, CHG)

clear_job() → None

Convenience function to clear job info after suspend. Mimics deletion of all the job info after suspend in a local test environment.

collect_errors()

Collects errors from the VASP run

collect_logfiles()

Collect errors and warnings.

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.

collect_structures(filter_function=None) → StructureStorage

Collects a copy of all structures in a compact StructureStorage.

This can be used to force lazily applied modifications with transform_structures() or simply to obtain a known object type from a generic HasStructure object.

Parameters:

filter_function (function) – include structure only if this function returns True for it

Returns:

a copy of all (filtered) structures

Return type:

StructureStorage

collect_warnings()

Collects warnings from the VASP run

compress(files_to_compress=None)

Compress the output files of a job object.

Parameters:

files_to_compress (list) – A list of files to compress (optional)

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:

convergence_check()

Checks for electronic and ionic convergence according to the user specified tolerance

Returns:

True if converged

Return type:

bool

copy() → GenericJob

Copy the GenericJob object which links to the job and its HDF5 file

Returns:

New GenericJob object pointing to the same job

Return type:

GenericJob

copy_file_to_working_directory(file: str) → None

Copy a specific file to the working directory before the job is executed.

Parameters:

file (str) – path of the file to be copied.

copy_hamiltonian(job_name)

Copies a job to new one with a different name.

Parameters:

job_name (str) – Job name

Returns:

New job

Return type:

pyiron.vasp.vasp.Vasp

copy_template(project: ProjectHDFio | JobCore | None = None, new_job_name: None = None) → GenericJob

Copy the content of the job including the HDF5 file but without the output data to a new location

Parameters:

• project (JobCore/ProjectHDFio/Project/None) – The project to copy the job to. (Default is None, use the same project.)

• new_job_name (str) – The new name to assign the duplicate job. Required if the project is None or the same project as the copied job. (Default is None, try to keep the same name.)

Returns:

GenericJob object pointing to the new location.

Return type:

GenericJob

copy_to(project: ProjectHDFio | JobCore | None = None, new_job_name: str | None = None, input_only: bool = False, new_database_entry: bool = True, delete_existing_job: bool = False, copy_files: bool = True)

Copy the content of the job including the HDF5 file to a new location.

Parameters:

• project (JobCore/ProjectHDFio/Project/None) – The project to copy the job to. (Default is None, use the same project.)

• new_job_name (str) – The new name to assign the duplicate job. Required if the project is None or the same project as the copied job. (Default is None, try to keep the same name.)

• input_only (bool) – [True/False] Whether to copy only the input. (Default is False.)

• new_database_entry (bool) – [True/False] Whether to create a new database entry. If input_only is True then new_database_entry is False. (Default is True.)

• delete_existing_job (bool) – [True/False] Delete existing job in case it exists already (Default is False.)

• copy_files (bool) – If True copy all files the working directory of the job, too

Returns:

GenericJob object pointing to the new location.

Return type:

GenericJob

create_job(job_type: str, job_name: str, delete_existing_job: bool = False) → GenericJob

Create one of the following jobs: - ‘StructureContainer’: - ‘StructurePipeline’: - ‘AtomisticExampleJob’: example job just generating random number - ‘ExampleJob’: example job just generating random number - ‘Lammps’: - ‘KMC’: - ‘Sphinx’: - ‘Vasp’: - ‘GenericMaster’: - ‘ParallelMaster’: series of jobs run in parallel - ‘KmcMaster’: - ‘ThermoLambdaMaster’: - ‘RandomSeedMaster’: - ‘MeamFit’: - ‘Murnaghan’: - ‘MinimizeMurnaghan’: - ‘ElasticMatrix’: - ‘ConvergenceEncutParallel’: - ‘ConvergenceKpointParallel’: - ’PhonopyMaster’: - ‘DefectFormationEnergy’: - ‘LammpsASE’: - ‘PipelineMaster’: - ’TransformationPath’: - ‘ThermoIntEamQh’: - ‘ThermoIntDftEam’: - ‘ScriptJob’: Python script or jupyter notebook job container - ‘ListMaster’: list of jobs

Parameters:

• job_type (str) – job type can be [‘StructureContainer’, ‘StructurePipeline’, ‘AtomisticExampleJob’, ‘ExampleJob’, ‘Lammps’, ‘KMC’, ‘Sphinx’, ‘Vasp’, ‘GenericMaster’, ‘ParallelMaster’, ‘KmcMaster’, ‘ThermoLambdaMaster’, ‘RandomSeedMaster’, ‘MeamFit’, ‘Murnaghan’, ‘MinimizeMurnaghan’, ‘ElasticMatrix’, ‘ConvergenceEncutParallel’, ‘ConvergenceKpointParallel’, ’PhonopyMaster’, ‘DefectFormationEnergy’, ‘LammpsASE’, ‘PipelineMaster’, ’TransformationPath’, ‘ThermoIntEamQh’, ‘ThermoIntDftEam’, ‘ScriptJob’, ‘ListMaster’]

• job_name (str) – name of the job

• delete_existing_job (bool) – delete an existing job - default false

Returns:

job object depending on the job_type selected

Return type:

GenericJob

create_pipeline(step_lst, delete_existing_job=False)

Create a job pipeline

Parameters:

step_lst (list) – List of functions which create calculations

Return type:

FlexibleMaster

db_entry()

Generate the initial database entry

Returns:

db_dict

Return type:

(dict)

decompress() → None

Decompress the output files of a compressed job object.

drop_status_to_aborted() → None

Change the job status to aborted when the job was intercepted.

property exchange_correlation_functional

The exchange correlation functional used (LDA or GGA)

property exclude_groups_hdf: list

Get the list of groups which are excluded from storing in the hdf5 file

Returns:

groups(list)

property exclude_nodes_hdf: list

Get the list of nodes which are excluded from storing in the hdf5 file

Returns:

nodes(list)

property executable: Executable

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

Returns:

exectuable path

Return type:

(str/pyiron_base.job.executable.Executable)

property files: FileBrowser

Allows to browse the files in a job directory.

By default this object prints itself as a listing of the job directory and the files inside.

>>> job.files
/path/to/my/job:
    pyiron.log
    error.out

Access to the names of files is provided with list()

>>> job.files.list()
['pyiron.log', 'error.out', 'INCAR']

Access to the contents of files is provided by indexing into this object, which returns a list of lines in the file

>>> job.files['error.out']
["Oh no

“, “Something went wrong! “]

The tail() method prints the last lines of a file to stdout

>>> job.files.tail('error.out', lines=1)
Something went wrong!

For files that have valid python variable names can also be accessed by attribute notation

>>> job.files.INCAR 
File('INCAR')

property fix_spin_constraint

Tells if the type of constraints the spins have for this calculation

Type:

bool

from_dict(obj_dict)

Populate the object from the serialized object.

Parameters:

• obj_dict (dict) – data previously returned from to_dict()

• version (str) – version tag written together with the data

from_directory(directory)

The Vasp instance is created by parsing the input and output from the specified directory

Parameters:

directory (str) – Path to the directory

from_hdf(hdf=None, group_name=None)

Recreates instance from the hdf5 file

Parameters:

• hdf (pyiron_base.generic.hdfio.ProjectHDFio) – The HDF file/path to read the data from

• group_name (str) – The name of the group under which the data must be stored as

classmethod from_hdf_args(hdf: ProjectHDFio) → dict

Read arguments for instance creation from HDF5 file

Parameters:

hdf (ProjectHDFio) – HDF5 group object

get(name: str, default: Any | None = None) → Any

Internal wrapper function for __getitem__() - self[name]

Parameters:

• key (str, slice) – path to the data or key of the data object

• default (any, optional) – return this if key cannot be found

Returns:

data or data object

Return type:

dict, list, float, int

Raises:

ValueError – key cannot be found and default is not given

get_bader_charges()

Returns the total charge on every atom determined by the Bader charge partitioning scheme.

Returns:

The Bader charges for each atom

Return type:

numpy.ndarray

get_bader_volumes()

Returns the integration volume around every atom from the Bader charge partitioning scheme.

Returns:

The Bader charges for each atom

Return type:

numpy.ndarray

get_calculate_function() → callable

Generate calculate() function

Example:

>>> calculate_function = job.get_calculate_function()
>>> shell_output, parsed_output, job_crashed = calculate_function(**job.calculate_kwargs)
>>> job.save_output(output_dict=parsed_output, shell_output=shell_output)

Returns:

calculate() functione

Return type:

callable

get_charge_density()

Gets the charge density from the hdf5 file. This value is normalized by the volume

Returns:

atomistics.volumetric.generic.VolumetricData instance

get_density_of_states(sigma=0.1, shift_by_fermi_energy=True, grid=None)

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_eddrmm_handling()

Returns:

status of EDDRMM handling

Return type:

str

get_electronic_structure()

Gets the electronic structure instance from the hdf5 file

Returns:

pyiron_atomistics.atomistics.waves.electronic.ElectronicStructure instance

get_electrostatic_potential()

Gets the electrostatic potential from the hdf5 file.

Returns:

atomistics.volumetric.generic.VolumetricData instance

get_final_structure()

Get the final structure calculated from the job.

Returns:

Atoms

get_final_structure_from_file(cwd, filename='CONTCAR')

Get the final structure of the simulation usually from the CONTCAR file

Parameters:

filename (str) – Path to the CONTCAR file in VASP

Returns:

The final structure

Return type:

pyiron.atomistics.structure.atoms.Atoms

get_from_table(path: str, name: str) → dict | list | float | int

Get a specific value from a pandas.Dataframe

Parameters:

• path (str) – relative path to the data object

• name (str) – parameter key

Returns:

the value associated to the specific parameter key

Return type:

dict, list, float, int

get_icharg_value(icharg=None, self_consistent_calc=None)

Gives the correct ICHARG value for the restart calculation.

Parameters:

• icharg (int/None) – If given, this value will be checked for validity and returned.

• self_consistent_calc (bool/None) – If ‘True’ returns 1, if ‘False’ returns 11, if ‘None’ returns based on the job either 1 or 11.

Returns:

the icharg tag

Return type:

int

get_input_parameter_dict() → dict

Get an hierarchical dictionary of input files. On the first level the dictionary is divided in file_to_create and files_to_copy. Both are dictionaries use the file names as keys. In file_to_create the values are strings which represent the content which is going to be written to the corresponding file. In files_to_copy the values are the paths to the source files to be copied.

The get_input_file_dict() function is called before the write_input() function to convert the input specified on the job object to strings which can be written to the working directory as well as files which are copied to the working directory. After the write_input() function wrote the input files the executable is called.

Returns:

hierarchical dictionary of input files

Return type:

dict

get_job_id(job_specifier: int | str | None = None) → int | None

get the job_id for job named job_name in the local project path from database

Parameters:

job_specifier (str, int) – name of the job or job ID

Returns:

job ID of the job

Return type:

int

get_k_mesh_by_cell(k_mesh_spacing, cell=None)

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_magnetic_moments(iteration_step=-1)

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_neighbors(start=0, stop=-1, stride=1, num_neighbors=12, **kwargs)

Get the neighbors for a given section of the trajectory

Parameters:

• start (int) – Start point of the slice of the trajectory to be sampled

• stop (int) – End point of of the slice of the trajectory to be sampled

• stride (int) – Samples the snapshots evert stride steps

• num_neighbors (int) – The cutoff for the number of neighbors

• **kwargs (dict) – Additional arguments to be passed to the get_neighbors() routine (eg. cutoff_radius, norm_order , etc.)

Returns:

NeighborsTraj instances

containing the neighbor information.

Return type:

pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory

get_neighbors_snapshots(snapshot_indices=None, num_neighbors=12, **kwargs)

Get the neighbors only for the required snapshots from the trajectory

Parameters:

• snapshot_indices (list/numpy.ndarray) – Snapshots for which the the neighbors need to be computed (eg. [1, 5, 10,…, 100]

• num_neighbors (int) – The cutoff for the number of neighbors

• **kwargs (dict) – Additional arguments to be passed to the get_neighbors() routine (eg. cutoff_radius, norm_order , etc.)

Returns:

NeighborsTraj instances

containing the neighbor information.

Return type:

pyiron_atomistics.atomistics.structure.neighbors.NeighborsTrajectory

get_nelect()

Returns the number of electrons in the systems

Returns:

Number of electrons in the system

Return type:

float

get_rwigs()

Gets the radii of Wigner-Seitz cell. (RWIGS tag)

Returns:

dictionary of radii

Return type:

dict

get_structure(frame=-1, wrap_atoms=True, iteration_step=None)

Retrieve structure from object. The number of available structures depends on the job and what kind of calculation has been run on it, see number_of_structures.

Parameters:

frame (int, object) – index of the structure requested, if negative count from the back; if

:param _translate_frame() is overridden: :param frame will pass through it: :param iteration_step: deprecated alias for frame :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 requested structure

Return type:

pyiron_atomistics.atomistics.structure.atoms.Atoms

Raises:

IndexError – if not -number_of_structures <= iteration_step < number_of_structures

get_valence_and_total_charge_density()

Gives the valence and total charge densities

Returns:

The required charge densities

Return type:

tuple

get_workdir_file(filename: str) → None

Checks if a given file exists within the job’s working directory and returns the absolute path to it.

ToDo: Move this to pyiron_base since this is more generic.

Parameters:

filename (str) – The name of the file

Returns:

The name absolute path of the file in the working directory

Return type:

str

Raises:

FileNotFoundError – Raised if the given file does not exist.

gui()

Returns:

property id: int

Unique id to identify the job in the pyiron database - use self.job_id instead

Returns:

job id

Return type:

int

inspect(job_specifier: str | int) → JobCore

Inspect an existing pyiron object - most commonly a job - from the database

Parameters:

job_specifier (str, int) – name of the job or job ID

Returns:

Access to the HDF5 object - not a GenericJob object - use load() instead.

Return type:

JobCore

classmethod instantiate(obj_dict: dict, version: str = None) → Self

Create a blank instance of this class.

This can be used when some values are already necessary for the objects __init__.

Parameters:

• obj_dict (dict) – data previously returned from to_dict()

• version (str) – version tag written together with the data

Returns:

a blank instance of the object that is sufficiently initialized to call _from_dict() on it

Return type:

object

interactive_close() → None

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. After the interactive execution, the job can be closed using the interactive_close function.

interactive_fetch() → None

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. To access the output data during the execution the interactive_fetch function is used.

interactive_flush(path: str = 'generic', include_last_step: bool = True) → None

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. To write the interactive cache to the HDF5 file the interactive flush function is used.

is_compressed() → bool

Check if the job is already compressed or not.

Returns:

[True/False]

Return type:

bool

is_master_id(job_id: int) → bool

Check if the job ID job_id is the master ID for any child job

Parameters:

job_id (int) – job ID of the master job

Returns:

[True/False]

Return type:

bool

is_self_archived() → bool

Check if the HDF5 file of the Job is compressed as tar-archive

Returns:

[True/False]

Return type:

bool

iter_structures(wrap_atoms=True)

Iterate over all structures in this object.

Parameters:

wrap_atoms (bool) – True if the atoms are to be wrapped back into the unit cell; passed to get_structure()

Yields:

pyiron_atomistics.atomistitcs.structure.atoms.Atoms – every structure attached to the object

job_file_name(file_name: str, cwd: str | None = None) → str

combine the file name file_name with the path of the current working directory

Parameters:

• file_name (str) – name of the file

• cwd (str) – current working directory - this overwrites self.project_hdf5.working_directory - optional

Returns:

absolute path to the file in the current working directory

Return type:

str

property job_id: int

Unique id to identify the job in the pyiron database

Returns:

job id

Return type:

int

property job_info_str: str

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

Returns:

job info string

Return type:

str

property job_name: str

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

Returns:

job name

Return type:

str

property job_type: str

[‘ExampleJob’, ‘ParallelMaster’, ‘ScriptJob’,

‘ListMaster’]

Returns:

Job type object

Return type:

JobTypeChoice

Type:

Job type object with all the available job types

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

kill() → None

Kill the job.

This function is used to terminate the execution of the job. It checks if the job is currently running or submitted, and if so, it removes and resets the job ID. If the job is not running or submitted, a ValueError is raised.

Returns:

None

list_all()

Returns dictionary of :method:`.list_groups()` and :method:`.list_nodes()`.

Returns:

results of :method:`.list_groups() under the key "groups"; results of :method:`.list_nodes()` und the

key “nodes”

Return type:

dict

list_childs() → list

List child jobs as JobPath objects - not loading the full GenericJob objects for each child

Returns:

list of child jobs

Return type:

list

list_files() → list

List files inside the working directory

Parameters:

extension (str) – filter by a specific extension

Returns:

list of file names

Return type:

list

list_groups()

Return a list of names of all nested groups.

Returns:

group names

Return type:

list of str

list_nodes()

Return a list of names of all nested nodes.

Returns:

node names

Return type:

list of str

list_potentials()

Lists all the possible POTCAR files for the elements in the structure depending on the XC functional

Returns:

a list of available potentials

Return type:

list

load(job_specifier: str | int, convert_to_object: bool = True) → pyiron_base.job.generic.GenericJob | JobCore

Load an existing pyiron object - most commonly a job - from the database

Parameters:

• job_specifier (str, int) – name of the job or job ID

• convert_to_object (bool) – convert the object to an pyiron object or only access the HDF5 file - default=True accessing only the HDF5 file is about an order of magnitude faster, but only provides limited functionality. Compare the GenericJob object to JobCore object.

Returns:

Either the full GenericJob object or just a reduced JobCore object

Return type:

GenericJob, JobCore

property logger

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

Returns:

logger object

Return type:

logging.getLogger()

map(function, parameter_lst)

Create MapMaster with the current job as reference job.

The job name is created as ‘map_{self.name}’

Parameters:

• function (callable) – passed as modify_function to the map master

• parameter_list (list) – passed as parameter_list to the map master

Returns:

newly created master job

Return type:

MapMaster

property master_id: int

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

Returns:

master id

Return type:

int

move_to(project: ProjectHDFio) → None

Move the content of the job including the HDF5 file to a new location

Parameters:

project (ProjectHDFio) – project to move the job to

property name: str

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

Returns:

job name

Return type:

str

nbands_convergence_check()

Function to check if there are a sufficient number of empty bands in the calculation to ensure electronic convergence.

Returns:

True if the highest band is unoccupied, False if the highest band is occupied

Return type:

bool

property number_of_structures

maximum iteration_step + 1 that can be passed to get_structure().

Type:

int

property parent_id: int

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

Returns:

parent id

Return type:

int

property path: str

Absolute path of the HDF5 group starting from the system root - combination of the absolute system path plus the absolute path inside the HDF5 file starting from the root group.

Returns:

absolute path

Return type:

str

property plane_wave_cutoff

Plane wave energy cutoff in eV

property project: pyiron_base.project.generic.Project

Project instance the jobs is located in

Returns:

project the job is located in

Return type:

Project

property project_hdf5: ProjectHDFio

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

Returns:

HDF5 project

Return type:

ProjectHDFio

property queue_id: int

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

Returns:

queue ID

Return type:

int

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

refresh_job_status() → None

Refresh job status by updating the job status with the status from the database if a job ID is available.

relocate_hdf5(h5_path: str | None = None)

Relocate the hdf file. This function is needed when the child job is spawned by a parent job (cf. pyiron_base.jobs.master.generic)

remove(_protect_childs: bool = True) → None

Remove the job - this removes the HDF5 file, all data stored in the HDF5 file an the corresponding database entry.

Parameters:

_protect_childs (bool) – [True/False] by default child jobs can not be deleted, to maintain the consistency - default=True

remove_and_reset_id(_protect_childs: bool = True) → None

Remove the job and reset its ID.

Parameters:

_protect_childs (bool) – Flag indicating whether to protect child jobs (default is True).

Returns:

None

remove_child() → None

internal function to remove command that removes also child jobs. Do never use this command, since it will destroy the integrity of your project.

rename(new_job_name: str) → None

Rename the job - by changing the job name

Parameters:

new_job_name (str) – new job name

reset_job_id(job_id: int | None = None) → None

Reset the job id sets the job_id to None in the GenericJob as well as all connected modules like JobStatus.

reset_output()

Resets the output instance

restart(job_name=None, job_type=None)

Creates a “restart” job from an existing Vasp calculation. (Default behaviour is to copy CONTCAR -> POSCAR, all other job inputs are copied from original job)

Usage: job.restart().run() restarts the job with job_name: “$(original_job_name)_restart”

Parameters:

• job_name (str) – Job name

• job_type (str) – Job type. If not specified a Vasp job type is assumed

Returns:

New job

Return type:

new_ham (vasp.vasp.Vasp instance)

property restart_file_dict: dict

A dictionary of the new name of the copied restart files

property restart_file_list: list

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

Returns:

list of files

Return type:

list

restart_for_band_structure_calculations(job_name=None)

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

Parameters:

job_name (str/None) – Job name

Returns:

New job

Return type:

new_ham (vasp.vasp.Vasp instance)

restart_from_charge_density(job_name=None, job_type=None, icharg=None, self_consistent_calc=None)

Restart a new job created from an existing Vasp calculation by reading the charge density.

Parameters:

• job_name (str/None) – Job name

• job_type (str/None) – Job type. If not specified a Vasp job type is assumed

• icharg (int/None) – If given, this value will be checked for validity and returned.

• self_consistent_calc (bool/None) – If ‘True’ returns 1, if ‘False’ returns 11, if ‘None’ returns based on the job either 1 or 11.

Returns:

New job

Return type:

new_ham (vasp.vasp.Vasp instance)

restart_from_wave_and_charge(job_name=None, job_type=None, icharg=None, self_consistent_calc=None, istart=1)

Restart a new job created from an existing Vasp calculation by reading the charge density and the wave function.

Parameters:

• job_name (str/None) – Job name

• job_type (str/None) – Job type. If not specified a Vasp job type is assumed

• icharg (int/None) – If given, this value will be checked for validity and returned.

• self_consistent_calc (bool/None) – If ‘True’ returns 1, if ‘False’ returns 11, if ‘None’ returns based on the job either 1 or 11.

• istart (int) – Vasp ISTART tag

Returns:

New job

Return type:

new_ham (vasp.vasp.Vasp instance)

restart_from_wave_functions(job_name=None, job_type=None, istart=1)

Restart a new job created from an existing Vasp calculation by reading the wave functions.

Parameters:

• job_name (str/None) – Job name

• job_type (str/None) – Job type. If not specified a Vasp job type is assumed

• istart (int) – Vasp ISTART tag

Returns:

New job

Return type:

new_ham (vasp.vasp.Vasp instance)

run(delete_existing_job: bool = False, repair: bool = False, debug: bool = False, run_mode: str | None = None, run_again: bool = False) → None

This is the main run function, depending on the job status [‘initialized’, ‘created’, ‘submitted’, ‘running’, ‘collect’,’finished’, ‘refresh’, ‘suspended’] the corresponding run mode is chosen.

Parameters:

• delete_existing_job (bool) – Delete the existing job and run the simulation again.

• repair (bool) – Set the job status to created and run the simulation again.

• debug (bool) – Debug Mode - defines the log level of the subprocess the job is executed in.

• run_mode (str) – [‘modal’, ‘non_modal’, ‘queue’, ‘manual’] overwrites self.server.run_mode

• run_again (bool) – Same as delete_existing_job (deprecated)

run_if_interactive() → None

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.

run_if_interactive_non_modal() → None

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.

run_if_modal() → None

The run if modal function is called by run to execute the simulation, while waiting for the output. For this we use subprocess.check_output()

run_if_refresh() → None

Internal helper function the run if refresh function is called when the job status is ‘refresh’. If the job was suspended previously, the job is going to be started again, to be continued.

run_if_scheduler() → None | int

The run if queue function is called by run if the user decides to submit the job to and queing system. The job is submitted to the queuing system using subprocess.Popen() :returns: Returns the queue ID for the job. :rtype: int

run_static() → None | int

The run static function is called by run to execute the simulation.

run_time_to_db() → None

Internal helper function to store the run_time in the database

save()

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)

save_output(output_dict: dict | None = None, shell_output: str | None = None)

Internal helper function to store the hierarchical output dictionary in the HDF5 file of the pyiron job object

Parameters:

output_dict (dict) – hierarchical output dictionary

self_archive() → None

Compress HDF5 file of the job object to tar-archive

self_unarchive() → None

Decompress HDF5 file of the job object from tar-archive

property server: Server

Get the server object to handle the execution environment for the job.

Returns:

server object

Return type:

Server

set_algorithm(algorithm='Fast', ialgo=None)

Sets the type of electronic minimization algorithm

Parameters:

• algorithm (str) – Algorithm defined by VASP (Fast, Normal etc.)

• ialgo (int) – Sets the IALGO tag in VASP. If not none, this overwrites algorithm

set_convergence_precision(ionic_energy_tolerance=0.001, electronic_energy=1e-07, ionic_force_tolerance=0.01)

Sets the electronic and ionic convergence precision. For ionic convergence either the energy or the force precision is required

Parameters:

• ionic_energy_tolerance (float) – Ionic energy convergence precision (eV)

• electronic_energy (float/NoneType) – Electronic energy convergence precision (eV)

• ionic_force_tolerance (float) – Ionic force convergence precision (eV/A)

set_coulomb_interactions(interaction_type=2, ldau_print=True)

Write the on-site Coulomb interactions in the INCAR file

Parameters:

• interaction_type (int) – Type of Coulombic interaction 1 - Asimov method 2 - Dudarev method

• ldau_print (boolean) – True/False

set_dipole_correction(direction=2, dipole_center=None)

Apply a dipole correction using the dipole layer method proposed by Neugebauer & Scheffler

Parameters:

• direction (int) – Direction along which the field has to be applied (0, 1, or 2)

• dipole_center (list/numpy.ndarray) – Position of the center of the dipole (not the center of the vacuum) in relative coordinates

set_eddrmm_handling(status='warn')

Sets the way, how EDDRMM warning is handled.

Parameters:

status (str) – new status of EDDRMM handling (can be ‘warn’, ‘ignore’, or ‘restart’)

set_electric_field(e_field=0.1, direction=2, dipole_center=None)

Set an external electric field using the dipole layer method proposed by Neugebauer & Scheffler

Parameters:

• e_field (float) – Magnitude of the external electric field (eV/A)

• direction (int) – Direction along which the field has to be applied (0, 1, or 2)

• dipole_center (list/numpy.ndarray) – Position of the center of the dipole (not the center of the vacuum) in relative coordinates

set_empty_states(n_empty_states=None)

Sets the number of empty states in the calculation :param n_empty_states: Required number of empty states :type n_empty_states: int

set_encut(encut)

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

set_fft_mesh(nx=None, ny=None, nz=None)

Set the number of points in the respective directions for the 3D FFT mesh used for computing the charge density or electrostatic potentials. In VASP, using PAW potentials, this refers to the “finer fft mesh”. If no values are set, the default settings from Vasp are used to set the number of grid points.

Parameters:

• nx (int) – Number of points on the x-grid

• ny (int) – Number of points on the y-grid

• nz (int) – Number of points on the z-grid

set_for_band_structure_calc(num_points, structure=None, read_charge_density=True)

Sets up the input for a non self-consistent bandstructure calculation

Parameters:

• num_points (int) – Number of k-points along the total BZ path

• structure (atomistics.structure.atoms.Atoms instance) – Structure for which the bandstructure is to be generated. (default is the input structure)

• read_charge_density (boolean) – If True, a charge density from a previous SCF run is used (recommended)

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, k_mesh_spacing=None, n_path=None, path_name=None)

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_

• set) (angstrom is)

• 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, density_residual_scaling=None, spin_residual_scaling=None)

Parameters:

• method (str) – mixing method ‘PULAY’ or ‘KERKER’ (default: PULAY)

• n_pulay_steps (int) – number of previous densities to use for the Pulay mixing (default: 7)

• density_mixing_parameter (float) – mixing ratio of rho_opt to rho_in

• spin_mixing_parameter (float) – linear mixing parameter for spin densities

• density_residual_scaling (float) – scaling for the residual contribution of the Kerker mixing. 1 means it takes as much rho_in (input density) as residual (where Kerker preconditioning applies). The lower the value, the smaller the residual contribution becomes.

• spin_residual_scaling (float) – scaling for the spin residual (cf. density_residual_scaling)

• by (Mixing ratio m is given) – rho^n = (m-1)*rho_in+m*preconditioner*rho_opt

A low value of density mixing parameter may lead to a more stable convergence, but will slow down the calculation if set too low. In systems with bands around the Fermi energy (i.e. metals, e.g. Fe, Mn), the mixing parameters should be small. In insulators (e.g. Al, Si) the mixing parameter should be high.

set_occupancy_smearing(smearing: str = None, width: float = None, order: int = 1, ismear: int = None) → None

Set how the finite temperature smearing is applied in determining partial occupancies

Parameters:

• smearing (str) – Type of smearing (Fermi, Gaussian, or Methfessel-Paxton)

• width (float) – Smearing width (eV)

• order (int) – order (int): Smearing order (only for Methfessel-Paxton)

• ismear (int) – (Deprecated) Directly sets the ISMEAR tag. Overwrites the smearing tag

set_rwigs(rwigs_dict)

Sets the radii of Wigner-Seitz cell. (RWIGS tag)

Parameters:

rwigs_dict (dict) – Dictionary of species and corresponding radii. (structure has to be defined before)

set_spin_constraint(lamb, rwigs_dict, direction=False, norm=False)

Sets spin constrains including ‘LAMBDA’ and ‘RWIGS’.

Parameters:

• lamb (float) – LAMBDA tag

• rwigs_dict (dict) – Dictionary of species and corresponding radii. (structure has to be defined before)

• direction (bool) – (True/False) constrain spin direction.

• norm (bool) – (True/False) constrain spin norm (magnitude).

show_hdf() → None

Iterating over the HDF5 datastructure and generating a human readable graph.

signal_intercept(sig) → None

Abort the job and log signal that caused it.

Expected to be called from pyiron_base.state.signal.catch_signals().

Parameters:

sig (int) – the signal that triggered the abort

property sorted_indices

How the original atom indices are ordered in the vasp format (species by species)

property spin_constraints

Returns True if the calculation is spin constrained

property status: str

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

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

Returns:

status

Return type:

(str/pyiron_base.job.jobstatus.JobStatus)

stop_calculation(next_electronic_step=False)

Call to stop the VASP calculation

Parameters:

next_electronic_step (bool) – True if the next electronic step should be calculated

store_structure()

Create StructureContainer job with the initial structure of the job and sets that jobs parent_id from this job.

Returns:

job containing initial structure of this job

Return type:

StructureContainer

property structure

Returns:

suspend() → None

Suspend the job by storing the object and its state persistently in HDF5 file and exit it.

to_dict()

Reduce the object to a dictionary.

Returns:

serialized state of this object

Return type:

dict

to_hdf(hdf=None, group_name=None)

Stores the instance attributes into the hdf5 file

Parameters:

• hdf (pyiron_base.generic.hdfio.ProjectHDFio) – The HDF file/path to write the data to

• group_name (str) – The name of the group under which the data must be stored as

to_object(object_type: str | None = None, **qwargs) → pyiron_base.job.generic.GenericJob

Load the full pyiron object from an HDF5 file

Parameters:

• object_type – if the ‘TYPE’ node is not available in the HDF5 file a manual object type can be set - optional

• **qwargs – optional parameters [‘job_name’, ‘project’] - to specify the location of the HDF5 path

Returns:

pyiron object

Return type:

GenericJob

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

Returns a Trajectory instance containing the necessary information to describe the evolution of the atomic structure during the atomistic simulation.

Parameters:

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

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

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

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

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

• overwrite_cells (list/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.atomistics.job.atomistic.Trajectory

transfer_from_remote() → None

Transfer the job from a remote location to the local machine.

This method transfers the job from a remote location to the local machine. It performs the following steps: 1. Retrieves the job from the remote location using the queue adapter. 2. Transfers the job file to the remote location, with the option to delete the file on the remote location after transfer. 3. Updates the project database if it is disabled, otherwise updates the file table in the database with the job information.

Parameters:

None

Returns:

None

transform_structures(modify) → TransformStructure

Return a modified object by applying a function to each object lazily.

Parameters:

modify (function) – applied to each structure, has to return the modified structure

Returns:

a container with the modified structures

Return type:

TransformStructure

update_master(force_update: bool = False) → None

After a job is finished it checks whether it is linked to any metajob - meaning the master ID is pointing to this jobs job ID. If this is the case and the master job is in status suspended - the child wakes up the master job, sets the status to refresh and execute run on the master job. During the execution the master job is set to status refresh. If another child calls update_master, while the master is in refresh the status of the master is set to busy and if the master is in status busy at the end of the update_master process another update is triggered.

Parameters:

force_update (bool) – Whether to check run mode for updating master

validate_ready_to_run()

Returns:

property version: str

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

Returns:

version number

Return type:

str

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

property working_directory: str

Get the working directory of the job is executed in - outside the HDF5 file. The working directory equals the path but it is represented by the filesystem:

/absolute/path/to/the/file.h5/path/inside/the/hdf5/file

becomes:

/absolute/path/to/the/file_hdf5/path/inside/the/hdf5/file

Returns:

absolute path to the working directory

Return type:

str

property write_charge_density

True if the charge density file CHGCAR file is/should be written

property write_electrostatic_potential

True if the local potential or electrostatic potential LOCPOT file is/should be written

write_input() → None

Call routines that generate the code specific input files Returns:

write_magmoms()

Write the magnetic moments in INCAR from that assigned to the species

property write_resolved_dos

True if the resolved DOS should be written (in the vasprun.xml file)

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

property write_wave_funct

True if the wave function file WAVECAR file is/should be written