pyiron_atomistics.sphinx.sphinx.Sphinx

pyiron_atomistics.sphinx.sphinx.Sphinx#

class pyiron_atomistics.sphinx.sphinx.Sphinx(project, job_name)[source]#

Bases: SphinxInteractive

Class to setup and run Sphinx simulations which is a derivative of pyiron_atomistics.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 Sphinx specific input and output.

Parameters:

project – Project object (defines path where job will be created and stored)
job_name (str) – name of the job (must be unique within this project path)

__init__(project, job_name)[source]#

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.
`calc_md`([temperature, n_ionic_steps, ...])
`calc_minimize`([electronic_steps, ...])	Setup the hamiltonian to perform ionic relaxations.
`calc_static`([electronic_steps])	Setup the hamiltonian to perform a static SCF run.
`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.
`check_vasp_potentials`()
`clear_job`()	Convenience function to clear job info after suspend.
`collect_errors`()	Collects errors from the SPHInX run
`collect_logfiles`()	Collect errors and warnings.
`collect_output`([force_update, compress_files])	Collects the outputs and stores them to the hdf file
`collect_structures`([filter_function])	Collects a copy of all structures in a compact `StructureStorage`.
`collect_warnings`()	Collects warnings from the SPHInX 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_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[, file_name])
`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_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_from_table`(path, name)	Get a specific value from a pandas.Dataframe
`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_n_ir_reciprocal_points`([...])
`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_output_parameter_dict`()
`get_scf_group`([maxSteps, keepRhoFixed, ...])	SCF group setting for SPHInX for all args refer to calc_static or calc_minimize
`get_structure`([frame, wrap_atoms, ...])	Retrieve structure from object.
`get_structure_group`([keep_angstrom])	create a SPHInX Group object based on self.structure
`get_valence_and_total_charge_density`()
`get_version_float`()
`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_atom_spin_constraints_getter`()
`interactive_atom_spins_getter`()
`interactive_cell_organizer`()
`interactive_cells_getter`()
`interactive_cells_setter`(cell)
`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_collect`()
`interactive_computation_time_getter`()
`interactive_energy_pot_getter`()
`interactive_energy_tot_getter`()
`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])	param path:
`interactive_forces_getter`()
`interactive_index_organizer`()
`interactive_indices_getter`()
`interactive_indices_setter`(indices)
`interactive_initialize_interface`()
`interactive_is_activated`()	Check if the interactive library is activated.
`interactive_magmom_organizer`()
`interactive_magnetic_forces_getter`()
`interactive_open`()	Set the run mode to interactive.
`interactive_positions_getter`()
`interactive_positions_organizer`()
`interactive_positions_setter`(positions)
`interactive_pressures_getter`()
`interactive_spin_constraints_getter`()
`interactive_spin_constraints_setter`(spins)
`interactive_spins_getter`()
`interactive_steps_getter`()
`interactive_store_in_cache`(key, value)	Store a value in the interactive cache.
`interactive_stress_getter`()
`interactive_structure_setter`(structure)
`interactive_temperatures_getter`()
`interactive_time_getter`()
`interactive_unwrapped_positions_getter`()
`interactive_volume_getter`()
`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
`load_basis_group`()	Load the basis Group.
`load_default_groups`()	Populates input groups with the default values.
`load_default_input`()	Set defaults for generic parameters and create SPHInX input groups.
`load_guess_group`([update_spins])	Load the initialGuess Group.
`load_hamilton_group`()	Load the PAWHamiltonian Group.
`load_main_group`()	Load the main Group.
`load_species_group`([check_overlap, potformat])	Build the species Group object based on self.structure
`load_structure_group`([keep_angstrom])	Build + load the structure group based on self.structure
`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.
`restart`([job_name, job_type, ...])	Restart a new job created from an existing calculation.
`restart_for_band_structure_calculations`([...])	Restart a new job created from an existing calculation by reading the charge density for band structures.
`restart_from_charge_density`([job_name, ...])	Restart a new job created from an existing calculation by reading the charge density.
`restart_from_wave_functions`([job_name, job_type])	Restart a new job created from an existing 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_addon`(addon[, args, from_tar, silent, ...])	Run a SPHInX addon
`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])	Store output of the calculate function in the HDF5 file.
`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_check_overlap`([check_overlap])	param check_overlap: Whether to check overlap
`set_convergence_precision`([...])	Sets the electronic and ionic convergence precision.
`set_empty_states`([n_empty_states])	Function to set the number of empty states.
`set_encut`(encut)	Sets the plane-wave energy cutoff :param encut: The energy cutoff in eV :type encut: float
`set_exchange_correlation_functional`(...)
`set_input_to_read_only`()	This function enforces read-only mode for the input classes, but it has to be implemented 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, order])	Set how the finite temperature smearing is applied in determining partial occupancies
`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.
`species_from_hdf`()
`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.
`update_sphinx`()
`validate_ready_to_run`()	Checks whether parameters are set appropriately.
`view_structure`([snapshot, spacefill, show_cell])	param snapshot: Snapshot of the trajectory one wants
`write_input`()	Generate all the required input files for the SPHInX job.
`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`
`current_structure`
`database_entry`
`encut`
`exchange_correlation_functional`
`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`
`fix_symmetry`
`id`	Unique id to identify the job in the pyiron database - use self.job_id instead
`id_pyi_to_spx`
`id_spx_to_pyi`
`initial_structure`
`interactive_enforce_structure_reset`
`interactive_flush_frequency`
`interactive_write_frequency`
`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`
`potential`
`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
`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.
`spin_constraints`
`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.
`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

calc_minimize(electronic_steps=None, ionic_steps=None, max_iter=None, pressure=None, ionic_energy_tolerance=None, ionic_force_tolerance=None, ionic_energy=None, ionic_forces=None, volume_only=False)#

Setup the hamiltonian to perform ionic relaxations.

The convergence goal can be set using either the ionic_energy_tolerance as a limit for fluctuations in energy or the ionic_force_tolerance.

Loads defaults for all SPHInX input groups, including a ricQN-based main Group.

Warning

Sphinx does not support volume minimizations! Calling this method with pressure or volume_only results in an error.

Parameters:

pressure
max_iter
electronic_steps (int) – maximum number of electronic steps per electronic convergence
ionic_steps (int) – maximum number of ionic steps
ionic_energy (float) – convergence goal in terms of energy (depreciated use ionic_energy_tolerance instead)
ionic_energy_tolerance (float) – convergence goal in terms of energy (optional)
ionic_forces (float) – convergence goal in terms of forces (depreciated use ionic_force_tolerance instead)
ionic_force_tolerance (float) – convergence goal in terms of forces (optional)
volume_only (bool)

calc_static(electronic_steps=100)#

Setup the hamiltonian to perform a static SCF run.

Loads defaults for all SPHInX input groups, including a static main Group.

Parameters:: electronic_steps (int) – max # of electronic steps

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()#: 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

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 SPHInX run

collect_logfiles()#: Collect errors and warnings.

collect_output(force_update=False, compress_files=True)#: Collects the outputs and stores them to the hdf file

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 SPHInX 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_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 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')

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_hdf(hdf=None, group_name=None)#

Recreates instance from the hdf5 file

Parameters:

hdf (str) – Path to the hdf5 file
group_name (str) – Name of the group which contains the object

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:: pyiron_atomistics.atomistics.volumetric.generic.VolumetricData

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_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:: pyiron_atomistics.atomistics.volumetric.generic.VolumetricData

get_final_structure()#

Get the final structure calculated from the job.

Returns:: 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_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.

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_scf_group(maxSteps=None, keepRhoFixed=False, dEnergy=None, algorithm='blockCCG')#: SCF group setting for SPHInX for all args refer to calc_static or calc_minimize

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_structure_group(keep_angstrom=False)#

create a SPHInX Group object based on self.structure

Parameters:: keep_angstrom (bool) – Store distances in Angstroms or Bohr

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()#: 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()#: 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='interactive', include_last_step=False)#

Parameters:

path
include_last_step

Returns:

interactive_is_activated() → bool#

Check if the interactive library is activated.

Returns:: True if the interactive library is activated, False otherwise.
Return type:: bool

interactive_open() → pyiron_base.jobs.job.interactive.InteractiveBase#

Set the run mode to interactive.

This is the same as setting server.run_mode.interactive.

Must be called before run() is called.

interactive_store_in_cache(key: str, value: Any) → None#

Store a value in the interactive cache.

Parameters:

key (str) – The key to store the value under.
value (Any) – The value to be stored.

Returns:

None

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

load_basis_group()#

Load the basis Group.

The group is populated using setdefault to avoid overwriting values that were previously (intentionally) modified.

load_default_groups()#

Populates input groups with the default values.

Nearly every default simply points to a variable stored in self.input.

Does not load job.input.structure or job.input.pawPot. These groups should usually be modified via job.structure, in which case they will be set at the last minute when the job is run. These groups can be synced to job.structure at any time using job.load_structure_group() and job.load_species_group().

load_default_input()#: Set defaults for generic parameters and create SPHInX input groups.

load_guess_group(update_spins=True)#

Load the initialGuess Group.

The group is populated using setdefault to avoid overwriting values that were previously (intentionally) modified.

Parameters:: update_spins (bool) – whether or not to reload the atomicSpin groups based on the latest structure. Defaults to True.

load_hamilton_group()#

Load the PAWHamiltonian Group.

The group is populated using setdefault to avoid overwriting values that were previously (intentionally) modified.

load_main_group()#

Load the main Group.

The group is populated based on the type of calculation and settings in the self.input.

load_species_group(check_overlap=True, potformat='VASP')#

Build the species Group object based on self.structure

Parameters:

check_overlap (bool) – Whether to check overlap (see set_check_overlap)
potformat (str) – type of pseudopotentials that will be read. Options are JTH or VASP.

load_structure_group(keep_angstrom=False)#

Build + load the structure group based on self.structure

Parameters:: keep_angstrom (bool) – Store distances in Angstroms or Bohr

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 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=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.

restart(job_name=None, job_type=None, from_charge_density=True, from_wave_functions=True)#

Restart a new job created from an existing calculation. :param project: Project instance at which the new job should be created :type project: pyiron_atomistics.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

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 calculation by reading the charge density for band structures.

Parameters:: job_name (str/None) – Job name
Returns:: new job instance
Return type:: pyiron_atomistics.sphinx.sphinx.sphinx

restart_from_charge_density(job_name=None, job_type='Sphinx', band_structure_calc=False)#

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

Parameters:

job_name (str/None) – Job name
job_type (str/None) – Job type. If not specified a SPHInX job type is assumed (actually this is all that’s currently supported)
band_structure_calc (bool) – has to be True for band structure calculations.

Returns:

new job instance

Return type:

pyiron_atomistics.sphinx.sphinx.sphinx

restart_from_wave_functions(job_name=None, job_type='Sphinx')#

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

Parameters:

job_name (str) – Job name
job_type (str) – Job type. If not specified a SPHInX job type is assumed (actually this is all that’s currently supported.)

Returns:

new job instance

Return type:

pyiron_atomistics.sphinx.sphinx.sphinx

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_addon(addon, args=None, from_tar=None, silent=False, log=True, version=None, debug=False)#

Run a SPHInX addon

addon - name of addon (str) args - arguments (str or list) from_tar - if job is compressed, extract these files (list) silent - do not print output for successful runs? log - produce log file? version - which sphinx version to load (str or None) debug - return subprocess.CompletedProcess ?

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.

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. 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) → None#

Store output of the calculate function in the HDF5 file.

Parameters:

output_dict (dict) – hierarchical output dictionary to be stored in the HDF5 file.
shell_output (str) – shell output from calling the external executable to be stored in the HDF5 file.

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_check_overlap(check_overlap=True)#

Parameters:: check_overlap (bool) – Whether to check overlap

Comments:: Certain PAW-pseudo-potentials have an intrinsic pathology: their PAW overlap operator is not generally positive definite (i.e., the PAW-corrected norm of a wavefunction could become negative). SPHInX usually refuses to use such problematic potentials. This behavior can be overridden by setting check_overlap to False.

set_convergence_precision(ionic_energy_tolerance=None, ionic_force_tolerance=None, ionic_energy=None, electronic_energy=None, ionic_forces=None)#

Sets the electronic and ionic convergence precision.

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

Parameters:

ionic_energy (float) – Ionic energy convergence precision (depreciated use ionic_energy_tolerance instead)
ionic_energy_tolerance (float) – Ionic energy convergence precision
electronic_energy (float) – Electronic energy convergence precision
ionic_forces (float) – Ionic force convergence precision (depreciated use ionic_force_tolerance instead)
ionic_force_tolerance (float) – Ionic force convergence precision

set_empty_states(n_empty_states=None)#

Function to set the number of empty states.

Parameters:

n_empty_states (int/None) – Number of empty states.
None (If)
'auto'. (sets it to)

Comments:

If this number is too low, the algorithm will not be able to able to swap wave functions near the chemical potential. If the number is too high, computation time will be wasted for the higher energy states and potentially lead to a memory problem.

In contrast to VASP, this function sets only the number of empty states and not the number of total states.

The default value is 0.5*NIONS+3 for non-magnetic systems and 1.5*NIONS+3 for magnetic systems

set_encut(encut)#: Sets the plane-wave energy cutoff :param encut: The energy cutoff in eV :type encut: float

set_input_to_read_only()#: This function enforces read-only mode for the input classes, but it has to be implemented 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.

Further information can be found on the website: https://sxrepo.mpie.de

set_occupancy_smearing(smearing=None, width=None, order=1)#

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

Parameters:

smearing (str) – Type of smearing, ‘FermiDirac’ or ‘MethfesselPaxton’
width (float) – Smearing width (eV) (default: 0.2)
order (int) – Smearing order

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 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)

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 (str) – Path to the hdf5 file
group_name (str) – Name of the group which contains the object

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()#: Checks whether parameters are set appropriately. It does not mean the simulation won’t run if it returns False.

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

write_input()#

Generate all the required input files for the SPHInX job.

Creates: structure.sx: structure associated w/ job all pseudopotential files spins.in (if necessary): constrained spin moments input.sx: main input file with all sub-groups

Automatically called by job.run()

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

pyiron_atomistics.sphinx.sphinx.Sphinx

Contents

pyiron_atomistics.sphinx.sphinx.Sphinx#