pyiron package

Subpackages

• pyiron.atomistics package
  • Subpackages
    • pyiron.atomistics.generic package
      • Submodules
      • pyiron.atomistics.generic.object_type module
      • Module contents
    • pyiron.atomistics.job package
      • Submodules
      • pyiron.atomistics.job.atomistic module
      • pyiron.atomistics.job.interactive module
      • pyiron.atomistics.job.interactivewrapper module
      • pyiron.atomistics.job.potentials module
      • pyiron.atomistics.job.structurecontainer module
      • Module contents
    • pyiron.atomistics.master package
      • Submodules
      • pyiron.atomistics.master.convergence_volume module
      • pyiron.atomistics.master.murnaghan module
      • pyiron.atomistics.master.parallel module
      • pyiron.atomistics.master.phonopy module
      • pyiron.atomistics.master.serial module
      • pyiron.atomistics.master.structure module
      • Module contents
    • pyiron.atomistics.md_analysis package
      • Submodules
      • pyiron.atomistics.md_analysis.trajectory_analysis module
      • pyiron.atomistics.md_analysis.water_analysis module
      • Module contents
    • pyiron.atomistics.structure package
      • Submodules
      • pyiron.atomistics.structure.atom module
      • pyiron.atomistics.structure.atoms module
      • pyiron.atomistics.structure.ovito module
      • pyiron.atomistics.structure.periodic_table module
      • pyiron.atomistics.structure.phonopy module
      • pyiron.atomistics.structure.pyironase module
      • pyiron.atomistics.structure.sparse_list module
      • Module contents
    • pyiron.atomistics.thermodynamics package
      • Submodules
      • pyiron.atomistics.thermodynamics.thermo_bulk module
      • Module contents
    • pyiron.atomistics.volumetric package
      • Submodules
      • pyiron.atomistics.volumetric.generic module
      • Module contents
  • Module contents
• pyiron.base package
  • Subpackages
    • pyiron.base.database package
      • Submodules
      • pyiron.base.database.generic module
      • pyiron.base.database.jobtable module
      • Module contents
    • pyiron.base.generic package
      • Submodules
      • pyiron.base.generic.hdfio module
      • pyiron.base.generic.parameters module
      • pyiron.base.generic.template module
      • pyiron.base.generic.util module
      • Module contents
    • pyiron.base.job package
      • Submodules
      • pyiron.base.job.core module
      • pyiron.base.job.executable module
      • pyiron.base.job.generic module
      • pyiron.base.job.interactive module
      • pyiron.base.job.jobstatus module
      • pyiron.base.job.jobtype module
      • pyiron.base.job.path module
      • pyiron.base.job.script module
      • pyiron.base.job.wrapper module
      • Module contents
    • pyiron.base.master package
      • Submodules
      • pyiron.base.master.generic module
      • pyiron.base.master.list module
      • pyiron.base.master.parallel module
      • pyiron.base.master.serial module
      • pyiron.base.master.submissionstatus module
      • Module contents
    • pyiron.base.project package
      • Submodules
      • pyiron.base.project.generic module
      • pyiron.base.project.gui module
      • pyiron.base.project.path module
      • pyiron.base.project.store module
      • Module contents
    • pyiron.base.pyio package
      • Submodules
      • pyiron.base.pyio.parser module
      • Module contents
    • pyiron.base.server package
      • Submodules
      • pyiron.base.server.generic module
      • pyiron.base.server.queuestatus module
      • pyiron.base.server.runmode module
      • Module contents
    • pyiron.base.settings package
      • Submodules
      • pyiron.base.settings.generic module
      • pyiron.base.settings.install module
      • pyiron.base.settings.logger module
      • pyiron.base.settings.update module
      • Module contents
  • Module contents
• pyiron.dft package
  • Subpackages
    • pyiron.dft.job package
      • Submodules
      • pyiron.dft.job.generic module
      • Module contents
    • pyiron.dft.master package
      • Submodules
      • pyiron.dft.master.convergence_encut_parallel module
      • pyiron.dft.master.convergence_encut_serial module
      • pyiron.dft.master.convergence_kpoint_parallel module
      • pyiron.dft.master.murnaghan_dft module
      • Module contents
    • pyiron.dft.waves package
      • Submodules
      • pyiron.dft.waves.bandstructure module
      • pyiron.dft.waves.dos module
      • pyiron.dft.waves.electronic module
      • Module contents
  • Module contents
• pyiron.lammps package
  • Submodules
  • pyiron.lammps.base module
  • pyiron.lammps.control module
  • pyiron.lammps.interactive module
  • pyiron.lammps.lammps module
  • pyiron.lammps.pipe module
  • pyiron.lammps.potential module
  • pyiron.lammps.structure module
  • Module contents
• pyiron.testing package
  • Submodules
  • pyiron.testing.executable module
  • pyiron.testing.randomatomistic module
  • Module contents
• pyiron.vasp package
  • Submodules
  • pyiron.vasp.base module
  • pyiron.vasp.interactive module
  • pyiron.vasp.outcar module
  • pyiron.vasp.potential module
  • pyiron.vasp.procar module
  • pyiron.vasp.structure module
  • pyiron.vasp.vasp module
  • pyiron.vasp.vasprun module
  • pyiron.vasp.volumetric_data module
  • Module contents

Submodules

pyiron.project module

class pyiron.project.Project(path='', user=None, sql_query=None)

Bases: pyiron.base.project.generic.Project

The project is the central class in pyiron, all other objects can be created from the project object.

Parameters:

• path (GenericPath, str) – path of the project defined by GenericPath, absolute or relative (with respect to current working directory) path
• user (str) – current pyiron user
• sql_query (str) – SQL query to only select a subset of the existing jobs within the current project

.. attribute:: root_path

the pyiron user directory, defined in the .pyiron configuration

.. attribute:: project_path

the relative path of the current project / folder starting from the root path of the pyiron user directory

.. attribute:: path

the absolute path of the current project / folder

.. attribute:: base_name

the name of the current project / folder

.. attribute:: history

previously opened projects / folders

.. attribute:: parent_group

parent project - one level above the current project

.. attribute:: user

current unix/linux/windows user who is running pyiron

.. attribute:: sql_query

an SQL query to limit the jobs within the project to a subset which matches the SQL query.

.. attribute:: db

connection to the SQL database

.. attribute:: job_type

Job Type object with all the available job types: [‘StructureContainer’, ‘StructurePipeline’, ‘AtomisticExampleJob’,

‘ExampleJob’, ‘Lammps’, ‘KMC’, ‘Sphinx’, ‘Vasp’, ‘GenericMaster’, ‘SerialMaster’, ‘AtomisticSerialMaster’, ‘ParallelMaster’, ‘KmcMaster’, ‘ThermoLambdaMaster’, ‘RandomSeedMaster’, ‘MeamFit’, ‘Murnaghan’, ‘MinimizeMurnaghan’, ‘ElasticMatrix’, ‘ConvergenceVolume’, ‘ConvergenceEncutParallel’, ‘ConvergenceKpointParallel’, ’PhonopyMaster’, ‘DefectFormationEnergy’, ‘LammpsASE’, ‘PipelineMaster’, ’TransformationPath’, ‘ThermoIntEamQh’, ‘ThermoIntDftEam’, ‘ScriptJob’, ‘ListMaster’]

copy()

Copy the project object - copying just the Python object but maintaining the same pyiron path

Returns:copy of the project object Return type:Project

static create_ase_bulk(name, crystalstructure=None, a=None, c=None, covera=None, u=None, orthorhombic=False, cubic=False)

Creating bulk systems using ASE bulk module.

Crystal structure and lattice constant(s) will be guessed if not provided.

name: str

Chemical symbol or symbols as in ‘MgO’ or ‘NaCl’.

crystalstructure: str

Must be one of sc, fcc, bcc, hcp, diamond, zincblende, rocksalt, cesiumchloride, fluorite or wurtzite.

a: float

Lattice constant.

c: float

Lattice constant.

c_over_a: float

c/a ratio used for hcp. Default is ideal ratio: sqrt(8/3).

u: float

Internal coordinate for Wurtzite structure.

orthorhombic: bool

Construct orthorhombic unit cell instead of primitive cell which is the default.

cubic: bool

Construct cubic unit cell if possible.

static create_atoms(symbols=None, positions=None, numbers=None, tags=None, momenta=None, masses=None, magmoms=None, charges=None, scaled_positions=None, cell=None, pbc=None, celldisp=None, constraint=None, calculator=None, info=None, indices=None, elements=None, dimension=None, species=None, **qwargs)

Creates a atomistics.structure.atoms.Atoms instance.

Parameters:

• elements (list/numpy.ndarray) – List of strings containing the elements or a list of atomistics.structure.periodic_table.ChemicalElement instances
• numbers (list/numpy.ndarray) – List of atomic numbers of elements
• symbols (list/numpy.ndarray) – List of chemical symbols
• positions (list/numpy.ndarray) – List of positions
• scaled_positions (list/numpy.ndarray) – List of scaled positions (relative coordinates)
• pbc (boolean) – Tells if periodic boundary conditions should be applied
• cell (list/numpy.ndarray) – A 3x3 array representing the lattice vectors of the structure
• momenta (list/numpy.ndarray) – List of momentum values
• tags (list/numpy.ndarray) – A list of tags
• masses (list/numpy.ndarray) – A list of masses
• magmoms (list/numpy.ndarray) – A list of magnetic moments
• charges (list/numpy.ndarray) – A list of point charges
• celldisp –
• constraint (list/numpy.ndarray) – A list of constraints
• calculator – ASE calculator
• info (list/str) – ASE compatibility
• indices (list/numpy.ndarray) – The list of species indices
• dimension (int) – Dimension of the structure
• species (list) – List of species

Returns:

The required structure instance

Return type:

pyiron.atomistics.structure.atoms.Atoms

static create_element(parent_element, new_element_name=None, spin=None, potential_file=None)

Parameters:

• parent_element (str, int) – The parent element eq. “N”, “O”, “Mg” etc.
• new_element_name (str) – The name of the new parent element (can be arbitrary)
• spin (float) – Value of the magnetic moment (with sign)
• potential_file (str) – Location of the new potential file if necessary

Returns:

atomistics.structure.periodic_table.ChemicalElement instance

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’: - ‘SerialMaster’: series of jobs run in serial - ‘AtomisticSerialMaster’: - ‘ParallelMaster’: series of jobs run in parallel - ‘KmcMaster’: - ‘ThermoLambdaMaster’: - ‘RandomSeedMaster’: - ‘MeamFit’: - ‘Murnaghan’: - ‘MinimizeMurnaghan’: - ‘ElasticMatrix’: - ‘ConvergenceVolume’: - ‘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’, ‘SerialMaster’, ‘AtomisticSerialMaster’, ‘ParallelMaster’, ‘KmcMaster’, ‘ThermoLambdaMaster’, ‘RandomSeedMaster’, ‘MeamFit’, ‘Murnaghan’, ‘MinimizeMurnaghan’, ‘ElasticMatrix’, ‘ConvergenceVolume’, ‘ConvergenceEncutParallel’, ‘ConvergenceKpointParallel’, ’PhonopyMaster’, ‘DefectFormationEnergy’, ‘LammpsASE’, ‘PipelineMaster’, ’TransformationPath’, ‘ThermoIntEamQh’, ‘ThermoIntDftEam’, ‘ScriptJob’, ‘ListMaster’]
• job_name (str) – name of the job

Returns:

job object depending on the job_type selected

Return type:

GenericJob

static create_object(object_type)

Parameters:object_type –

Returns:

static create_structure(element, bravais_basis, lattice_constant)

Parameters:

• element –
• bravais_basis –
• lattice_constant –

Returns:

static create_surface(element, surface_type, size=(1, 1, 1), vacuum=1.0, center=False, **kwargs)

Generates surfaces instances based on the ase.build.surface module. :param element: Element name :type element: str :param surface_type: The string specifying the surface type generators available through ase (fcc111, :type surface_type: str :param hcp0001 etc.): :param size: Size of the surface :type size: turple :param vacuum: Length of vacuum layer added to the surface along the z direction :type vacuum: float :param center: Tells if the surface layers have to be at the center or at one end along the z-direction :type center: boolean :param **kwargs: Additional, arguments you would normally pass to the structure generator like ‘a’, ‘b’, :param ‘orthogonal’ etc.:

Returns:surface (atomistics.structure.atoms.Atoms instance)

get_structure(job_specifier, iteration_step=-1)

Gets the structure from a given iteration step of the simulation (MD/ionic relaxation). For static calculations there is only one ionic iteration step :param job_specifier: name of the job or job ID :type job_specifier: str, int :param iteration_step: Step for which the structure is requested :type iteration_step: int

Returns:atomistics.structure.atoms.Atoms object

gui()

Returns:

import_from_path(path, recursive=True)

Parameters:

• path –
• recursive –

Returns:

import_single_calculation(project_to_import_from, rel_path=None, job_type='Vasp')

Parameters:

• rel_path –
• project_to_import_from –
• job_type (str) – Type of the calculation which is going to be imported

static inspect_emperical_potentials()

static inspect_periodic_table()

static inspect_pseudo_potentials()

load_from_jobpath(job_id=None, db_entry=None, convert_to_object=True)

Internal function to load an existing job either based on the job ID or based on the database entry dictionary.

Parameters:

• job_id (int) – Job ID - optional, but either the job_id or the db_entry is required.
• db_entry (dict) – database entry dictionary - optional, but either the job_id or the db_entry is required.
• 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

Module contents