pyiron.atomistics.structure.factory module

class pyiron.atomistics.structure.factory.StructureFactory

Bases: pyiron_base.generic.factory.PyironFactory

static 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.

Returns

Required bulk structure

Return type

pyiron.atomistics.structure.atoms.Atoms

ase_read(*args, **kwargs)

Returns a ASE’s read result, wrapped as a pyiron.atomstic.structure.atoms.Atoms object.

ase.io.read docstring: Read Atoms object(s) from file.

filename: str or file

Name of the file to read from or a file descriptor.

index: int, slice or str

The last configuration will be returned by default. Examples:

• index=0: first configuration

• index=-2: second to last

• index=':' or index=slice(None): all

• index='-3:' or index=slice(-3, None): three last

• index='::2' or index=slice(0, None, 2): even

• index='1::2' or index=slice(1, None, 2): odd

format: str

Used to specify the file-format. If not given, the file-format will be guessed by the filetype function.

parallel: bool

Default is to read on master and broadcast to slaves. Use parallel=False to read on all slaves.

do_not_split_by_at_sign: bool

If False (default) filename is splited by at sign @

Many formats allow on open file-like object to be passed instead of filename. In this case the format cannot be auto-decected, so the format argument should be explicitly given.

static 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 crystal(element, bravais_basis, lattice_constant)

Create a crystal structure using pyiron’s native crystal structure generator

Parameters

• element (str) – Element name

• bravais_basis (str) – Basis type

• lattice_constant (float/list) – Lattice constants

Returns

The required crystal structure

Return type

pyiron.atomistics.structure.atoms.Atoms

static 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

static surface(element, surface_type, size=(1, 1, 1), vacuum=1.0, center=False, pbc=True, **kwargs)

Generate a surface based on the ase.build.surface module.

Parameters

• element (str) – Element name

• surface_type (str) – The string specifying the surface type generators available through ase (fcc111,

• etc.) (hcp0001) –

• size (tuple) – Size of the surface

• vacuum (float) – Length of vacuum layer added to the surface along the z direction

• center (bool) – Tells if the surface layers have to be at the center or at one end along the z-direction

• pbc (list/numpy.ndarray) – List of booleans specifying the periodic boundary conditions along all three directions.

• **kwargs – Additional, arguments you would normally pass to the structure generator like ‘a’, ‘b’,

• etc. ('orthogonal') –

Returns

Required surface

Return type

pyiron.atomistics.structure.atoms.Atoms instance

static surface_hkl(lattice, hkl, layers, vacuum=1.0, center=False, pbc=True)

Use ase.build.surface to build a surface with surface normal (hkl).

Parameters

• lattice (pyiron.atomistics.structure.atoms.Atoms/str) – bulk Atoms instance or str, e.g. “Fe”, from which to build the surface

• hkl (list) – miller indices of surface to be created

• layers (int) – # of atomic layers in the surface

• vacuum (float) – vacuum spacing

• center (bool) – shift all positions to center the surface in the cell

Returns

Required surface

Return type

pyiron.atomistics.structure.atoms.Atoms instance