aim2dat.strct.surface

Module implementing a class to generate surfaces.

Module Contents

Classes

SurfaceGeneration

Generates a surfaces and surface slabs based on a bulk crystal structure.
class aim2dat.strct.surface.SurfaceGeneration(structure: aim2dat.strct.strct.Structure)[source]

Generates a surfaces and surface slabs based on a bulk crystal structure.

Overview

Methods

create_surface(miller_indices, termination, tolerance, symprec, angle_tolerance, hall_number)

Create surface from a bulk crystal structure.

generate_surface_slabs(miller_indices, nr_layers, periodic, vacuum, vacuum_factor, symmetrize, tolerance, symprec, angle_tolerance, hall_number)

Generate surface slabs with all terminations for a certain direction given by its

store_surfaces_in_aiida_db(miller_indices, tolerance, symprec, angle_tolerance, hall_number, group_label, group_description)

Store surfaces into the AiiDA-database.

to_aiida_surfacedata(miller_indices, termination, tolerance, symprec, angle_tolerance, hall_number)

Create surface from a bulk crystal structure.
create_surface(miller_indices: tuple[int] | list[int] = (1, 0, 0), termination: int = 1, tolerance: float = 0.005, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: int = 0) → dict[source]

Create surface from a bulk crystal structure.

Parameters:

  • miller_indices (list or tuple (optional)) – Miller indices of the surface. The default value is (1, 0, 0).

  • termination (int (optional)) – Determine termination of the surface.

  • tolerance (float (optional)) – Numerical tolerance. The default value is 0.005.

  • symprec (float (optional)) – Tolerance parameter for spglib. The default value is 0.005.

  • angle_tolerance (float (optional)) – Tolerance parameter for spglib. The default value is -1.0.

  • hall_number (int (optional)) – The argument to constrain the space-group-type search only for the Hall symbol corresponding to it. The default number is 0.

Returns:

dict – Dictionary containing the surface data.

generate_surface_slabs(miller_indices: tuple[int] | list[int] = (1, 0, 0), nr_layers: int = 5, periodic: bool = False, vacuum: float = 10.0, vacuum_factor: float = 0.0, symmetrize: bool = True, tolerance: float = 0.01, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: int = 0) → aim2dat.strct.structure_collection.StructureCollection | None[source]

Generate surface slabs with all terminations for a certain direction given by its miller indices.

Parameters:

  • miller_indices (list or tuple (optional)) – Miller indices of the surface. The default value is (1, 0, 0).

  • nr_layers (int (optional)) – Number of repititions of the underlying periodic surface cell. The default value is 5.

  • periodic (bool (optional)) – Whether to apply periodic boundary conditions in the direction normal to the surface plane. The default value is False.

  • vacuum (float (optional)) – Vacuum space added at the top and bottom of the slab. The default value is 10.0.

  • vacuum_factor (float (optional)) – Alternatively to the vacuum-parameter the amount of vacuum can be set as a multiple of the slab size. The method is only applied if the parameter is larger than zero. The default value is 0.0.

  • symmetrize (bool (optional)) – Create slabs that have the same termination on both sides. The default value is True.

  • tolerance (float (optional)) – Numerical tolerance. The default value is 0.005.

  • symprec (float (optional)) – Tolerance parameter for spglib. The default value is 0.005.

  • angle_tolerance (float (optional)) – Tolerance parameter for spglib. The default value is -1.0.

  • hall_number (int (optional)) – The argument to constrain the space-group-type search only for the Hall symbol corresponding to it. The default number is 0.

Returns:

StructureCollection – Collection of the generated surface slabs.

store_surfaces_in_aiida_db(miller_indices: tuple[int] = (1, 0, 0), tolerance: float = 0.005, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: int = 0, group_label: str = None, group_description: str = None)[source]

Store surfaces into the AiiDA-database.

Parameters:

  • miller_indices (list or tuple (optional)) – Miller indices of the surface. The default value is (1, 0, 0).

  • tolerance (float (optional)) – Numerical tolerance. The default value is 0.005.

  • symprec (float (optional)) – Tolerance parameter for spglib. The default value is 0.005.

  • angle_tolerance (float (optional)) – Tolerance parameter for spglib. The default value is -1.0.

  • hall_number (int (optional)) – The argument to constrain the space-group-type search only for the Hall symbol corresponding to it. The default number is 0.

  • group_label (str (optional)) – Label of the AiiDA group.

  • group_description (str (optional)) – Description of the AiiDA group.

Returns:

list – List containing dictionary of all surface nodes.

to_aiida_surfacedata(miller_indices: tuple[int] | list[int] = (1, 0, 0), termination: int = 1, tolerance: float = 0.005, symprec: float = 0.005, angle_tolerance: float = -1.0, hall_number: int = 0)[source]

Create surface from a bulk crystal structure.

Parameters:

  • miller_indices (list or tuple (optional)) – Miller indices of the surface. The default value is (1, 0, 0).

  • termination (int (optional)) – Determine termination of the surface.

  • tolerance (float (optional)) – Numerical tolerance. The default value is 0.005.

  • symprec (float (optional)) – Tolerance parameter for spglib. The default value is 0.005.

  • angle_tolerance (float (optional)) – Tolerance parameter for spglib. The default value is -1.0.

  • hall_number (int (optional)) – The argument to constrain the space-group-type search only for the Hall symbol corresponding to it. The default number is 0.

Returns:

SurfaceData – AiiDA surface data node.