ectoolkits.structures.slab module

class ectoolkits.structures.slab.RutileSlab(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, velocities=None)

Bases: Slab

class atoms used for rutile like(structure) system space group: P42/mnm Usage: rutile = read(“Rutile-exp.cif”) x = RutileType(rutile) slab = [] for i in range(3, 7):

slab.append(x.get_slab(indices=(1, 1, 0), n_layers=i, lateral_repeat=(2, 4)))

get_slab(indices: Tuple[int], n_layers, lateral_repeat: Tuple[int] = (2, 4), vacuum=10.0)

rutile_slab_001(n_layers=5, lateral_repeat: tuple = (2, 2), vacuum=10.0)

function for create symmetry slab for rutile structure 001 surface space group: P42/mnm this function is valid only for 6 atoms conventional cell.

rutile_slab_100(n_layers=5, lateral_repeat: tuple = (2, 3), vacuum=10.0)

function for create symmetry slab for rutile structure 100 surface space group: P42/mnm this function is valid only for 6 atoms conventional cell.

rutile_slab_101(n_layers=5, lateral_repeat: tuple = (2, 2), vacuum=10.0)

function for create symmetry slab for rutile structure 101 surface space group: P42/mnm this function is valid only for 6 atoms conventional cell.

rutile_slab_110(n_layers=5, lateral_repeat: tuple = (2, 4), vacuum=10.0)

function for create symmetry slab for rutile structure 110 surface space group: P42/mnm this function is valid only for 6 atoms conventional cell.

class ectoolkits.structures.slab.Slab(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, velocities=None)

Bases: Atoms

Object inherent from Atoms object in ASE. Add method for vacuum slab model

Parameters:

Atoms (_type_) – Atoms object int ASE

add_adsorbate(ad_site_idx: int, vertical_dist: float, adsorbate: Atoms, contact_atom_idx: int = 0, lateral_shift: Tuple[float] = (0, 0))

add_adsorbates(ad_site_idx_list: List[int], vertical_dist: float, adsorbate: Atoms, contact_atom_idx: int = 0, lateral_shift: Tuple[float] = (0, 0))

del_from_range(zmin: int, zmax: int, element: Optional[str] = None) → Atoms

_summary_

_extended_summary_

Parameters:

• zmin (int) – _description_

• zmax (int) – _description_

• element (str, optional) – _description_. Defaults to None.

Returns:

_description_

Return type:

Atoms

del_surf_layer(element: Optional[str] = None, tolerance=0.1, dsur='up', check_cross_boundary=False)

delete the layer atoms,

_extended_summary_

Parameters:

• element (str, optional) – _description_. Defaults to None.

• tolerance (float, optional) – _description_. Defaults to 0.1.

• dsur (str, optional) – _description_. Defaults to ‘up’.

Returns:

_description_

Return type:

_type_

find_element_idx_list(element: str) → list

find atom index provided that element symbol

_extended_summary_

Parameters:

element (str) – element symbol

Returns:

list of atom indices

Return type:

list

find_idx_from_range(zmin: int, zmax: int, element: Optional[str] = None) → list

_summary_

_extended_summary_

Parameters:

• zmin (int) – minimum in z

• zmax (int) – maximum in z

• element (str, optional) – element symbol, None means all atoms. Defaults to None.

Returns:

list of atom indices

Return type:

list

find_surf_idx(element: Optional[str] = None, tolerance: float = 0.1, dsur: str = 'up', check_cross_boundary=False, trans_z_dist=5) → list

find atom indexs at surface

_extended_summary_

Parameters:

• element (str) – element symbol

• tolerance (float, optional) – tolerance for define a layer. Defaults to 0.1.

• dsur (str, optional) – direction of surface, ‘up’ or ‘dw’. for a vacuum-slab model,

• 'up'. (you have up surface and down surface. Defaults to) –

Returns:

list of atom indices

Return type:

list

generate_components_symmetry_box(water_box_len, ads_components_smiles: list, ads_components_counts: list, bulk_components_smiles: list, bulk_components_counts: list, ads_limit=0.5, bulk_dw=None, bulk_up=None)

Generate a slab-aligned box with symmetric distribution of water, adsorbed molecules, and bulk components.

Parameters:

• water_box_len (float) – Height of the water box along z-direction.

• ads_components_smiles (list) – SMILES list of adsorbed components.

• ads_components_counts (list) – Corresponding counts of adsorbed components.

• bulk_components_smiles (list) – SMILES list of bulk components.

• bulk_components_counts (list) – Corresponding counts of bulk components.

• ads_limit (float) – Vertical range (in Å) above and below the surface for placing adsorbed species. Default = 0.5 Å.

• bulk_dw (float, optional) – Lower boundary (Å) of the symmetric bulk region (below box center).

• bulk_up (float, optional) – Upper boundary (Å) of the symmetric bulk region (below box center). Must satisfy: 0 < bulk_dw < bulk_up < water_box_len / 2. If set, creates symmetric regions for bulk placement.

Returns:

None. Generates a Packmol input file and runs Packmol to generate watbox.xyz.

Example

>>> from ectoolkits.structures.tools import generate_components_symmetry_box
>>> generate_components_symmetry_box(
...     water_box_len = 20
...     ads_components_smiles=["[Cl-]"],
...     ads_components_counts=[2],
...     bulk_components_smiles=["[K+]", "[Cl-]"],
...     bulk_components_counts=[3, 3],
...     ads_limit=0.5,
...     bulk_dw = 3,
...     bulk_up = 6
)

generate_interface(water_box_len: float, top_surface_idx: List[int], bottom_surface_idx: List[int])

merge slab model and water box together

Parameters:

• water_box_len –

• top_surface_idx –

• bottom_surface_idx –

Return type:

tmp

generate_water_box(water_box_len)

function to generate water box x and y length is from self length :param water_box_len:

Returns:

get_cus(input_idx, coord_num, cutoff)

function to get atom index of coordinate unsaturated sites. slab: Atoms object, the slab model input_idx: the index of the atom you want get the coordination number coord_num: coordination number for coordinate unsaturated sites, the number must be less then the full coordination cutoff: the cutoff radius defining coordination. something like: {(‘Ti’, ‘O’): 2.2} return: the index for cus atoms

get_neighbor_list(idx: int, cutoff: dict) → list

provided that atom index and return its neighbor in list

Parameters:

• idx (int) – atom index

• cutoff (dict) – cutoff for neighbor pair

Returns:

list of atom indices

Return type:

list

Examples

get_neighbor_list(16, {(“O”, “H”): 1.4})

is_cross_z_boundary(element: Optional[str] = None)

remove_cell_vacuum(adopt_space=2)

remove the vacuum of z direction cell z must be perpendicular to xy plane