data.oc.core.adsorbate_slab_config

data.oc.core.adsorbate_slab_config#

Classes#

AdsorbateSlabConfig

Initializes a list of adsorbate-catalyst systems for a given Adsorbate and Slab.

Functions#

get_random_sites_on_triangle(vertices[, num_sites])

Sample num_sites random sites uniformly on a given 3D triangle.

custom_tile_atoms(atoms)

Tile the atoms so that the center tile has the indices and positions of the

get_interstitial_distances(adsorbate_slab_config)

Check to see if there is any atomic overlap between surface atoms

there_is_overlap(adsorbate_slab_config)

Check to see if there is any atomic overlap between surface atoms

Module Contents#

class data.oc.core.adsorbate_slab_config.AdsorbateSlabConfig(slab: fairchem.data.oc.core.slab.Slab, adsorbate: fairchem.data.oc.core.slab.Adsorbate, num_sites: int = 100, num_augmentations_per_site: int = 1, interstitial_gap: float = 0.1, mode: str = 'random')#

Initializes a list of adsorbate-catalyst systems for a given Adsorbate and Slab.

Parameters:

  • slab (Slab) – Slab object.

  • adsorbate (Adsorbate) – Adsorbate object.

  • num_sites (int) – Number of sites to sample.

  • num_augmentations_per_site (int) – Number of augmentations of the adsorbate per site. Total number of generated structures will be num_sites * num_augmentations_per_site.

  • interstitial_gap (float) – Minimum distance in Angstroms between adsorbate and slab atoms.

  • mode (str) –

    “random”, “heuristic”, or “random_site_heuristic_placement”. This affects surface site sampling and adsorbate placement on each site.

    In “random”, we do a Delaunay triangulation of the surface atoms, then sample sites uniformly at random within each triangle. When placing the adsorbate, we randomly rotate it along xyz, and place it such that the center of mass is at the site.

    In “heuristic”, we use Pymatgen’s AdsorbateSiteFinder to find the most energetically favorable sites, i.e., ontop, bridge, or hollow sites. When placing the adsorbate, we randomly rotate it along z with only slight rotation along x and y, and place it such that the binding atom is at the site.

    In “random_site_heuristic_placement”, we do a Delaunay triangulation of the surface atoms, then sample sites uniformly at random within each triangle. When placing the adsorbate, we randomly rotate it along z with only slight rotation along x and y, and place it such that the binding atom is at the site.

    In all cases, the adsorbate is placed at the closest position of no overlap with the slab plus interstitial_gap along the surface normal.

slab#
adsorbate#
num_sites#
num_augmentations_per_site#
interstitial_gap#
mode#
sites#
get_binding_sites(num_sites: int)#

Returns up to num_sites sites given the surface atoms’ positions.

place_adsorbate_on_site(adsorbate: fairchem.data.oc.core.slab.Adsorbate, site: numpy.ndarray, interstitial_gap: float = 0.1)#

Place the adsorbate at the given binding site.

place_adsorbate_on_sites(sites: list, num_augmentations_per_site: int = 1, interstitial_gap: float = 0.1)#

Place the adsorbate at the given binding sites.

_get_scaled_normal(adsorbate_c: ase.Atoms, slab_c: ase.Atoms, site: numpy.ndarray, unit_normal: numpy.ndarray, interstitial_gap: float = 0.1)#

Get the scaled normal that gives a proximate configuration without atomic overlap by:

  1. Projecting the adsorbate and surface atoms onto the surface plane.

  2. Identify all adsorbate atom - surface atom combinations for which

    an itersection when translating along the normal would occur. This is where the distance between the projected points is less than r_surface_atom + r_adsorbate_atom

  3. Explicitly solve for the scaled normal at which the distance between

    surface atom and adsorbate atom = r_surface_atom + r_adsorbate_atom + interstitial_gap. This exploits the superposition of vectors and the distance formula, so it requires root finding.

Assumes that the adsorbate’s binding atom or center-of-mass (depending on mode) is already placed at the site.

Parameters:

  • adsorbate_c (ase.Atoms) – A copy of the adsorbate with coordinates at the site

  • slab_c (ase.Atoms) – A copy of the slab

  • site (np.ndarray) – the coordinate of the site

  • adsorbate_atoms (ase.Atoms) – the translated adsorbate

  • unit_normal (np.ndarray) – the unit vector normal to the surface

  • interstitial_gap (float) – the desired distance between the covalent radii of the closest surface and adsorbate atom

Returns:

the magnitude of the normal vector for placement

Return type:

(float)

_find_combos_to_check(adsorbate_c2: ase.Atoms, slab_c2: ase.Atoms, unit_normal: numpy.ndarray, interstitial_gap: float)#

Find the pairs of surface and adsorbate atoms that would have an intersection event while traversing the normal vector. For each pair, return pertanent information for finding the point of intersection. :param adsorbate_c2: A copy of the adsorbate with coordinates at the centered site :type adsorbate_c2: ase.Atoms :param slab_c2: A copy of the slab with atoms wrapped s.t. things are centered

about the site

Parameters:

  • unit_normal (np.ndarray) – the unit vector normal to the surface

  • interstitial_gap (float) – the desired distance between the covalent radii of the closest surface and adsorbate atom

Returns:

each entry in the list corresponds to one pair to check. With the
following information:

[(adsorbate_idx, slab_idx), r_adsorbate_atom + r_slab_atom, slab_atom_position]

Return type:

(list[lists])

_get_projected_points(adsorbate_c2: ase.Atoms, slab_c2: ase.Atoms, unit_normal: numpy.ndarray)#

Find the x and y coordinates of each atom projected onto the surface plane. :param adsorbate_c2: A copy of the adsorbate with coordinates at the centered site :type adsorbate_c2: ase.Atoms :param slab_c2: A copy of the slab with atoms wrapped s.t. things are centered

about the site

Parameters:

unit_normal (np.ndarray) – the unit vector normal to the surface

Returns:

{“ads”: [[x1, y1], [x2, y2], …], “slab”: [[x1, y1], [x2, y2], …],}

Return type:

(dict)

get_metadata_dict(ind)#

Returns a dict containing the atoms object and metadata for one specified config, used for writing to files.

data.oc.core.adsorbate_slab_config.get_random_sites_on_triangle(vertices: numpy.ndarray, num_sites: int = 10)#

Sample num_sites random sites uniformly on a given 3D triangle. Following Sec. 4.2 from https://www.cs.princeton.edu/~funk/tog02.pdf.

data.oc.core.adsorbate_slab_config.custom_tile_atoms(atoms: ase.Atoms)#

Tile the atoms so that the center tile has the indices and positions of the untiled structure.

Parameters:

atoms (ase.Atoms) – the atoms object to be tiled

Returns:

the tiled atoms which has been repeated 3 times in

the x and y directions but maintains the original indices on the central unit cell.

Return type:

(ase.Atoms)

data.oc.core.adsorbate_slab_config.get_interstitial_distances(adsorbate_slab_config: ase.Atoms)#

Check to see if there is any atomic overlap between surface atoms and adsorbate atoms.

Parameters:

adsorbate_slab_configuration (ase.Atoms) – an slab atoms object with an adsorbate placed

Returns:

True if there is atomic overlap, otherwise False

Return type:

(bool)

data.oc.core.adsorbate_slab_config.there_is_overlap(adsorbate_slab_config: ase.Atoms)#

Check to see if there is any atomic overlap between surface atoms and adsorbate atoms.

Parameters:

adsorbate_slab_configuration (ase.Atoms) – an slab atoms object with an adsorbate placed

Returns:

True if there is atomic overlap, otherwise False

Return type:

(bool)

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