pymatgen.analysis.adsorption module

This module provides classes used to enumerate surface sites and to find adsorption sites on slabs.

class AdsorbateSiteFinder(slab, selective_dynamics=False, height=0.9, mi_vec=None)

Bases: object

This class finds adsorbate sites on slabs and generates adsorbate structures according to user-defined criteria.

The algorithm for finding sites is essentially as follows:

1. Determine “surface sites” by finding those within

   a height threshold along the miller index of the highest site

2. Create a network of surface sites using the Delaunay

   triangulation of the surface sites

3. Assign on-top, bridge, and hollow adsorption sites

   at the nodes, edges, and face centers of the Del. Triangulation

4. Generate structures from a molecule positioned at

   these sites

Create an AdsorbateSiteFinder object.

Parameters:

• slab (Slab) – slab object for which to find adsorbate sites

• selective_dynamics (bool) – flag for whether to assign non-surface sites as fixed for selective dynamics

• height (float) – height criteria for selection of surface sites

• mi_vec (3-D array-like) – vector corresponding to the vector concurrent with the miller index, this enables use with slabs that have been reoriented, but the miller vector must be supplied manually

add_adsorbate(molecule, ads_coord, repeat=None, translate=True, reorient=True)

Adds an adsorbate at a particular coordinate. Adsorbate represented by a Molecule object and is translated to (0, 0, 0) if translate is True, or positioned relative to the input adsorbate coordinate if translate is False.

Parameters:

• molecule (Molecule) – molecule object representing the adsorbate

• ads_coord (array) – coordinate of adsorbate position

• repeat (3-tuple or list) – input for making a supercell of slab prior to placing the adsorbate

• translate (bool) – flag on whether to translate the molecule so that its CoM is at the origin prior to adding it to the surface

• reorient (bool) – flag on whether to reorient the molecule to have its z-axis concurrent with miller index

adsorb_both_surfaces(molecule, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)

Function that generates all adsorption structures for a given molecular adsorbate on both surfaces of a slab. This is useful for calculating surface energy where both surfaces need to be equivalent or if we want to calculate nonpolar systems.

Parameters:

• molecule (Molecule) – molecule corresponding to adsorbate

• repeat (3-tuple or list) – repeat argument for supercell generation

• min_lw (float) – minimum length and width of the slab, only used if repeat is None

• reorient (bool) – flag on whether or not to reorient adsorbate along the miller index

• find_args (dict) – dictionary of arguments to be passed to the call to self.find_adsorption_sites, e.g. {“distance”:2.0}

classmethod assign_selective_dynamics(slab)

Helper function to assign selective dynamics site_properties based on surface, subsurface site properties.

Parameters:

slab (Slab) – slab for which to assign selective dynamics

assign_site_properties(slab, height=0.9)

Assigns site properties.

classmethod ensemble_center(site_list, indices, cartesian=True)

Finds the center of an ensemble of sites selected from a list of sites. Helper method for the find_adsorption_sites algorithm.

Parameters:

• site_list (list of sites) – list of sites

• indices (list of ints) – list of ints from which to select sites from site list

• cartesian (bool) – whether to get average fractional or Cartesian coordinate

find_adsorption_sites(distance=2.0, put_inside=True, symm_reduce=0.01, near_reduce=0.01, positions=('ontop', 'bridge', 'hollow'), no_obtuse_hollow=True)

Finds surface sites according to the above algorithm. Returns a list of corresponding Cartesian coordinates.

Parameters:

• distance (float) – distance from the coordinating ensemble of atoms along the miller index for the site (i. e. the distance from the slab itself)

• put_inside (bool) – whether to put the site inside the cell

• symm_reduce (float) – symm reduction threshold

• near_reduce (float) – near reduction threshold

• positions (list) –

  which positions to include in the site finding “ontop”: sites on top of surface sites “bridge”: sites at edges between surface sites in Delaunay

  triangulation of surface sites in the miller plane

  ”hollow”: sites at centers of Delaunay triangulation faces “subsurface”: subsurface positions projected into miller plane

• no_obtuse_hollow (bool) – flag to indicate whether to include obtuse triangular ensembles in hollow sites

find_surface_sites_by_height(slab, height=0.9, xy_tol=0.05)

This method finds surface sites by determining which sites are within a threshold value in height from the topmost site in a list of sites.

Parameters:

• site_list (list) – list of sites from which to select surface sites

• height (float) – threshold in angstroms of distance from topmost site in slab along the slab c-vector to include in surface site determination

• xy_tol (float) – if supplied, will remove any sites which are within a certain distance in the miller plane.

Returns:

list of sites selected to be within a threshold of the highest

classmethod from_bulk_and_miller(structure, miller_index, min_slab_size=8.0, min_vacuum_size=10.0, max_normal_search=None, center_slab=True, selective_dynamics=False, undercoord_threshold=0.09)

This method constructs the adsorbate site finder from a bulk structure and a miller index, which allows the surface sites to be determined from the difference in bulk and slab coordination, as opposed to the height threshold.

Parameters:

• structure (Structure) – structure from which slab input to the ASF is constructed

• miller_index (3-tuple or list) – miller index to be used

• min_slab_size (float) – min slab size for slab generation

• min_vacuum_size (float) – min vacuum size for slab generation

• max_normal_search (int) – max normal search for slab generation

• center_slab (bool) – whether to center slab in slab generation

• dynamics (selective) – whether to assign surface sites to selective dynamics

• undercoord_threshold (float) – threshold of “undercoordation” to use for the assignment of surface sites. Default is 0.1, for which surface sites will be designated if they are 10% less coordinated than their bulk counterpart

generate_adsorption_structures(molecule, repeat=None, min_lw=5.0, translate=True, reorient=True, find_args=None)

Function that generates all adsorption structures for a given molecular adsorbate. Can take repeat argument or minimum length/width of precursor slab as an input.

Parameters:

• molecule (Molecule) – molecule corresponding to adsorbate

• repeat (3-tuple or list) – repeat argument for supercell generation

• min_lw (float) – minimum length and width of the slab, only used if repeat is None

• translate (bool) – flag on whether to translate the molecule so that its CoM is at the origin prior to adding it to the surface

• reorient (bool) – flag on whether or not to reorient adsorbate along the miller index

• find_args (dict) – dictionary of arguments to be passed to the call to self.find_adsorption_sites, e.g. {“distance”:2.0}

generate_substitution_structures(atom, target_species=None, sub_both_sides=False, range_tol=0.01, dist_from_surf=0)

Function that performs substitution-type doping on the surface and returns all possible configurations where one dopant is substituted per surface. Can substitute one surface or both.

Parameters:

• atom (str) – atom corresponding to substitutional dopant

• sub_both_sides (bool) – If true, substitute an equivalent site on the other surface

• target_species (list) – List of specific species to substitute

• range_tol (float) – Find viable substitution sites at a specific distance from the surface +- this tolerance

• dist_from_surf (float) – Distance from the surface to find viable substitution sites, defaults to 0 to substitute at the surface

get_extended_surface_mesh(repeat=(5, 5, 1))

Gets an extended surface mesh for to use for adsorption site finding by constructing supercell of surface sites.

Parameters:

repeat (3-tuple) – repeat for getting extended surface mesh

near_reduce(coords_set, threshold=0.0001)

Prunes coordinate set for coordinates that are within threshold.

Parameters:

• coords_set (Nx3 array-like) – list or array of coordinates

• threshold (float) – threshold value for distance

subsurface_sites()

convenience method to return list of subsurface sites.

property surface_sites

convenience method to return a list of surface sites.

symm_reduce(coords_set, threshold=1e-06)

Reduces the set of adsorbate sites by finding removing symmetrically equivalent duplicates.

Parameters:

• coords_set – coordinate set in Cartesian coordinates

• threshold – tolerance for distance equivalence, used as input to in_coord_list_pbc for dupl. checking

get_mi_vec(slab)

Convenience function which returns the unit vector aligned with the miller index.

get_rot(slab)

Gets the transformation to rotate the z axis into the miller index.

plot_slab(slab, ax, scale=0.8, repeat=5, window=1.5, draw_unit_cell=True, decay=0.2, adsorption_sites=True, inverse=False)

Function that helps visualize the slab in a 2-D plot, for convenient viewing of output of AdsorbateSiteFinder.

Parameters:

• slab (slab) – Slab object to be visualized

• ax (axes) – matplotlib axes with which to visualize

• scale (float) – radius scaling for sites

• repeat (int) – number of repeating unit cells to visualize

• window (float) – window for setting the axes limits, is essentially a fraction of the unit cell limits

• draw_unit_cell (bool) – flag indicating whether or not to draw cell

• decay (float) – how the alpha-value decays along the z-axis

• inverse (bool) – invert z axis to plot opposite surface

put_coord_inside(lattice, cart_coordinate)

converts a Cartesian coordinate such that it is inside the unit cell.

reorient_z(structure)

reorients a structure such that the z axis is concurrent with the normal to the A-B plane.