pymatgen.analysis.adsorption module

class AdsorbateSiteFinder(slab, selective_dynamics=False, height=0.9, mi_vec=None, top_surface=True)[source]

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
  • top_surface (bool) – Which surface to adsorb, True for the surface above the center of mass, False for the surface below center of mass
add_adsorbate(molecule, ads_coord, repeat=None, reorient=True)[source]

Adds an adsorbate at a particular coordinate. Adsorbate represented by a Molecule object, and is positioned relative to the input adsorbate coordinate.

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

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)[source]

Assigns site properties.

ensemble_center(site_list, indices, cartesian=True)[source]

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)[source]

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)[source]

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)[source]

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, reorient=True, find_args={})[source]

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
  • 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}
get_extended_surface_mesh(repeat=(5, 5, 1))[source]

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)[source]

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()[source]

convenience method to return list of subsurface sites

surface_sites

convenience method to return a list of surface sites

symm_reduce(coords_set, threshold=1e-06)[source]

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
adsorb_both_surfaces(slab, molecule, selective_dynamics=False, height=0.9, mi_vec=None, repeat=None, min_lw=5.0, reorient=True, find_args={})[source]

Function that generates all adsorption structures for a given molecular adsorbate on both surfaces of a slab.

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
  • molecule (Molecule) – molecule corresponding to adsorbate
  • selective_dynamics – 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
  • 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}
cart_to_frac(lattice, cart_coord)[source]

converts cartesian coordinates to fractional

frac_to_cart(lattice, frac_coord)[source]

converts fractional coordinates to cartesian

get_mi_vec(slab)[source]

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

get_rot(slab)[source]

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)[source]

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
put_coord_inside(lattice, cart_coordinate)[source]

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

reorient_z(structure)[source]

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