Usage

This package has been implemented in a Streamlit-based web app, accessible here.

Ionic slabs with polyatomic anions

Given a bulk structure of an ionic compound with a polyatomic anionic subunit (e.g., Mg₂SiO₄), PolyCleaver is able to generate all surfaces from a list of Miller indices as follows:

from polycleaver.core import mnx
miller_indices_list = [(0,0,1), (1,0,1)]
slabs = mnx.generate_mnx_slabs('bulk_mg2sio4.cif', miller_indices_list, save=True)

This will generate all non-polar terminations of the selected bulk with the specified Miller indices. The approximate thickness and vacuum of the slab (by default, 15 Å each) can be specified as follows:

slabs = mnx.generate_mnx_slabs('bulk_mg2sio4.cif', miller_indices_list, thickness=15, vacuum=15, save=True)

This will save all structures in cif files, with an integer index plus the Miller three indices of the generated plane (e.g., 1_001.cif). Alternatively, if planes with all hkl indices up to a maximum Miller index of n are to be modelled, instead of a Miller indices list, the user can specify a single integer corresponding to n, and the package will construct a list containing all non-equivalent Miller indices based on the bulk symmetry:

from polycleaver.core import mnx
max_index = 2
slabs = mnx.generate_mnx_slabs('bulk_mg2sio4.cif', max_index, save=True)

Visualization of slabs

The slabs can be visualized using ASE as follows:

from pymatgen.io.ase import AseAtomsAdaptor
from ase.visualize import view

view([AseAtomsAdaptor.get_atoms(slab.atoms) for slab in slabs])

Calculation of slab parameters

After generation of surfaces, PolyCleaver can be used to display relevant surface parameters (only working for ionic surfaces with polyatomic anions, generated with the generate_mnx_slabs module):

for slab in slabs:
    print(slab.thickness)    # Prints the final thickness of the reconstructed slabs
    print(slab.cations)      # Prints list of all cationic atoms (e.g., Mg2+ in Mg2SiO4).
    print(slab.anions)       # Prints list of all anionic atoms (e.g., O2- in Mg2SiO4).
    print(slab.centers)      # Prints list of the center atoms of all polyatomic anions (e.g., Si4+ in Mg2SiO4).
    print(slab.undercoordinated_sites(slab.cations)) # Prints all undercoordinated cations at both sides of the slab.

This allows for rapid selection of most interesting slabs for reactivity or adsorption studies.

Ionic slabs with monoatomic anions

Alternatively, this package can also generate bare slabs from ionic compounds with monoatomic ions such as FeS₂ in a similar fashion, using the polycleaver.core.mx module:

from polycleaver.core import mx
miller_indices_list = [(0,0,1), (1,0,1)]
slabs = mx.generate_mx_slabs('bulk_fes2.cif', miller_indices_list, save=True)