Enumerate surface morphology

General Discussion
1

Hi everyone,

I’m new to the community and would like to know if this tool can help with generating surfaces with various morphologies.

I have a simple organic monomer to start with (.cif file I have), for which I’d like to explore surface reactions with some gases. I wonder if I can use this tool to create and enumerate automatically over different surface morphs.

Appreciate your thoughts and ideas on this!

Regards,

Jo

2

Sort of. By far the best way to do this is with the pymatgen Python package from the Materials Project. (I answered a similar question on Stack Exchange )

If you’re using Avogadro2 (e.g. 1.101) I can finish up the Python script which helps automate the generation.

But if you want to enumerate automatically, I think the Python code needed with pymatgen is easy enough: (this is untested)

# Import the neccesary tools to generate surfaces
from pymatgen.core.surface import SlabGenerator, generate_all_slabs
from pymatgen.core import Structure

# Read the CIF file and create a pymatgen Structure object
structure = Structure.from_file("path/to/your/structure.cif")

# get a list of all slabs up to a Miller index of 3
# with a minimum thickness of 10Ang
# and a vacuum layer of 25̄A
all_slabs = generate_all_slabs(structure, 3, 10, 25)
for slab in all_slabs:
    h, j, k = slab.miller_index
    # save the slab, e.g. to XYZ or something