How to cut properly a slab from a cif file?

Question

I am trying to do DFT calculations on ethanol adsorbed on Pd, both surfaces 111 and 100. I have the cif file from the database and also I have built the new unit cell that explicitly shows face 111.

I need to slab of Pd, one of 100, the other 111, made by 5 layers of metal, 9 atoms per layer. I have tried with VESTA (with this software I have obtained the new unit cell), but I cannot reproduce the slabs from the reference article, both in number and in geometry. Do you have a sort of guide/recipe idiot-proof to prepare correctly a slab for DFT simulations?

Answer 1

You can use ASE.

• For your case, I assume you are using the Pd crystal structure with space group 225.

• Cut the (111) surface with ASE:

  from ase.io import read, write
  from ase.build import surface
  
  ####================================================
  A=read('Pd_mp-2_conventional_standard.cif',format='cif')
  B=surface(A,(1,1,1),5,vacuum=10)
  write('111.vasp',B,format='vasp')
  

• The 111 slab with five atomic layers:

To obtain 9 atoms in each layer you may need to make a matrix transformation with VESTA.

Hope it helps.