I’m currently working on calculations involving Voronoi tessellation and bond valence site energy. One hurdle I’m facing is the requirement for CIF files with full occupancy. In my quest for solutions, I’ve come across the Supercell program, enumlib, and similar tools. However, I’m grappling with the decision-making process for selecting a supercell that closely aligns with the original compound. Can anyone offer guidance on this? Additionally, I’d appreciate insights into computational strategies for addressing the occupancy problem.
As far as GULP is concerned, you can have partial occupancy on sites, so things don’t have to be fully occupied. Using supercells is broad general topic for anyone modelling defects with any code, so it’s worth just going through the literature for the field.
Thank you for your response. I’m a bit confused, but here’s a clear example. Consider an orthorhombic system with no partial occupation. In the study, the formation energy of defects was examined using a 2x2x2 supercell. In the methods section, they provided the following details: “Short-range interactions were represented using Buckingham potentials (see Table S2). Simulation boxes and corresponding atom positions were optimized using the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm. The Mott-Littleton method was employed to analyze lattice relaxation concerning point defects and migrating ions.”
Does this imply the following?
Generate a 2x2x2 supercell, for instance, in Vesta, utilizing a .gin file to model the structure with Buckingham potential.
Subsequently, perform relaxation using the BFGS algorithm on the simulation boxes and associated atom positions.
Once an optimized cell is obtained, employ the Mott-Littleton method to calculate defect energies.
Your reading is correct. My comment would be, that it’s not necessary to use the supercell for Mott-Littleton since the defects are introduced into an otherwise perfect bulk structure. So using the supercell just makes it slower for no good reason. I’d also note that GULP can build the supercell without using Vesta, so it’s not clear what the point of step 1 was, but the other 2 make sense.