Hello everyone,
I have been using pymatgen and ASE to generate crystal slabs with different Miller indices for medium-sized organic molecules (e.g., Aspirin, Ibuprofen) based on CIF files. However, I am encountering an issue where the SlabGenerator appears to fracture molecules when applying surface terminations. The resulting slabs contain fragmented molecules on the surface, which are physically unrealistic and cause issues in subsequent molecular modeling.
This doesn’t happen when I use other tools like GDIS, which can generate slabs without breaking molecules, but I need the programmability that pymatgen provides.
Is there a known workaround or best practice to ensure whole molecules remain intact when generating slabs? Or is pymatgen not well suited for organic crystals in this context?
Any advice would be greatly appreciated! Thanks in advance!