How to Generate Crystal Slabs Without Fragmented Molecules in Pymatgen?

[richy330]

Hello everyone!

I’m working with organic molecular crystals (e.g., Aspirin) from CIF files and need help generating clean crystal slabs in pymatgen. Right now, I’m running into a major issue: my slabs always contain fragmented molecules at the boundaries, which could cause problems in later simulations.

The Problem

When I create a slab, molecules at the boundaries are cut, leaving fragments instead of intact structures. Example:

I suspect this happens because the unit cell in the CIF file already contains fragmented molecules, as seen here:

Other programs seem to handle this automatically. For example, in this video tutorial (0:43), they
mention "tidying up" the unit cell before slab generation. However, I haven’t found a clear way to do this in pymatgen.

What I’ve Tried

I’ve searched through pymatgen’s and ASE's documentation, discussions, and issues for over a week but haven’t found a solution.

My current idea is:

• Detect fragmented molecules in the unit cell.
• Identify which unit cell face the broken bonds pass through.
• Shift the fragments so that they align properly.

But I’m not sure if this is the right approach or if pymatgen has a built-in way to handle this.

Question

Has anyone encountered this issue before? Is there a recommended way to generate clean slabs without fragmented molecules in pymatgen, or another library more suitable to my needs?

Any advice or pointers would be greatly appreciated! Thanks in advance.