Hi! Could anyone advise me on how to constrain the atoms to stay within the unit cell when performing a geometry optimization? Thank you!
Hi Sophie - it would help to know a bit more about what you’re trying to do:
- what kind of unit cell (you mention molecular)
- what kind of optimizing you’re using (e.g, what method)
- what version of Avogadro / operating system
In general, the current force fields (except Lennard Jones) are for isolated molecules.
That said, in Avogadro2 it’s possible to install force field scripts that handle unit cells, including some of the more recent ML models.
Hi!
Of course. I’m trying to optimize a metallic slab with explicit water in the unit cell. I’m freezing the slab atoms, I just want to get a better water configuration around the slab that what I have at the moment. I want to use UFF. I’m using Avogadro 1.2.0 on macOS. Ideally, I would have periodic boundary conditions, but I’m unsure if it’s possible currently. I don’t need anything to precise, just trying to get an okay starting configuration for the water for future more expensive calculations.
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Unfortunately, there’s no good way to handle this in Avogadro 1.2.
Yeah, this is why I’m re-writing the UFF implementation for Avogadro2 - to handle periodic boundary conditions.
My suggestion right at the moment (i.e., before I finish up the new UFF code) would be to export to LAMMPS or use ASE and run something quick with XTB or DFTB+
But I’m well aware that it would be nice to have a working UFF that handles this use case… soon.