UFF can be used to optimize the geometries of periodic systems. However, some limitations apply:
- UFF cannot handle systems with unit cells that are too small, each lattice direction should be at least 6 Angstrom. If the unit cells are too small, UFF will confuse bonds through periodic boundaries with internal bonds. If you need to use UFF for a very small system, You can create a supercell to increase the sizes of the unit cell.
- When building a periodic system, one should also specify the bonds that pass through a periodic boundary. These have the same format as the other UFF bonds and there is no distinction between normal bonds and bonds passing through periodic boundaries in the UFF input file. For an example on how this works: open the GUI, go to the UFF interface and use the magnifying glass to find ‘zeolite ABW’. The UFF input file can now be seen by going to details Run Script.
If your system shows strange geometries when optimizing with UFF, it is probably one of the above problems. To fix problems with bonds, you can try to disable Use existing bonds on the main UFF tab. This will enable automatic bond detection by UFF, which might work if your system has a reasonable geometry. If your unit cell is too small, use the structure tool (the snowflake) to generate a supercell of 2x2x2, and try again.