How to convert primitive cell to conventional cell?

ASE
1

I have used ase to read atoms object with a primitive cell. When using ase.build.surface module to cleave surface, a conventional cell is needed.

How can i convert the atoms object from primitive cell to conventional cell? ( there is magmom information in primitive cell, and hoping it still exists after converting)

Thank you !!!

2

Hi zihao

Atoms objects aren’t really aware of whether they are primitive or conventional or something else.

If you know that a cell is primitive, you can in principle transform it to conventional by means of the information on the Bravais objects inside ase.lattice. They have a matrix called conventional_cellmap which serves as a transformation that maps to the conventional lattice. But it’s a bit involved as I/someone never got around to making a very clean programming interface for using it.

3

…also your primitive cell probably needs to be in AFlow form in order for that mapping to be necessarily correct. So yes, it’s a little bit involved.

4

I’d suggest one has to identify the space group using spglib.get_spacegroup and the corresponding standard unit cell using spglib.standardize_cell (see the API docs). The standardize_cell method has a boolean flag to_primitive (which on my experience should be however carefully aligned with the symprec tolerance).