Open ahmedabdelkawy opened 5 months ago
@pmrv @jyang2009
The xyz file format is not clearly specified - so there are different versions how the chemical elements are stored in those file. Can you upload an example?
It's a bit manual still, but what you can try is use this class. Once you have populated positions and cells, you can call .animate_structures()
to get the 3D view. Alternatively use StructureStorage and .add_structure()
each structure separately before calling .anime_structures()
. In both cases you will still need to load the structures using ase.io
. Be aware also that nglview doesn't understand changes to the cell along the trajectory, so it will use the first cell.
Ah and with ase.io.read
you may have to specify format='extxyz'
, otherwise it will try to read in numeric element ids instead of chemical symbols.
using the ase.io.read and then ase_to_pyiron did not work (get_chemical_species error), do we have another function to do so directly?