Closed lnnbig closed 1 year ago
The original implementation of LJ does not support multiple species -- but I just updated it to allow multiple species. ForSi-O systems, you need to modify two lines in the example:
model = LennardJones(species = ['Si', 'O'])
and
model.set_opt_params(sigma=[["default"], ["default"], ["default"]], epsilon=[["default"], ["default"],["default"]])
we need to set 3 "default" for sigma
and epsilon
now because for a binary Si-O system, the model assumes interactions between Si-Si, Si-O, and O-O. You can change the "default" to other numerical values as the initial guess.
See more of the model here: https://github.com/openkim/kliff/blob/68db8956f2b38bc0846ff37cf4b72832278066f5/kliff/models/lennard_jones.py#L167
Note, the model supporting multiple species currently only exists in the master
branch, not on PyPI. So you will need to reinstall kliff from source. See https://kliff.readthedocs.io/en/latest/installation.html
Hi Mingjian,
I have a dataset for silica SiO2, with two species “Si” and “O”. Could you please give me a help about how to modify the LJ template which is for a single Si species at https://kliff.readthedocs.io/en/latest/auto_examples/example_lennard_jones.html?
Many thanks!