This repository stores all the code necessary to reproduce (at least stochastically) all the data, figures, and text for the atomistic simulations associated with MANSUCRIPTTBA.
Steps to run:
- Be in a unix environment
- Clone repo
- Create the necessary python environment using
environment.yml
- (Optional, if you really want to re-run the whole project from scratch) If you have an existing pyiron installation on a compute cluster, and already have the queue adapter configured, then set the
SERVER
value inproject.ipynb
to match the server queue appropriate for single-core jobs taking <4 days. Otherwise set this value toNone
/remove all instances ofserver.queue =
from the notebook, and make sure your machine is ready for a week of up-time...
With steps (0-2) you can already play around in example.ipynb
, which will recreate one of the early manuscript figures with minimal computational cost.
The purpose here is simply to provide scientific reproducibility, not to supply a fully extensible/reusable/magical and beautiful software package, but nonetheless at least a little effort has been put into documentation and usability -- we hope it's helpful.
pyiron, the pyiron publication template, and this fork of it are all licensed under the BSD-3-Clause license which is included in the LICENSE
file.
In addition an CODE_OF_CONDUCT.md
file is included to foster an open and welcoming environment.