Mkphuthi/multiple engines

mkphuthi commented 1 year ago

Breaking changes

Changed asimtools.utils.get_atoms i.e. the way images are supplied so that you can now use any function in ase.build, ase.io.read or direct Atoms object and the keywords match exactly with ase + lots of test cases. See examples and test cases.
Changed input_file to image_file in get_atoms so that it doesn't clash with other things which might be called input_file
Changed asimtools.utils.get_images so that it can take in a file with many images, all images matching a pattern or a list of Atoms directly + tests

New features

Added a data dir to tests to store useful input data for tests such as structures, scripts etc.
Added atom_relax.py which can relax a structure using any optimizer in ASE
Added lammps.py which can run an arbitrary lammps script or use a template with variables and/or an image specified by the user. Needs tests

Next steps

Job dependency is the next big thing. Need to agree on how to build scripts with lots of steps and will likely lead to breaking changes in the calc_input, sim_input format and script.
In the meantime, I will wok on job arrays + adding calculators and other things which shouldn't introduce breaking changes until next meeting

emilannevelink commented 1 year ago

Test Changes

needed to change dictionary for singlepoint_sim_input keys to name and crystalstructure to work with ase.build.bulk

All the tests are now passing for me. Do we want tests for each of the scripts?

mkphuthi commented 1 year ago

Ideally yes. It would make it much easier if we make changes to job.py etc. to make sure we didn't break anything. Especially for the ones we iterate on i.e. singlepoint, eos etc. Maybe adding a scripts directory in tests. This seems high priority

emilannevelink commented 1 year ago

Maybe we can merge this and then add an issue for adding tests for the rest of the scripts.

I think issues is how people generally keep track of a to-do list.

BattModels / asimtools