Input files and scripts for benchmarking OpenFF force fields with yammbs
Create a new branch starting from the master
branch.
Create a new entry in the submissions
directory, with the general format
YYYY-MM-DD-Name
. For example:
mkdir submissions/$(date +%Y-%m-%d)-Sage-2.1.0
Add a YAML input file in this directory specifying the force field and datasets to use for the run. For example:
forcefield: openff-2.1.0.offxml
datasets:
- datasets/cache/industry.json
All paths should be relative to the root of the repository, and cached datasets must be used. Force fields can also correspond to built-in force fields recognized by the toolkit (as in the example). Currently only single datasets are supported.
Push your branch and open a PR.
Request a review, and get the PR approved.
Make a comment of the form /run-benchmark path/to/submission [conda-env.yaml]
on the PR. The brackets indicate an optional argument. If
the path to the conda environment is omitted, the default environment will be
used (devtools/env.yaml).
Wait for the benchmarks to finish.
Review the results, and update your submission with a README containing a link to the Zenodo archive created by CI.
Merge your PR!
This will produce CSV files corresponding to the DDE, RMSD, TFD, and internal-coordinate RMSD (ICRMSD) metrics computed by yammbs.
Submission | Description | DOI |
---|---|---|
Sage-2.1.0 | Constrained openff-2.1.0.offxml | 10.5281/zenodo.14053221 |
Sage-2.1.0-unconstrained | Unconstrained openff-2.1.0.offxml | 10.5281/zenodo.14058464 |