yammbs-dataset-submission

Input files and scripts for benchmarking OpenFF force fields with yammbs

Usage

Running benchmarks in CI

0. Create a new branch starting from the master branch.

1. 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

2. 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.

3. Push your branch and open a PR.

4. Request a review, and get the PR approved.

5. 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).

6. Wait for the benchmarks to finish and merge your PR!

Output

This will produce CSV files corresponding to the DDE, RMSD, TFD, and internal-coordinate RMSD (ICRMSD) metrics computed by yammbs.

Generating datasets

See datasets/README.md