Must have: | A feature freeze on ParameterHandlers while this milestone is being undertaken Nonbonded force combination kwarg equivalence Implementation of charge_from_molecules and partial_bondorders_from_molecules kwargs Regression tests that achieve agreement to 6 decimal places while comparing serialized OpenMM System objects generated by the 0.10.3 6 toolkit and the 0.11.0 release candidate. Included in this test set are: The 9104 SMILES from the public industry data set parameterized with Sage, with default conformer generation. Using this file: | Github link macro |
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| link | https://github.com/openforcefield/qca-dataset-submission/blob/master/submissions/2021-03-30-OpenFF-Industry-Benchmark-Season-1-v1.0/dataset.smi |
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| extended | false |
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All condensed phase systems used for fitting Sage, using Sage parameters Using this file: | Github link macro |
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| link | https://github.com/openforcefield/openff-sage/blob/main/data-set-curation/physical-property/optimizations/data-sets/sage-train-v1.json |
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For 5-10 diverse molecules that have interpolated parameters assigned with WBO-interpolated bonds WBO-interpolated torsions SB drew up some molecules and made up torsion terms, sent to MT. MT chose these molecules without much expertise or care: input needed
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| link | https://github.com/openforcefield/qca-dataset-submission/blob/f5be666d368a8781379fe229df8ab6ecc865c61a/submissions/2020-10-06-OpenFF-Phenyl-Set/molecules.smi#L1-L10 |
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For 5 diverse molecules, ensure equal (to 6 decimal places) systems, identical (6 d.p.) vsite geometries, ensure that parameters are applied consistently with 0.10.2 and ensure that test parameters are not default for every type of VirtualSite and permutation of the match keyword (VSite FF and molecules were generated by JW)The 0.11.0 toolkit release candidate + Interchange will pass the vsite test suite as added in #1252 Further, since the above test suite examines everything except exceptions and energies, one molecule+FF permutation from the 0.10.6 vsite geometry tests will be used to compare single-point energies in both 0.10.6 and the 0.11.0 release candidate.
Every built-in handler and their associated attributes must be able to be stored in an Interchange object and be exported to an OpenMM system (with exceptions for things that shouldn’t be passed on, like that OpenMM shouldn’t know partial_bondorder_method="am1-wiberg" , or that PME was requested if the topology is non-periodic, though the structure of the regression tests should make it clear that these AREN’T being checked). Value propagation testing: “for every attribute of every built-in parameter handler (e.g. cutoff, v-site distance, bond length): an OpenMM system created using openff-2.0.0.offxml but with the attribute of the handler perturbed yields an OpenMM system with that value also modified, again to ensure that changes to parameter attributes are actually captured and its not just the default values that get passed through” In most cases, only the value of one attribute needs to be changed at a time. The propagation of these changed values can be tested by comparing the output OpenMM systems, written as XML, and compared via deepdiff
Disagreements between Interchange and Toolkit found as a result of this testing will be resolved as follows: The SMIRNOFF committee may decide to modify or extend the SMIRNOFF spec in response to issues that arise from this, and only the resulting SMIRNOFF spec should be considered correct behavior. If the Toolkit had a bug or was violating the SMIRNOFF spec, then Interchange should proceed with the correct values per the spec If the difference is within allowed error or is agreed to be acceptable (as determined by both Primary Driver and Approver), then it is acceptable. Either the Primary Driver or Approver may require that the difference be documented. For externally-calculated properties such as partial charges and Wiberg bond orders, differences with a relative magnitude over 1e-6 must be shown to be either:
OpenFF Toolkit 0.11.0 will only support the Interchange backend for create_openmm_system. There will be a feature freeze on 0.10.Z line except for backporting critical bugfixes (“bugs that affect assigned parameters to 6 decimal places (kcal/mol)”, or “bugs that both Approver and Driver agree need to be backported”).
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