0.4.0 Support qcportal >=0.50 + Update Default FF

In this release we updated espaloma to support newer versions of qcportal and updated the default forcefield for load_forcefield to be openff_unconstrained-2.2.1 (it was openff_unconstrained-2.0.0).

The other fix was in some edge cases the data split did not work as intended, see #149 for details.

We have attached espaloma-0.4.0.pt to this release for convince, but this model is identical to espaloma-0.3.2.pt. espaloma-latest.pt is also the same as espaloma-0.3.1.pt. Please see https://github.com/choderalab/espaloma/releases/tag/0.3.1 for more information about the espaloma 0.3.x family of models.

Automatic Changelog

• include date in cache key by @mikemhenry in #204
• Check if dgl 2.3.0 works by @mikemhenry in #220
• Update README.md Install Steps by @mikemhenry in #198
• switch install docs to use mamba by @mikemhenry in #223
• Qcarchive update by @chrisiacovella in #187
• Fix syntax issue on docker file build by @mikemhenry in #184
• update to openff_unconstrained-2.1.0 as the default ff by @mikemhenry in #201
• switch install docs to use mamba by @mikemhenry in #226
• Fix data split by @kntkb in #151

New Contributors

• @chrisiacovella made their first contribution in #187

Full Changelog: 0.3.2...0.3.3

Note

This release updates espaloma to support the newest version (1.1.2) of DGL. There are no API breaking changes or updates to the espaloma model. We have attached espaloma-0.3.2.pt to this release for convince, but this model is identical to espaloma-0.3.1.pt. espaloma-latest.pt is also the same as espaloma-0.3.1.pt. Please see https://github.com/choderalab/espaloma/releases/tag/0.3.1 for more information about the espaloma 0.3.x family of models.

What's Changed

• Support latest (1.1.2) DGL version

Bug fixes, packaging, and documentation updates

• Installation Guide Update by @mikemhenry in #175
• Add docker and apptainer image building on demand by @mikemhenry in #176
• Update to new dgl version (1.1.1) by @mikemhenry in #179
• Add Instructions on loading local model by @ijpulidos in #183
• Test & Update to newest DGL Version (1.1.2) by @mikemhenry in #186
• Update readme and docs for version 0.3.2 @mikemhenry in #188

Full Changelog: 0.3.1...0.3.2

What's Changed

• Fix CI -- updated by @ijpulidos in #152
• Support newer versions of OpenFF Toolkit by @mattwthompson in #155
• Support for modern openff-toolkit versions (>=0.11) by @ijpulidos in #153
• Support different improper torsion multiplicity by @kntkb in #157
• Update default reference force field when creating a system from graph (fix #160) by @kntkb in #161
• Add comments to why some of the input features were commented out by @kntkb in #163
• Improved deployment testing with different charge-method options by @ijpulidos in #164
• Changed default charge method to nn by @madilynpaul in #142
• Fix loading molecules serialized with older openff-toolkit versions (<=0.11) by @ijpulidos in #166
• Use rtd for docs by @mikemhenry in #167
• Speed up and improve CI and update readme by @mikemhenry in #169
• First pass at model fetch by @mikemhenry in #172
• Use dgl.to_homogeneous instead of the old deprecated name by @ijpulidos in #173

New Contributors

• @ijpulidos made their first contribution in #152
• @mattwthompson made their first contribution in #155
• @madilynpaul made their first contribution in #142

Full Changelog: 0.3.0...0.3.1

Model updates

• Note that espaloma-0.3.0.pt is also deployed which is compatible with espaloma-0.3.1.pt. espaloma-0.3.0.pt was renamed to espaloma-0.3.1.ptto maintain consistency with the release version.
• espaloma-0.3.1.pt (espaloma-0.3.0.pt) is a new espaloma model (see notes_for_espaloma-0.3.1.pdf for more details) with the improved features:
  • Trained with curated quantum chemical dataset covering small molecules, peptides, and nucleic acids, containing over 15,000 unique molecules and 1M conformations
  • Improved training strategy that uses both energies and forces, as well as L2 regularization to proper and improper torsion force constants to reduce the model complexity and variance
  • Restrict improper torsion multiplicity to n=1,2

Notes

• espaloma-0.3.1.pt (espaloma-0.3.0.pt) was trained and created using a dev version (commit: 4c6155b) of v0.3.1 release based on openff-toolkit 0.10.6
• A manuscript describing the complete fitting process and assessment is forthcoming
• Please warn that v0.3.0 is no longer compatible with v0.3.1, and espaloma-0.3.1.pt is not supported by v0.3.0

What's Changed

• Get rid of large storage by @yuanqing-wang in #133
• Fix nonbonded force subtraction by @kntkb in #134, #140
• Exclude resonance variant input features by @yuanqing-wang in #148

Full Changelog: 0.2.4...0.3.0

Model Update

• espaloma_0.3.0rc1.pt is deployed as a release candidate for espaloma_0.3.0 (see notes_for_espaloma-0.3.0rc1.pdf for more details).
• Please note that notes_for_espaloma-0.3.0rc1.pdf are temporal and manuscript describing the complete fitting process and assessment is forthcoming.
• Please warn that espaloma_0.3.0 is no longer compatible with the 0.2.x models, and vice versa.

What's Changed

• Formal charge fix by @jthorton in #122
• Subtract nonbonded by @kntkb in #124
• Fix readme link to docs by @mikemhenry in #117
• Fix docstring for JanossyPoolingNonbonded class. by @kaminow in #102
• Pin to older toolkit + fix CI by @mikemhenry in #129
• fix yaml syntax issue by @mikemhenry in #132

New Contributors

• @jthorton made their first contribution in #122
• @kntkb made their first contribution in #124

Full Changelog: 0.2.3...0.2.4

Fixed the index casting bug caught by new version of DGL.

Used Smirnoff-style 3-termed improper torsion in stead of 6-termed. (#105)

This version is concurrent with: https://arxiv.org/abs/2010.01196v3

Erased global DGL import to make package compatible with Conda-forge.

Code base for https://arxiv.org/abs/2010.01196 v2.

This release is responsible for generating the results for https://arxiv.org/abs/2010.01196.