Foyer 0.9.2

Bug fixes

• This is a patch release for the issue related to the combining rule used to calculate 1-4 nonbonded interactions (#435)
  • Currently, the 1-4 nonbonded calculations are calculated using the Lorentz Berthelot combining rule (https://en.wikipedia.org/wiki/Combining_rules#Lorentz-Berthelot_rules), and the parameters are not updated when forcefield.combining_rule is updated. This release adds a patch to recalculate sigma when forcefield.combining_rule is updated to “geometric” (#433)
  • NOTE - This applies to all instances of parametrizing with foyer, all mixing rules were calculated using Lorentz-Berthelot, even when geometric was specified

Features

• Include combination_rule as top-level metadata in forcefield XMLs (#433)
• Update references and SMARTS strings for ester groups in oplsaa.xml, refer to CHANGELOG for list of affected atomtypes (#429)

Maintenance

• Explicitly list default cloud-based pre-commit options in .pre-commit-config.yaml (#425)
• Include detailed tests for forcefield metadata (#435)
• Increase performance for unit testing gmso integration (#437)

Foyer 0.9.1

Bug fixes

• This is a bug fix release. Add __init__py for the foyer.tests module. Fixing a bug in mbuild tests when importing get_fn from foyer.tests.utils. (#421)

Maintenance

• Pre-commit autoupdate (#420)

Foyer 0.9.0

Features

• Add new general Forcefield class which supports gmso backend (#358)
• Add atomtyping support for gmso.Topology and openff.Topology objects (#399)

Maintenance

• Add pre-commit (#417, #418)
• Refactor tests (#385)

Foyer 0.8.1

Features

• Add SMARTS definition for esters in oplsaa.xml (#346)
• Add SMARTS definition for lithium ion in oplsaa.xml (#383)
• Add lj14scale and coulomb14scale to Forcefield (#398)
• Add SMARTS definition for chloride ion in oplsaa.xml (#403)
• Add SMARTS definition for acetate ion in oplsaa.xml (#404)

Maintenance

• Refactor the creation of a structure from a residue (#373)
• Default to environment.yml files for environment creation (#400)
• Include pytest.ini for sane pytest defaults (#400)
• Make environment.yml files more consistent among the mosdef-hub organization (#410)
• Fix regression in Dockerfile and automated image building (#412)
• Add link and blurb about the TRUE paper and methodology (#413)
• Pin networkx dependency to >=2.5 (#416)
• Add Units tab to our documentation at foyer.mosdef.org (#402)

Foyer 0.8.0

Features

• Native method to get parameters from a Forcefield object (#382)
• Decouple parmed from the foyer atomtyper (#389)
• Return a list of available Forcefield loaders based on currently installed plugins (#388)

Maintenance

• Upload CodeCov reports without tokens (#393)
• Update user documentation (#376)
• Update README badge for conda-forge (#372)

Foyer 0.7.7

Maintenance

• Entrypoints Conda (To ensure that we have our plugins supported) (#345)
• Update foyer docs link (#347)
• Add link to GitHub/homepage in docs footer (#351)
• Update copyright years in docs (#353)
• Use bump2version for versioning (#357)
• Fix typo in desc (#361)
• Remove travis (#366, #368)
• Fix typo in forcefield.py (#362)
• Fix docker link in README (#367)
• Fix OpenMM _SystemData changes (#369)
• Pin OpenMM version (#370)

Breaking Changes

This version of foyer is no longer compatible with OpenMM < v7.5.

Foyer 0.7.6

Features

• Add warning for non-zero charge structure (#338)
• Add SMARTS string for opls_207 and more test files (#343)

Bug Fixes

• Fix error in Forcefield.apply() verbose mode when dihedrals are missed (#335)
• Resolve issue with latest version of lark-parser (0.8.6) (#341)

Foyer 0.7.5

Attention

The lark-parser package recently updated to version 0.8.6, which has broken certain SMARTS functionality within foyer. Until these issues are resolved, do not use lark-parser version 0.8.6. This has been hotfixed until the issue has been resolved (#337)

Features

• Automate Docker Image publishing with AZP (#334)
• Add OPLS SMARTS strings for Sulfur Compounds (#307)

Bug Fixes

• Pin lark-parser to version 0.8.5 (#337)

Foyer 0.7.4

Features

• Add version attribute to ForceField class and XML schema (#298)
• Expand OPLS-AA XML coverage:
  - Amides (#278)
  - Isopropyl and tert-butyl ether (#311)
  - Chlorobenzene and benzonitrile (#308)
  - Methyl-nitro aniline (#319)
  - Secondary and Tertiary alcohols (#320)
  - Update to use smaller files for testing (#313)
• Remove OpenMM from atom-typing step (#296)

Maintenance

• Fix travis by not installing md5sha1sum (#302)
• Refactor unit tests to use mbuild recipes instead of mbuild examples (#303)
• Remove six from requirements (#325)
• Drop Appveyor YML and update README (#329)

Miscellaneous

• Add LICENSE.rst to MANIFEST.in (#324)
• Build documentation on ReadTheDocs (#316)

Foyer 0.7.3

Features

• Establish entry points for external force fields (#282)
• Separate parametrization step into a discrete function (#294)

Bug Fixes

• Reorder _check_angles function in order for verbose messages to be printed (#293)
• Fix TravisCI build errors (#300)
• Pass assert_improper_params argument to parametrize_system (#299)

Miscellaneous

• Remove coveralls badge from README (#289)
• Switch force field entry points to functions that load classes (#288)