Release v0.21.0

What's Changed

• Catch LennardJonesGenerator made NB functions. by @Lnaden in #511
• Remove logic for missing file when retrying to open a dataset by @mikemhenry in #515
• Constants codata 2018 update by @ijpulidos in #525
• deal with openmm 7.6 package unwrapping by @sroet in #528
• Overriding deepcopying behavior to avoid creating new ContextCaches. by @ijpulidos in #524
• Try closing reporter in test for windows fix by @Lnaden in #535
• Add Git Attributes File Required by Versioneer by @SimonBoothroyd in #496
• Fix for issue #435 by @mjw99 in #534
• Update changelog for #511 by @Lnaden in #512
• Testing updated python versions by @ijpulidos in #542
• ContextCache usage cleanup by @ijpulidos in #538
• Release 0.21.0 by @mikemhenry in #545

New Contributors

• @ijpulidos made their first contribution in #525
• @SimonBoothroyd made their first contribution in #496
• @mjw99 made their first contribution in #534

Full Changelog: 0.20.3...0.21.0

0.20.3 Bugfix Release

Fix critical bug in which GPU contexts would fail to recognize mixed precision was available PR #506 (Resolves issue #505 )

0.20.2 Bugfix Release

Remove leftover six imports and xrange See PR #504

0.20.1 Bugfix Release

This release fixes several bugs and eliminates cython compiled acceleration of replica-exchange all-swap (replacing it with numba) to enable working release on conda-forge.

Bug Fixes

• #485: Replace cython-accelerated all-swap replica mixing with numba implementation
• #488: Fix ParallelTemperingSampler temperature spacing
• #501: Do unit conversion first to improve precision (fixes issue #500)

0.20.0 - Periodic nonequilibrium integrator

New features

• (#466) Adds PeriodicNonequilibriumIntegrator for periodic nonequilibrium simulations

Bug fixes

• (#462) Bugfix for restrained atom indices

0.19.0 - Multiple alchemical regions

New features

• Added support in AbsoluteAlchemicalFactory for handling multiple independent alchemical regions (#438).
• Added support for anisotropic and membrane barostats in ThermodynamicState (#437`).
• Added support for platform properties in ContextCache (e.g. for mixed and double precision CUDA in multistate sampler) (#437).

Bugfixes

• The multistate samplers now issue experimental API warnings via logger.warn() rather than warnings.warn() (#446).
• Fix return value in states.reduced_potential_at_states (#444).

Known issues

• Using parallel MPI processes causes poor mixing of the odd thermodynamic states while the mixing of the even states is normal. We're still investigating whether the issue is caused by a change in the MPI library or an internal bug. For now, we recommend running calculations using only 1 GPU (see also #449 and choderalab/yank#1130).

0.18.3 - Storage enhancements and bugfixes

Bugfixes

• Fixed a bug in multistateanalyzer.py where a function was imported from openmmtools.utils instead of openmmtools.multistate.utils (#430).
• Fixed a few imprecisions in the documentation (#432).

Enhancements

• Writing on disk is much faster when the checkpoint_interval of multi-state samplers is large. This was due to the dimension of the netcdf chunk size increasing with the checkpoint interval and surpassing the dimension of the netcdf chunk cache. The chunk size of the iteration dimension is now always set to 1 (#432).

0.18.2 - Bugfix release

Bugfixes

• A bug in the multistate samplers wherelogsumexp was imported from scipy.misc (now in scipy.special) was fixed (#423).
• Improve the robustness of opening the netcdf file on resuming of the multi-state samplers by setting the environment variable HDF5_USE_FILE_LOCKING to 'FALSE' after 4 failed attempts (#426).
• Fixed a bug causing a crash during exception handling (#426).

Other

• Update build infrastructure to match MolSSI cookiecutter (#424, #426).

0.18.1 - Bugfix release

This is a minor bugfix release.

New features

• Improvements for HostGuest* classes
  • add oemols, host_oemol, and guest_oemol properties to retrieve OpenEye Toolkit OEMol objects (requires toolkit license and installation)
  • these classes can now accept overriding kwargs

Bugfixes

• openmmtools.multistate experimental API warning is only issued when openmmtools.multistate is imported
• AlchemicalNonequilibriumLangevinIntegrator.reset() now correctly resets the nonequilibrium work

0.18.0 - Added multistate samplers

Add a number of classes that can use MCMC to sample from multiple thermodynamic states:

• MultiStateSampler: sample independently from multiple thermodynamic states
• ReplicaExchangeSampler: replica exchange among thermodynamic states
• SAMSSampler: self-adjusted mixture sampling (SAMS) sampling

All samplers can use MPI via the mpiplus package.