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@dwhswenson dwhswenson released this Nov 5, 2018 · 169 commits to master since this release

OpenPathSampling 0.9.6 includes several new features, as well as many improvements to the examples and documentation. Highlights include:

  • Interface constrained shooting, an efficient technique in TIS
  • Better ways to load trajectories for the OpenMM engine (especially from Gromacs trajectories)
  • bugfix for minus interface ensemble in cases where the transition is not particularly rare

New features

  • Tools to get correctly reduced box vectors for OpenMM (#799)
  • Simple function to load TRR files (#799)
  • "Part-In-B" network (used in TPS rate calculation) (#796)
  • Interface constrained shooting (#788, #791, #790, #800) [parts by @bolhuis]

Bugs fixed

  • maskedarray fixes (#803)
  • bugfix in minus ensemble (#803)
  • Attempt to fix for old openmmtools as well as new (#768)
  • Fix push-docs-to-s3 for pip 10 (#785)

Miscellaneous improvements

  • Updates to Examples (#798)
  • Fix notebook tests (#797)
  • Updates to docs (#795, #793)
  • Changes to .gitignore files (#792)
  • Fixes for continuous integration (#802)
Assets 2
Nov 5, 2018
Merge pull request #801 from dwhswenson/0.9.6
OpenPathSampling 0.9.6

@dwhswenson dwhswenson released this Jun 20, 2018 · 261 commits to master since this release

OpenPathSampling 0.9.5 includes various minor bug fixes and improvements, but also marks a significant milestone in our movement toward 1.0: we now have drafts of the articles describing OPS that we consider ready for submission!

Bugs fixed

  • Only keep existing value stores in attribute_list (#783)
  • Omit using rejected paths in correlation visualization (#782)
  • Fix problems in notebook tests (#776)
  • Fix problem with netCDF not playing nicely with simtk.unit (#776)
  • Volumes should only be bounded on one side (#772)
  • Fix TISEnsemble so it allows 0 frames between interface and state B (#772)

Miscellaneous improvements

  • Fix pandas deprecation warning : replace df.as_matrix() with df.values (#781)
  • Update minus ensemble implementation (#772)
  • Fix openmmtools.RestorableIntegrator error (#764)
  • Better source code organization and management (#754, #760)
  • Add acknowledgments to docs (#766)
Assets 2

@dwhswenson dwhswenson released this Feb 25, 2018 · 318 commits to master since this release

OpenPathSampling 0.9.4 includes a few new features, several important bug fixes, and a lot of minor improvements. A few highlights include:

  • New ability to include velocities when creating an OPS trajectory from an MDTraj trajectory
  • New default colors in visualizations (better visibility for the most common type of color blindness)
  • Significant updates to the documentation
  • Major improvements in Python 3 support
  • Critical bug fix in the direct MD flux calculation
  • Critical bug fix in two-way shooting

Details on all improvements below.

New features

  • Add velocities as input to trajectory_from_mdtraj (#750)
  • Tools for converting flux to pandas structures (#735)

Bugs fixed

  • Allow unicode for string options in engine option check (#757)
  • Fix bug in BackwardFirstTwoWayShooting (#752)
  • Fix problem with HistogramPlotter2D limits (#732)
  • Fix bug in box_vectors (#731)
  • Fix bug in DirectSimulation flux (#726)

Miscellaneous improvements

Assets 2

@dwhswenson dwhswenson released this Sep 26, 2017 · 485 commits to master since this release

Long-overdue release, with several new features and lots of little fixes. Includes significant progress toward Python 3 support, which should be fully complete within the next few releases.

New features

  • Velocity direction modifiers (traditional delta-p) for 2-way shooting (#650)
  • Channel analysis tools to study switching between reaction channels (or different transitions) (#658)
  • resampling_statistics module to get uncertainties from pandas.DataFrame results (#684)
  • safemode to load CVs without loading the stored functions (#695)
  • PseudoAttributes: caching storage for generalized CollectiveVariable-like functions (not just of snapshots) (#691)
  • New TIS analysis subsystem in openpathsampling.analysis.tis (#686)

Miscellaneous improvements

  • Major progress toward Python 3 support (#690, #696, #708, #713)
  • storage.tags works, as well as storage.tag (#698)
  • Faster ensemble check for the case that the trajectory was generated using can_append/can_prepend (#669)
  • Refactor CommittorSimulation into reusable ShootFromSnapshotsSimulation (#667)
  • Miscellaneous storage improvements
  • Miscellaneous performance improvements
  • Miscellaneous updates to docs, testing, and continuous integration procedures

Bugs fixed

  • Fix bug in OpenMM instantaneous temperature (#649)
  • Fix (rare) bug in acceptance probability for 2-way shooting (#652)
  • Fix bug in deserialization/reloading of OpenMMTools integrators (#675)
  • Fix bug in multiple state rate calculation from DirectSimulation (#706)
Assets 2

@dwhswenson dwhswenson released this Dec 1, 2016 · 977 commits to master since this release

A few new features and some significant clean-up as we prepare for 1.0.

Note that the changes in the Details object have the potential to break compatibility with older code. Please check PRs #629 and #633 if that is likely to be a problem for you.

Changes in this release include:

  • Added two-way shooting (#600)
  • Clean-up of how Details are handled (details are only for move changes; not samples) (#629, #633)
  • Load a trajectory to OPS (via MDTraj) with ops_load_trajectory (#645)
  • Items from storage can be loaded with negative numbers, following Python list index convention (#612)
  • CSS for visualizations moved to separate file (#574)
  • New conveniences for restarting a simulation (#616)
  • RandomVelocities respects constraints (#618)
  • Miscellaneous bugfixes, documentation improvements, and other minor improvements
Assets 2

@dwhswenson dwhswenson released this Oct 4, 2016 · 1148 commits to master since this release

Continuing clean-up and adding conveniences as we prepare for 1.0.

Some improvements new in this release:

  • switch JSON library to ujson (#582)
  • masses, n_degrees_of_freedom, and instantaneous_temperature snapshot features (#579, #589)
  • renamings surrounding what used to be live_visualization (#596)
  • end checking for "safe imports" in CVs (#599)
  • improvements to the committor calculation (#601)

In addition, we removed lots of unnecessary/outdated code, reorganized several sections for better modularity, cleaned up our examples, and gave the documentation a long-overdue update.

Assets 2

@dwhswenson dwhswenson released this Sep 16, 2016 · 1315 commits to master since this release

First public (pre)release of OpenPathSampling.

OPS is now feature-complete for 1.0, and mostly API-stable. While we clean up the code and check the corners for bugs on our way to 1.0, we'd like to encourage people to get familiar with us by trying our 0.9 release.

Assets 2
Sep 15, 2016


Merge pull request #581 from jhprinz/copyreplace
Implement `Copy_with_replacements`
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