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Release 2026.2.0 - #208

Merged

lohedges merged 85 commits into

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release_2026.2.0

Sep 15, 2026

Merged

Release 2026.2.0#208
lohedges merged 85 commits into
mainfrom
release_2026.2.0

Commits on Jun 29, 2026
- Update BioSimSpace development pin.
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- Update CHANGELOG for 2026.2.0 development.
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- Add note regarding PyMBAR JAX issues.
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Commits on Jul 1, 2026
- Remove pre-release warning. [ci skip]
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- Clarify perturbed_system option. [ci skip]
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Commits on Jul 2, 2026
- Add support for generating Boresch restraints for ABFE.
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- Add support for split restraint levers in ABFE schedules.
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Commits on Jul 3, 2026
Commits on Jul 4, 2026
- Seed simulation from least strained restraint search structure.
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Commits on Jul 21, 2026
- Use persistent thread pools for the production block.
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- Merge pull request #175 from OpenBioSim/fix_174
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- Add oversubscription_factor to allowed_diffs.
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- Merge pull request #177 from OpenBioSim/fix_176
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Commits on Jul 22, 2026
- Restrict energy decomposition to force groups used for integration.
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- Merge pull request #180 from OpenBioSim/fix_178
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- Parallelise replica mixing.
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- Merge pull request #181 from OpenBioSim/feature_parallel_mixing
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Commits on Jul 27, 2026
- Query the correct GPU when checking device memory. [closes #182]
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- Merge pull request #183 from OpenBioSim/fix_182
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Commits on Jul 28, 2026
- Store GCMC statistics per lambda value.
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- Merge pull request #185 from OpenBioSim/feature_gcmc_stats
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- Use pip_check: false to avoid NumPy pin errors with AmberTools.
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Commits on Aug 4, 2026
- Link restart systems to the reference end state.
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- Merge pull request #189 from OpenBioSim/fix_188
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- Cap the number of OpenMM contexts used for replica exchange.
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- Fix constrained bond lengths at a common lambda value.
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- Seed the end state from the middle of a group.
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- Check that replicas resume from where they stopped.
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- Read positions from a legacy checkpoint when logging the GCMC sphere.
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- Set the box vectors before the positions.
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- Accumulate the flags for replicas whose state has moved.
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- Don't minimise on restart.
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- Consolidate the duplicated context count and GPU load warnings.
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  b05c162
- Document max_contexts in the replica exchange section of the README.
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- Fix typos and formatting errors in README.
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- Pin the perturbed system coordinate path in the seeding test.
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- Respect swap_end_states when seeding from the perturbed system.
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- Clarify what the perturbed_system input must contain.
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- Suggest a max_contexts value when the replicas don't fit in memory.
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- Remove the redundant post-equilibration GCMC water count.
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- Assert that GCMC water occupancy follows the replica through a mix.
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- Count the GCMC waters against the context in the regular runner.
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- Cover GCMC with no sampling region in the regular runner.
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- Pre-equilibrate the water before minimising in the regular runner.
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- Give each replica its own terminal flip statistics list.
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- Link CHANGELOG entries to PR.
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- Add a precision option for GPU platforms.
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Commits on Aug 5, 2026
- Pin the recorded times in the energy trajectory tests.
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- Merge pull request #191 from OpenBioSim/feature_dynamics_cache
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Commits on Aug 24, 2026
- Add section on keeping up-to-date during a development cycle. [ci skip]
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- Add support for auto-generating Morse restraints for ring-breaking.
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- Document schedules, ABFE, and ring-breaking. [ci skip]
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- Merge pull request #194 from OpenBioSim/feature_auto_rb_restraint
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- Document intended use of standard_morph schedule. [ci skip]
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- Remove redundant prepareFEP option. [ci skip]
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- Make package name formatting consistent. [ci skip]
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- Correct version scheme. [ci skip]
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Commits on Aug 26, 2026
- Remove redundant kappa lever equations from ring-breaking/making schedules.
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- Merge pull request #195 from OpenBioSim/fix_redundant_terms
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Commits on Aug 28, 2026
- Don't silently swallow errors when adding coalchemical restraints.
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- Add section on charge-change perturbations. [ci skip]
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- Add features section to the top of the README. [ci skip]
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- Add link to somd2_examples repository. [ci skip]
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  d1bc0d6
- Accept stream file paths for restraints and lambda schedules.
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  3384ca7
- Merge pull request #198 from OpenBioSim/feature_stream_file_input
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  9b7651b
- Fix log message.
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Commits on Sep 1, 2026
- Fix platform section. [ci skip]
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Commits on Sep 4, 2026
- Account for v-site charges when checking for charge change.
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- Merge pull request #200 from OpenBioSim/fix_199
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Commits on Sep 8, 2026
- Handle num_lambda=1.
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- Update CHANGELOG and add missing entries and links.
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- Merge pull request #203 from OpenBioSim/fix_202
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Commits on Sep 14, 2026
- Default to single precision until benchmarks are done.
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Commits on Sep 15, 2026
- Use the configured platform when detecting available GPUs.
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  2e4d519
- Fix the OpenCL constant used to query AMD GPU free memory.
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  e25aa48
- Merge pull request #206 from OpenBioSim/fix_204_205
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- Merge branch 'main' into release_2026.2.0
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  c4d831d
- Update BioSimSpace pin.
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  ca848fc
- Update CHANGELOG.
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  b60f2ab

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Commits on Jun 29, 2026

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Commits on Aug 28, 2026

Commits on Sep 1, 2026

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Commits on Sep 15, 2026