Turn on heavy matches heavy by default#66
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* Not to be merged until full benchmarks are back
badisa
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February 12, 2026 23:33
badisa
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* WIP * WIP * Initial change, it must be broken * WIP * WIP * REVERT * Clean up * Fixes a bug in the setup of the free * Fix issue with construction of system idxs * Fix linting * Skip testing large batches in CI with memcheck on * Adds Amber AM1CCC Forcefield (#69) * Use Amber AM1BCCs as the base charges then add correctable charge corrections. * The aromaticity model doesn't match, but for training this should be a fine starting point. OpenFF prefers MDL which is the standard for TMD as well. * Clean up tests related to OE * Remove batch tests from memcheck * Causing ooms * Skip memory check in failing test * Running enough RBFE at this stage that it doesn't seem like we will be caught unaware. But running with pytest-xdist has inconsistent memory behavior * Add CCC refitting test (#71) * Fix resetting of nonbonded ixn group * More memory allocated than strictly needed, but that is fine for now * JANK * REMOVESYNC * jank * Fixes incorrect predictions in CSVs (#72) * Was not performing conversion of units correctly * Bump to 0.2.2 (#73) * CMake Fixes + RPath (#67) * Remove quotes around CMAKE vars * No reason to do this * Add lib directory as additional rpath * Include shared objects in package * Fix links to old repo * Add docs * Include versions in shared objects * PR Feedback: Remove build dependecy * Not strictly necessary * Ensure that water atoms are contiguous after prep (#74) * Remove restriction that waters are at the end of the PDB * Make waters contiguous to ensure water sampler is setup correctly * Probably can make the water sampler more flexible. May need to be revisited for performance later * Add FlatBottomRestraint (#75) * Similar to FlatBottomBond except it restraints particles to positions * Useful for minimization * jank * Working * Further * Add tests of batching on and off * Fix up water sampling * Revert "REMOVESYNC" This reverts commit 41cef11. * Fix the tests * Fix environment variable and examples * Update hashes * Update hashes * Fix output dirs * Turn on heavy matches heavy by default (#66) * Turn on heavy matches heavy by default * Not to be merged until full benchmarks are back * Fix failing graph building tests * Update hashes * Update shas * Update missed sha * Loosen tolerance on failing nightly test
badisa
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Feb 25, 2026
* Batch Bonded Potentials + Integrators (#8) * Support Batching in Harmonic Bond * Lots of boilplate to handle changes to the API * execute_dim is janky, but need to figure out how to handle this correctly * Enforce potentials must have batch size 1 in context * To be fixed later on * Add EnergyAccumulator utility class * Modifies all the potentials to use it instead * Reduces boilerplate and makes it easier to batch everything * Batch PeriodicTorsions * Fix tests * Adds num_atoms to all other valence terms * HarmonicAngle Batch Support * ChiralAtomRestraint Batch Support * Adds some jank around params, since they are flat for ChiralAtomRestraint * Improve test robustness * ChiralBondRestraint Batch Support * FlatBottomBond Batch Support * Fix up the tests * LogFlatBottomBond Batch support * NonbondedPairList Batching Support * Should batching of JAX methods be supported? * NonbondedPrecomputedPairlist Batching support * Enforce idxs more consistently * Fixes test * Fix failing tests * Exclusions were flat * Initial Batching of Vacuum simulations * Expand test to cover langevin integrator * Fix up some typing * Batch Neighborlist and Nonbonded Potentials (#38) * Swap ordering of row/col in set_idxs_device * Fix number of atoms for precomputed pairlist * Fix up the integrators * Rename batch_size to num_systems in older code * Batch Movers (#45) * WIP * WIP: Fix up the barostat * Expose num systems to move signature * Remove memcheck for tests * OOMing * Return scale factors * Fix up the existing tests * Fix memory leak in energy accumulator * Support batching in TIBD/BD ExchangeMover * Update tests * Fix batching for single topology * Add verification that the size of the system matches the potentials * Add tests for exchange movers * Reduce memory usage during CI * Fix test * Tweak memory usage in CI * Probably need more ram still * Reduce number of workers further * Fix a neighborlist test * Reduce vacuum tests memory usage * Add batching benchmarks * Appears slower than MPS. The issues with rebuilding the nblist constnatly may be a problem for global. * Reduce memory consumption further * Reduce the memory usage * Disable float64 tests * Remove batch simulations from memcheck * Absurd how much memory these things are taking * Disable memory checks under x-dist * Mixture of tests impacts RSS * Undo change * Fix failing test * Re-enable parallelism in memory tests * Adds Batch Support for Local MD (#70) * WIP * WIP * Initial change, it must be broken * WIP * WIP * REVERT * Clean up * Fixes a bug in the setup of the free * Fix issue with construction of system idxs * Fix linting * Skip testing large batches in CI with memcheck on * Remove batch tests from memcheck * Causing ooms * Skip memory check in failing test * Running enough RBFE at this stage that it doesn't seem like we will be caught unaware. But running with pytest-xdist has inconsistent memory behavior * Fix resetting of nonbonded ixn group * More memory allocated than strictly needed, but that is fine for now * Batch Flat Bottom Restraint (#76) * Adds Amber AM1CCC Forcefield (#69) * Use Amber AM1BCCs as the base charges then add correctable charge corrections. * The aromaticity model doesn't match, but for training this should be a fine starting point. OpenFF prefers MDL which is the standard for TMD as well. * Clean up tests related to OE * Add CCC refitting test (#71) * Fixes incorrect predictions in CSVs (#72) * Was not performing conversion of units correctly * Bump to 0.2.2 (#73) * CMake Fixes + RPath (#67) * Remove quotes around CMAKE vars * No reason to do this * Add lib directory as additional rpath * Include shared objects in package * Fix links to old repo * Add docs * Include versions in shared objects * PR Feedback: Remove build dependecy * Not strictly necessary * Ensure that water atoms are contiguous after prep (#74) * Remove restriction that waters are at the end of the PDB * Make waters contiguous to ensure water sampler is setup correctly * Probably can make the water sampler more flexible. May need to be revisited for performance later * Add FlatBottomRestraint (#75) * Similar to FlatBottomBond except it restraints particles to positions * Useful for minimization * Batch HREX (#77) * WIP * WIP * Initial change, it must be broken * WIP * WIP * REVERT * Clean up * Fixes a bug in the setup of the free * Fix issue with construction of system idxs * Fix linting * Skip testing large batches in CI with memcheck on * Adds Amber AM1CCC Forcefield (#69) * Use Amber AM1BCCs as the base charges then add correctable charge corrections. * The aromaticity model doesn't match, but for training this should be a fine starting point. OpenFF prefers MDL which is the standard for TMD as well. * Clean up tests related to OE * Remove batch tests from memcheck * Causing ooms * Skip memory check in failing test * Running enough RBFE at this stage that it doesn't seem like we will be caught unaware. But running with pytest-xdist has inconsistent memory behavior * Add CCC refitting test (#71) * Fix resetting of nonbonded ixn group * More memory allocated than strictly needed, but that is fine for now * JANK * REMOVESYNC * jank * Fixes incorrect predictions in CSVs (#72) * Was not performing conversion of units correctly * Bump to 0.2.2 (#73) * CMake Fixes + RPath (#67) * Remove quotes around CMAKE vars * No reason to do this * Add lib directory as additional rpath * Include shared objects in package * Fix links to old repo * Add docs * Include versions in shared objects * PR Feedback: Remove build dependecy * Not strictly necessary * Ensure that water atoms are contiguous after prep (#74) * Remove restriction that waters are at the end of the PDB * Make waters contiguous to ensure water sampler is setup correctly * Probably can make the water sampler more flexible. May need to be revisited for performance later * Add FlatBottomRestraint (#75) * Similar to FlatBottomBond except it restraints particles to positions * Useful for minimization * jank * Working * Further * Add tests of batching on and off * Fix up water sampling * Revert "REMOVESYNC" This reverts commit 41cef11. * Fix the tests * Fix environment variable and examples * Update hashes * Update hashes * Fix output dirs * Turn on heavy matches heavy by default (#66) * Turn on heavy matches heavy by default * Not to be merged until full benchmarks are back * Fix failing graph building tests * Update hashes * Update shas * Update missed sha * Loosen tolerance on failing nightly test * Reduce memory consumption of energy accumulation in the batched mode (#80) * Batch Bisection (#78) * Bisection initial implementation * Lots of duplicate code * Handle bisection where more than 2 initial lambdas provided * Disable batching by default * Enabled by the TMD_BATCH_MODE=on flag * Update vacuum sha * Fix bug in bisection * Was running 1 more iteration than it should * Fix test * Update hashes
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