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Changelog#

0.5.0#

Improvements#

  • Use MDTraj to calculate torsions rather than doing this manually
  • Make metadynamics more aggressive, allow user to specify torsions targeted by metadynamics, and include in-ring aliphatic torsions by default in #26

Fixes#

  • Remove unused settings fields in #25

0.4.0#

Improvements#

  • Improve cleanliness/prettiness of CLI output
  • Reduce memory use during congeneric series fitting in #17
  • Improve test quality, speed, and coverage in #19
  • Update environments with explicit python and cuda versions and document installation with different cuda versions
  • Plot sampling of rotatable torsions in #23

Fixes#

  • Update ParameterConfig defaults so that linear torsions are not trained in #18

0.3.0#

  • Renamed bespokefit_smee -> presto (Parameter Refinement Engine for Smirnoff Training / Optimisation)
  • Added more documentation on the method, recommended settings, and outputs.

0.2.0#

New Features#

  • Implement new default protocol with MLP-minimised configurations
  • Add support for loading multiple pre-computed datasets for training
  • Implement flexible bespoke SMARTS type generation with MergeQueryHs
  • Add support for multi-molecule simultaneous fits
  • Add dataset filtering function for preprocessing
  • Add function for calculating Hessian matrices

Improvements#

  • GPU Memory Management: Significantly improved GPU memory handling
  • Add GPU memory cleanup utility function
  • Clear GPU memory after sampling operations
  • Reduce GPU memory usage throughout training pipeline
  • Fix GPU memory leaks with LM optimizer
  • Make CUDA operations conditional on availability for CPU-only environments
  • Modified Seminario Method (MSM)
  • Complete reimplementation of MSM for better performance
  • ML Potential Updates
  • Add aceff-2.0 and make it the default MLP
  • Update default sampling settings (consistent with higher speed of aceff-2.0)
  • Force Field Updates
  • Update default MM-FF to 2.3.0
  • Ensure we train FF with bespoke types added
  • Ensure parameter names are not overwritten
  • Regularization Improvements
  • Overhaul regularization and calculation of loss
  • Normalize regularization per-parameter
  • Decouple type generation from regularization
  • Optimizer Fixes
  • Fix LM optimizer implementation
  • Clear cache between iterations with Adam
  • Avoid GPU memory leaks with LM optimizer
  • Path Management
  • Fix path management for multiple molecules
  • Improve handling of output paths for per-molecule outputs

Maintenance#

  • Remove bespoke toolkit wrapper

0.1.1#

Documentation#

  • Added example notebook

0.1.0#

  • Initial implementation.