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Release 0.9.0 - Langevin splitting integrators, MCMC framework and alchemy

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@andrrizzi andrrizzi released this 03 Apr 21:32

This version adds several improvements to the integrators module, it introduces a general framework to perform MCMC simulations, and it imports the functionalities of choderalab/alchemy.

  • Added a LangevinSplittingIntegrator class that includes several popular integrators of Langevin dynamics as special cases.
  • Added BAOABIntegrator and GeodesicBAOABIntegrator.
  • New base CustomIntegrators: ThermostatedIntegrator, which offers utilities for integrators that maintain the distribution at a certain temperature, and RestorableIntegrator that enable restoring class members (e.g. temperature getter/setters) that are otherwise lost with OpenMM serialization.
  • New state classes ThermodynamicState, SamplerState and CompoundThermodynamicState that can be used to store and manipulate OpenMM Systems and Contexts.
  • New class ContextCache that centralizes the creation and caching of OpenMM Contexts by exploiting the mechanism of compatibility between ThermodynamicStates.
  • Imported existing MCMC framework (previously in choderalab/openmmmcmc) and adapted it to the new state classes. MCMCMoves share a ContextCache to minimize the number of created Contexts during the simulation.
  • Imported the alchemy module and adapted it to the new framework. AlchemicalState can be used with CompoundThermodynamicState to extend ThermodynamicState by composition.