Release 0.9.0 - Langevin splitting integrators, MCMC framework and alchemy
Pre-release
Pre-release
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
andGeodesicBAOABIntegrator
. - New base
CustomIntegrator
s:ThermostatedIntegrator
, which offers utilities for integrators that maintain the distribution at a certain temperature, andRestorableIntegrator
that enable restoring class members (e.g. temperature getter/setters) that are otherwise lost with OpenMM serialization. - New state classes
ThermodynamicState
,SamplerState
andCompoundThermodynamicState
that can be used to store and manipulate OpenMMSystem
s andContext
s. - New class
ContextCache
that centralizes the creation and caching of OpenMMContext
s by exploiting the mechanism of compatibility betweenThermodynamicState
s. - Imported existing MCMC framework (previously in
choderalab/openmmmcmc
) and adapted it to the new state classes.MCMCMove
s share aContextCache
to minimize the number of createdContext
s during the simulation. - Imported the
alchemy
module and adapted it to the new framework.AlchemicalState
can be used withCompoundThermodynamicState
to extendThermodynamicState
by composition.