Releases: choderalab/openmmtools
Releases · choderalab/openmmtools
0.20.3 Bugfix Release
0.20.2 Bugfix Release
Remove leftover six
imports and xrange
See PR #504
0.20.1 Bugfix Release
This release fixes several bugs and eliminates cython compiled acceleration of replica-exchange all-swap
(replacing it with numba
) to enable working release on conda-forge.
Bug Fixes
0.20.0 - Periodic nonequilibrium integrator
0.19.0 - Multiple alchemical regions
New features
- Added support in
AbsoluteAlchemicalFactory
for handling multiple independent alchemical regions (#438). - Added support for anisotropic and membrane barostats in
ThermodynamicState
(#437`). - Added support for platform properties in ContextCache (e.g. for mixed and double precision CUDA in multistate sampler) (#437).
Bugfixes
- The multistate samplers now issue experimental API warnings via
logger.warn()
rather thanwarnings.warn()
(#446). - Fix return value in
states.reduced_potential_at_states
(#444).
Known issues
- Using parallel MPI processes causes poor mixing of the odd thermodynamic states while the mixing of the even states is normal. We're still investigating whether the issue is caused by a change in the MPI library or an internal bug. For now, we recommend running calculations using only 1 GPU (see also #449 and choderalab/yank#1130).
0.18.3 - Storage enhancements and bugfixes
Bugfixes
- Fixed a bug in
multistateanalyzer.py
where a function was imported fromopenmmtools.utils
instead ofopenmmtools.multistate.utils
(#430). - Fixed a few imprecisions in the documentation (#432).
Enhancements
- Writing on disk is much faster when the
checkpoint_interval
of multi-state samplers is large. This was due to the dimension of the netcdf chunk size increasing with the checkpoint interval and surpassing the dimension of the netcdf chunk cache. The chunk size of the iteration dimension is now always set to 1 (#432).
0.18.2 - Bugfix release
Bugfixes
- A bug in the multistate samplers where
logsumexp
was imported fromscipy.misc
(now inscipy.special
) was fixed (#423). - Improve the robustness of opening the netcdf file on resuming of the multi-state samplers by setting the environment variable
HDF5_USE_FILE_LOCKING
to'FALSE'
after 4 failed attempts (#426). - Fixed a bug causing a crash during exception handling (#426).
Other
- Update build infrastructure to match MolSSI cookiecutter (#424, #426).
0.18.1 - Bugfix release
This is a minor bugfix release.
New features
- Improvements for
HostGuest*
classes- add
oemols
,host_oemol
, andguest_oemol
properties to retrieve OpenEye ToolkitOEMol
objects (requires toolkit license and installation) - these classes can now accept overriding
kwargs
- add
Bugfixes
openmmtools.multistate
experimental API warning is only issued whenopenmmtools.multistate
is importedAlchemicalNonequilibriumLangevinIntegrator.reset()
now correctly resets the nonequilibrium work
0.18.0 - Added multistate samplers
Add a number of classes that can use MCMC to sample from multiple thermodynamic states:
MultiStateSampler
: sample independently from multiple thermodynamic statesReplicaExchangeSampler
: replica exchange among thermodynamic statesSAMSSampler
: self-adjusted mixture sampling (SAMS) sampling
All samplers can use MPI via the mpiplus
package.
0.17.0 - Removed Py2 support, faster exact PME treatment
New features
- Add
GlobalParameterFunction
that allows to enslave aGlobalParameter
to an arbitrary function of controlling variables (#380). - Allow ignoring velocities when building the dict representation of a
SamplerState
. This can be useful for example to save bandwidth when sending aSamplerState
over the network and velocities are not required (#386). - Add
DoubleWellDimer_WCAFluid
andDoubleWellChain_WCAFluid
test systems (#389).
Enhancements
- New implementation of the exact PME handling that uses the parameter offset feature in OpenMM 7.3. This comes with a
considerable speed improvement over the previous implementation (#380). - Exact PME is now the default for the
alchemical_pme_treatment
parameter in the constructor of
AbsoluteAchemicalFactory
(#386). - It is now possible to have multiple composable states exposing the same attributes/getter/setter in a
CompoundThermodynamicState
(#380).
Bug fixes
- Fixed a bug involving the
NoseHooverChainVelocityVerletIntegrator
withSystem
with constraints. The constraints were not taken into account when calculating the number of degrees of freedom resulting in the temperature not converging to the target value. (#384) - Fixed a bug affecting
reduced_potential_at_states
when computing the reduced potential of systems in differentAlchemicalState
s when the same alchemical parameter appeared in force objects split into different force groups. (#385)
Deprecated and API breaks
- Python 2 and 3.5 is not supported anymore.
- The
update_alchemical_charges
attribute ofAlchemicalState
, which was deprecated in 0.16.0, has now been removed since it doesn't make sense with the new parameter offset implementation. - The methods
AlchemicalState.get_alchemical_variable
andAlchemicalState.set_alchemical_variable
have been deprecated. UseAlchemicalState.get_alchemical_function
andAlchemicalState.set_alchemical_function
instead.