Release History¶
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 to ignore velocities when building the dict representation of a SamplerState
. This can be useful for example
to save bandwidth when sending a SamplerState
over the network and velocities are not required (#386).
- Add DoubleWellDimer_WCAFluid
and DoubleWellChain_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 different
``AlchemicalState``s when the same alchemical parameter appeared in force objects split in different force groups. (#385)
Deprecated and API breaks¶
- Python 2 is not supported anymore.
- The
update_alchemical_charges
attribute of ``AlchemicalState`, 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
and AlchemicalState.set_alchemical_variable
have been
deprecated. Use AlchemicalState.get_alchemical_function
and AlchemicalState.set_alchemical_function
instead.
0.16.0 - Py2 deprecated, GlobalParameterState class, SamplerState reads CVs¶
New features¶
- Add ability for
SamplerState
to access new OpenMM Custom CV Force Variables (#362). SamplerState.update_from_context
now has keywords to support finer grain updating from the Context. This is only recommended for advanced users (#362).- Added the new class
states.GlobalParameterState
designed to simplify the implementation of composable states that control global variables (#363). - Allow restraint force classes to be controlled by a parameter other than
lambda_restraints
. This will enable multi-restraints simulations (#363).
Enhancements¶
- Global variables of integrators are now automatically copied over the integrator returned by
ContextCache.get_context
. It is possible to specify exception throughContextCache.INCOMPATIBLE_INTEGRATOR_ATTRIBUTES
(#364).
Others¶
- Integrator
MCMCMove``s now attempt to recover from NaN automatically by default (with ``n_restart_attempts
set to 4) (#364).
Deprecated¶
- Python2 is officially deprecated. Support will be dropped in future versions.
- Deprecated the signature of
IComposableState._on_setattr
to fix a bug where the objects were temporarily left in an inconsistent state when an exception was raised and caught. - Deprecated
update_alchemical_charges
inAlchemicalState
in anticipation of the new implementation of the exact PME that will be based on theNonbondedForce
offsets rather thanupdateParametersInContext()
.
0.15.0 - Restraint forces¶
0.14.0 - Exact treatment of alchemical PME electrostatics, water cluster test system, optimizations¶
New features¶
Enhancements¶
0.13.4 - Barostat/External Force Bugfix, Restart Robustness¶
Bug fixes¶
- Fixed implementation bug where
CustomExternalForce
restraining atoms to absolute coordinates caused an issue when a Barostat was used (#310)
Enhancements¶
- MCMC Integrators now attempt to re-initialize the
Context
object on the last restart attempt when NaN’s are encountered. This has internally been shown to correct some instances where normally resetting positions does not work around the NaN’s. This is a slow step relative to just resetting positions, but better than simulation crashing.
0.13.3 - Critical Bugfix to SamplerState Context Manipulation¶
0.13.2 - SamplerState Slicing and BitWise And/Or Ops¶
Added support for SamplerState slicing (#298)
Added bit operators and
and or
to math_eval
(#301)
0.13.1 - Bugfix release¶
0.13.0 - Alternative reaction field models, Langevin splitting MCMCMove¶
New Features¶
- Storage Interface module with automatic disk IO handling
- Option for shifted or switched Reaction Field
LangevinSplittingDynamic
MCMC move with specifiable sub step ordering- Nose-Hoover Chain Thermostat
Bug Fixes¶
- Many doc string cleanups
- Tests are based on released versions of OpenMM
- Tests also compare against development OpenMM, but do not fail because of it
- Fixed bug in Harmonic Oscillator tests’ error calculation
- Default collision rate in Langevin Integrators now matches docs
0.12.1 - Add virtual sites support in alchemy¶
0.12.0 - GB support in alchemy and new forces module¶
New features¶
- Add AbsoluteAlchemicalFactory support for all GB models (#250)
- Added
forces
andforcefactories
modules implementingUnishiftedReactionFieldForce
andreplace_reaction_field
respectively. The latter has been moved fromAbsoluteAlchemicalFactory
(#253) - Add
restrain_atoms
to restrain molecule conformation through an harmonic restrain (#255)
0.11.2 - Bugfix release¶
- Hotfix in fringe Python2/3 compatibility issue when using old style serialization systems in Python 2
0.11.1 - Optimizations¶
0.11.0 - Conda forge installation¶
New Features¶
LangevinIntegrator
now setsmeasure_heat=False
by default for increased performance (#211)AbsoluteAlchemicalFactory
now supportsdisable_alchemical_dispersion_correction
to prevent 600x slowdowns with nonequilibrium integration (#218)- We now require conda-forge as a dependency for testing and deployment (#216)
- Conda-forge added as channel to conda packages
0.10.0 - Optimizations of ThermodynamicState, renamed AlchemicalFactory¶
BREAKS API: Renamed AlchemicalFactory to AbsoluteAlchemicalFactory (#206)
Major optimizations of ThermodynamicState (#200, #205)
- Keep in memory only a single System object per compatible state
- Fast copy/deepcopy
- Enable custom optimized serialization for multiple states
Added readthedocs documentation (#191)
Bugfix for serialization of context when NaN encountered (#199)
Added tests for Python 3.6 (#184)
0.9.4 - Nonequilibrium integrators overhaul¶
Major changes¶
- Overhaul of
LangevinIntegrator
and subclasses to better support nonequilibrium integrators - Add true reaction-field support to
AlchemicalFactory
- Add some alchemical test systems
Updates to openmmtools.integrators.LangevinIntegrator
and friends¶
API-breaking changes¶
- The nonequilibrium integrators are now called
AlchemicalNonequilibriumLangevinIntegrator
andExternalPerturbationLangevinIntegrator
, and both are subclasses of a commonNonequilibriumLangevinIntegrator
that provides a consistent interface to setting and gettingprotocol_work
AlchemicalNonequilibriumLangevinIntegrator
now has a defaultalchemical_functions
to eliminate need for every test to treat it as a special case (#180)- The
get_protocol_work()
method allows you to retrieve the protocol work from anyNonequilibriumLangevinIntegrator
subclass and returns a unit-bearing work. The optionaldimensionless=True
argument returns a dimensionless float in units of kT. - Integrator global variables now store all energies in natural OpenMM units (kJ/mol) but the new accessor methods (see below) should b used instead of getting integrator global variables for work and heat. (#181)
- Any private methods for adding steps to the integrator have been prepended with
_
to hide them from the public API.
New features¶
- Order of arguments for all
LangevinIntegrator
derivatives matchesopenmm.LangevinIntegrator
so it can act as a drop-in replacement. (#176) - The
get_shadow_work()
andget_heat()
methods are now available for anyLangevinIntegrator
subclass, as well as the corresponding propertiesshadow_work
and heat. The functions also supportdimensionless=True.
(#163) - The
shadow_work
andheat
properties were added to all LangevinIntegrator subclasses, returning the values of these properties (if the integrator was constructed with the appropriatemeasure_shadow_work=True
ormeasure_heat=True
flags) as unit-bearing quantities - The
get_protocol_work()
andget_total_work()
methods are now available for anyNonequilibriumLangevinIntegrator
, returning unit-bearing quantities unlessdimensionless=True
is provided in which case they return the work in implicit units of kT.get_total_work()
requires the integrator to have been constructed withmeasure_shadow_work=True
. - The
protocol_work
andtotal_work
properties were added to allNonequilibriumLangevinIntegrator
subclasses, and return the unit-bearing work quantities.total_work
requires the integrator to have been constructed withmeasure_shadow_work=True
. - The subclasses have been reworked to support any kwargs that the base classes support, and defaults have all been made consistent.
- Various reset() methods have been added to reset statistics for all
LangevinIntegrator
subclasses. - All custom integrators support
.pretty_format()
and.pretty_print()
with optional highlighting of specific step types.
Bugfixes¶
- Zero-step perturbations now work correctly (#177)
AlchemicalNonequilibriumLangevinIntegrator
now correctly supports multipleH
steps.
Internal changes¶
- Adding new LangevinIntegrator step methods now uses a
self._register_step_method(step_string, callback_function, supports_force_groups=False)
call to simplify this process. - Code duplication has been reduced through the use of calling base class methods whenever possible.
run_nonequilibrium_switching()
test now uses BAR to test dragging a harmonic oscillator and tests a variety of integrator splittings(["O { V R H R V } O", "O V R H R V O", "R V O H O V R", "H R V O V R H"])
.- Integrator tests use deterministic PME and mixed precision when able.
Updates to openmmtools.alchemy.AlchemicalFactory¶
- Reaction field electrostatics now removes the shift, setting
c_rf = 0
. - A convenience method AlchemicalFactory.replace_reaction_field() has been added to allow fully-interacting systems to
be modified to force
c_rf = 0
by recoding reaction-field electrostatics as aCustomNonbondedForce
New openmmtools.testsystems
classes¶
- AlchemicalWaterBox was added, which has the first water molecule in the system alchemically modified