openmmtools.integrators.PeriodicNonequilibriumIntegrator¶

class openmmtools.integrators.PeriodicNonequilibriumIntegrator(alchemical_functions=None, nsteps_eq=1000, nsteps_neq=100, splitting='V R H O R V', **kwargs)[source]¶

Periodic nonequilibrium integrator where master alchemical parameter lambda is driven through a periodic protocol:

eq 0 for nsteps_eq | neq 0->1 over nsteps_neq | eq 1 for nsteps_eq | neq 1->0 for nsteps_neq

Arbitrary Langevin splitting strings can be provided.

Warning

This API is experimental, and subject to change.

Examples

Create a nonequilibrium integrator to switch the center of a harmonic oscillator between two locations, dwelling in either state to allow equilibration. This example uses BAOAB (V R O R V) for integration.

>>> # Create harmonic oscillator testsystem
>>> from openmmtools import testsystems
>>> import openmm
>>> from openmm import unit
>>> testsystem = testsystems.HarmonicOscillator()
>>> # Create a nonequilibrium alchemical integrator
>>> alchemical_functions = { 'testsystems_HarmonicOscillator_x0' : 'lambda' }
>>> nsteps_eq = 100 # number of steps to dwell in equilibrium at lambda = 0 or 1
>>> nsteps_neq = 50 # number of steps in the switching trajectory where lambda is switched from 0 to 1
>>> integrator = PeriodicAlchemicalNonequilibriumLangevinIntegrator(
...                  temperature=300*unit.kelvin, collision_rate=1.0/unit.picoseconds, timestep=1.0*unit.femtoseconds,
...                  alchemical_functions=alchemical_functions, splitting="V R H O R V",
...                  nsteps_eq=nsteps_eq, nsteps_neq=nsteps_neq)
>>> # Create a Context
>>> context = openmm.Context(testsystem.system, integrator)
>>> # Run one periodic cycle: (eq 0) > (neq 0->1) > (eq 1) > (neq 1->0)
>>> context.setPositions(testsystem.positions)
>>> nsteps_per_period = 2*nsteps_eq + 2*nsteps_neq
>>> integrator.step(nsteps_per_period)
>>> protocol_work = integrator.protocol_work # retrieve protocol work (excludes shadow work)
>>> total_work = integrator.total_work # retrieve total work (includes shadow work, if requested)
>>> # Run another cycle
>>> integrator.step(nsteps_per_period)
>>> # Reset and run again
>>> context.setPositions(testsystem.positions)
>>> integrator.reset()
>>> integrator.step(nsteps_per_period)

Attributes:

acceptance_rate: Get acceptance rate for Metropolized integrators.
global_variable_names: The set of global variable names defined for this integrator.
heat
is_metropolized: Return True if this integrator is Metropolized, False otherwise.
kT: The thermal energy in openmm.Quantity
protocol_work: Total protocol work in energy units.
shadow_work
thisown: The membership flag
total_work: Total work (protocol work plus shadow work) in energy units.

Methods

`addComputeGlobal`(self, variable, expression)	Add a step to the integration algorithm that computes a global value.
`addComputePerDof`(self, variable, expression)	Add a step to the integration algorithm that computes a per-DOF value.
`addComputeSum`(self, variable, expression)	Add a step to the integration algorithm that computes a sum over degrees of freedom.
`addComputeTemperatureDependentConstants`(...)	Wrap the ComputePerDof into an if-block executed only when kT changes.
`addConstrainPositions`(self)	Add a step to the integration algorithm that updates particle positions so all constraints are satisfied.
`addConstrainVelocities`(self)	Add a step to the integration algorithm that updates particle velocities so the net velocity along all constraints is 0.
`addGlobalVariable`(self, name, initialValue)	Define a new global variable.
`addPerDofVariable`(self, name, initialValue)	Define a new per-DOF variable.
`addTabulatedFunction`(self, name, function)	Add a tabulated function that may appear in expressions.
`addUpdateContextState`(self)	Add a step to the integration algorithm that allows Forces to update the context state.
`beginIfBlock`(self, condition)	Add a step which begins a new "if" block.
`beginWhileBlock`(self, condition)	Add a step which begins a new "while" block.
`deserialize_xml`(xml_serialization)	Shortcut to deserialize the XML representation and the restore interface.
`endBlock`(self)	Add a step which marks the end of the most recently begun "if" or "while" block.
`getComputationStep`(self, index)	Get the details of a computation step that has been added to the integration algorithm.
`getConstraintTolerance`(self)	Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
`getGlobalVariable`(self, index)	Get the current value of a global variable.
`getGlobalVariableByName`(self, name)	Get the current value of a global variable, specified by name.
`getGlobalVariableName`(self, index)	Get the name of a global variable.
`getIntegrationForceGroups`(self)	Get which force groups to use for integration.
`getKineticEnergyExpression`(self)	Get the expression to use for computing the kinetic energy.
`getNumComputations`(self)	Get the number of computation steps that have been added.
`getNumGlobalVariables`(self)	Get the number of global variables that have been defined.
`getNumPerDofVariables`(self)	Get the number of per-DOF variables that have been defined.
`getNumTabulatedFunctions`(self)	Get the number of tabulated functions that have been defined.
`getPerDofVariable`()
`getPerDofVariableByName`(self, name)	Get the value of a per-DOF variable, specified by name.
`getPerDofVariableName`(self, index)	Get the name of a per-DOF variable.
`getRandomNumberSeed`(self)	Get the random number seed.
`getStepSize`(self)	Get the size of each time step, in picoseconds.
`getTabulatedFunction`(-> TabulatedFunction)	Get a reference to a tabulated function that may appear in expressions.
`getTabulatedFunctionName`(self, index)	Get the name of a tabulated function that may appear in expressions.
`getTemperature`()	Return the temperature of the heat bath.
`get_acceptance_rate`()	Get acceptance rate for Metropolized integrators.
`get_heat`([dimensionless])	Get the current accumulated heat.
`get_protocol_work`([dimensionless])	Get the current accumulated protocol work.
`get_shadow_work`([dimensionless])	Get the current accumulated shadow work.
`get_total_work`([dimensionless])	Get the current accumulated total work.
`is_restorable`(openmm_object)	Check if the custom integrator or force has a restorable interface.
`is_thermostated`(integrator)	Return true if the integrator is a ThermostatedIntegrator.
`pretty_format`([as_list, step_types_to_highlight])	Generate a human-readable version of each integrator step.
`pretty_print`()	Pretty-print the computation steps of this integrator.
`reset`()	Reset all statistics, alchemical parameters, and work.
`reset_ghmc_statistics`()	Reset GHMC acceptance rate statistics.
`reset_heat`()	Reset heat.
`reset_protocol_work`()	Reset the protocol work.
`reset_shadow_work`()	Reset shadow work.
`restore_interface`(integrator)	Restore the original interface of a CustomIntegrator.
`setConstraintTolerance`(self, tol)	Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
`setGlobalVariable`(self, index, value)	Set the value of a global variable.
`setGlobalVariableByName`(self, name, value)	Set the value of a global variable, specified by name.
`setIntegrationForceGroups`(groups)	Set which force groups to use for integration.
`setKineticEnergyExpression`(self, expression)	Set the expression to use for computing the kinetic energy.
`setPerDofVariable`(self, index, values)	Set the value of a per-DOF variable.
`setPerDofVariableByName`(self, name, values)	Set the value of a per-DOF variable, specified by name.
`setRandomNumberSeed`(self, seed)	Set the random number seed.
`setStepSize`(self, size)	Set the size of each time step, in picoseconds.
`setTemperature`(temperature)	Set the temperature of the heat bath.
`step`(self, steps)	Advance a simulation through time by taking a series of time steps.

__init__(alchemical_functions=None, nsteps_eq=1000, nsteps_neq=100, splitting='V R H O R V', **kwargs)[source]¶

Parameters:

nsteps_eqint, optional, default=1000

Number of equilibration steps to dwell within lambda = 0 or 1 when reached

nsteps_neqint, optional, default=100

Number of nonequilibrium switching steps for 0->1 and 1->0 switches

splittingstring, default: “V R H O R V”

Sequence of “R”, “V”, “O” (and optionally “{”, “}”, “V0”, “V1”, …) substeps to be executed each timestep. “H” increments the global parameter lambda by 1/nsteps_neq for each step and accumulates protocol work.

Forces are only used in V-step. Handle multiple force groups by appending the force group index to V-steps, e.g. “V0” will only use forces from force group 0. “V” will perform a step using all forces. { will cause Metropolization, and must be followed later by a }.

Methods

`__init__`([alchemical_functions, nsteps_eq, ...])	Parameters:
`addComputeGlobal`(self, variable, expression)	Add a step to the integration algorithm that computes a global value.
`addComputePerDof`(self, variable, expression)	Add a step to the integration algorithm that computes a per-DOF value.
`addComputeSum`(self, variable, expression)	Add a step to the integration algorithm that computes a sum over degrees of freedom.
`addComputeTemperatureDependentConstants`(...)	Wrap the ComputePerDof into an if-block executed only when kT changes.
`addConstrainPositions`(self)	Add a step to the integration algorithm that updates particle positions so all constraints are satisfied.
`addConstrainVelocities`(self)	Add a step to the integration algorithm that updates particle velocities so the net velocity along all constraints is 0.
`addGlobalVariable`(self, name, initialValue)	Define a new global variable.
`addPerDofVariable`(self, name, initialValue)	Define a new per-DOF variable.
`addTabulatedFunction`(self, name, function)	Add a tabulated function that may appear in expressions.
`addUpdateContextState`(self)	Add a step to the integration algorithm that allows Forces to update the context state.
`beginIfBlock`(self, condition)	Add a step which begins a new "if" block.
`beginWhileBlock`(self, condition)	Add a step which begins a new "while" block.
`deserialize_xml`(xml_serialization)	Shortcut to deserialize the XML representation and the restore interface.
`endBlock`(self)	Add a step which marks the end of the most recently begun "if" or "while" block.
`getComputationStep`(self, index)	Get the details of a computation step that has been added to the integration algorithm.
`getConstraintTolerance`(self)	Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
`getGlobalVariable`(self, index)	Get the current value of a global variable.
`getGlobalVariableByName`(self, name)	Get the current value of a global variable, specified by name.
`getGlobalVariableName`(self, index)	Get the name of a global variable.
`getIntegrationForceGroups`(self)	Get which force groups to use for integration.
`getKineticEnergyExpression`(self)	Get the expression to use for computing the kinetic energy.
`getNumComputations`(self)	Get the number of computation steps that have been added.
`getNumGlobalVariables`(self)	Get the number of global variables that have been defined.
`getNumPerDofVariables`(self)	Get the number of per-DOF variables that have been defined.
`getNumTabulatedFunctions`(self)	Get the number of tabulated functions that have been defined.
`getPerDofVariable`()
`getPerDofVariableByName`(self, name)	Get the value of a per-DOF variable, specified by name.
`getPerDofVariableName`(self, index)	Get the name of a per-DOF variable.
`getRandomNumberSeed`(self)	Get the random number seed.
`getStepSize`(self)	Get the size of each time step, in picoseconds.
`getTabulatedFunction`(-> TabulatedFunction)	Get a reference to a tabulated function that may appear in expressions.
`getTabulatedFunctionName`(self, index)	Get the name of a tabulated function that may appear in expressions.
`getTemperature`()	Return the temperature of the heat bath.
`get_acceptance_rate`()	Get acceptance rate for Metropolized integrators.
`get_heat`([dimensionless])	Get the current accumulated heat.
`get_protocol_work`([dimensionless])	Get the current accumulated protocol work.
`get_shadow_work`([dimensionless])	Get the current accumulated shadow work.
`get_total_work`([dimensionless])	Get the current accumulated total work.
`is_restorable`(openmm_object)	Check if the custom integrator or force has a restorable interface.
`is_thermostated`(integrator)	Return true if the integrator is a ThermostatedIntegrator.
`pretty_format`([as_list, step_types_to_highlight])	Generate a human-readable version of each integrator step.
`pretty_print`()	Pretty-print the computation steps of this integrator.
`reset`()	Reset all statistics, alchemical parameters, and work.
`reset_ghmc_statistics`()	Reset GHMC acceptance rate statistics.
`reset_heat`()	Reset heat.
`reset_protocol_work`()	Reset the protocol work.
`reset_shadow_work`()	Reset shadow work.
`restore_interface`(integrator)	Restore the original interface of a CustomIntegrator.
`setConstraintTolerance`(self, tol)	Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
`setGlobalVariable`(self, index, value)	Set the value of a global variable.
`setGlobalVariableByName`(self, name, value)	Set the value of a global variable, specified by name.
`setIntegrationForceGroups`(groups)	Set which force groups to use for integration.
`setKineticEnergyExpression`(self, expression)	Set the expression to use for computing the kinetic energy.
`setPerDofVariable`(self, index, values)	Set the value of a per-DOF variable.
`setPerDofVariableByName`(self, name, values)	Set the value of a per-DOF variable, specified by name.
`setRandomNumberSeed`(self, seed)	Set the random number seed.
`setStepSize`(self, size)	Set the size of each time step, in picoseconds.
`setTemperature`(temperature)	Set the temperature of the heat bath.
`step`(self, steps)	Advance a simulation through time by taking a series of time steps.

Attributes

`BlockEnd`
`ComputeGlobal`
`ComputePerDof`
`ComputeSum`
`ConstrainPositions`
`ConstrainVelocities`
`IfBlockStart`
`UpdateContextState`
`WhileBlockStart`
`acceptance_rate`	Get acceptance rate for Metropolized integrators.
`global_variable_names`	The set of global variable names defined for this integrator.
`heat`
`is_metropolized`	Return True if this integrator is Metropolized, False otherwise.
`kT`	The thermal energy in openmm.Quantity
`protocol_work`	Total protocol work in energy units.
`shadow_work`
`thisown`	The membership flag
`total_work`	Total work (protocol work plus shadow work) in energy units.

openmmtools.integrators.PeriodicNonequilibriumIntegrator¶

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