openmmtools.integrators.GHMCIntegrator

class openmmtools.integrators.GHMCIntegrator(*args, **kwargs)

Create a generalized hybrid Monte Carlo (GHMC) integrator.

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

shadow_work

thisown

The membership flag

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_shadow_work([dimensionless])	Get the current accumulated shadow 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 (heat, shadow work, acceptance rates, step).
reset_ghmc_statistics()	Reset GHMC acceptance rate statistics.
reset_heat()	Reset heat.
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__(*args, **kwargs)

Parameters:

temperatureunit.Quantity compatible with kelvin, default: 298*unit.kelvin

The temperature.

collision_rateunit.Quantity compatible with 1/picoseconds, default: 91.0/unit.picoseconds

The collision rate.

timestepunit.Quantity compatible with femtoseconds, default: 1.0*unit.femtoseconds

The integration timestep.

Notes

This integrator is equivalent to a Langevin integrator in the velocity Verlet discretization with a Metrpolization step to ensure sampling from the appropriate distribution.

Additional global variables ‘ntrials’ and ‘naccept’ keep track of how many trials have been attempted and accepted, respectively.

References

Lelievre T, Stoltz G, and Rousset M. Free Energy Computations: A Mathematical Perspective http://www.amazon.com/Free-Energy-Computations-Mathematical-Perspective/dp/1848162472

Examples

Create a GHMC integrator.

>>> temperature = 298.0 * unit.kelvin
>>> collision_rate = 1.0 / unit.picoseconds
>>> timestep = 1.0 * unit.femtoseconds
>>> integrator = GHMCIntegrator(temperature, collision_rate, timestep)

Methods

__init__(*args, **kwargs)	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_shadow_work([dimensionless])	Get the current accumulated shadow 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 (heat, shadow work, acceptance rates, step).
reset_ghmc_statistics()	Reset GHMC acceptance rate statistics.
reset_heat()	Reset heat.
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
shadow_work
thisown	The membership flag