openmmtools.integrators.LangevinIntegrator¶
- class openmmtools.integrators.LangevinIntegrator(temperature=Quantity(value=298.0, unit=kelvin), collision_rate=Quantity(value=1.0, unit=/picosecond), timestep=Quantity(value=1.0, unit=femtosecond), splitting='V R O R V', constraint_tolerance=1e-08, measure_shadow_work=False, measure_heat=False)[source]¶
Integrates Langevin dynamics with a prescribed operator splitting.
- One way to divide the Langevin system is into three parts which can each be solved “exactly:”
- R: Linear “drift” / Constrained “drift”
Deterministic update of positions, using current velocities x <- x + v dt
- V: Linear “kick” / Constrained “kick”
Deterministic update of velocities, using current forces v <- v + (f/m) dt
where f = force, m = mass
- O: Ornstein-Uhlenbeck
Stochastic update of velocities, simulating interaction with a heat bath v <- av + b sqrt(kT/m) R
where a = e^(-gamma dt) b = sqrt(1 - e^(-2gamma dt)) R is i.i.d. standard normal
We can then construct integrators by solving each part for a certain timestep in sequence. (We can further split up the V step by force group, evaluating cheap but fast-fluctuating forces more frequently than expensive but slow-fluctuating forces. Since forces are only evaluated in the V step, we represent this by including in our “alphabet” V0, V1, …)
When the system contains holonomic constraints, these steps are confined to the constraint manifold.
References
[Leimkuhler and Matthews, 2015] Molecular dynamics: with deterministic and stochastic numerical methods, Chapter 7
Examples
- VVVR
splitting=”O V R V O”
- BAOAB:
splitting=”V R O R V”
- g-BAOAB, with K_r=3:
splitting=”V R R R O R R R V”
- g-BAOAB with solvent-solute splitting, K_r=K_p=2:
splitting=”V0 V1 R R O R R V1 R R O R R V1 V0”
- Attributes:
- _kinetic_energystr
This is 0.5*m*v*v by default, and is the expression used for the kinetic energy
- shadow_workunit.Quantity with units of energy
Shadow work (if integrator was constructed with measure_shadow_work=True)
- heatunit.Quantity with units of energy
Heat (if integrator was constructed with measure_heat=True)
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__(temperature=Quantity(value=298.0, unit=kelvin), collision_rate=Quantity(value=1.0, unit=/picosecond), timestep=Quantity(value=1.0, unit=femtosecond), splitting='V R O R V', constraint_tolerance=1e-08, measure_shadow_work=False, measure_heat=False)[source]¶
Create a Langevin integrator with the prescribed operator splitting.
- Parameters:
- splittingstring, default: “V R O R V”
Sequence of “R”, “V”, “O” (and optionally “{”, “}”, “V0”, “V1”, …) substeps to be executed each timestep.
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 “}”.
- temperaturenp.unit.Quantity compatible with kelvin, default: 298.0*unit.kelvin
Fictitious “bath” temperature
- collision_ratenp.unit.Quantity compatible with 1/picoseconds, default: 1.0/unit.picoseconds
Collision rate
- timestepnp.unit.Quantity compatible with femtoseconds, default: 1.0*unit.femtoseconds
Integration timestep
- constraint_tolerancefloat, default: 1.0e-8
Tolerance for constraint solver
- measure_shadow_workboolean, default: False
Accumulate the shadow work performed by the symplectic substeps, in the global shadow_work
- measure_heatboolean, default: False
Accumulate the heat exchanged with the bath in each step, in the global heat
Methods
__init__
([temperature, collision_rate, ...])Create a Langevin integrator with the prescribed operator splitting.
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