openmmtools.integrators.GeodesicBAOABIntegrator

class openmmtools.integrators.GeodesicBAOABIntegrator(*args, **kwargs)[source]

Create a geodesic-BAOAB integrator.

Attributes:
acceptance_rate

Get acceptance rate for Metropolized integrators.

heat
is_metropolized

Return True if this integrator is Metropolized, False otherwise.

kT

The thermal energy in simtk.openmm.Quantity

shadow_work

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.
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(self, index) getPerDofVariable(self, index) -> PyObject *
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(self, index) getTabulatedFunction(self, index) -> TabulatedFunction
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.
reset_steps() Reset step counter.
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.
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)[source]

Create a geodesic BAOAB Langevin integrator.

Parameters:
K_r : integer, default: 2

Number of geodesic drift steps.

temperature : np.unit.Quantity compatible with kelvin, default: 298.0*unit.kelvin

Fictitious “bath” temperature

collision_rate : np.unit.Quantity compatible with 1/picoseconds, default: 1.0/unit.picoseconds

Collision rate

timestep : np.unit.Quantity compatible with femtoseconds, default: 1.0*unit.femtoseconds

Integration timestep

constraint_tolerance : float, default: 1.0e-8

Tolerance for constraint solver

measure_shadow_work : boolean, default: False

Accumulate the shadow work performed by the symplectic substeps, in the global shadow_work

measure_heat : boolean, default: False

Accumulate the heat exchanged with the bath in each step, in the global heat

References

[Leimkuhler and Matthews, 2016] Efficient molecular dynamics using geodesic integration and solvent-solute splitting http://rspa.royalsocietypublishing.org/content/472/2189/20160138

Examples

Create a geodesic BAOAB integrator. >>> temperature = 298.0 * unit.kelvin >>> collision_rate = 1.0 / unit.picoseconds >>> timestep = 1.0 * unit.femtoseconds >>> integrator = GeodesicBAOABIntegrator(K_r=3, temperature=temperature, collision_rate=collision_rate, timestep=timestep)

Methods

__init__(*args, **kwargs) Create a geodesic BAOAB Langevin integrator.
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.
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(self, index) getPerDofVariable(self, index) -> PyObject *
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(self, index) getTabulatedFunction(self, index) -> TabulatedFunction
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.
reset_steps() Reset step counter.
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.
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.
heat
is_metropolized Return True if this integrator is Metropolized, False otherwise.
kT The thermal energy in simtk.openmm.Quantity
shadow_work
acceptance_rate

Get acceptance rate for Metropolized integrators.

addComputeGlobal(self, variable, expression) → int

Add a step to the integration algorithm that computes a global value.

Parameters:
variable : string

the global variable to store the computed value into

expression : string

a mathematical expression involving only global variables. In each integration step, its value is computed and stored into the specified variable.

Returns:
int

the index of the step that was added

addComputePerDof(self, variable, expression) → int

Add a step to the integration algorithm that computes a per-DOF value.

Parameters:
variable : string

the per-DOF variable to store the computed value into

expression : string

a mathematical expression involving both global and per-DOF variables. In each integration step, its value is computed for every degree of freedom and stored into the specified variable.

Returns:
int

the index of the step that was added

addComputeSum(self, variable, expression) → int

Add a step to the integration algorithm that computes a sum over degrees of freedom.

Parameters:
variable : string

the global variable to store the computed value into

expression : string

a mathematical expression involving both global and per-DOF variables. In each integration step, its value is computed for every degree of freedom. Those values are then added together, and the sum is stored in the specified variable.

Returns:
int

the index of the step that was added

addComputeTemperatureDependentConstants(compute_per_dof)

Wrap the ComputePerDof into an if-block executed only when kT changes.

Parameters:
compute_per_dof : dict of str: str

A dictionary of variable_name: expression.

addConstrainPositions(self) → int

Add a step to the integration algorithm that updates particle positions so all constraints are satisfied.

Returns:
int

the index of the step that was added

addConstrainVelocities(self) → int

Add a step to the integration algorithm that updates particle velocities so the net velocity along all constraints is 0.

Returns:
int

the index of the step that was added

addGlobalVariable(self, name, initialValue) → int

Define a new global variable.

Parameters:
name : string

the name of the variable

initialValue : double

the variable will initially be set to this value

Returns:
int

the index of the variable that was added

addPerDofVariable(self, name, initialValue) → int

Define a new per-DOF variable.

Parameters:
name : string

the name of the variable

initialValue : double

the variable will initially be set to this value for all degrees of freedom

Returns:
int

the index of the variable that was added

addTabulatedFunction(self, name, function) → int

Add a tabulated function that may appear in expressions.

Parameters:
name : string

the name of the function as it appears in expressions

function : TabulatedFunction *

a TabulatedFunction object defining the function. The TabulatedFunction should have been created on the heap with the “new” operator. The integrator takes over ownership of it, and deletes it when the integrator itself is deleted.

Returns:
int

the index of the function that was added

addUpdateContextState(self) → int

Add a step to the integration algorithm that allows Forces to update the context state.

Returns:
int

the index of the step that was added

beginIfBlock(self, condition) → int

Add a step which begins a new “if” block.

Parameters:
condition : string

a mathematical expression involving a comparison operator and global variables. All steps between this one and the end of the block are executed only if the condition is true.

Returns:
int

the index of the step that was added

beginWhileBlock(self, condition) → int

Add a step which begins a new “while” block.

Parameters:
condition : string

a mathematical expression involving a comparison operator and global variables. All steps between this one and the end of the block are executed repeatedly as long as the condition remains true.

Returns:
int

the index of the step that was added

classmethod deserialize_xml(xml_serialization)

Shortcut to deserialize the XML representation and the restore interface.

Parameters:
xml_serialization : str

The XML representation of the OpenMM custom force/integrator.

Returns:
openmm_object

The deserialized OpenMM force/integrator with the original interface restored (if restorable).

endBlock(self) → int

Add a step which marks the end of the most recently begun “if” or “while” block.

Returns:
int

the index of the step that was added

getComputationStep(self, index)

Get the details of a computation step that has been added to the integration algorithm.

Parameters:
index : int

the index of the computation step to get

Returns:
type : ComputationType

the type of computation this step performs

variable : string

the variable into which this step stores its result. If this step does not store a result in a variable, this will be an empty string.

expression : string

the expression this step evaluates. If this step does not evaluate an expression, this will be an empty string.

getConstraintTolerance(self) → double

Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.

getGlobalVariable(self, index) → double

Get the current value of a global variable.

Parameters:
index : int

the index of the variable to get

Returns:
double

the current value of the variable

getGlobalVariableByName(self, name) → double

Get the current value of a global variable, specified by name.

Parameters:
name : string

the name of the variable to get

Returns:
double

the current value of the parameter

getGlobalVariableName(self, index) → std::string const &

Get the name of a global variable.

Parameters:
index : int

the index of the variable to get

Returns:
string

the name of the variable

getKineticEnergyExpression(self) → std::string const &

Get the expression to use for computing the kinetic energy. The expression is evaluated for every degree of freedom. Those values are then added together, and the sum is reported as the current kinetic energy.

getNumComputations(self) → int

Get the number of computation steps that have been added.

getNumGlobalVariables(self) → int

Get the number of global variables that have been defined.

getNumPerDofVariables(self) → int

Get the number of per-DOF variables that have been defined.

getNumTabulatedFunctions(self) → int

Get the number of tabulated functions that have been defined.

getPerDofVariable(self, index)

getPerDofVariable(self, index) -> PyObject *

getPerDofVariableByName(self, name)

Get the value of a per-DOF variable, specified by name.

Parameters:
name : string

the name of the variable to get

Returns:
values : vector< Vec3 >

the values of the variable for all degrees of freedom are stored into this

getPerDofVariableName(self, index) → std::string const &

Get the name of a per-DOF variable.

Parameters:
index : int

the index of the variable to get

Returns:
string

the name of the variable

getRandomNumberSeed(self) → int

Get the random number seed. See setRandomNumberSeed() for details.

getStepSize(self) → double

Get the size of each time step, in picoseconds. If this integrator uses variable time steps, the size of the most recent step is returned.

Returns:
double

the step size, measured in ps

getTabulatedFunction(self, index) → TabulatedFunction

getTabulatedFunction(self, index) -> TabulatedFunction

Get a reference to a tabulated function that may appear in expressions.

Parameters:
index : int

the index of the function to get

Returns:
TabulatedFunction

the TabulatedFunction object defining the function

getTabulatedFunctionName(self, index) → std::string const &

Get the name of a tabulated function that may appear in expressions.

Parameters:
index : int

the index of the function to get

Returns:
string

the name of the function as it appears in expressions

getTemperature()

Return the temperature of the heat bath.

Returns:
temperature : unit.Quantity

The temperature of the heat bath in kelvins.

get_acceptance_rate()

Get acceptance rate for Metropolized integrators.

Returns:
acceptance_rate : float

Acceptance rate. An Exception is thrown if the integrator is not Metropolized.

get_heat(dimensionless=False)

Get the current accumulated heat.

Parameters:
dimensionless : bool, optional, default=False

If specified, the work is returned in reduced (kT) unit.

Returns:
work : unit.Quantity or float

If dimensionless=True, the heat in kT (float). Otherwise, the unit-bearing heat in units of energy.

get_shadow_work(dimensionless=False)

Get the current accumulated shadow work.

Parameters:
dimensionless : bool, optional, default=False

If specified, the work is returned in reduced (kT) unit.

Returns:
work : unit.Quantity or float

If dimensionless=True, the protocol work in kT (float). Otherwise, the unit-bearing protocol work in units of energy.

is_metropolized

Return True if this integrator is Metropolized, False otherwise.

classmethod is_restorable(openmm_object)

Check if the custom integrator or force has a restorable interface.

Parameters:
openmm_object : object

The custom integrator or force to check.

Returns:
True if the object has a restorable interface, False otherwise.
classmethod is_thermostated(integrator)

Return true if the integrator is a ThermostatedIntegrator.

This can be useful when you only have access to the Context CustomIntegrator, which loses all extra function during serialization.

Parameters:
integrator : simtk.openmm.Integrator

The integrator to check.

Returns:
True if the original CustomIntegrator class inherited from
ThermostatedIntegrator, False otherwise.
kT

The thermal energy in simtk.openmm.Quantity

pretty_format(as_list=False, step_types_to_highlight=None)

Generate a human-readable version of each integrator step.

Parameters:
as_list : bool, optional, default=False

If True, a list of human-readable strings will be returned. If False, these will be concatenated into a single human-readable string.

step_types_to_highlight : list of int, optional, default=None

If specified, these step types will be highlighted.

Returns:
readable_lines : list of str

A list of human-readable versions of each step of the integrator

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.

reset_steps()

Reset step counter.

classmethod restore_interface(integrator)

Restore the original interface of a CustomIntegrator.

The function restore the methods of the original class that inherited from ThermostatedIntegrator. Return False if the interface could not be restored.

Parameters:
integrator : simtk.openmm.CustomIntegrator

The integrator to which add methods.

Returns:
True if the original class interface could be restored, False otherwise.
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.

Parameters:
index : int

the index of the variable to set

value : double

the new value of the variable

setGlobalVariableByName(self, name, value)

Set the value of a global variable, specified by name.

Parameters:
name : string

the name of the variable to set

value : double

the new value of the variable

setKineticEnergyExpression(self, expression)

Set the expression to use for computing the kinetic energy. The expression is evaluated for every degree of freedom. Those values are then added together, and the sum is reported as the current kinetic energy.

setPerDofVariable(self, index, values)

Set the value of a per-DOF variable.

Parameters:
index : int

the index of the variable to set

values : vector< Vec3 >

the new values of the variable for all degrees of freedom

setPerDofVariableByName(self, name, values)

Set the value of a per-DOF variable, specified by name.

Parameters:
name : string

the name of the variable to set

values : vector< Vec3 >

the new values of the variable for all degrees of freedom

setRandomNumberSeed(self, seed)

Set the random number seed. The precise meaning of this parameter is undefined, and is left up to each Platform to interpret in an appropriate way. It is guaranteed that if two simulations are run with different random number seeds, the sequence of random numbers will be different. On the other hand, no guarantees are made about the behavior of simulations that use the same seed. In particular, Platforms are permitted to use non-deterministic algorithms which produce different results on successive runs, even if those runs were initialized identically.

If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context is created from this Force. This is done to ensure that each Context receives unique random seeds without you needing to set them explicitly.

setStepSize(self, size)

Set the size of each time step, in picoseconds. If this integrator uses variable time steps, the effect of calling this method is undefined, and it may simply be ignored.

Parameters:
size : double

the step size, measured in ps

setTemperature(temperature)

Set the temperature of the heat bath.

Parameters:
temperature : unit.Quantity

The new temperature of the heat bath (temperature units).

step(self, steps)

Advance a simulation through time by taking a series of time steps.

Parameters:
steps : int

the number of time steps to take