openmmtools.integrators.MTSIntegrator

class openmmtools.integrators.MTSIntegrator(timestep=Quantity(value=1.0, unit=femtosecond), groups=[(0, 1)])[source]

MTSIntegrator implements the rRESPA multiple time step integration algorithm.

This integrator allows different forces to be evaluated at different frequencies, for example to evaluate the expensive, slowly changing forces less frequently than the inexpensive, quickly changing forces.

To use it, you must first divide your forces into two or more groups (by calling setForceGroup() on them) that should be evaluated at different frequencies. When you create the integrator, you provide a tuple for each group specifying the index of the force group and the frequency (as a fraction of the outermost time step) at which to evaluate it. For example:

>>> integrator = MTSIntegrator(4*unit.femtoseconds, [(0,1), (1,2), (2,8)])

This specifies that the outermost time step is 4 fs, so each step of the integrator will advance time by that much. It also says that force group 0 should be evaluated once per time step, force group 1 should be evaluated twice per time step (every 2 fs), and force group 2 should be evaluated eight times per time step (every 0.5 fs).

For details, see Tuckerman et al., J. Chem. Phys. 97(3) pp. 1990-2001 (1992).

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.
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.
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.
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.
step(self, steps) Advance a simulation through time by taking a series of time steps.
__init__(timestep=Quantity(value=1.0, unit=femtosecond), groups=[(0, 1)])[source]

Create an MTSIntegrator.

Parameters:
timestep : unit.Quantity with units compatible with femtoseconds, optional default=1*femtoseconds

The largest (outermost) integration time step to use.

groups : list of tuples, optional, default=(0,1)

A list of tuples defining the force groups. The first element of each tuple is the force group index, and the second element is the number of times that force group should be evaluated in one time step.

Methods

__init__([timestep, unit, groups]) Create an MTSIntegrator.
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.
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.
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.
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.
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
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

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

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

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

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