CustomIntegrator Class Reference

This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms. More...

Inheritance diagram for CustomIntegrator:

Public Member Functions
def	getNumGlobalVariables
	getNumGlobalVariables(CustomIntegrator self) -> int
def	getNumPerDofVariables
	getNumPerDofVariables(CustomIntegrator self) -> int
def	getNumComputations
	getNumComputations(CustomIntegrator self) -> int
def	addGlobalVariable
	addGlobalVariable(CustomIntegrator self, std::string const & name, double initialValue) -> int
def	getGlobalVariableName
	getGlobalVariableName(CustomIntegrator self, int index) -> std::string const &
def	addPerDofVariable
	addPerDofVariable(CustomIntegrator self, std::string const & name, double initialValue) -> int
def	getPerDofVariableName
	getPerDofVariableName(CustomIntegrator self, int index) -> std::string const &
def	getGlobalVariable
	getGlobalVariable(CustomIntegrator self, int index) -> double
def	setGlobalVariable
	setGlobalVariable(CustomIntegrator self, int index, double value)
def	setGlobalVariableByName
	setGlobalVariableByName(CustomIntegrator self, std::string const & name, double value)
def	setPerDofVariable
	setPerDofVariable(CustomIntegrator self, int index, std::vector< Vec3,std::allocator< Vec3 > > const & values)
def	setPerDofVariableByName
	setPerDofVariableByName(CustomIntegrator self, std::string const & name, std::vector< Vec3,std::allocator< Vec3 > > const & values)
def	addComputeGlobal
	addComputeGlobal(CustomIntegrator self, std::string const & variable, std::string const & expression) -> int
def	addComputePerDof
	addComputePerDof(CustomIntegrator self, std::string const & variable, std::string const & expression) -> int
def	addComputeSum
	addComputeSum(CustomIntegrator self, std::string const & variable, std::string const & expression) -> int
def	addConstrainPositions
	addConstrainPositions(CustomIntegrator self) -> int
def	addConstrainVelocities
	addConstrainVelocities(CustomIntegrator self) -> int
def	addUpdateContextState
	addUpdateContextState(CustomIntegrator self) -> int
def	getComputationStep
	getComputationStep(CustomIntegrator self, int index)
def	getKineticEnergyExpression
	getKineticEnergyExpression(CustomIntegrator self) -> std::string const &
def	setKineticEnergyExpression
	setKineticEnergyExpression(CustomIntegrator self, std::string const & expression)
def	getRandomNumberSeed
	getRandomNumberSeed(CustomIntegrator self) -> int
def	setRandomNumberSeed
	setRandomNumberSeed(CustomIntegrator self, int seed)
def	step
	step(CustomIntegrator self, int steps)
def	getPerDofVariable
	getPerDofVariable(CustomIntegrator self, int index, std::vector< Vec3,std::allocator< Vec3 > > & values) getPerDofVariable(CustomIntegrator self, int index) -> PyObject *
def	__init__
	init(OpenMM::CustomIntegrator self, double stepSize) -> CustomIntegrator init(OpenMM::CustomIntegrator self, CustomIntegrator other) -> CustomIntegrator
def	__del__
	del(OpenMM::CustomIntegrator self)
Public Member Functions inherited from Integrator
def	__init__
def	__del__
	del(OpenMM::Integrator self)
def	getStepSize
	getStepSize(Integrator self) -> double
def	setStepSize
	setStepSize(Integrator self, double size)
def	getConstraintTolerance
	getConstraintTolerance(Integrator self) -> double
def	setConstraintTolerance
	setConstraintTolerance(Integrator self, double tol)
def	step
	step(Integrator self, int steps)

Public Attributes
	this

Static Public Attributes
	ComputeGlobal _openmm.CustomIntegrator_ComputeGlobal
	ComputePerDof _openmm.CustomIntegrator_ComputePerDof
	ComputeSum _openmm.CustomIntegrator_ComputeSum
	ConstrainPositions _openmm.CustomIntegrator_ConstrainPositions
	ConstrainVelocities _openmm.CustomIntegrator_ConstrainVelocities
	UpdateContextState _openmm.CustomIntegrator_UpdateContextState

Detailed Description

This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms.

It is flexible enough to support a wide range of methods including both deterministic and stochastic integrators, Metropolized integrators, and integrators that must integrate additional quantities along with the particle positions and momenta.

To create an integration algorithm, you first define a set of variables the integrator will compute. Variables come in two types: global variables have a single value, while per-DOF variables have a value for every degree of freedom (x, y, or z coordinate of a particle). You can define as many variables as you want of each type. The value of any variable can be computed by the integration algorithm, or set directly by calling a method on the CustomIntegrator. All variables are persistent between integration steps; once a value is set, it keeps that value until it is changed by the user or recomputed in a later integration step.

Next, you define the algorithm as a series of computations. To execute a time step, the integrator performs the list of computations in order. Each computation updates the value of one global or per-DOF value. There are several types of computations that can be done:

• Global: You provide a mathematical expression involving only global variables. It is evaluated and stored into a global variable.

• Per-DOF: You provide a mathematical expression involving both global and per-DOF variables. It is evaluated once for every degree of freedom, and the values are stored into a per-DOF variable.

• Sum: You provide a mathematical expression involving both global and per-DOF variables. It is evaluated once for every degree of freedom. All of those values are then added together, and the sum is stored into a global variable.

• Constrain Positions: The particle positions are updated so that all distance constraints are satisfied.

• Constrain Velocities: The particle velocities are updated so the net velocity along any constrained distance is 0.

Like all integrators, CustomIntegrator ignores any particle whose mass is 0. It is skipped when doing per-DOF computations, and is not included when computing sums over degrees of freedom.

In addition to the variables you define by calling addGlobalVariable() and addPerDofVariable(), the integrator provides the following pre-defined variables:

• dt: (global) This is the step size being used by the integrator.

• energy: (global, read-only) This is the current potential energy of the system.

• energy0, energy1, energy2, ...: (global, read-only) This is similar to energy, but includes only the contribution from forces in one force group. A single computation step may only depend on a single energy variable (energy, energy0, energy1, etc.).

• x: (per-DOF) This is the current value of the degree of freedom (the x, y, or z coordinate of a particle).

• v: (per-DOF) This is the current velocity associated with the degree of freedom (the x, y, or z component of a particle's velocity).

• f: (per-DOF, read-only) This is the current force acting on the degree of freedom (the x, y, or z component of the force on a particle).

• f0, f1, f2, ...: (per-DOF, read-only) This is similar to f, but includes only the contribution from forces in one force group. A single computation step may only depend on a single force variable (f, f0, f1, etc.).

• m: (per-DOF, read-only) This is the mass of the particle the degree of freedom is associated with.

• uniform: (either global or per-DOF, read-only) This is a uniformly distributed random number between 0 and 1. Every time an expression is evaluated, a different value will be used. When used in a per-DOF expression, a different value will be used for every degree of freedom. Note, however, that if this variable appears multiple times in a single expression, the same value is used everywhere it appears in that expression.

• gaussian: (either global or per-DOF, read-only) This is a Gaussian distributed random number with mean 0 and variance 1. Every time an expression is evaluated, a different value will be used. When used in a per-DOF expression, a different value will be used for every degree of freedom. Note, however, that if this variable appears multiple times in a single expression, the same value is used everywhere it appears in that expression.

• A global variable is created for every adjustable parameter defined in the integrator's Context.

The following example uses a CustomIntegrator to implement a velocity Verlet integrator:

CustomIntegrator integrator(0.001);
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("v", "v+0.5*dt*f/m");

The first step updates the velocities based on the current forces. The second step updates the positions based on the new velocities, and the third step updates the velocities again. Although the first and third steps look identical, the forces used in them are different. You do not need to tell the integrator that; it will recognize that the positions have changed and know to recompute the forces automatically.

The above example has two problems. First, it does not respect distance constraints. To make the integrator work with constraints, you need to add extra steps to tell it when and how to apply them. Second, it never gives Forces an opportunity to update the context state. This should be done every time step so that, for example, an AndersenThermostat can randomize velocities or a MonteCarloBarostat can scale particle positions. You need to add a step to tell the integrator when to do this. The following example corrects both these problems, using the RATTLE algorithm to apply constraints:

CustomIntegrator integrator(0.001);
integrator.addPerDofVariable("x1", 0);
integrator.addUpdateContextState();
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("x1", "x");
integrator.addConstrainPositions();
integrator.addComputePerDof("v", "v+0.5*dt*f/m+(x-x1)/dt");
integrator.addConstrainVelocities();

CustomIntegrator can be used to implement multiple time step integrators. The following example shows an r-RESPA integrator. It assumes the quickly changing forces are in force group 0 and the slowly changing ones are in force group 1. It evaluates the "fast" forces four times as often as the "slow" forces.

CustomIntegrator integrator(0.004);
integrator.addComputePerDof("v", "v+0.5*dt*f1/m");
for (int i = 0; i < 4; i++) {
integrator.addComputePerDof("v", "v+0.5*(dt/4)*f0/m");
integrator.addComputePerDof("x", "x+(dt/4)*v");
integrator.addComputePerDof("v", "v+0.5*(dt/4)*f0/m");
}
integrator.addComputePerDof("v", "v+0.5*dt*f1/m");

An Integrator has one other job in addition to evolving the equations of motion: it defines how to compute the kinetic energy of the system. Depending on the integration method used, simply summing mv/2 over all degrees of freedom may not give the correct answer. For example, in a leapfrog integrator the velocities are "delayed" by half a time step, so the above formula would give the kinetic energy half a time step ago, not at the current time.

Call setKineticEnergyExpression() to set an expression for the kinetic energy. It is computed for every degree of freedom (excluding ones whose mass is 0) and the result is summed. The default expression is "m*v*v/2", which is correct for many integrators.

As example, the following line defines the correct way to compute kinetic energy when using a leapfrog algorithm:

integrator.setKineticEnergyExpression("m*v1*v1/2; v1=v+0.5*dt*f/m");

The kinetic energy expression may depend on the following pre-defined variables: x, v, f, m, dt. It also may depend on user-defined global and per-DOF variables, and on the values of adjustable parameters defined in the integrator's Context. It may not depend on any other variable, such as the potential energy, the force from a single force group, or a random number.

Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise. delta(x) = 1 if x is 0, 0 otherwise. An expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.

Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

init(OpenMM::CustomIntegrator self, double stepSize) -> CustomIntegrator init(OpenMM::CustomIntegrator self, CustomIntegrator other) -> CustomIntegrator

Create a CustomIntegrator.

Parameters

stepSize

the step size with which to integrate the system (in picoseconds)

def __del__

(

self

)

del(OpenMM::CustomIntegrator self)

Member Function Documentation

def addComputeGlobal	(		self,
			args
	)

addComputeGlobal(CustomIntegrator self, std::string const & variable, std::string const & expression) -> int

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

Parameters

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

def addComputePerDof	(		self,
			args
	)

addComputePerDof(CustomIntegrator self, std::string const & variable, std::string const & expression) -> int

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

Parameters

variable	the per-DOF variable to store the computed value into
expression	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.

def addComputeSum	(		self,
			args
	)

addComputeSum(CustomIntegrator self, std::string const & variable, std::string const & expression) -> int

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

Parameters

variable	the global variable to store the computed value into
expression	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.

def addConstrainPositions

(

self

)

addConstrainPositions(CustomIntegrator self) -> int

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

def addConstrainVelocities

(

self

)

addConstrainVelocities(CustomIntegrator self) -> int

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

def addGlobalVariable	(		self,
			args
	)

addGlobalVariable(CustomIntegrator self, std::string const & name, double initialValue) -> int

Define a new global variable.

Parameters

name	the name of the variable
initialValue	the variable will initially be set to this value

def addPerDofVariable	(		self,
			args
	)

addPerDofVariable(CustomIntegrator self, std::string const & name, double initialValue) -> int

Define a new per-DOF variable.

Parameters

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

def addUpdateContextState

(

self

)

addUpdateContextState(CustomIntegrator self) -> int

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

def getComputationStep	(		self,
			args
	)

getComputationStep(CustomIntegrator self, int index)

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

Parameters

index	the index of the computation step to get
type	on exit, the type of computation this step performs
variable	on exit, 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	on exit, the expression this step evaluates. If this step does not evaluate an expression, this will be an empty string.

def getGlobalVariable	(		self,
			args
	)

getGlobalVariable(CustomIntegrator self, int index) -> double

Get the current value of a global variable.

Parameters

index

the index of the variable to get

def getGlobalVariableName	(		self,
			args
	)

getGlobalVariableName(CustomIntegrator self, int index) -> std::string const &

Get the name of a global variable.

Parameters

index

the index of the variable to get

def getKineticEnergyExpression

(

self

)

getKineticEnergyExpression(CustomIntegrator 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.

def getNumComputations

(

self

)

getNumComputations(CustomIntegrator self) -> int

Get the number of computation steps that have been added.

def getNumGlobalVariables

(

self

)

getNumGlobalVariables(CustomIntegrator self) -> int

Get the number of global variables that have been defined.

def getNumPerDofVariables

(

self

)

getNumPerDofVariables(CustomIntegrator self) -> int

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

def getPerDofVariable	(		self,
			args
	)

getPerDofVariable(CustomIntegrator self, int index, std::vector< Vec3,std::allocator< Vec3 > > & values) getPerDofVariable(CustomIntegrator self, int index) -> PyObject *

def getPerDofVariableName	(		self,
			args
	)

getPerDofVariableName(CustomIntegrator self, int index) -> std::string const &

Get the name of a per-DOF variable.

Parameters

index

the index of the variable to get

def getRandomNumberSeed

(

self

)

getRandomNumberSeed(CustomIntegrator self) -> int

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

def setGlobalVariable	(		self,
			args
	)

setGlobalVariable(CustomIntegrator self, int index, double value)

Set the value of a global variable.

Parameters

index	the index of the variable to set
value	the new value of the variable

def setGlobalVariableByName	(		self,
			args
	)

setGlobalVariableByName(CustomIntegrator self, std::string const & name, double value)

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

Parameters

name	the name of the variable to set
value	the new value of the variable

def setKineticEnergyExpression	(		self,
			args
	)

setKineticEnergyExpression(CustomIntegrator self, std::string const & 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.

def setPerDofVariable	(		self,
			args
	)

setPerDofVariable(CustomIntegrator self, int index, std::vector< Vec3,std::allocator< Vec3 > > const & values)

Set the value of a per-DOF variable.

Parameters

index	the index of the variable to set
values	the new values of the variable for all degrees of freedom

def setPerDofVariableByName	(		self,
			args
	)

setPerDofVariableByName(CustomIntegrator self, std::string const & name, std::vector< Vec3,std::allocator< Vec3 > > const & values)

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

Parameters

name	the name of the variable to set
values	the new values of the variable for all degrees of freedom

def setRandomNumberSeed	(		self,
			args
	)

setRandomNumberSeed(CustomIntegrator self, int 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.

def step	(		self,
			args
	)

step(CustomIntegrator self, int steps)

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

Parameters

steps

the number of time steps to take

Member Data Documentation

ComputeGlobal _openmm.CustomIntegrator_ComputeGlobal

static

ComputePerDof _openmm.CustomIntegrator_ComputePerDof

static

ComputeSum _openmm.CustomIntegrator_ComputeSum

static

ConstrainPositions _openmm.CustomIntegrator_ConstrainPositions

static

ConstrainVelocities _openmm.CustomIntegrator_ConstrainVelocities

static

this

UpdateContextState _openmm.CustomIntegrator_UpdateContextState

static

---

The documentation for this class was generated from the following file:

• openmm.py