Package ffx.openmm
Class Integrator
java.lang.Object
ffx.openmm.Integrator
- Direct Known Subclasses:
BrownianIntegrator
,CompoundIntegrator
,CustomIntegrator
,DrudeIntegrator
,LangevinMiddleIntegrator
,NoseHooverIntegrator
,VariableLangevinIntegrator
,VariableVerletIntegrator
,VerletIntegrator
An Integrator defines a method for simulating a System by integrating the equations of motion.
This is an abstract class. Subclasses define particular integration methods.
Each Integrator object is bound to a particular Context which it integrates. This connection is specified by passing the Integrator as an argument to the constructor of the Context.
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected com.sun.jna.ptr.PointerByReference
OpenMM Integrator pointer. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionabstract void
destroy()
This method will be called by subclasses when the integrator is destroyed.double
Get the tolerance within which constraints must be satisfied during the simulation.int
Get the set of force groups this integrator acts on.com.sun.jna.ptr.PointerByReference
Get the OpenMM Integrator pointer.double
Get the size of each time step, in picoseconds.void
setConstraintTolerance
(double tolerance) Set the tolerance within which constraints must be satisfied during the simulation.void
setIntegrationForceGroups
(int groups) Set the force groups this integrator acts on.void
setPointer
(com.sun.jna.ptr.PointerByReference pointer) Set the OpenMM Integrator pointer.void
setStepSize
(double stepSize) Set the size of each time step, in picoseconds.void
step
(int steps) Integrate the system forward in time by the specified number of time steps.
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Field Details
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pointer
protected com.sun.jna.ptr.PointerByReference pointerOpenMM Integrator pointer.
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Constructor Details
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Integrator
public Integrator(com.sun.jna.ptr.PointerByReference pointer) Constructor.
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Method Details
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destroy
public abstract void destroy()This method will be called by subclasses when the integrator is destroyed. -
getConstraintTolerance
public double getConstraintTolerance()Get the tolerance within which constraints must be satisfied during the simulation.- Returns:
- The constraint tolerance in nm.
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getIntegrationForceGroups
public int getIntegrationForceGroups()Get the set of force groups this integrator acts on.- Returns:
- The bit flags indicating which force groups this integrator acts on.
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getPointer
public com.sun.jna.ptr.PointerByReference getPointer()Get the OpenMM Integrator pointer.- Returns:
- The OpenMM Integrator pointer.
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getStepSize
public double getStepSize()Get the size of each time step, in picoseconds.- Returns:
- The step size in ps.
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setConstraintTolerance
public void setConstraintTolerance(double tolerance) Set the tolerance within which constraints must be satisfied during the simulation. The default value is 1e-5 nm.- Parameters:
tolerance
- The tolerance within which constraints must be satisfied.
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setIntegrationForceGroups
public void setIntegrationForceGroups(int groups) Set the force groups this integrator acts on.- Parameters:
groups
- The bit flags indicating which force groups this integrator acts on.
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setPointer
public void setPointer(com.sun.jna.ptr.PointerByReference pointer) Set the OpenMM Integrator pointer.- Parameters:
pointer
- The OpenMM Integrator pointer.
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setStepSize
public void setStepSize(double stepSize) Set the size of each time step, in picoseconds.- Parameters:
stepSize
- The step size in ps.
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step
public void step(int steps) Integrate the system forward in time by the specified number of time steps.- Parameters:
steps
- The number of steps to take.
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