Package ffx.openmm

Class CompoundIntegrator

java.lang.Object
ffx.openmm.Integrator
ffx.openmm.CompoundIntegrator
public class CompoundIntegrator extends Integrator
This class allows you to use multiple integration algorithms within a single simulation, switching back and forth between them. To use it, create whatever other Integrators you need, then add all of them to a CompoundIntegrator: 
    CompoundIntegrator compoundIntegrator = new CompoundIntegrator();
    compoundIntegrator.addIntegrator(new VerletIntegrator(0.001));
    compoundIntegrator.addIntegrator(new LangevinIntegrator(300.0, 1.0, 0.001));

Next create a Context, specifying the CompoundIntegrator as the Integrator to use for the Context: 

     Context context = new Context(system, compoundIntegrator);

Finally, call setCurrentIntegrator() to set which Integrator is active. That one will be used for all calls to step() until the next time you change it. 

     compoundIntegrator.setCurrentIntegrator(0);
     compoundIntegrator.step(1000); // Take 1000 steps of Verlet dynamics
     compoundIntegrator.setCurrentIntegrator(1);
     compoundIntegrator.step(1000); // Take 1000 steps of Langevin dynamics

When switching between integrators, it is important to make sure they are compatible with each other, and that they will interpret the positions and velocities in the same way. Remember that leapfrog style integrators assume the positions and velocities are offset from each other by half a time step. When switching between a leapfrog and non-leapfrog integrator, you must first adjust the velocities to avoid introducing error. This is also true when switching between two leapfrog integrators that use different step sizes, since they will interpret the velocities as corresponding to different times.

  • Constructor Details

    • CompoundIntegrator

      public CompoundIntegrator()
      Create a CompoundIntegrator.

  • Method Details

    • addIntegrator

      public int addIntegrator(Integrator integrator)
      Add an Integrator to this CompoundIntegrator. The Integrator object should have been created on the heap with the "new" operator. The CompoundIntegrator takes over ownership of it, and deletes it when the CompoundIntegrator itself is deleted. All Integrators must be added before the Context is created.
      Parameters:
      integrator - the Integrator to add
      Returns:
      the index of the Integrator that was added

    • destroy

      public void destroy()
      Destroy the integrator.
      Specified by:
      destroy in class Integrator

    • getConstraintTolerance

      public double getConstraintTolerance()
      Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance. This method calls getConstraintTolerance() on whichever Integrator has been set as current.
      Overrides:
      getConstraintTolerance in class Integrator
      Returns:
      The constraint tolerance in nm.

    • getCurrentIntegrator

      public int getCurrentIntegrator()
      Get the index of the current Integrator.

    • getIntegrationForceGroups

      public int getIntegrationForceGroups()
      Get which force groups to use for integration. By default, all force groups are included. This is interpreted as a set of bit flags: the forces from group i will be included if (groups&(1<<i)) != 0.

      This method returns the integration force groups for the current Integrator.

      Overrides:
      getIntegrationForceGroups in class Integrator
      Returns:
      The bit flags indicating which force groups this integrator acts on.

    • getIntegrator

      public com.sun.jna.ptr.PointerByReference getIntegrator(int index)
      Get a reference to one of the Integrators that have been added to this CompoundIntegrator.
      Parameters:
      index - the index of the Integrator to get

    • getNumIntegrators

      public int getNumIntegrators()
      Get the number of Integrators that have been added to this CompoundIntegrator.

    • getStepSize

      public double getStepSize()
      Get the size of each time step, in picoseconds. This method calls getStepSize() on whichever Integrator has been set as current.
      Overrides:
      getStepSize in class Integrator
      Returns:
      the step size, measured in ps

    • setConstraintTolerance

      public void setConstraintTolerance(double tol)
      Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance. This method calls setConstraintTolerance() on whichever Integrator has been set as current.
      Overrides:
      setConstraintTolerance in class Integrator
      Parameters:
      tol - The tolerance within which constraints must be satisfied.

    • setCurrentIntegrator

      public void setCurrentIntegrator(int index)
      Set the current Integrator.
      Parameters:
      index - the index of the Integrator to use

    • setIntegrationForceGroups

      public void setIntegrationForceGroups(int groups)
      Set which force groups to use for integration. By default, all force groups are included. This is interpreted as a set of bit flags: the forces from group i will be included if (groups&(1<<i)) != 0.

      Calling this method sets the integration force groups for all Integrators contained in this CompoundIntegrator.

      Overrides:
      setIntegrationForceGroups in class Integrator
      Parameters:
      groups - The bit flags indicating which force groups this integrator acts on.

    • setStepSize

      public void setStepSize(double size)
      Set the size of each time step, in picoseconds. This method calls setStepSize() on whichever Integrator has been set as current.
      Overrides:
      setStepSize in class Integrator
      Parameters:
      size - the step size, measured in ps

    • step

      public void step(int steps)
      Advance a simulation through time by taking a series of time steps. This method calls step() on whichever Integrator has been set as current.
      Overrides:
      step in class Integrator
      Parameters:
      steps - the number of time steps to take