Package ffx.potential

Class ForceFieldEnergyOpenMM.Context

java.lang.Object
ffx.potential.ForceFieldEnergyOpenMM.Context
Enclosing class:
ForceFieldEnergyOpenMM
public class ForceFieldEnergyOpenMM.Context extends Object
Creates and manage an OpenMM Context.

A Context stores the complete state of a simulation. More specifically, it includes: The current time The position of each particle The velocity of each particle The values of configurable parameters defined by Force objects in the System

You can retrieve a snapshot of the current state at any time by calling getState(). This allows you to record the state of the simulation at various points, either for analysis or for checkpointing. getState() can also be used to retrieve the current forces on each particle and the current energy of the System.

  • Method Summary

    Modifier and Type
    Method
    Description
    com.sun.jna.ptr.PointerByReference
    getContextPointer()
    Get a Pointer to the OpenMM Context.
    com.sun.jna.ptr.PointerByReference
    getIntegrator()
    Get a Pointer to the OpenMM Integrator.
    void
    integrate(int numSteps)
    Use the Context / Integrator combination to take the requested number of steps.
    void
    optimize(double eps, int maxIterations)
    Use the Context to optimize the system to the requested tolerance.
    void
    setOpenMMPositions(double[] x)
    The array x contains atomic coordinates only for active atoms.
    void
    setOpenMMVelocities(double[] v)
    The array v contains velocity values for active atomic coordinates.
    void
    setPeriodicBoxVectors()
    Set the periodic box vectors for a context based on the crystal instance.
    String
    toString()

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Method Details

    • getContextPointer

      public com.sun.jna.ptr.PointerByReference getContextPointer()
      Get a Pointer to the OpenMM Context. A Context is created if none has been instantiated yet.
      Returns:
      Context pointer.

    • getIntegrator

      public com.sun.jna.ptr.PointerByReference getIntegrator()
      Get a Pointer to the OpenMM Integrator.
      Returns:
      Integrator pointer.

    • integrate

      public void integrate(int numSteps)
      Use the Context / Integrator combination to take the requested number of steps.
      Parameters:
      numSteps - Number of steps to take.

    • optimize

      public void optimize(double eps, int maxIterations)
      Use the Context to optimize the system to the requested tolerance.
      Parameters:
      eps - Convergence criteria (kcal/mole/A).
      maxIterations - Maximum number of iterations.

    • setOpenMMPositions

      public void setOpenMMPositions(double[] x)
      The array x contains atomic coordinates only for active atoms.
      Parameters:
      x - Atomic coordinate array for only active atoms.

    • setOpenMMVelocities

      public void setOpenMMVelocities(double[] v)
      The array v contains velocity values for active atomic coordinates.
      Parameters:
      v - Velocity array for active atoms.

    • setPeriodicBoxVectors

      public void setPeriodicBoxVectors()
      Set the periodic box vectors for a context based on the crystal instance.

    • toString

      public String toString()
      Overrides:
      toString in class Object