Package ffx.openmm.drude

Class DrudeForce

java.lang.Object
ffx.openmm.Force
ffx.openmm.drude.DrudeForce
public class DrudeForce extends Force
This class implements forces that are specific to Drude oscillators. There are two distinct forces it applies: an anisotropic harmonic force connecting each Drude particle to its parent particle; and a screened Coulomb interaction between specific pairs of dipoles. The latter is typically used between closely bonded particles whose Coulomb interaction would otherwise be fully excluded.

To use this class, create a DrudeForce object, then call addParticle() once for each Drude particle in the System to define its parameters. After a particle has been added, you can modify its force field parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext(). Likewise, call addScreenedPair() for each pair of dipoles (each dipole consisting of a Drude particle and its parent) that should be computed.

  • Field Summary

    Fields inherited from class ffx.openmm.Force

    pointer

  • Constructor Summary

    Constructors
    Constructor
    Description
    DrudeForce()
    Create a DrudeForce.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    addParticle(int particle, int particle1, int particle2, int particle3, int particle4, double charge, double polarizability, double aniso12, double aniso34)
    Add a Drude particle to which forces should be applied.
    int
    addScreenedPair(int particle1, int particle2, double thole)
    Add an interaction to the list of screened pairs.
    void
    destroy()
    Destroy the force.
    int
    getNumParticles()
    Get the number of particles for which force field parameters have been defined.
    int
    getNumScreenedPairs()
    Get the number of special interactions that should be calculated differently from other interactions.
    void
    getParticleParameters(int index, com.sun.jna.ptr.IntByReference particle, com.sun.jna.ptr.IntByReference particle1, com.sun.jna.ptr.IntByReference particle2, com.sun.jna.ptr.IntByReference particle3, com.sun.jna.ptr.IntByReference particle4, com.sun.jna.ptr.DoubleByReference charge, com.sun.jna.ptr.DoubleByReference polarizability, com.sun.jna.ptr.DoubleByReference aniso12, com.sun.jna.ptr.DoubleByReference aniso34)
    Get the parameters for a Drude particle.
    void
    getScreenedPairParameters(int index, com.sun.jna.ptr.IntByReference particle1, com.sun.jna.ptr.IntByReference particle2, com.sun.jna.ptr.DoubleByReference thole)
    Get the force field parameters for a screened pair.
    void
    getScreenedPairParameters(int index, IntBuffer particle1, IntBuffer particle2, DoubleBuffer thole)
    Get the force field parameters for a screened pair.
    void
    setParticleParameters(int index, int particle, int particle1, int particle2, int particle3, int particle4, double charge, double polarizability, double aniso12, double aniso34)
    Set the parameters for a Drude particle.
    void
    setScreenedPairParameters(int index, int particle1, int particle2, double thole)
    Set the force field parameters for a screened pair.
    void
    setUsesPeriodicBoundaryConditions(boolean periodic)
    Set whether this force should apply periodic boundary conditions when calculating displacements.
    void
    updateParametersInContext(Context context)
    Update the particle and screened pair parameters in a Context to match those stored in this Force object.
    boolean
    usesPeriodicBoundaryConditions()
    Returns whether or not this force makes use of periodic boundary conditions.

    Methods inherited from class ffx.openmm.Force

    getForceGroup, getForceIndex, getName, getPointer, setForceGroup, setForceIndex, setName

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • DrudeForce

      public DrudeForce()
      Create a DrudeForce.

  • Method Details

    • addParticle

      public int addParticle(int particle, int particle1, int particle2, int particle3, int particle4, double charge, double polarizability, double aniso12, double aniso34)
      Add a Drude particle to which forces should be applied.
      Parameters:
      particle - the index within the System of the Drude particle
      particle1 - the index within the System of the particle to which the Drude particle is attached
      particle2 - the index within the System of the second particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso12 will be ignored.
      particle3 - the index within the System of the third particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso34 will be ignored.
      particle4 - the index within the System of the fourth particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso34 will be ignored.
      charge - The charge on the Drude particle
      polarizability - The isotropic polarizability
      aniso12 - The scale factor for the polarizability along the direction defined by particle1 and particle2
      aniso34 - The scale factor for the polarizability along the direction defined by particle3 and particle4
      Returns:
      the index of the particle that was added

    • addScreenedPair

      public int addScreenedPair(int particle1, int particle2, double thole)
      Add an interaction to the list of screened pairs.
      Parameters:
      particle1 - the index within this Force of the first particle involved in the interaction
      particle2 - the index within this Force of the second particle involved in the interaction
      thole - the Thole screening factor
      Returns:
      the index of the screenedPair that was added

    • destroy

      public void destroy()
      Destroy the force.

      This method releases the memory associated with the DrudeForce object. After calling this method, the force should not be used.

      Specified by:
      destroy in class Force

    • getNumParticles

      public int getNumParticles()
      Get the number of particles for which force field parameters have been defined.

    • getNumScreenedPairs

      public int getNumScreenedPairs()
      Get the number of special interactions that should be calculated differently from other interactions.

    • getParticleParameters

      public void getParticleParameters(int index, com.sun.jna.ptr.IntByReference particle, com.sun.jna.ptr.IntByReference particle1, com.sun.jna.ptr.IntByReference particle2, com.sun.jna.ptr.IntByReference particle3, com.sun.jna.ptr.IntByReference particle4, com.sun.jna.ptr.DoubleByReference charge, com.sun.jna.ptr.DoubleByReference polarizability, com.sun.jna.ptr.DoubleByReference aniso12, com.sun.jna.ptr.DoubleByReference aniso34)
      Get the parameters for a Drude particle.
      Parameters:
      index - the index of the Drude particle for which to get parameters
      particle - the index within the System of the Drude particle
      particle1 - the index within the System of the particle to which the Drude particle is attached
      particle2 - the index within the System of the second particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso12 will be ignored.
      particle3 - the index within the System of the third particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso34 will be ignored.
      particle4 - the index within the System of the fourth particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso34 will be ignored.
      charge - The charge on the Drude particle
      polarizability - The isotropic polarizability
      aniso12 - The scale factor for the polarizability along the direction defined by particle1 and particle2
      aniso34 - The scale factor for the polarizability along the direction defined by particle3 and particle4

    • getScreenedPairParameters

      public void getScreenedPairParameters(int index, com.sun.jna.ptr.IntByReference particle1, com.sun.jna.ptr.IntByReference particle2, com.sun.jna.ptr.DoubleByReference thole)
      Get the force field parameters for a screened pair.
      Parameters:
      index - the index of the pair for which to get parameters
      particle1 - the index within this Force of the first particle involved in the interaction
      particle2 - the index within this Force of the second particle involved in the interaction
      thole - the Thole screening factor

    • getScreenedPairParameters

      public void getScreenedPairParameters(int index, IntBuffer particle1, IntBuffer particle2, DoubleBuffer thole)
      Get the force field parameters for a screened pair.
      Parameters:
      index - the index of the pair for which to get parameters
      particle1 - the index within this Force of the first particle involved in the interaction
      particle2 - the index within this Force of the second particle involved in the interaction
      thole - the Thole screening factor

    • setParticleParameters

      public void setParticleParameters(int index, int particle, int particle1, int particle2, int particle3, int particle4, double charge, double polarizability, double aniso12, double aniso34)
      Set the parameters for a Drude particle.
      Parameters:
      index - the index of the Drude particle for which to set parameters
      particle - the index within the System of the Drude particle
      particle1 - the index within the System of the particle to which the Drude particle is attached
      particle2 - the index within the System of the second particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso12 will be ignored.
      particle3 - the index within the System of the third particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso34 will be ignored.
      particle4 - the index within the System of the fourth particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso34 will be ignored.
      charge - The charge on the Drude particle
      polarizability - The isotropic polarizability
      aniso12 - The scale factor for the polarizability along the direction defined by particle1 and particle2
      aniso34 - The scale factor for the polarizability along the direction defined by particle3 and particle4

    • setScreenedPairParameters

      public void setScreenedPairParameters(int index, int particle1, int particle2, double thole)
      Set the force field parameters for a screened pair.
      Parameters:
      index - the index of the pair for which to get parameters
      particle1 - the index within this Force of the first particle involved in the interaction
      particle2 - the index within this Force of the second particle involved in the interaction
      thole - the Thole screening factor

    • setUsesPeriodicBoundaryConditions

      public void setUsesPeriodicBoundaryConditions(boolean periodic)
      Set whether this force should apply periodic boundary conditions when calculating displacements. Usually this is not appropriate for bonded forces, but there are situations when it can be useful.

      Periodic boundary conditions are only applied to screened pairs. They are never used for the force between a Drude particle and its parent particle, regardless of this setting.

    • updateParametersInContext

      public void updateParametersInContext(Context context)
      Update the particle and screened pair parameters in a Context to match those stored in this Force object. This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setParticleParameters() and setScreenedPairParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.

      This method has several limitations. It can be used to modify the numeric parameters associated with a particle or screened pair (polarizability, thole, etc.), but not the identities of the particles they involve. It also cannot be used to add new particles or screenedPairs, only to change the parameters of existing ones.

    • usesPeriodicBoundaryConditions

      public boolean usesPeriodicBoundaryConditions()
      Returns whether or not this force makes use of periodic boundary conditions.
      Overrides:
      usesPeriodicBoundaryConditions in class Force
      Returns:
      True if the force uses periodic boundary conditions.