Package ffx.potential.nonbonded

Interface MaskingInterface

All Known Implementing Classes:
PermanentFieldRegion, RealSpaceEnergyRegion, VanDerWaals, VanDerWaalsTornado
public interface MaskingInterface
By implementing the MaskingInterface interface, interaction pairs can be excluded during NeighborList construction.

During non-bonded calculations, the interactions between bonded atoms (1-2, 1-3 or 1-4, for example) may be masked to zero. The interaction energy between excluded atoms is described by the bonded energy terms.

Since:
1.0
Author:
Michael J. Schnieders

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    applyMask(int i, boolean[] is14, double[]... masks)
    Interactions with atom i that should not be included in the NeighborList should be set to 0.
    void
    removeMask(int i, boolean[] is14, double[]... masks)
    After calling removeMask, all entries in the mask array should be 1 and is14 array false.

  • Method Details

    • applyMask

      void applyMask(int i, boolean[] is14, double[]... masks)
      Interactions with atom i that should not be included in the NeighborList should be set to 0.
      Parameters:
      i - The atom whose masking rules should be applied.
      is14 - True if atom i and the current atom are 1-4 to each other.
      masks - One or more masking arrays.
      Since:
      1.0

    • removeMask

      void removeMask(int i, boolean[] is14, double[]... masks)
      After calling removeMask, all entries in the mask array should be 1 and is14 array false.
      Parameters:
      i - The atom whose masking rules should be removed.
      is14 - True if atom i and the current atom are 1-4 to each other.
      masks - One or more masking arrays.
      Since:
      1.0