Package ffx.potential.constraint

Class ShakeChargeConstraint

java.lang.Object
ffx.potential.constraint.ShakeChargeConstraint
All Implemented Interfaces:
Constraint
public class ShakeChargeConstraint extends Object implements Constraint

  • Constructor Summary

    Constructors
    Constructor
    Description
    ShakeChargeConstraint(int nConstraints, int c, double tol)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    applyChargeConstraintToStep(double[] x, double[] a, double[] masses, double dt)
     
    void
    applyConstraintToStep(double[] xPrior, double[] xNew, double[] masses, double tol)
    Applies this Constraint in the context of a partially calculated MD time-step.
    void
    applyConstraintToVelocities(double[] x, double[] v, double[] masses, double tol)
    Applies this Constraint to velocities, ensuring relative velocities are perpendicular to constrained bonds, etc., without affecting positions.
    int[]
    constrainedAtomIndices()
    Returns the atomic XYZ indices of all Atoms constrained.
    boolean
    constraintSatisfied(double[] x, double tol)
    Checks if this Constraint is satisfied.
    boolean
    constraintSatisfied(double[] x, double[] v, double xTol, double vTol)
    Checks if this Constraint is satisfied.
    int
    getNumDegreesFrozen()
    Returns the number of degrees of freedom this Constraint constrains.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • ShakeChargeConstraint

      public ShakeChargeConstraint(int nConstraints, int c, double tol)

  • Method Details

    • applyConstraintToStep

      public void applyConstraintToStep(double[] xPrior, double[] xNew, double[] masses, double tol)
      Description copied from interface: Constraint
      Applies this Constraint in the context of a partially calculated MD time-step. All arrays are globally indexed (i.e. includes all system atoms, not just the constrained ones).

      If there is no prior step (e.g. a newly loaded system that has not yet been rigidified), xPrior and xNew can be copies of each other when passed to the method.

      xPrior corresponds to atomCoordinates in the OpenMM constraint code. Ours will be in Angstroms, not nm. xNew corresponds to atomCoordinatesP in the OpenMM constraint code. Ours will be in Angstroms, not nm.

      Specified by:
      applyConstraintToStep in interface Constraint
      Parameters:
      xPrior - Atomic coordinates prior to the time-step to be constrained.
      xNew - Atomic coordinates after the time-step; updated in-place to satisfy the constraint.
      masses - Masses.
      tol - Acceptable constraint tolerance for numerical methods, as a fraction of bond length.

    • applyChargeConstraintToStep

      public boolean applyChargeConstraintToStep(double[] x, double[] a, double[] masses, double dt)

    • applyConstraintToVelocities

      public void applyConstraintToVelocities(double[] x, double[] v, double[] masses, double tol)
      Description copied from interface: Constraint
      Applies this Constraint to velocities, ensuring relative velocities are perpendicular to constrained bonds, etc., without affecting positions. All arrays are globally indexed (i.e. includes all system atoms, not just the constrained ones).

      Our positions will be in Angstroms, and velocities in Angstroms/ps, compared to the OpenMM nm and nm/ps.

      Specified by:
      applyConstraintToVelocities in interface Constraint
      Parameters:
      x - Atomic coordinates (unchanged).
      v - Velocities (updated in-place to satisfy constraints).
      masses - Masses.
      tol - Acceptable constraint tolerance for numerical methods; likely in Angstroms/ps

    • constrainedAtomIndices

      public int[] constrainedAtomIndices()
      Description copied from interface: Constraint
      Returns the atomic XYZ indices of all Atoms constrained. Guaranteed to be unique. The primary assumption will be that variables are in sets of 3x Cartesian coordinates.
      Specified by:
      constrainedAtomIndices in interface Constraint
      Returns:
      All indices of constrained Atoms.

    • constraintSatisfied

      public boolean constraintSatisfied(double[] x, double tol)
      Description copied from interface: Constraint
      Checks if this Constraint is satisfied.
      Specified by:
      constraintSatisfied in interface Constraint
      Parameters:
      x - Input coordinates to check.
      tol - Numerical tolerance as a fraction of bond stretch.
      Returns:
      Whether this Constraint is satisfied.

    • constraintSatisfied

      public boolean constraintSatisfied(double[] x, double[] v, double xTol, double vTol)
      Description copied from interface: Constraint
      Checks if this Constraint is satisfied. Also checks velocities; bond constraints, for example, require that relative velocity be orthogonal to the bond. If the velocities vector is null or the tolerance is zero, velocity checks are skipped.
      Specified by:
      constraintSatisfied in interface Constraint
      Parameters:
      x - Input coordinates to check.
      v - Input velocities to check. If null, velocity check disabled.
      xTol - Numerical tolerance for bond lengths.
      vTol - Numerical tolerance for velocity checks (typically in degrees). If zero, velocity check disabled.
      Returns:
      Whether this Constraint is satisfied.

    • getNumDegreesFrozen

      public int getNumDegreesFrozen()
      Description copied from interface: Constraint
      Returns the number of degrees of freedom this Constraint constrains.
      Specified by:
      getNumDegreesFrozen in interface Constraint
      Returns:
      Number of frozen DoF.