Package ffx.potential.constraint

Class SettleConstraint

java.lang.Object

ffx.potential.constraint.SettleConstraint

All Implemented Interfaces:

Constraint

public class SettleConstraint
extends Object
implements Constraint

SETTLE triatomic distance constraints, intended for rigid water models.

S. Miyamoto and P.A. Kollman, "SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithm for Rigid Water Models", Journal of Computational Chemistry, Vol. 13, No. 8, 952-962 (1992)

Since:

1.0

Author:

Michael J. Schnieders, Jacob M. Litman

Method Summary

Modifier and Type	Method	Description
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.
static SettleConstraint	settleFactory(Angle a012)	Constructs a SETTLE constraint from an angle and its two bonds.

Methods inherited from class java.lang.Object

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

Method Details

settleFactory

public static SettleConstraint settleFactory(Angle a012)

Constructs a SETTLE constraint from an angle and its two bonds. Factory used mostly to avoid a leaking-this scenario, as this method also passes the new SETTLE constraint to a012.

Parameters:

a012 - Angle to construct a SETTLE constraint from.

Returns:

New SettleConstraint.

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.

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.