Package ffx.potential.bonded

Class RestrainDistance

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

ffx.potential.bonded.RestrainDistance

All Implemented Interfaces:

BondedEnergy, LambdaInterface, ROLS, Serializable, Cloneable, Comparable<BondedTerm>, MutableTreeNode, TreeNode

public class RestrainDistance
extends BondedTerm
implements LambdaInterface

RestraintDistance class.

Since:

1.0

Author:

Michael J. Schnieders

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class ffx.potential.bonded.BondedTerm

BondedTerm.BondedComparator

Field Summary

Fields

Modifier and Type	Field	Description
BondType	bondType
static final double	DEFAULT_RB_LAM_END
static final double	DEFAULT_RB_LAM_START

Fields inherited from class ffx.potential.bonded.BondedTerm

atoms, bonds, energy, id, value

Fields inherited from class ffx.potential.bonded.MSNode

selected

Fields inherited from class javax.swing.tree.DefaultMutableTreeNode

allowsChildren, children, EMPTY_ENUMERATION, parent, userObject

Fields inherited from interface ffx.potential.bonded.ROLS

MaxLengthScale

Constructor Summary

Constructors

Constructor	Description
RestrainDistance(Atom a1, Atom a2, Crystal crystal, boolean lambdaTerm, double lamStart, double lamEnd, UnivariateSwitchingFunction sf)	Creates a distance restraint between two Atoms.

Method Summary

Modifier and Type	Method	Description
double	energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
Atom	get1_2(Atom a)	Find the other Atom in this Bond.
BondType	getBondType()	Getter for the field bondType.
double	getd2EdL2()	Get the 2nd partial derivative of the energy with respect to lambda.
double	getdEdL()	Get the partial derivative of the energy with respect to lambda.
void	getdEdXdL(double[] gradient)	Get the gradient of dEdL with respect to each parameter.
double	getLambda()	Get the current value of the state variable.
boolean	isLambdaScaled()	Check if this BondedTerm is lambda-sensitive (e.g., a softcore dihedral).
void	log()	Log details for this Bond energy term.
void	setBondType(BondType bondType)	Set a reference to the force field parameters.
void	setLambda(double lambda)	Set the current value of the state variable.
String	toString()

Methods inherited from class ffx.potential.bonded.BondedTerm

applyLambda, compareTo, containsHydrogen, containsResolution, destroy, equals, getAtom, getAtomArray, getAtomArray, getAtoms, getBond, getID, getUse, getValue, hashCode, isConstrained, isNeuralNetwork, print, removeNeuralNetworkTerms, setAtoms, setBonds, setColor, setConstraint, setID, setID_Key, setSelected, setValue, setView

Methods inherited from class ffx.potential.bonded.MSNode

contains, drawLabel, getAngleList, getAngleTorsionList, getAtomList, getAtomList, getBondList, getCenter, getChildList, getExtent, getImproperTorsionList, getList, getList, getMSCount, getMSNode, getMW, getName, getOutOfPlaneBendList, getPiOrbitalTorsionList, getStretchBendList, getStretchTorsionList, getTorsionList, getTorsionTorsionList, getTotalMass, getUreyBradleyList, isSelected, removeChild, setName, update

Methods inherited from class javax.swing.tree.DefaultMutableTreeNode

add, breadthFirstEnumeration, children, clone, depthFirstEnumeration, getAllowsChildren, getChildAfter, getChildAt, getChildBefore, getChildCount, getDepth, getFirstChild, getFirstLeaf, getIndex, getLastChild, getLastLeaf, getLeafCount, getLevel, getNextLeaf, getNextNode, getNextSibling, getParent, getPath, getPathToRoot, getPreviousLeaf, getPreviousNode, getPreviousSibling, getRoot, getSharedAncestor, getSiblingCount, getUserObject, getUserObjectPath, insert, isLeaf, isNodeAncestor, isNodeChild, isNodeDescendant, isNodeRelated, isNodeSibling, isRoot, pathFromAncestorEnumeration, postorderEnumeration, preorderEnumeration, remove, remove, removeAllChildren, removeFromParent, setAllowsChildren, setParent, setUserObject

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface ffx.potential.bonded.BondedEnergy

energy, energy, update

Methods inherited from interface ffx.potential.bonded.LambdaInterface

dEdLZeroAtEnds

Field Details

DEFAULT_RB_LAM_START

public static final double DEFAULT_RB_LAM_START

See Also:

• Constant Field Values

DEFAULT_RB_LAM_END

public static final double DEFAULT_RB_LAM_END

See Also:

• Constant Field Values

bondType

public BondType bondType

Constructor Details

RestrainDistance

public RestrainDistance(Atom a1,
 Atom a2,
 Crystal crystal,
 boolean lambdaTerm,
 double lamStart,
 double lamEnd,
 UnivariateSwitchingFunction sf)

Creates a distance restraint between two Atoms.

Parameters:

a1 - First Atom.

a2 - Second Atom.

crystal - The Crystal used by the system.

lambdaTerm - Whether lambda affects this restraint.

lamStart - At what lambda does the restraint begin to take effect?

lamEnd - At what lambda does the restraint hit full strength?

sf - Switching function determining lambda dependence; null produces a ConstantSwitch.

Method Details

energy

public double energy(boolean gradient,
 int threadID,
 AtomicDoubleArray3D grad,
 AtomicDoubleArray3D lambdaGrad)

energy.

Evaluate this Bond energy.

Specified by:

energy in interface BondedEnergy

Parameters:

gradient - If true, compute the gradient.

threadID - The thread ID.

grad - a AtomicDoubleArray3D object.

lambdaGrad - a AtomicDoubleArray3D object.

Returns:

a double.

get1_2

public Atom get1_2(Atom a)

Find the other Atom in this Bond. These two atoms are said to be 1-2.

Parameters:

a - The known Atom.

Returns:

The other Atom that makes up this Bond, or Null if Atom a is not part of this Bond.

getBondType

public BondType getBondType()

Getter for the field bondType.

Returns:

a BondType object.

setBondType

public void setBondType(BondType bondType)

Set a reference to the force field parameters.

Parameters:

bondType - a BondType object.

getLambda

public double getLambda()

Get the current value of the state variable.

Specified by:

getLambda in interface LambdaInterface

Returns:

state

setLambda

public void setLambda(double lambda)

Set the current value of the state variable. May be ignored if lambda is not being applied.

Specified by:

setLambda in interface LambdaInterface

Parameters:

lambda - a double.

getd2EdL2

public double getd2EdL2()

Get the 2nd partial derivative of the energy with respect to lambda.

Specified by:

getd2EdL2 in interface LambdaInterface

Returns:

d2EdL2

getdEdL

public double getdEdL()

Get the partial derivative of the energy with respect to lambda.

Specified by:

getdEdL in interface LambdaInterface

Returns:

dEdL

getdEdXdL

public void getdEdXdL(double[] gradient)

Get the gradient of dEdL with respect to each parameter.

Specified by:

getdEdXdL in interface LambdaInterface

Parameters:

gradient - - A double array of length the number of parameters in the model (commonly 3 * number of atoms).

isLambdaScaled

public boolean isLambdaScaled()

Description copied from class: BondedTerm

Check if this BondedTerm is lambda-sensitive (e.g., a softcore dihedral).

Overrides:

isLambdaScaled in class BondedTerm

Returns:

True if Lambda affects the energy of this term.

log

public void log()

Log details for this Bond energy term.

toString

public String toString()

Description copied from class: BondedTerm

Overridden toString method returns the MSNode's name

Overridden toString Method returns the Term's id.

Overrides:

toString in class BondedTerm