Package ffx.potential.nonbonded

Class VanDerWaalsTornado

java.lang.Object

ffx.potential.nonbonded.VanDerWaals

ffx.potential.nonbonded.VanDerWaalsTornado

All Implemented Interfaces:

LambdaInterface, MaskingInterface

public class VanDerWaalsTornado
extends VanDerWaals

The Van der Waals class computes Van der Waals interaction in parallel using a NeighborList for P1 (no symmetry) Crystal systems.

The repulsive power (e.g. 12), attractive power (e.g. 6) and buffering (e.g. for the AMOEBA buffered-14-7) can all be specified such that both Lennard-Jones and AMOEBA are supported.

Since:

1.0

Author:

Michael J. Schnieders

Nested Class Summary

Nested classes/interfaces inherited from class ffx.potential.nonbonded.VanDerWaals

VanDerWaals.LambdaFactors, VanDerWaals.LambdaFactorsOST

Constructor Summary

Constructors

Constructor	Description
VanDerWaalsTornado(Atom[] atoms, Crystal crystal, ForceField forceField, double vdwCutoff)	The VanDerWaalsTornado class constructor.

Method Summary

Modifier and Type	Method	Description
double	energy(boolean gradient, boolean print)	The energy routine may be called repeatedly.
double	getEnergy()	Get the total Van der Waals potential energy.
int	getInteractions()	Get the number of interacting pairs.
void	setAtoms(Atom[] atoms)	Setter for the field atoms.
void	setCrystal(Crystal crystal)	If the crystal being passed in is not equal to the current crystal, then some Van der Waals data structures may need to updated.
String	toString()

Methods inherited from class ffx.potential.nonbonded.VanDerWaals

applyMask, attachExtendedSystem, destroy, getAlpha, getBeta, getBuffer, getd2EdL2, getdEdL, getdEdXdL, getDoLongRangeCorrection, getExtendedSystem, getIntramolecularSoftcore, getLambda, getLambdaTerm, getMask12, getMask13, getMask14, getNeighborList, getNeighborLists, getNonbondedCutoff, getReductionIndex, getVDWForm, removeMask, setAtoms, setLambda

Methods inherited from class java.lang.Object

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

Methods inherited from interface ffx.potential.bonded.LambdaInterface

dEdLZeroAtEnds

Constructor Details

VanDerWaalsTornado

public VanDerWaalsTornado(Atom[] atoms,
 Crystal crystal,
 ForceField forceField,
 double vdwCutoff)

The VanDerWaalsTornado class constructor.

Parameters:

atoms - Atom array to do Van Der Waals calculations on.

crystal - The periodic boundary conditions information.

forceField - the ForceField parameters to apply.

vdwCutoff - vdW cutoff.

Since:

1.0

Method Details

energy

public double energy(boolean gradient,
 boolean print)

The energy routine may be called repeatedly.

Overrides:

energy in class VanDerWaals

Parameters:

gradient - If true, gradients with respect to atomic coordinates are computed.

print - If true, there is verbose printing.

Returns:

The energy.

Since:

1.0

getEnergy

public double getEnergy()

Get the total Van der Waals potential energy.

Overrides:

getEnergy in class VanDerWaals

Returns:

The energy.

Since:

1.0

getInteractions

public int getInteractions()

Get the number of interacting pairs.

Overrides:

getInteractions in class VanDerWaals

Returns:

The interaction count.

Since:

1.0

setAtoms

public void setAtoms(Atom[] atoms)

Setter for the field atoms.

Parameters:

atoms - an array of Atom objects.

setCrystal

public void setCrystal(Crystal crystal)

If the crystal being passed in is not equal to the current crystal, then some Van der Waals data structures may need to updated. If nSymm has changed, update arrays dimensioned by nSymm. Finally, rebuild the neighbor-lists.

Overrides:

setCrystal in class VanDerWaals

Parameters:

crystal - The new crystal instance defining the symmetry and boundary conditions.

toString

public String toString()

Overrides:

toString in class VanDerWaals