Uses of Class
ffx.potential.extended.ExtendedSystem

Packages that use ExtendedSystem

Package	Description
ffx.algorithms.dynamics	The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.nonbonded	The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and Particle Mesh Ewald electrostastics.
ffx.potential.nonbonded.pme
ffx.potential.parsers	The Parsers package handles reading/writing files to/from the internal data structure.

Uses of ExtendedSystem in ffx.algorithms.dynamics

Methods in ffx.algorithms.dynamics with parameters of type ExtendedSystem

Modifier and Type	Method	Description
void	MolecularDynamics.attachExtendedSystem(ExtendedSystem system, double reportFreq)	attachExtendedSystem.

Constructors in ffx.algorithms.dynamics with parameters of type ExtendedSystem

Modifier	Constructor	Description
	PhReplicaExchange(MolecularDynamics molecularDynamics, File structureFile, double pH, double[] pHLadder, double temp, ExtendedSystem extendedSystem, double[] x)	pHReplicaExchange constructor.
	PhReplicaExchange(MolecularDynamics molecularDynamics, File structureFile, double pH, double[] pHLadder, double temp, ExtendedSystem extendedSystem, double[] x, MolecularDynamicsOpenMM molecularDynamicsOpenMM, Potential potential)	OpenMM cycled pHReplicaExchange constructor.

Uses of ExtendedSystem in ffx.algorithms.optimize

Fields in ffx.algorithms.optimize declared as ExtendedSystem

Modifier and Type	Field	Description
protected final ExtendedSystem	PhMinimize.esvSystem	The extended system that contains the fictitious particle

Constructors in ffx.algorithms.optimize with parameters of type ExtendedSystem

Modifier	Constructor	Description
	PhMinimize(MolecularAssembly molecularAssembly, AlgorithmListener algorithmListener, ExtendedSystem esvSystem)	Constructor for Minimize.
	PhMinimize(MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, ExtendedSystem esvSystem)	Constructor for Minimize.

Uses of ExtendedSystem in ffx.potential

Methods in ffx.potential that return ExtendedSystem

Modifier and Type	Method	Description
ExtendedSystem	ForceFieldEnergy.getExtendedSystem()	getExtendedSystem.

Methods in ffx.potential with parameters of type ExtendedSystem

Modifier and Type	Method	Description
void	ForceFieldEnergy.attachExtendedSystem(ExtendedSystem system)	Overwrites current esvSystem if present.

Uses of ExtendedSystem in ffx.potential.nonbonded

Methods in ffx.potential.nonbonded that return ExtendedSystem

Modifier and Type	Method	Description
ExtendedSystem	VanDerWaals.getExtendedSystem()	Get the ExtendedSystem instance.

Methods in ffx.potential.nonbonded with parameters of type ExtendedSystem

Modifier and Type	Method	Description
void	ParticleMeshEwald.attachExtendedSystem(ExtendedSystem system)	Attach system with extended variable such as titrations.
void	VanDerWaals.attachExtendedSystem(ExtendedSystem system)	attachExtendedSystem.

Uses of ExtendedSystem in ffx.potential.nonbonded.pme

Methods in ffx.potential.nonbonded.pme with parameters of type ExtendedSystem

Modifier and Type	Method	Description
void	InitializationRegion.init(boolean lambdaTerm, ExtendedSystem esvSystem, Atom[] atoms, double[][][] coordinates, Crystal crystal, MultipoleType.MultipoleFrameDefinition[] frame, int[][] axisAtom, double[][][] globalMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[] polarizability, double[] titrationPolarizability, double[] tautomerPolarizability, double[] thole, double[] ipdamp, boolean[] use, int[][][] neighborLists, int[][][] realSpaceLists, int[][][] vaporLists, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque)
void	RealSpaceEnergyRegion.init(Atom[] atoms, Crystal crystal, ExtendedSystem extendedSystem, boolean esvTerm, double[][][] coordinates, MultipoleType.MultipoleFrameDefinition[] frame, int[][] axisAtom, double[][][] globalMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, boolean[] use, int[] molecule, int[][] ip11, int[][] mask12, int[][] mask13, int[][] mask14, int[][] mask15, boolean[] isSoft, double[] ipdamp, double[] thole, RealSpaceNeighborParameters realSpaceNeighborParameters, boolean gradient, boolean lambdaTerm, boolean nnTerm, LambdaMode lambdaMode, Polarization polarization, EwaldParameters ewaldParameters, ScaleParameters scaleParameters, AlchemicalParameters alchemicalParameters, long[] realSpaceEnergyTime, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque, SharedDouble shareddEdLambda, SharedDouble sharedd2EdLambda2)
void	ReciprocalEnergyRegion.init(Atom[] atoms, Crystal crystal, boolean gradient, boolean lambdaTerm, boolean esvTerm, boolean[] use, double[][][] globalMultipole, double[][][] globalFracMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[][] cartMultipolePhi, double[][] fracMultipolePhi, Polarization polarization, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] cartesianDipolePhi, double[][] cartesianDipolePhiCR, double[][] fracInducedDipolePhi, double[][] fracInducedDipolePhiCR, ReciprocalSpace reciprocalSpace, AlchemicalParameters alchemicalParameters, ExtendedSystem extendedSystem, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque, SharedDouble shareddEdLambda, SharedDouble sharedd2EdLambda2)

Uses of ExtendedSystem in ffx.potential.parsers

Methods in ffx.potential.parsers that return ExtendedSystem

Modifier and Type	Method	Description
ExtendedSystem	XPHFilter.getExtendedSystem()

Methods in ffx.potential.parsers with parameters of type ExtendedSystem

Modifier and Type	Method	Description
void	XPHFilter.setExtendedSystem(ExtendedSystem esvSystem)

Constructors in ffx.potential.parsers with parameters of type ExtendedSystem

Modifier	Constructor	Description
	XPHFilter(SystemFilter systemFilter, ExtendedSystem esvSystem)
	XPHFilter(File file, MolecularAssembly system, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties, ExtendedSystem esvSystem)	Constructor for XPHFilter.