Uses of Interface
ffx.numerics.Potential

Packages that use Potential

Package	Description
ffx.algorithms	The Algorithms package has support for local and global optimization, molecular dynamics simulations, and calculation of free energy differences.
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.commands
ffx.algorithms.commands.test
ffx.algorithms.dynamics	The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
ffx.algorithms.dynamics.integrators	The Integrators package implements integrators for molecular dynamics simulations.
ffx.algorithms.mc	The MC package implements a variety of Monte Carlo moves for optimization and simulation algorithms.
ffx.algorithms.misc	The Misc package contains a few miscellaneous algorithms.
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.algorithms.optimize.anneal	The anneal package implements simulated annealing-based optimization, including an interface for annealing schedules and several concrete schedule implementations (linear, exponential, and flat-end) used to control temperature during optimization runs.
ffx.algorithms.optimize.manybody	The manybody package implements many-body rotamer optimization infrastructure, including distance matrices, an energy expansion (self, two-body, three-body, and four-body), Dead-end elimination criteria, Goldstein elimination criteria, and supporting data structures for efficient optimization.
ffx.algorithms.thermodynamics	The Thermodynamics package computes free energy differences using Orthogonal Space Tempering (OST) sampling via pure Java or OpenMM (via Monte Carlo OST).
ffx.crystal	The Crystal package implements space group symmetry and periodic boundary condition support.
ffx.numerics	The Numerics package has support for atomic double arrays, FFTs (1D and 3D), numerical integration (1D), complex numbers, vector operations, multipole tensors, multi-dimensional optimization, special functions, splines and switching functions.
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.cli	The Potential CLI package defines reusable options for PicoCLI command line scripts.
ffx.potential.commands
ffx.potential.commands.test
ffx.potential.extended	The Extended package is progress toward support for constant pH molecular dynamics using extended system variables (i.e. lambda dynamics on protonation).
ffx.potential.openmm	The openmm package contains utilities to construct and run Force Field X potentials on the OpenMM platform, including system builders, custom forces, alchemical fixed-charge forces, and integrators tailored to FFX simulations.
ffx.potential.utils	The Utils package implements core functionality needed for using the Potential package, such as opening and closing structure files, basic force field energy evaluations, etc.
ffx.realspace	The Real Space package implements real space structure refinement.
ffx.realspace.commands
ffx.realspace.commands.test
ffx.ui	The UI package provides views and controllers for manipulating molecular systems.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.
ffx.xray.commands
ffx.xray.commands.test

Uses of Potential in ffx.algorithms

Methods in ffx.algorithms that return Potential

Modifier and Type	Method	Description
Potential	AlgorithmFunctions.minimize(MolecularAssembly assembly, double eps)	Relax the coordinates of a MolecularAssembly and minimize its potential energy
Potential	AlgorithmUtils.minimize(MolecularAssembly assembly, double eps)	Relax the coordinates of a MolecularAssembly and minimize its potential energy

Constructors in ffx.algorithms with parameters of type Potential

Modifier	Constructor	Description
	ParallelStateEnergy(int nStates, double[] lambdaValues, MolecularAssembly[] molecularAssemblies, Potential potential, String[][] fullFilePaths, SystemFilter[] openers)	The ParallelEnergy constructor.

Uses of Potential in ffx.algorithms.cli

Methods in ffx.algorithms.cli that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	AlgorithmsCommand.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	AlgorithmsCommand.getPotentialsFromAssemblies(MolecularAssembly[] assemblies)	Returns a List of all Potential objects from the supplied MolecularAssembly array.

Methods in ffx.algorithms.cli with parameters of type Potential

Modifier and Type	Method	Description
SimulatedAnnealing	AnnealOptions.createAnnealer(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener)	Creates a SimulatedAnnealing object.
SimulatedAnnealing	AnnealOptions.createAnnealer(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, File dynFile)	Creates a SimulatedAnnealing object.
void	MultiDynamicsOptions.distribute(MolecularAssembly[] molecularAssemblies, Potential[] potentials, CrystalPotential crystalPotential, AlgorithmFunctions algorithmFunctions, int rank, int worldSize)	If residues selected for distributing initial configurations, performs many-body optimization for this distribution.
MolecularDynamics	DynamicsOptions.getDynamics(WriteoutOptions writeoutOptions, Potential potential, MolecularAssembly activeAssembly, AlgorithmListener algorithmListener)	Initialize a MolecularDynamics from the parsed options.
MolecularDynamics	DynamicsOptions.getDynamics(WriteoutOptions writeoutOptions, Potential potential, MolecularAssembly activeAssembly, AlgorithmListener algorithmListener, MDEngine requestedEngine)	Initialize a MolecularDynamics from the parsed options.

Uses of Potential in ffx.algorithms.commands

Fields in ffx.algorithms.commands declared as Potential

Modifier and Type	Field	Description
Potential	Dynamics.potential	Creation of a public field to try and make the JUnit test work, original code does not declare this as a public field.

Methods in ffx.algorithms.commands that return Potential

Modifier and Type	Method	Description
Potential	Dynamics.getPotentialObject()
Potential	PhDynamics.getPotentialObject()

Methods in ffx.algorithms.commands that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	AnalyzeNEQ.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	Anneal.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	BAR.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	Cluster.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	Dynamics.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	ForEachFile.getPotentials()
List<Potential>	Histogram.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	ManyBody.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	MBAR.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	Minimize.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	MinimizeCrystals.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	MinimizeOpenMM.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	MutatePDB.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	PhDynamics.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	SaveRotamers.getPotentials()
List<Potential>	SortArc.getPotentials()
List<Potential>	Superpose.getPotentials()
List<Potential>	SuperposeCrystals.getPotentials()
List<Potential>	Thermodynamics.getPotentials()
List<Potential>	TorsionScan.getPotentials()

Uses of Potential in ffx.algorithms.commands.test

Fields in ffx.algorithms.commands.test declared as Potential

Modifier and Type	Field	Description
Potential	FindRestraints.potential	Creation of a public field to try and make the JUnit test work, original code does not declare this as a public field.

Methods in ffx.algorithms.commands.test that return Potential

Modifier and Type	Method	Description
Potential	FindRestraints.getPotentialObject()	Get the potential object.

Methods in ffx.algorithms.commands.test that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	OSTGradient.getPotentials()	Returns a List of all Potential objects associated with this script.
List<Potential>	RepexThermo.getPotentials()

Uses of Potential in ffx.algorithms.dynamics

Classes in ffx.algorithms.dynamics that implement Potential

Modifier and Type	Class	Description
class	Barostat	The Barostat class maintains constant pressure using random trial moves in lattice parameters, which are consistent with the space group.

Methods in ffx.algorithms.dynamics that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	Barostat.getUnderlyingPotentials()

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

Modifier and Type	Method	Description
static MolecularDynamics	MolecularDynamics.dynamicsFactory(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator)	Method that determines whether a dynamics is done by the java implementation native to ffx or the OpenMM implementation
static MolecularDynamics	MolecularDynamics.dynamicsFactory(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator, MDEngine engine)	dynamicsFactory.

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

Modifier	Constructor	Description
	MolecularDynamics(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator)	Constructor for MolecularDynamics.
	MolecularDynamicsOpenMM(MolecularAssembly assembly, Potential potential, AlgorithmListener listener, ThermostatEnum thermostat, IntegratorEnum integrator)	Constructs a MolecularDynamicsOpenMM object, to perform molecular dynamics using native OpenMM routines, avoiding the cost of communicating coordinates, gradients, and energies back and forth across the PCI bus.
	PhReplicaExchange(MolecularDynamics molecularDynamics, File structureFile, double pH, double[] pHLadder, double temp, ExtendedSystem extendedSystem, double[] x, MolecularDynamicsOpenMM molecularDynamicsOpenMM, Potential potential, int worldSize)	OpenMM cycled pHReplicaExchange constructor.

Uses of Potential in ffx.algorithms.dynamics.integrators

Methods in ffx.algorithms.dynamics.integrators with parameters of type Potential

Modifier and Type	Method	Description
void	BetterBeeman.preForce(Potential potential)	Integrator pre-force evaluation operation.
abstract void	Integrator.preForce(Potential potential)	Integrator pre-force evaluation operation.
void	Respa.preForce(Potential potential)	Integrator pre-force evaluation operation.
void	Stochastic.preForce(Potential potential)	Integrator pre-force evaluation operation.
void	VelocityVerlet.preForce(Potential potential)	Integrator pre-force evaluation operation.

Uses of Potential in ffx.algorithms.mc

Methods in ffx.algorithms.mc that return Potential

Modifier and Type	Method	Description
Potential	MolecularMC.getPotential()	Returns the associated Potential.

Constructors in ffx.algorithms.mc with parameters of type Potential

Modifier	Constructor	Description
	MDMove(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, DynamicsOptions dynamics, long stepsPerCycle, File dynRestartFile)	Constructor for MDMove.
	MolecularMC(MolecularAssembly molecularAssembly, Potential potential)	Constructs a DefaultMC instance with a molecular assembly and a specific Potential.

Uses of Potential in ffx.algorithms.misc

Constructors in ffx.algorithms.misc with parameters of type Potential

Modifier	Constructor	Description
	GenerateRotamers(MolecularAssembly molecularAssembly, Potential potential, Residue residue, File file, int nChi, AlgorithmListener listener)	Intended to create rotamer sets for nonstandard amino acids.
	GenerateRotamers(MolecularAssembly molecularAssembly, Potential potential, Residue residue, File file, int nChi, AlgorithmListener listener, RotamerLibrary library)	Intended to create rotamer sets for nonstandard amino acids.

Uses of Potential in ffx.algorithms.optimize

Fields in ffx.algorithms.optimize declared as Potential

Modifier and Type	Field	Description
protected final Potential	Minimize.potential	The potential energy to optimize.
protected final Potential	PhMinimize.potential	The potential energy to optimize.
protected final Potential	RotamerOptimization.potential	The Potential to evaluate during rotamer optimization.

Methods in ffx.algorithms.optimize that return Potential

Modifier and Type	Method	Description
Potential	CrystalMinimize.minimize(int m, double eps, int maxIterations)	minimize
Potential	Minimize.minimize()	minimize
Potential	Minimize.minimize(double eps)	minimize
Potential	Minimize.minimize(double eps, int maxIterations)	minimize
Potential	Minimize.minimize(int m, double eps, int maxIterations)	minimize
Potential	MinimizeOpenMM.minimize(double eps, int maxIterations)	minimize
Potential	MinimizeOpenMM.minimize(int m, double eps, int maxIterations)	Note the OpenMM L-BFGS minimizer does not accept the parameter "m" for the number of previous steps used to estimate the Hessian.
Potential	PhMinimize.minimizeCoordinates()	minimize
Potential	PhMinimize.minimizeCoordinates(double eps)	minimize
Potential	PhMinimize.minimizeCoordinates(double eps, int maxIterations)	minimize
Potential	PhMinimize.minimizeCoordinates(int m, double eps, int maxIterations)	minimize
Potential	PhMinimize.minimizeTitration(double eps, int maxIterations)	minimize
Potential	PhMinimize.minimizeTitration(int m, double eps, int maxIterations)	minimize

Methods in ffx.algorithms.optimize with parameters of type Potential

Modifier and Type	Method	Description
static Minimize.MinimizationEngine	Minimize.defaultEngine(MolecularAssembly molecularAssembly, Potential potentialEnergy)
static Minimize	Minimize.minimizeFactory(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, Minimize.MinimizationEngine engine)	dynamicsFactory.

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

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

Uses of Potential in ffx.algorithms.optimize.anneal

Constructors in ffx.algorithms.optimize.anneal with parameters of type Potential

Modifier	Constructor	Description
	SimulatedAnnealing(MolecularAssembly molecularAssembly, Potential potentialEnergy, AlgorithmListener algorithmListener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator, AnnealingSchedule annealingSchedule, long mdSteps, double timeStep, boolean reInitVelocity, File dynFile)	Constructor for SimulatedAnnealing.

Uses of Potential in ffx.algorithms.optimize.manybody

Constructors in ffx.algorithms.optimize.manybody with parameters of type Potential

Modifier	Constructor	Description
	EnergyExpansion(RotamerOptimization rO, DistanceMatrix dM, EliminatedRotamers eR, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, List<Residue> allResiduesList, int[][] resNeighbors, boolean threeBodyTerm, boolean decomposeOriginal, boolean usingBoxOptimization, boolean verbose, boolean pruneClashes, boolean prunePairClashes, boolean master)

Uses of Potential in ffx.algorithms.thermodynamics

Classes in ffx.algorithms.thermodynamics that implement Potential

Modifier and Type	Class	Description
class	OrthogonalSpaceTempering	An implementation of the Orthogonal Space Tempering algorithm.

Methods in ffx.algorithms.thermodynamics that return Potential

Modifier and Type	Method	Description
Potential	OrthogonalSpaceTempering.getPotentialEnergy()	getPotentialEnergy.

Constructors in ffx.algorithms.thermodynamics with parameters of type Potential

Modifier	Constructor	Description
	MonteCarloOST(Potential potentialEnergy, OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly molecularAssembly, org.apache.commons.configuration2.CompositeConfiguration properties, AlgorithmListener listener, DynamicsOptions dynamics, boolean verbose, int cycleLength, File dynRestartFile)	Constructor for MonteCarloOST.

Uses of Potential in ffx.crystal

Subinterfaces of Potential in ffx.crystal

Modifier and Type	Interface	Description
interface	CrystalPotential	The CrystalPotential interface extends Potential to provide methods that change the periodic boundary conditions and symmetry via a Crystal instance.

Uses of Potential in ffx.numerics

Methods in ffx.numerics that return types with arguments of type Potential

Modifier and Type	Method	Description
default List<Potential>	OptimizationInterface.getUnderlyingPotentials()	Returns a List of Potentials this Potential depends on with a recursive search, excluding the top level of this call.

Uses of Potential in ffx.potential

Classes in ffx.potential that implement Potential

Modifier and Type	Class	Description
class	ANIEnergy
class	DualTopologyEnergy	Compute the potential energy and derivatives for a dual-topology system.
class	ForceFieldEnergy	Compute the potential energy and derivatives of a molecular system described by a force field.
class	QuadTopologyEnergy	Implements an error-canceling quad topology, where two large dual-topology simulation legs are run simultaneously to arrive at a small sum.
class	XtalEnergy	This class computes the energy and Cartesian coordinate gradient, plus finite difference derivatives of lattice parameters.

Methods in ffx.potential that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	DualTopologyEnergy.getUnderlyingPotentials()
List<Potential>	QuadTopologyEnergy.getUnderlyingPotentials()

Methods in ffx.potential with parameters of type Potential

Modifier and Type	Method	Description
static double	FiniteDifferenceUtils.computedEdL(Potential potential, LambdaInterface lambdaInterface, ForceField forceField)	Compute dE/dL using finite differences.

Uses of Potential in ffx.potential.cli

Methods in ffx.potential.cli that return Potential

Modifier and Type	Method	Description
Potential	TopologyOptions.assemblePotential(MolecularAssembly[] assemblies, StringBuilder sb)	Performs the bulk of the work of setting up a multi-topology system.
Potential	TopologyOptions.getTopology(MolecularAssembly[] topologies, UnivariateSwitchingFunction sf, List<Integer> uniqueA, List<Integer> uniqueB, int numParallel, StringBuilder sb)	Configure a Dual-, Quad- or Oct- Topology.

Methods in ffx.potential.cli that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	PotentialCommand.getPotentials()	Returns a List of all Potential objects associated with this command.
List<Potential>	PotentialCommand.getPotentialsFromAssemblies(MolecularAssembly[] assemblies)	Returns a List of all Potential objects from the supplied MolecularAssembly array.

Uses of Potential in ffx.potential.commands

Methods in ffx.potential.commands that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	Cart2Frac.getPotentials()
List<Potential>	Energy.getPotentials()
List<Potential>	Frac2Cart.getPotentials()
List<Potential>	ImportCIF.getPotentials()
List<Potential>	MoveIntoUnitCell.getPotentials()
List<Potential>	PhEnergy.getPotentials()
List<Potential>	PrepareSpaceGroups.getPotentials()
List<Potential>	Solvator.getPotentials()
List<Potential>	Timer.getPotentials()

Uses of Potential in ffx.potential.commands.test

Methods in ffx.potential.commands.test that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	Gradient.getPotentials()
List<Potential>	LambdaGradient.getPotentials()
List<Potential>	PhGradient.getPotentials()

Uses of Potential in ffx.potential.extended

Classes in ffx.potential.extended that implement Potential

Modifier and Type	Class	Description
class	ExtendedSystem	ExtendedSystem class.

Uses of Potential in ffx.potential.openmm

Classes in ffx.potential.openmm that implement Potential

Modifier and Type	Class	Description
class	OpenMMDualTopologyEnergy
class	OpenMMEnergy	Compute the potential energy and derivatives using OpenMM.

Methods in ffx.potential.openmm that return Potential

Modifier and Type	Method	Description
Potential	OpenMMDualTopologySystem.getPotential()	Get the Potential in use.
Potential	OpenMMSystem.getPotential()	Get the Potential in use.

Uses of Potential in ffx.potential.utils

Constructors in ffx.potential.utils with parameters of type Potential

Modifier	Constructor	Description
	GradientUtils(Potential potential)	Constructor.

Uses of Potential in ffx.realspace

Classes in ffx.realspace that implement Potential

Modifier and Type	Class	Description
class	RealSpaceEnergy	Combine the Real Space target and chemical potential energy.

Uses of Potential in ffx.realspace.commands

Methods in ffx.realspace.commands that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	Anneal.getPotentials()
List<Potential>	Dynamics.getPotentials()
List<Potential>	ManyBody.getPotentials()

Uses of Potential in ffx.realspace.commands.test

Methods in ffx.realspace.commands.test that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	Alchemical.getPotentials()
List<Potential>	LambdaGradient.getPotentials()

Uses of Potential in ffx.ui

Methods in ffx.ui that return Potential

Modifier and Type	Method	Description
Potential	UIUtils.minimize(MolecularAssembly assembly, double eps)

Uses of Potential in ffx.xray

Classes in ffx.xray that implement Potential

Modifier and Type	Class	Description
class	RefinementEnergy	Combine the X-ray target and chemical potential energy using the CrystalPotential interface
class	XRayEnergy	Combine the X-ray target and chemical potential energy.

Methods in ffx.xray that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	RefinementEnergy.getUnderlyingPotentials()

Uses of Potential in ffx.xray.commands

Methods in ffx.xray.commands that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	Anneal.getPotentials()
List<Potential>	AverageMTZ.getPotentials()
List<Potential>	CIFtoMTZ.getPotentials()
List<Potential>	ComputeFc.getPotentials()
List<Potential>	Deuterate.getPotentials()
List<Potential>	Dynamics.getPotentials()
List<Potential>	GenZ.getPotentials()
List<Potential>	ManyBody.getPotentials()
List<Potential>	Minimize.getPotentials()
List<Potential>	ModelvsData.getPotentials()
List<Potential>	MTZInfo.getPotentials()
List<Potential>	Timer.getPotentials()

Uses of Potential in ffx.xray.commands.test

Methods in ffx.xray.commands.test that return types with arguments of type Potential

Modifier and Type	Method	Description
List<Potential>	Alchemical.getPotentials()
List<Potential>	Gradient.getPotentials()
List<Potential>	LambdaGradient.getPotentials()	Returns a List of all Potential objects associated with this script.