Uses of Interface
ffx.numerics.OptimizationInterface

Packages that use OptimizationInterface

Package	Description
ffx.algorithms.dynamics	The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
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.numerics.estimator
ffx.numerics.optimization	The Optimization package implements the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm for large-scale multidimensional unconstrained optimization problems.
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
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
ffx.realspace	The Real Space package implements real space structure refinement.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.

Uses of OptimizationInterface in ffx.algorithms.dynamics

Classes in ffx.algorithms.dynamics that implement OptimizationInterface

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.

Uses of OptimizationInterface in ffx.algorithms.thermodynamics

Classes in ffx.algorithms.thermodynamics that implement OptimizationInterface

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

Uses of OptimizationInterface in ffx.crystal

Subinterfaces of OptimizationInterface 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 OptimizationInterface in ffx.numerics

Subinterfaces of OptimizationInterface in ffx.numerics

Modifier and Type	Interface	Description
interface	Potential	The Potential interface defines methods required by an optimizer or molecular dynamics.

Uses of OptimizationInterface in ffx.numerics.estimator

Classes in ffx.numerics.estimator that implement OptimizationInterface

Modifier and Type	Class	Description
class	MultistateBennettAcceptanceRatio	The MultistateBennettAcceptanceRatio class defines a statistical estimator based on a generalization to the Bennett Acceptance Ratio (BAR) method for multiple lambda windows.

Uses of OptimizationInterface in ffx.numerics.optimization

Methods in ffx.numerics.optimization with parameters of type OptimizationInterface

Modifier and Type	Method	Description
static int	LBFGS.minimize(int n, int mSave, double[] x, double f, double[] g, double eps, int maxIterations, OptimizationInterface potential, OptimizationListener listener)	This method solves the unconstrained minimization problem
static int	LBFGS.minimize(int n, int mSave, double[] x, double f, double[] g, double eps, OptimizationInterface potential, OptimizationListener listener)	This method solves the unconstrained minimization problem
double	LineSearch.search(int n, double[] x, double f, double[] g, double[] p, double[] angle, double fMove, LineSearch.LineSearchResult[] info, int[] functionEvaluations, OptimizationInterface optimizationSystem)	Minimize a function along a search direction.

Uses of OptimizationInterface in ffx.potential

Classes in ffx.potential that implement OptimizationInterface

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.

Uses of OptimizationInterface in ffx.potential.extended

Classes in ffx.potential.extended that implement OptimizationInterface

Modifier and Type	Class	Description
class	ExtendedSystem	ExtendedSystem class.

Uses of OptimizationInterface in ffx.potential.openmm

Classes in ffx.potential.openmm that implement OptimizationInterface

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

Uses of OptimizationInterface in ffx.realspace

Classes in ffx.realspace that implement OptimizationInterface

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

Uses of OptimizationInterface in ffx.xray

Classes in ffx.xray that implement OptimizationInterface

Modifier and Type	Class	Description
class	RefinementEnergy	Combine the X-ray target and chemical potential energy using the CrystalPotential interface
class	ScaleBulkEnergy	Fit bulk solvent and aniso B scaling terms to correct calculated structure factors against data
class	SigmaAEnergy	Optimize SigmaA coefficients (using spline coefficients) and structure factor derivatives using a likelihood target function.
class	SplineEnergy	Fit structure factors using spline coefficients
class	XRayEnergy	Combine the X-ray target and chemical potential energy.