Uses of Interface
ffx.numerics.switching.UnivariateSwitchingFunction
Package
Description
The Switching package implements univariate switching functions.
The Potential package implements molecular mechanics force fields with shared memory Parallel
Java and via OpenMM.
The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions,
etc.
The Potential CLI package defines reusable options for PicoCLI command line scripts.
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Uses of UnivariateSwitchingFunction in ffx.numerics.switching
Modifier and TypeClassDescriptionclass
Implements a bell-shaped switching function by stitching together a pair of MultiplicativeSwitches. f(midpoint - 0.5*width) = 0, f(midpoint) = 1, f(midpoint + 0.5*width) = 0.class
The CompositeSwitch uses a primary switch in the middle, and then two secondary switches at the ends of the path to smoothly switch to the primary switch.class
The ConstantSwitch returns a constant value for all input values x.class
A LinearDerivativeSwitch interpolates between 0 and 1 vi f(x) = 2*x - x^2.class
The 6 coefficients of the multiplicative polynomial switch are unique given the distances "a" and "b".class
A PowerSwitch interpolates between 0 and 1 vi f(x) = (ax)^beta, where x must be between 0 and 1/a.class
A SquaredTrigSwitch implements a 0-1 switch of form f(x) = sin^2(ax) or of form f(x) = cos^2(ax).Modifier and TypeMethodDescriptionstatic UnivariateSwitchingFunction
Parse an array of Strings describing a univariate switching function.static UnivariateSwitchingFunction
Parse an array of Strings terminating in the description of a univariate switching function.ModifierConstructorDescriptionBuilds a switch that uses MultiplicativeSwitches at the ends (0-0.1, 0.9-1.0) to smoothly interpolate a provided switch between 0 and 1 with smooth 2'nd and 3'rd derivatives.CompositeSwitch
(UnivariateSwitchingFunction primary, UnivariateSwitchingFunction start, UnivariateSwitchingFunction end, double lbPrimary, double ubPrimary) Builds a composite switch in .CompositeSwitch
(UnivariateSwitchingFunction primary, UnivariateSwitchingFunction start, UnivariateSwitchingFunction end, double lbPrimary, double ubPrimary, double lb, double ub) Builds a composite switch in . -
Uses of UnivariateSwitchingFunction in ffx.potential
Modifier and TypeMethodDescriptionDualTopologyEnergy.getSwitch()
Returns the switching function used by this DualTopologyEnergy; presently, switching functions are immutable, and cannot be changed once a DualTopologyEnergy is constructed.ModifierConstructorDescriptionDualTopologyEnergy
(MolecularAssembly topology1, MolecularAssembly topology2, UnivariateSwitchingFunction switchFunction) Constructor for DualTopologyEnergy. -
Uses of UnivariateSwitchingFunction in ffx.potential.bonded
ModifierConstructorDescriptionRestrainDistance
(Atom a1, Atom a2, Crystal crystal, boolean lambdaTerm, double lamStart, double lamEnd, UnivariateSwitchingFunction sf) Creates a distance restraint between two Atoms. -
Uses of UnivariateSwitchingFunction in ffx.potential.cli
Modifier and TypeMethodDescriptionTopologyOptions.getSwitchingFunction()
Return the switching function between topology energies.Modifier and TypeMethodDescriptionTopologyOptions.getTopology
(MolecularAssembly[] topologies, UnivariateSwitchingFunction sf, List<Integer> uniqueA, List<Integer> uniqueB, int numParallel, StringBuilder sb) Configure a Dual-, Quad- or Oct- Topology.