Package ffx.potential.openmm

Class OpenMMDualTopologyEnergy

java.lang.Object

ffx.potential.DualTopologyEnergy

ffx.potential.openmm.OpenMMDualTopologyEnergy

All Implemented Interfaces:

CrystalPotential, OptimizationInterface, Potential, LambdaInterface, OpenMMPotential

public class OpenMMDualTopologyEnergy
extends DualTopologyEnergy
implements OpenMMPotential

Nested Class Summary

Nested classes/interfaces inherited from interface ffx.numerics.Potential

Potential.STATE, Potential.VARIABLE_TYPE

Constructor Summary

Constructors

Constructor	Description
OpenMMDualTopologyEnergy(MolecularAssembly topology1, MolecularAssembly topology2, UnivariateSwitchingFunction switchFunction, Platform requestedPlatform)	Constructor for DualTopologyEnergy.

Method Summary

Modifier and Type	Method	Description
double	energy(double[] x)	This method is called repeatedly to compute the function energy.
double	energy(double[] x, boolean verbose)	This method is called repeatedly to compute the function energy.
double	energyFFX(double[] x)	Compute the energy using the pure Java code path.
double	energyFFX(double[] x, boolean verbose)	Compute the energy using the pure Java code path.
OpenMMContext	getContext()	Returns the Context instance.
ForceFieldEnergy	getForceFieldEnergy(int topology)	Get the OpenMMEnergy for the specified topology.
MolecularAssembly	getMolecularAssembly(int topology)	Get the MolecularAssembly.
OpenMMState	getOpenMMState(int mask)	Create an immutable OpenMM State.
OpenMMSystem	getSystem()	Get a reference to the System instance.
boolean	setActiveAtoms()	Update active atoms.
void	setCoordinates(double[] x)	Coordinates for active atoms in units of Angstroms.
void	setVelocity(double[] v)	Velocities for active atoms in units of Angstroms.
void	updateContext(String integratorName, double timeStep, double temperature, boolean forceCreation)	Create an OpenMM Context.
void	updateParameters(Atom[] atoms)	Update parameters if the Use flags and/or Lambda value has changed.

Methods inherited from class ffx.potential.DualTopologyEnergy

dEdLZeroAtEnds, destroy, energyAndGradient, energyAndGradient, energyFactory, getAcceleration, getCoordinates, getCrystal, getd2EdL2, getdEdL, getdEdXdL, getDualTopologyAtom, getDualTopologyAtoms, getDualTopologyIndex1, getDualTopologyIndex2, getEnergyTermState, getForceFieldEnergy1, getForceFieldEnergy2, getLambda, getMass, getNumberOfAtoms, getNumberOfVariables, getNumSharedVariables, getPreviousAcceleration, getScaling, getSwitch, getTopologyScale, getTotalEnergy, getUnderlyingPotentials, getVariableTypes, getVelocity, mapToDualTopologyIndex, setAcceleration, setCrystal, setEnergyTermState, setLambda, setParallel, setPreviousAcceleration, setPrintOnFailure, setScaling

Methods inherited from class java.lang.Object

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

Methods inherited from interface ffx.numerics.OptimizationInterface

scaleCoordinates, scaleCoordinatesAndGradient, unscaleCoordinates

Methods inherited from interface ffx.numerics.Potential

getConstraints, writeAdditionalRestartInfo

Constructor Details

OpenMMDualTopologyEnergy

public OpenMMDualTopologyEnergy(MolecularAssembly topology1,
 MolecularAssembly topology2,
 UnivariateSwitchingFunction switchFunction,
 Platform requestedPlatform)

Constructor for DualTopologyEnergy.

Parameters:

topology1 - a MolecularAssembly object.

topology2 - a MolecularAssembly object.

switchFunction - a UnivariateSwitchingFunction object.

requestedPlatform - a Platform object.

Method Details

energy

public double energy(double[] x)

This method is called repeatedly to compute the function energy.

Specified by:

energy in interface OptimizationInterface

Overrides:

energy in class DualTopologyEnergy

Parameters:

x - Input parameters.

Returns:

Function value at x.

energy

public double energy(double[] x,
 boolean verbose)

This method is called repeatedly to compute the function energy. The verbose flag may not be used by all implementations.

Specified by:

energy in interface OptimizationInterface

Overrides:

energy in class DualTopologyEnergy

Parameters:

x - Input parameters.

verbose - Display extra information.

Returns:

Function value at x

energyFFX

public double energyFFX(double[] x)

Compute the energy using the pure Java code path.

Parameters:

x - Atomic coordinates.

Returns:

The energy (kcal/mol)

energyFFX

public double energyFFX(double[] x,
 boolean verbose)

Compute the energy using the pure Java code path.

Parameters:

x - Input atomic coordinates

verbose - Use verbose logging.

Returns:

The energy (kcal/mol)

setCoordinates

public void setCoordinates(double[] x)

Coordinates for active atoms in units of Angstroms.

Specified by:

setCoordinates in interface OptimizationInterface

Overrides:

setCoordinates in class DualTopologyEnergy

Parameters:

x - Atomic coordinates active atoms.

setVelocity

public void setVelocity(double[] v)

Velocities for active atoms in units of Angstroms.

Specified by:

setVelocity in interface Potential

Overrides:

setVelocity in class DualTopologyEnergy

Parameters:

v - Velocities for active atoms.

getMolecularAssembly

public MolecularAssembly getMolecularAssembly(int topology)

Get the MolecularAssembly.

Parameters:

topology - The topology index (0 for topology 1, 1 for topology 2).

Returns:

a MolecularAssembly object for topology 1.

getForceFieldEnergy

public ForceFieldEnergy getForceFieldEnergy(int topology)

Get the OpenMMEnergy for the specified topology.

Parameters:

topology - The topology index (0 for topology 1, 1 for topology 2).

Returns:

The OpenMMEnergy for the specified topology.

updateParameters

public void updateParameters(@Nullable
 Atom[] atoms)

Update parameters if the Use flags and/or Lambda value has changed.

Specified by:

updateParameters in interface OpenMMPotential

Parameters:

atoms - Atoms in this list are considered.

getContext

public OpenMMContext getContext()

Returns the Context instance.

Specified by:

getContext in interface OpenMMPotential

Returns:

context

updateContext

public void updateContext(String integratorName,
 double timeStep,
 double temperature,
 boolean forceCreation)

Create an OpenMM Context.

Context.free() must be called to free OpenMM memory.

Specified by:

updateContext in interface OpenMMPotential

Parameters:

integratorName - Integrator to use.

timeStep - Time step.

temperature - Temperature (K).

forceCreation - Force a new Context to be created, even if the existing one matches the request.

getOpenMMState

public OpenMMState getOpenMMState(int mask)

Create an immutable OpenMM State.

State.free() must be called to free OpenMM memory.

Specified by:

getOpenMMState in interface OpenMMPotential

Parameters:

mask - The State mask.

Returns:

Returns the State.

getSystem

public OpenMMSystem getSystem()

Get a reference to the System instance.

Specified by:

getSystem in interface OpenMMPotential

Returns:

a reference to the OpenMMSystem.

setActiveAtoms

public boolean setActiveAtoms()

Update active atoms.

Specified by:

setActiveAtoms in interface OpenMMPotential

Returns:

True if there are inactive atoms.