Package ffx.potential.openmm

Class OpenMMEnergy

java.lang.Object

ffx.potential.ForceFieldEnergy

ffx.potential.openmm.OpenMMEnergy

All Implemented Interfaces:

CrystalPotential, OptimizationInterface, Potential, LambdaInterface

public class OpenMMEnergy
extends ForceFieldEnergy

Compute the potential energy and derivatives using OpenMM.

Since:

1.0

Author:

Michael J. Schnieders

Nested Class Summary

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

Potential.STATE, Potential.VARIABLE_TYPE

Field Summary

Fields inherited from class ffx.potential.ForceFieldEnergy

DEFAULT_CONSTRAINT_TOLERANCE, lambdaBondedTerms, lambdaTerm, maxDebugGradient, molecularAssembly, optimizationScaling

Constructor Summary

Constructors

Constructor	Description
OpenMMEnergy(MolecularAssembly molecularAssembly, Platform requestedPlatform, int nThreads)	ForceFieldEnergyOpenMM constructor; offloads heavy-duty computation to an OpenMM Platform while keeping track of information locally.

Method Summary

Modifier and Type	Method	Description
boolean	destroy()	Frees up assets associated with this ForceFieldEnergy, such as worker Threads.
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	energyAndGradient(double[] x, double[] g)	This method is called repeatedly to compute the function energy and gradient.
double	energyAndGradient(double[] x, double[] g, boolean verbose)	This method is called repeatedly to compute the function energy and gradient.
double	energyAndGradientFFX(double[] x, double[] g)	Compute the energy and gradient using the pure Java code path.
double	energyAndGradientFFX(double[] x, double[] g, boolean verbose)	Compute the energy and gradient using the pure Java code path.
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.
double	getd2EdL2()	Get the 2nd partial derivative of the energy with respect to lambda.
double	getdEdL()	Get the partial derivative of the energy with respect to lambda.
void	getdEdXdL(double[] gradients)	Get the gradient of dEdL with respect to each parameter.
static int	getDefaultDevice(org.apache.commons.configuration2.CompositeConfiguration props)	Gets the default coprocessor device, ignoring any CUDA_DEVICE over-ride.
double[]	getGradient(double[] g)	Re-compute the gradient using OpenMM and return it.
boolean	getLambdaTerm()	Get the lambdaTerm flag.
MolecularAssembly	getMolecularAssembly()	Returns the MolecularAssembly instance.
OpenMMState	getOpenMMState(int mask)	Create an immutable OpenMM State.
Platform	getPlatform()	Gets the Platform associated with this force field energy.
OpenMMSystem	getSystem()	Get a reference to the System instance.
void	setActiveAtoms()	Update active atoms.
void	setCoordinates(double[] x)	Set FFX and OpenMM coordinates for active atoms.
void	setCrystal(Crystal crystal)	Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
void	setLambda(double lambda)	Set the current value of the state variable.
void	setLambdaTerm(boolean lambdaTerm)	Set the lambdaTerm flag.
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.ForceFieldEnergy

applyAllConstraintPositions, applyAllConstraintPositions, attachExtendedSystem, dEdLZeroAtEnds, energy, energy, energyFactory, energyFactory, getAcceleration, getAngleEnergy, getAngleEnergyString, getAngles, getAngles, getAngleTorsionEnergy, getAngleTorsions, getBondEnergy, getBondEnergyString, getBonds, getCavitationEnergy, getConstraints, getCoordinates, getCrystal, getCutoffPlusBuffer, getDispersionEnergy, getElectrostaticEnergy, getEnergyTermState, getEsvBiasEnergy, getExtendedSystem, getGK, getGKEnergy, getImproperTorsionEnergy, getImproperTorsions, getInPlaneAngleEnergyString, getLambda, getMass, getNeutralNetworkEnergy, getNumberofAngles, getNumberofAngleTorsions, getNumberofBonds, getNumberofImproperTorsions, getNumberofOutOfPlaneBends, getNumberofPiOrbitalTorsions, getNumberofStretchBends, getNumberofStretchTorsions, getNumberofTorsions, getNumberofTorsionTorsions, getNumberofUreyBradleys, getNumberOfVariables, getOutOfPlaneBendEnergy, getOutOfPlaneBends, getOutOfPlaneEnergyString, getParallelTeam, getPDBHeaderString, getPermanentInteractions, getPermanentMultipoleEnergy, getPermanentRealSpaceEnergy, getPermanentReciprocalMpoleEnergy, getPermanentReciprocalSelfEnergy, getPiOrbitalTorsionEnergy, getPiOrbitalTorsionEnergyString, getPiOrbitalTorsions, getPmeNode, getPolarizationEnergy, getPreviousAcceleration, getRelativeSolvationEnergy, getRestrainDistances, getRestrainGroups, getRestrainPositions, getRestrainTorsions, getScaling, getSolvationEnergy, getSolvationInteractions, getStrenchBendEnergy, getStretchBendEnergyString, getStretchBends, getStretchTorsionEnergy, getStretchTorsions, getTorsionEnergy, getTorsions, getTorsionTorsionEnergy, getTorsionTorsions, getTotalElectrostaticEnergy, getTotalEnergy, getUreyBradleyEnergy, getUreyBradleys, getVanDerWaalsEnergy, getVanDerWaalsInteractions, getVariableTypes, getVdwNode, getVelocity, logBondedTerms, setAcceleration, setCrystal, setEnergyTermState, setPreviousAcceleration, setPrintOnFailure, setScaling, setVelocity, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface ffx.numerics.OptimizationInterface

getUnderlyingPotentials, scaleCoordinates, scaleCoordinatesAndGradient, unscaleCoordinates

Methods inherited from interface ffx.numerics.Potential

writeAdditionalRestartInfo

Constructor Details

OpenMMEnergy

public OpenMMEnergy(MolecularAssembly molecularAssembly,
 Platform requestedPlatform,
 int nThreads)

ForceFieldEnergyOpenMM constructor; offloads heavy-duty computation to an OpenMM Platform while keeping track of information locally.

Parameters:

molecularAssembly - Assembly to construct energy for.

requestedPlatform - requested OpenMM platform to be used.

nThreads - Number of threads to use in the super class ForceFieldEnergy instance.

Method Details

getDefaultDevice

public static int getDefaultDevice(org.apache.commons.configuration2.CompositeConfiguration props)

Gets the default coprocessor device, ignoring any CUDA_DEVICE over-ride. This is either determined by process rank and the availableDevices/CUDA_DEVICES property, or just 0 if neither property is sets.

Parameters:

props - Properties in use.

Returns:

Pre-override device index.

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.

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.

Parameters:

mask - The State mask.

Returns:

Returns the State.

destroy

public boolean destroy()

Frees up assets associated with this ForceFieldEnergy, such as worker Threads.

Specified by:

destroy in interface OptimizationInterface

Overrides:

destroy in class ForceFieldEnergy

Returns:

If successful in freeing up assets.

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 ForceFieldEnergy

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 ForceFieldEnergy

Parameters:

x - Input parameters.

verbose - Display extra information.

Returns:

Function value at x

energyAndGradient

public double energyAndGradient(double[] x,
 double[] g)

This method is called repeatedly to compute the function energy and gradient.

Specified by:

energyAndGradient in interface OptimizationInterface

Overrides:

energyAndGradient in class ForceFieldEnergy

Parameters:

x - Input parameters.

g - Output gradients with respect to each parameter.

Returns:

Function value at x.

energyAndGradient

public double energyAndGradient(double[] x,
 double[] g,
 boolean verbose)

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

Specified by:

energyAndGradient in interface OptimizationInterface

Overrides:

energyAndGradient in class ForceFieldEnergy

Parameters:

x - Input parameters.

g - Output gradients with respect to each parameter.

verbose - Display extra information.

Returns:

Function value at x.

energyAndGradientFFX

public double energyAndGradientFFX(double[] x,
 double[] g)

Compute the energy and gradient using the pure Java code path.

Parameters:

x - Input atomic coordinates

g - Storage for the gradient vector.

Returns:

The energy (kcal/mol)

energyAndGradientFFX

public double energyAndGradientFFX(double[] x,
 double[] g,
 boolean verbose)

Compute the energy and gradient using the pure Java code path.

Parameters:

x - Input atomic coordinates

g - Storage for the gradient vector.

verbose - Use verbose logging.

Returns:

The energy (kcal/mol)

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)

getContext

public OpenMMContext getContext()

Returns the Context instance.

Returns:

context

getMolecularAssembly

public MolecularAssembly getMolecularAssembly()

Returns the MolecularAssembly instance.

Returns:

molecularAssembly

setLambdaTerm

public void setLambdaTerm(boolean lambdaTerm)

Set the lambdaTerm flag.

Parameters:

lambdaTerm - The value to set.

getLambdaTerm

public boolean getLambdaTerm()

Get the lambdaTerm flag.

Returns:

lambdaTerm.

getGradient

public double[] getGradient(double[] g)

Re-compute the gradient using OpenMM and return it.

Overrides:

getGradient in class ForceFieldEnergy

Parameters:

g - Gradient array.

Returns:

an array of

invalid reference

double

objects.

getPlatform

public Platform getPlatform()

Gets the Platform associated with this force field energy. For the reference platform, always returns FFX.

Overrides:

getPlatform in class ForceFieldEnergy

Returns:

A Platform.

getSystem

public OpenMMSystem getSystem()

Get a reference to the System instance.

Returns:

Java wrapper to an OpenMM system.

getd2EdL2

public double getd2EdL2()

Get the 2nd partial derivative of the energy with respect to lambda.

Specified by:

getd2EdL2 in interface LambdaInterface

Overrides:

getd2EdL2 in class ForceFieldEnergy

Returns:

d2EdL2

getdEdL

public double getdEdL()

Get the partial derivative of the energy with respect to lambda.

Specified by:

getdEdL in interface LambdaInterface

Overrides:

getdEdL in class ForceFieldEnergy

Returns:

dEdL

getdEdXdL

public void getdEdXdL(double[] gradients)

Get the gradient of dEdL with respect to each parameter.

Specified by:

getdEdXdL in interface LambdaInterface

Overrides:

getdEdXdL in class ForceFieldEnergy

Parameters:

gradients - - A double array of length the number of parameters in the model (commonly 3 * number of atoms).

setActiveAtoms

public void setActiveAtoms()

Update active atoms.

setCoordinates

public void setCoordinates(double[] x)

Set FFX and OpenMM coordinates for active atoms.

Overrides:

setCoordinates in class ForceFieldEnergy

Parameters:

x - Atomic coordinates.

setCrystal

public void setCrystal(Crystal crystal)

Set the Crystal instance that specifies the periodic boundary conditions and symmetry.

Set the boundary conditions for this calculation.

Specified by:

setCrystal in interface CrystalPotential

Overrides:

setCrystal in class ForceFieldEnergy

Parameters:

crystal - a Crystal instance.

setLambda

public void setLambda(double lambda)

Set the current value of the state variable. May be ignored if lambda is not being applied.

Specified by:

setLambda in interface LambdaInterface

Overrides:

setLambda in class ForceFieldEnergy

Parameters:

lambda - a double.

updateParameters

public void updateParameters(@Nullable
 Atom[] atoms)

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

Parameters:

atoms - Atoms in this list are considered.