#ifndef OPENMM_REFERENCEKERNELS_H_
#define OPENMM_REFERENCEKERNELS_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "ReferencePlatform.h"
#include "openmm/kernels.h"
#include "SimTKOpenMMRealType.h"
#include "ReferenceNeighborList.h"
#include "lepton/ExpressionProgram.h"
class CpuObc;
class CpuGBVI;
class ReferenceAndersenThermostat;
class ReferenceCustomCompoundBondIxn;
class ReferenceCustomHbondIxn;
class ReferenceBrownianDynamics;
class ReferenceStochasticDynamics;
class ReferenceConstraintAlgorithm;
class ReferenceMonteCarloBarostat;
class ReferenceVariableStochasticDynamics;
class ReferenceVariableVerletDynamics;
class ReferenceVerletDynamics;
class ReferenceCustomDynamics;
namespace OpenMM {
/**
* This kernel is invoked at the beginning and end of force and energy computations. It gives the
* Platform a chance to clear buffers and do other initialization at the beginning, and to do any
* necessary work at the end to determine the final results.
*/
class ReferenceCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
public:
ReferenceCalcForcesAndEnergyKernel(std::string name, const Platform& platform) : CalcForcesAndEnergyKernel(name, platform) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
*/
void initialize(const System& system);
/**
* This is called at the beginning of each force/energy computation, before calcForcesAndEnergy() has been called on
* any ForceImpl.
*
* @param context the context in which to execute this kernel
* @param includeForce true if forces should be computed
* @param includeEnergy true if potential energy should be computed
* @param groups a set of bit flags for which force groups to include
*/
void beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups);
/**
* This is called at the end of each force/energy computation, after calcForcesAndEnergy() has been called on
* every ForceImpl.
*
* @param context the context in which to execute this kernel
* @param includeForce true if forces should be computed
* @param includeEnergy true if potential energy should be computed
* @param groups a set of bit flags for which force groups to include
* @return the potential energy of the system. This value is added to all values returned by ForceImpls'
* calcForcesAndEnergy() methods. That is, each force kernel may either return its contribution to the
* energy directly, or add it to an internal buffer so that it will be included here.
*/
double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups);
private:
std::vector savedForces;
};
/**
* This kernel provides methods for setting and retrieving various state data: time, positions,
* velocities, and forces.
*/
class ReferenceUpdateStateDataKernel : public UpdateStateDataKernel {
public:
ReferenceUpdateStateDataKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : UpdateStateDataKernel(name, platform), data(data) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
*/
void initialize(const System& system);
/**
* Get the current time (in picoseconds).
*
* @param context the context in which to execute this kernel
*/
double getTime(const ContextImpl& context) const;
/**
* Set the current time (in picoseconds).
*
* @param context the context in which to execute this kernel
*/
void setTime(ContextImpl& context, double time);
/**
* Get the positions of all particles.
*
* @param positions on exit, this contains the particle positions
*/
void getPositions(ContextImpl& context, std::vector& positions);
/**
* Set the positions of all particles.
*
* @param positions a vector containg the particle positions
*/
void setPositions(ContextImpl& context, const std::vector& positions);
/**
* Get the velocities of all particles.
*
* @param velocities on exit, this contains the particle velocities
*/
void getVelocities(ContextImpl& context, std::vector& velocities);
/**
* Set the velocities of all particles.
*
* @param velocities a vector containg the particle velocities
*/
void setVelocities(ContextImpl& context, const std::vector& velocities);
/**
* Get the current forces on all particles.
*
* @param forces on exit, this contains the forces
*/
void getForces(ContextImpl& context, std::vector& forces);
/**
* Get the current periodic box vectors.
*
* @param a on exit, this contains the vector defining the first edge of the periodic box
* @param b on exit, this contains the vector defining the second edge of the periodic box
* @param c on exit, this contains the vector defining the third edge of the periodic box
*/
void getPeriodicBoxVectors(ContextImpl& context, Vec3& a, Vec3& b, Vec3& c) const;
/**
* Set the current periodic box vectors.
*
* @param a the vector defining the first edge of the periodic box
* @param b the vector defining the second edge of the periodic box
* @param c the vector defining the third edge of the periodic box
*/
void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const;
/**
* Create a checkpoint recording the current state of the Context.
*
* @param stream an output stream the checkpoint data should be written to
*/
void createCheckpoint(ContextImpl& context, std::ostream& stream);
/**
* Load a checkpoint that was written by createCheckpoint().
*
* @param stream an input stream the checkpoint data should be read from
*/
void loadCheckpoint(ContextImpl& context, std::istream& stream);
private:
ReferencePlatform::PlatformData& data;
};
/**
* This kernel modifies the positions of particles to enforce distance constraints.
*/
class ReferenceApplyConstraintsKernel : public ApplyConstraintsKernel {
public:
ReferenceApplyConstraintsKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) :
ApplyConstraintsKernel(name, platform), data(data), constraints(0) {
}
~ReferenceApplyConstraintsKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
*/
void initialize(const System& system);
/**
* Update particle positions to enforce constraints.
*
* @param context the context in which to execute this kernel
* @param tol the distance tolerance within which constraints must be satisfied.
*/
void apply(ContextImpl& context, double tol);
/**
* Update particle velocities to enforce constraints.
*
* @param context the context in which to execute this kernel
* @param tol the velocity tolerance within which constraints must be satisfied.
*/
void applyToVelocities(ContextImpl& context, double tol);
private:
ReferencePlatform::PlatformData& data;
ReferenceConstraintAlgorithm* constraints;
std::vector masses;
std::vector inverseMasses;
std::vector > constraintIndices;
std::vector constraintDistances;
int numConstraints;
};
/**
* This kernel recomputes the positions of virtual sites.
*/
class ReferenceVirtualSitesKernel : public VirtualSitesKernel {
public:
ReferenceVirtualSitesKernel(std::string name, const Platform& platform) : VirtualSitesKernel(name, platform) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
*/
void initialize(const System& system);
/**
* Compute the virtual site locations.
*
* @param context the context in which to execute this kernel
*/
void computePositions(ContextImpl& context);
};
/**
* This kernel is invoked by HarmonicBondForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcHarmonicBondForceKernel : public CalcHarmonicBondForceKernel {
public:
ReferenceCalcHarmonicBondForceKernel(std::string name, const Platform& platform) : CalcHarmonicBondForceKernel(name, platform) {
}
~ReferenceCalcHarmonicBondForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the HarmonicBondForce this kernel will be used for
*/
void initialize(const System& system, const HarmonicBondForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the HarmonicBondForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const HarmonicBondForce& force);
private:
int numBonds;
int **bondIndexArray;
RealOpenMM **bondParamArray;
};
/**
* This kernel is invoked by CustomBondForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcCustomBondForceKernel : public CalcCustomBondForceKernel {
public:
ReferenceCalcCustomBondForceKernel(std::string name, const Platform& platform) : CalcCustomBondForceKernel(name, platform) {
}
~ReferenceCalcCustomBondForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the CustomBondForce this kernel will be used for
*/
void initialize(const System& system, const CustomBondForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomBondForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomBondForce& force);
private:
int numBonds;
int **bondIndexArray;
RealOpenMM **bondParamArray;
Lepton::ExpressionProgram energyExpression, forceExpression;
std::vector parameterNames, globalParameterNames;
};
/**
* This kernel is invoked by HarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
public:
ReferenceCalcHarmonicAngleForceKernel(std::string name, const Platform& platform) : CalcHarmonicAngleForceKernel(name, platform) {
}
~ReferenceCalcHarmonicAngleForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the HarmonicAngleForce this kernel will be used for
*/
void initialize(const System& system, const HarmonicAngleForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the HarmonicAngleForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force);
private:
int numAngles;
int **angleIndexArray;
RealOpenMM **angleParamArray;
};
/**
* This kernel is invoked by CustomAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcCustomAngleForceKernel : public CalcCustomAngleForceKernel {
public:
ReferenceCalcCustomAngleForceKernel(std::string name, const Platform& platform) : CalcCustomAngleForceKernel(name, platform) {
}
~ReferenceCalcCustomAngleForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the CustomAngleForce this kernel will be used for
*/
void initialize(const System& system, const CustomAngleForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomAngleForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomAngleForce& force);
private:
int numAngles;
int **angleIndexArray;
RealOpenMM **angleParamArray;
Lepton::ExpressionProgram energyExpression, forceExpression;
std::vector parameterNames, globalParameterNames;
};
/**
* This kernel is invoked by PeriodicTorsionForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcPeriodicTorsionForceKernel : public CalcPeriodicTorsionForceKernel {
public:
ReferenceCalcPeriodicTorsionForceKernel(std::string name, const Platform& platform) : CalcPeriodicTorsionForceKernel(name, platform) {
}
~ReferenceCalcPeriodicTorsionForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the PeriodicTorsionForce this kernel will be used for
*/
void initialize(const System& system, const PeriodicTorsionForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the PeriodicTorsionForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const PeriodicTorsionForce& force);
private:
int numTorsions;
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
};
/**
* This kernel is invoked by RBTorsionForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcRBTorsionForceKernel : public CalcRBTorsionForceKernel {
public:
ReferenceCalcRBTorsionForceKernel(std::string name, const Platform& platform) : CalcRBTorsionForceKernel(name, platform) {
}
~ReferenceCalcRBTorsionForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the RBTorsionForce this kernel will be used for
*/
void initialize(const System& system, const RBTorsionForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the RBTorsionForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const RBTorsionForce& force);
private:
int numTorsions;
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
};
/**
* This kernel is invoked by CMAPTorsionForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcCMAPTorsionForceKernel : public CalcCMAPTorsionForceKernel {
public:
ReferenceCalcCMAPTorsionForceKernel(std::string name, const Platform& platform) : CalcCMAPTorsionForceKernel(name, platform) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the CMAPTorsionForce this kernel will be used for
*/
void initialize(const System& system, const CMAPTorsionForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
std::vector > > coeff;
std::vector torsionMaps;
std::vector > torsionIndices;
};
/**
* This kernel is invoked by CustomTorsionForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcCustomTorsionForceKernel : public CalcCustomTorsionForceKernel {
public:
ReferenceCalcCustomTorsionForceKernel(std::string name, const Platform& platform) : CalcCustomTorsionForceKernel(name, platform) {
}
~ReferenceCalcCustomTorsionForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the CustomTorsionForce this kernel will be used for
*/
void initialize(const System& system, const CustomTorsionForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomTorsionForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomTorsionForce& force);
private:
int numTorsions;
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
Lepton::ExpressionProgram energyExpression, forceExpression;
std::vector parameterNames, globalParameterNames;
};
/**
* This kernel is invoked by NonbondedForce to calculate the forces acting on the system.
*/
class ReferenceCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public:
ReferenceCalcNonbondedForceKernel(std::string name, const Platform& platform) : CalcNonbondedForceKernel(name, platform) {
}
~ReferenceCalcNonbondedForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the NonbondedForce this kernel will be used for
*/
void initialize(const System& system, const NonbondedForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @param includeReciprocal true if reciprocal space interactions should be included
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the NonbondedForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const NonbondedForce& force);
private:
int numParticles, num14;
int **bonded14IndexArray;
RealOpenMM **particleParamArray, **bonded14ParamArray;
RealOpenMM nonbondedCutoff, switchingDistance, rfDielectric, ewaldAlpha, dispersionCoefficient;
int kmax[3], gridSize[3];
bool useSwitchingFunction;
std::vector > exclusions;
NonbondedMethod nonbondedMethod;
NeighborList* neighborList;
};
/**
* This kernel is invoked by CustomNonbondedForce to calculate the forces acting on the system.
*/
class ReferenceCalcCustomNonbondedForceKernel : public CalcCustomNonbondedForceKernel {
public:
ReferenceCalcCustomNonbondedForceKernel(std::string name, const Platform& platform) : CalcCustomNonbondedForceKernel(name, platform), forceCopy(NULL) {
}
~ReferenceCalcCustomNonbondedForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the CustomNonbondedForce this kernel will be used for
*/
void initialize(const System& system, const CustomNonbondedForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomNonbondedForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
private:
int numParticles;
RealOpenMM **particleParamArray;
RealOpenMM nonbondedCutoff, switchingDistance, periodicBoxSize[3], longRangeCoefficient;
bool useSwitchingFunction, hasInitializedLongRangeCorrection;
CustomNonbondedForce* forceCopy;
std::map globalParamValues;
std::vector > exclusions;
Lepton::ExpressionProgram energyExpression, forceExpression;
std::vector parameterNames, globalParameterNames;
std::vector, std::set > > interactionGroups;
NonbondedMethod nonbondedMethod;
NeighborList* neighborList;
};
/**
* This kernel is invoked by GBSAOBCForce to calculate the forces acting on the system.
*/
class ReferenceCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
public:
ReferenceCalcGBSAOBCForceKernel(std::string name, const Platform& platform) : CalcGBSAOBCForceKernel(name, platform) {
}
~ReferenceCalcGBSAOBCForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the GBSAOBCForce this kernel will be used for
*/
void initialize(const System& system, const GBSAOBCForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the GBSAOBCForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force);
private:
CpuObc* obc;
std::vector charges;
bool isPeriodic;
};
/**
* This kernel is invoked by GBVIForce to calculate the forces acting on the system.
*/
class ReferenceCalcGBVIForceKernel : public CalcGBVIForceKernel {
public:
ReferenceCalcGBVIForceKernel(std::string name, const Platform& platform) : CalcGBVIForceKernel(name, platform) {
}
~ReferenceCalcGBVIForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the GBVIForce this kernel will be used for
* @param scaled radii the scaled radii (Eq. 5 of Labute paper)
*/
void initialize(const System& system, const GBVIForce& force, const std::vector & scaledRadii);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
CpuGBVI * gbvi;
std::vector charges;
bool isPeriodic;
};
/**
* This kernel is invoked by CustomGBForce to calculate the forces acting on the system.
*/
class ReferenceCalcCustomGBForceKernel : public CalcCustomGBForceKernel {
public:
ReferenceCalcCustomGBForceKernel(std::string name, const Platform& platform) : CalcCustomGBForceKernel(name, platform) {
}
~ReferenceCalcCustomGBForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the CustomGBForce this kernel will be used for
*/
void initialize(const System& system, const CustomGBForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomGBForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomGBForce& force);
private:
int numParticles;
bool isPeriodic;
RealOpenMM **particleParamArray;
RealOpenMM nonbondedCutoff;
std::vector > exclusions;
std::vector particleParameterNames, globalParameterNames, valueNames;
std::vector valueExpressions;
std::vector > valueDerivExpressions;
std::vector > valueGradientExpressions;
std::vector valueTypes;
std::vector energyExpressions;
std::vector > energyDerivExpressions;
std::vector > energyGradientExpressions;
std::vector energyTypes;
NonbondedMethod nonbondedMethod;
NeighborList* neighborList;
};
/**
* This kernel is invoked by CustomExternalForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcCustomExternalForceKernel : public CalcCustomExternalForceKernel {
public:
ReferenceCalcCustomExternalForceKernel(std::string name, const Platform& platform) : CalcCustomExternalForceKernel(name, platform) {
}
~ReferenceCalcCustomExternalForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the CustomExternalForce this kernel will be used for
*/
void initialize(const System& system, const CustomExternalForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomExternalForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force);
private:
int numParticles;
std::vector particles;
RealOpenMM **particleParamArray;
Lepton::ExpressionProgram energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ;
std::vector parameterNames, globalParameterNames;
};
/**
* This kernel is invoked by CustomHbondForce to calculate the forces acting on the system.
*/
class ReferenceCalcCustomHbondForceKernel : public CalcCustomHbondForceKernel {
public:
ReferenceCalcCustomHbondForceKernel(std::string name, const Platform& platform) : CalcCustomHbondForceKernel(name, platform), ixn(NULL) {
}
~ReferenceCalcCustomHbondForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the CustomHbondForce this kernel will be used for
*/
void initialize(const System& system, const CustomHbondForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomHbondForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomHbondForce& force);
private:
int numDonors, numAcceptors, numParticles;
bool isPeriodic;
RealOpenMM **donorParamArray, **acceptorParamArray;
RealOpenMM nonbondedCutoff;
ReferenceCustomHbondIxn* ixn;
std::vector > exclusions;
std::vector globalParameterNames;
};
/**
* This kernel is invoked by CustomCompoundBondForce to calculate the forces acting on the system.
*/
class ReferenceCalcCustomCompoundBondForceKernel : public CalcCustomCompoundBondForceKernel {
public:
ReferenceCalcCustomCompoundBondForceKernel(std::string name, const Platform& platform) : CalcCustomCompoundBondForceKernel(name, platform), ixn(NULL) {
}
~ReferenceCalcCustomCompoundBondForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the CustomCompoundBondForce this kernel will be used for
*/
void initialize(const System& system, const CustomCompoundBondForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomCompoundBondForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force);
private:
int numBonds, numParticles;
RealOpenMM **bondParamArray;
ReferenceCustomCompoundBondIxn* ixn;
std::vector globalParameterNames;
};
/**
* This kernel is invoked by VerletIntegrator to take one time step.
*/
class ReferenceIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
public:
ReferenceIntegrateVerletStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVerletStepKernel(name, platform),
data(data), dynamics(0), constraints(0) {
}
~ReferenceIntegrateVerletStepKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param integrator the VerletIntegrator this kernel will be used for
*/
void initialize(const System& system, const VerletIntegrator& integrator);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the VerletIntegrator this kernel is being used for
*/
void execute(ContextImpl& context, const VerletIntegrator& integrator);
/**
* Compute the kinetic energy.
*
* @param context the context in which to execute this kernel
* @param integrator the VerletIntegrator this kernel is being used for
*/
double computeKineticEnergy(ContextImpl& context, const VerletIntegrator& integrator);
private:
ReferencePlatform::PlatformData& data;
ReferenceVerletDynamics* dynamics;
ReferenceConstraintAlgorithm* constraints;
std::vector masses;
int numConstraints;
double prevStepSize;
};
/**
* This kernel is invoked by LangevinIntegrator to take one time step.
*/
class ReferenceIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
public:
ReferenceIntegrateLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateLangevinStepKernel(name, platform),
data(data), dynamics(0), constraints(0) {
}
~ReferenceIntegrateLangevinStepKernel();
/**
* Initialize the kernel, setting up the particle masses.
*
* @param system the System this kernel will be applied to
* @param integrator the LangevinIntegrator this kernel will be used for
*/
void initialize(const System& system, const LangevinIntegrator& integrator);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the LangevinIntegrator this kernel is being used for
*/
void execute(ContextImpl& context, const LangevinIntegrator& integrator);
/**
* Compute the kinetic energy.
*
* @param context the context in which to execute this kernel
* @param integrator the LangevinIntegrator this kernel is being used for
*/
double computeKineticEnergy(ContextImpl& context, const LangevinIntegrator& integrator);
private:
ReferencePlatform::PlatformData& data;
ReferenceStochasticDynamics* dynamics;
ReferenceConstraintAlgorithm* constraints;
std::vector masses;
int numConstraints;
double prevTemp, prevFriction, prevStepSize;
};
/**
* This kernel is invoked by BrownianIntegrator to take one time step.
*/
class ReferenceIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
public:
ReferenceIntegrateBrownianStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateBrownianStepKernel(name, platform),
data(data), dynamics(0), constraints(0) {
}
~ReferenceIntegrateBrownianStepKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param integrator the BrownianIntegrator this kernel will be used for
*/
void initialize(const System& system, const BrownianIntegrator& integrator);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the BrownianIntegrator this kernel is being used for
*/
void execute(ContextImpl& context, const BrownianIntegrator& integrator);
/**
* Compute the kinetic energy.
*
* @param context the context in which to execute this kernel
* @param integrator the BrownianIntegrator this kernel is being used for
*/
double computeKineticEnergy(ContextImpl& context, const BrownianIntegrator& integrator);
private:
ReferencePlatform::PlatformData& data;
ReferenceBrownianDynamics* dynamics;
ReferenceConstraintAlgorithm* constraints;
std::vector masses;
int numConstraints;
double prevTemp, prevFriction, prevStepSize;
};
/**
* This kernel is invoked by VariableLangevinIntegrator to take one time step.
*/
class ReferenceIntegrateVariableLangevinStepKernel : public IntegrateVariableLangevinStepKernel {
public:
ReferenceIntegrateVariableLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVariableLangevinStepKernel(name, platform),
data(data), dynamics(0), constraints(0) {
}
~ReferenceIntegrateVariableLangevinStepKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param integrator the VariableLangevinIntegrator this kernel will be used for
*/
void initialize(const System& system, const VariableLangevinIntegrator& integrator);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the VariableLangevinIntegrator this kernel is being used for
* @param maxTime the maximum time beyond which the simulation should not be advanced
* @return the size of the step that was taken
*/
double execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime);
/**
* Compute the kinetic energy.
*
* @param context the context in which to execute this kernel
* @param integrator the VariableLangevinIntegrator this kernel is being used for
*/
double computeKineticEnergy(ContextImpl& context, const VariableLangevinIntegrator& integrator);
private:
ReferencePlatform::PlatformData& data;
ReferenceVariableStochasticDynamics* dynamics;
ReferenceConstraintAlgorithm* constraints;
std::vector masses;
int numConstraints;
double prevTemp, prevFriction, prevErrorTol;
};
/**
* This kernel is invoked by VariableVerletIntegrator to take one time step.
*/
class ReferenceIntegrateVariableVerletStepKernel : public IntegrateVariableVerletStepKernel {
public:
ReferenceIntegrateVariableVerletStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVariableVerletStepKernel(name, platform),
data(data), dynamics(0), constraints(0) {
}
~ReferenceIntegrateVariableVerletStepKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param integrator the VariableVerletIntegrator this kernel will be used for
*/
void initialize(const System& system, const VariableVerletIntegrator& integrator);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the VariableVerletIntegrator this kernel is being used for
* @param maxTime the maximum time beyond which the simulation should not be advanced
* @return the size of the step that was taken
*/
double execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime);
/**
* Compute the kinetic energy.
*
* @param context the context in which to execute this kernel
* @param integrator the VariableVerletIntegrator this kernel is being used for
*/
double computeKineticEnergy(ContextImpl& context, const VariableVerletIntegrator& integrator);
private:
ReferencePlatform::PlatformData& data;
ReferenceVariableVerletDynamics* dynamics;
ReferenceConstraintAlgorithm* constraints;
std::vector masses;
int numConstraints;
double prevErrorTol;
};
/**
* This kernel is invoked by CustomIntegrator to take one time step.
*/
class ReferenceIntegrateCustomStepKernel : public IntegrateCustomStepKernel {
public:
ReferenceIntegrateCustomStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateCustomStepKernel(name, platform),
data(data), dynamics(0), constraints(0) {
}
~ReferenceIntegrateCustomStepKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param integrator the CustomIntegrator this kernel will be used for
*/
void initialize(const System& system, const CustomIntegrator& integrator);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the CustomIntegrator this kernel is being used for
* @param forcesAreValid if the context has been modified since the last time step, this will be
* false to show that cached forces are invalid and must be recalculated.
* On exit, this should specify whether the cached forces are valid at the
* end of the step.
*/
void execute(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid);
/**
* Compute the kinetic energy.
*
* @param context the context in which to execute this kernel
* @param integrator the CustomIntegrator this kernel is being used for
* @param forcesAreValid if the context has been modified since the last time step, this will be
* false to show that cached forces are invalid and must be recalculated.
* On exit, this should specify whether the cached forces are valid at the
* end of the step.
*/
double computeKineticEnergy(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid);
/**
* Get the values of all global variables.
*
* @param context the context in which to execute this kernel
* @param values on exit, this contains the values
*/
void getGlobalVariables(ContextImpl& context, std::vector& values) const;
/**
* Set the values of all global variables.
*
* @param context the context in which to execute this kernel
* @param values a vector containing the values
*/
void setGlobalVariables(ContextImpl& context, const std::vector& values);
/**
* Get the values of a per-DOF variable.
*
* @param context the context in which to execute this kernel
* @param variable the index of the variable to get
* @param values on exit, this contains the values
*/
void getPerDofVariable(ContextImpl& context, int variable, std::vector& values) const;
/**
* Set the values of a per-DOF variable.
*
* @param context the context in which to execute this kernel
* @param variable the index of the variable to get
* @param values a vector containing the values
*/
void setPerDofVariable(ContextImpl& context, int variable, const std::vector& values);
private:
ReferencePlatform::PlatformData& data;
ReferenceCustomDynamics* dynamics;
ReferenceConstraintAlgorithm* constraints;
std::vector masses, globalValues;
std::vector > perDofValues;
int numConstraints;
};
/**
* This kernel is invoked by AndersenThermostat at the start of each time step to adjust the particle velocities.
*/
class ReferenceApplyAndersenThermostatKernel : public ApplyAndersenThermostatKernel {
public:
ReferenceApplyAndersenThermostatKernel(std::string name, const Platform& platform) : ApplyAndersenThermostatKernel(name, platform), thermostat(0) {
}
~ReferenceApplyAndersenThermostatKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param thermostat the AndersenThermostat this kernel will be used for
*/
void initialize(const System& system, const AndersenThermostat& thermostat);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
*/
void execute(ContextImpl& context);
private:
ReferenceAndersenThermostat* thermostat;
std::vector > particleGroups;
std::vector masses;
};
/**
* This kernel is invoked by MonteCarloBarostat to adjust the periodic box volume
*/
class ReferenceApplyMonteCarloBarostatKernel : public ApplyMonteCarloBarostatKernel {
public:
ReferenceApplyMonteCarloBarostatKernel(std::string name, const Platform& platform) : ApplyMonteCarloBarostatKernel(name, platform), barostat(NULL) {
}
~ReferenceApplyMonteCarloBarostatKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param barostat the MonteCarloBarostat this kernel will be used for
*/
void initialize(const System& system, const Force& barostat);
/**
* Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
* This version scales the x, y, and z positions independently.
* This is called BEFORE the periodic box size is modified. It should begin by translating each particle
* or cluster into the first periodic box, so that coordinates will still be correct after the box size
* is changed.
*
* @param context the context in which to execute this kernel
* @param scaleX the scale factor by which to multiply particle x-coordinate
* @param scaleY the scale factor by which to multiply particle y-coordinate
* @param scaleZ the scale factor by which to multiply particle z-coordinate
*/
void scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ);
/**
* Reject the most recent Monte Carlo step, restoring the particle positions to where they were before
* scaleCoordinates() was last called.
*
* @param context the context in which to execute this kernel
*/
void restoreCoordinates(ContextImpl& context);
private:
ReferenceMonteCarloBarostat* barostat;
};
/**
* This kernel is invoked to remove center of mass motion from the system.
*/
class ReferenceRemoveCMMotionKernel : public RemoveCMMotionKernel {
public:
ReferenceRemoveCMMotionKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : RemoveCMMotionKernel(name, platform), data(data) {
}
/**
* Initialize the kernel, setting up the particle masses.
*
* @param system the System this kernel will be applied to
* @param force the CMMotionRemover this kernel will be used for
*/
void initialize(const System& system, const CMMotionRemover& force);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
*/
void execute(ContextImpl& context);
private:
ReferencePlatform::PlatformData& data;
std::vector masses;
int frequency;
};
} // namespace OpenMM
#endif /*OPENMM_REFERENCEKERNELS_H_*/