ReferenceKernels.h

#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) 2008-2009 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 "SimTKUtilities/SimTKOpenMMRealType.h"
#include "SimTKReference/ReferenceNeighborList.h"
#include "lepton/ExpressionProgram.h"

class CpuObc;
class CpuGBVI;
class ReferenceAndersenThermostat;
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 <i>either</i> return its contribution to the
     * energy directly, <i>or</i> 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<RealVec> 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<Vec3>& positions);
    /**
     * Set the positions of all particles.
     *
     * @param positions  a vector containg the particle positions
     */
    void setPositions(ContextImpl& context, const std::vector<Vec3>& positions);
    /**
     * Get the velocities of all particles.
     *
     * @param velocities  on exit, this contains the particle velocities
     */
    void getVelocities(ContextImpl& context, std::vector<Vec3>& velocities);
    /**
     * Set the velocities of all particles.
     *
     * @param velocities  a vector containg the particle velocities
     */
    void setVelocities(ContextImpl& context, const std::vector<Vec3>& velocities);
    /**
     * Get the current forces on all particles.
     *
     * @param forces  on exit, this contains the forces
     */
    void getForces(ContextImpl& context, std::vector<Vec3>& 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;
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), constraintDistances(0), constraintIndices(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);
private:
    ReferencePlatform::PlatformData& data;
    ReferenceConstraintAlgorithm* constraints;
    std::vector<RealOpenMM> masses;
    std::vector<RealOpenMM> inverseMasses;
    RealOpenMM* constraintDistances;
    int** constraintIndices;
    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);
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);
private:
    int numBonds;
    int **bondIndexArray;
    RealOpenMM **bondParamArray;
    Lepton::ExpressionProgram energyExpression, forceExpression;
    std::vector<std::string> 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);
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);
private:
    int numAngles;
    int **angleIndexArray;
    RealOpenMM **angleParamArray;
    Lepton::ExpressionProgram energyExpression, forceExpression;
    std::vector<std::string> 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);
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);
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<std::vector<std::vector<RealOpenMM> > > coeff;
    std::vector<int> torsionMaps;
    std::vector<std::vector<int> > 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);
private:
    int numTorsions;
    int **torsionIndexArray;
    RealOpenMM **torsionParamArray;
    Lepton::ExpressionProgram energyExpression, forceExpression;
    std::vector<std::string> 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);
private:
    int numParticles, num14;
    int **exclusionArray, **bonded14IndexArray;
    RealOpenMM **particleParamArray, **bonded14ParamArray;
    RealOpenMM nonbondedCutoff, rfDielectric, ewaldAlpha, dispersionCoefficient;
    int kmax[3], gridSize[3];
    std::vector<std::set<int> > 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) {
    }
    ~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);
private:
    int numParticles;
    int **exclusionArray;
    RealOpenMM **particleParamArray;
    RealOpenMM nonbondedCutoff, periodicBoxSize[3];
    std::vector<std::set<int> > exclusions;
    Lepton::ExpressionProgram energyExpression, forceExpression;
    std::vector<std::string> parameterNames, globalParameterNames;
    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);
private:
    CpuObc* obc;
    std::vector<RealOpenMM> 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<double> & 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<RealOpenMM> 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);
private:
    int numParticles;
    bool isPeriodic;
    RealOpenMM **particleParamArray;
    RealOpenMM nonbondedCutoff;
    std::vector<std::set<int> > exclusions;
    std::vector<std::string> particleParameterNames, globalParameterNames, valueNames;
    std::vector<Lepton::ExpressionProgram> valueExpressions;
    std::vector<std::vector<Lepton::ExpressionProgram> > valueDerivExpressions;
    std::vector<std::vector<Lepton::ExpressionProgram> > valueGradientExpressions;
    std::vector<OpenMM::CustomGBForce::ComputationType> valueTypes;
    std::vector<Lepton::ExpressionProgram> energyExpressions;
    std::vector<std::vector<Lepton::ExpressionProgram> > energyDerivExpressions;
    std::vector<std::vector<Lepton::ExpressionProgram> > energyGradientExpressions;
    std::vector<OpenMM::CustomGBForce::ComputationType> 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);
private:
    int numParticles;
    std::vector<int> particles;
    RealOpenMM **particleParamArray;
    Lepton::ExpressionProgram energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ;
    std::vector<std::string> 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);
private:
    int numDonors, numAcceptors, numParticles;
    bool isPeriodic;
    int **exclusionArray;
    RealOpenMM **donorParamArray, **acceptorParamArray;
    RealOpenMM nonbondedCutoff;
    ReferenceCustomHbondIxn* ixn;
    std::vector<std::set<int> > exclusions;
    std::vector<std::string> 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), constraintDistances(0), constraintIndices(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);
private:
    ReferencePlatform::PlatformData& data;
    ReferenceVerletDynamics* dynamics;
    ReferenceConstraintAlgorithm* constraints;
    std::vector<RealOpenMM> masses;
    RealOpenMM* constraintDistances;
    int** constraintIndices;
    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), constraintDistances(0), constraintIndices(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);
private:
    ReferencePlatform::PlatformData& data;
    ReferenceStochasticDynamics* dynamics;
    ReferenceConstraintAlgorithm* constraints;
    std::vector<RealOpenMM> masses;
    RealOpenMM* constraintDistances;
    int** constraintIndices;
    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), constraintDistances(0), constraintIndices(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);
private:
    ReferencePlatform::PlatformData& data;
    ReferenceBrownianDynamics* dynamics;
    ReferenceConstraintAlgorithm* constraints;
    std::vector<RealOpenMM> masses;
    RealOpenMM* constraintDistances;
    int** constraintIndices;
    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), constraintDistances(0), constraintIndices(0) {
    }
    ~ReferenceIntegrateVariableLangevinStepKernel();
    /**
     * Initialize the kernel.
     *
     * @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 VariableLangevinIntegrator& integrator);
    /**
     * Execute the kernel.
     *
     * @param context    the context in which to execute this kernel
     * @param integrator the LangevinIntegrator 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);
private:
    ReferencePlatform::PlatformData& data;
    ReferenceVariableStochasticDynamics* dynamics;
    ReferenceConstraintAlgorithm* constraints;
    std::vector<RealOpenMM> masses;
    RealOpenMM* constraintDistances;
    int** constraintIndices;
    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), constraintDistances(0), constraintIndices(0) {
    }
    ~ReferenceIntegrateVariableVerletStepKernel();
    /**
     * 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 VariableVerletIntegrator& integrator);
    /**
     * Execute the kernel.
     *
     * @param context    the context in which to execute this kernel
     * @param integrator the VerletIntegrator 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);
private:
    ReferencePlatform::PlatformData& data;
    ReferenceVariableVerletDynamics* dynamics;
    ReferenceConstraintAlgorithm* constraints;
    std::vector<RealOpenMM> masses;
    RealOpenMM* constraintDistances;
    int** constraintIndices;
    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), constraintDistances(0), constraintIndices(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);
    /**
     * 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<double>& 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<double>& 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<Vec3>& 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<Vec3>& values);
private:
    ReferencePlatform::PlatformData& data;
    ReferenceCustomDynamics* dynamics;
    ReferenceConstraintAlgorithm* constraints;
    std::vector<RealOpenMM> masses, globalValues;
    std::vector<std::vector<OpenMM::RealVec> > perDofValues; 
    RealOpenMM* constraintDistances;
    int** constraintIndices;
    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<std::vector<int> > particleGroups;
    std::vector<RealOpenMM> 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 MonteCarloBarostat& barostat);
    /**
     * Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
     * 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 scale      the scale factor by which to multiply particle positions
     */
    void scaleCoordinates(ContextImpl& context, double scale);
    /**
     * 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 calculate the kinetic energy of the system.
 */
class ReferenceCalcKineticEnergyKernel : public CalcKineticEnergyKernel {
public:
    ReferenceCalcKineticEnergyKernel(std::string name, const Platform& platform) : CalcKineticEnergyKernel(name, platform) {
    }
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     */
    void initialize(const System& system);
    /**
     * Execute the kernel.
     * 
     * @param context    the context in which to execute this kernel
     */
    double execute(ContextImpl& context);
private:
    std::vector<double> masses;
};

/**
 * 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<double> masses;
    int frequency;
};

} // namespace OpenMM

#endif /*OPENMM_REFERENCEKERNELS_H_*/