CudaKernels.h

#ifndef OPENMM_CUDAKERNELS_H_
#define OPENMM_CUDAKERNELS_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) 2008-2012 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
 * This program is free software: you can redistribute it and/or modify       *
 * it under the terms of the GNU Lesser General Public License as published   *
 * by the Free Software Foundation, either version 3 of the License, or       *
 * (at your option) any later version.                                        *
 *                                                                            *
 * This program is distributed in the hope that it will be useful,            *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of             *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
 * GNU Lesser General Public License for more details.                        *
 *                                                                            *
 * You should have received a copy of the GNU Lesser General Public License   *
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
 * -------------------------------------------------------------------------- */

#include "CudaPlatform.h"
#include "CudaArray.h"
#include "CudaContext.h"
//#include "CudaParameterSet.h"
#include "CudaSort.h"
#include "openmm/kernels.h"
#include "openmm/System.h"

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 CudaCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
public:
    CudaCalcForcesAndEnergyKernel(std::string name, const Platform& platform, CudaContext& cu) : CalcForcesAndEnergyKernel(name, platform), cu(cu) {
    }
    /**
     * 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:
   CudaContext& cu;
};

/**
 * This kernel provides methods for setting and retrieving various state data: time, positions,
 * velocities, and forces.
 */
class CudaUpdateStateDataKernel : public UpdateStateDataKernel {
public:
    CudaUpdateStateDataKernel(std::string name, const Platform& platform, CudaContext& cu) : UpdateStateDataKernel(name, platform), cu(cu) {
    }
    /**
     * 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;
    /**
     * 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:
    CudaContext& cu;
};

/**
 * This kernel modifies the positions of particles to enforce distance constraints.
 */
class CudaApplyConstraintsKernel : public ApplyConstraintsKernel {
public:
    CudaApplyConstraintsKernel(std::string name, const Platform& platform, CudaContext& cu) : ApplyConstraintsKernel(name, platform),
            cu(cu), hasInitializedKernel(false) {
    }
    /**
     * 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:
    CudaContext& cu;
    bool hasInitializedKernel;
    CUfunction applyDeltasKernel;
};

/**
 * This kernel recomputes the positions of virtual sites.
 */
class CudaVirtualSitesKernel : public VirtualSitesKernel {
public:
    CudaVirtualSitesKernel(std::string name, const Platform& platform, CudaContext& cu) : VirtualSitesKernel(name, platform), cu(cu) {
    }
    /**
     * 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);
private:
    CudaContext& cu;
};

/**
 * This kernel is invoked by HarmonicBondForce to calculate the forces acting on the system and the energy of the system.
 */
class CudaCalcHarmonicBondForceKernel : public CalcHarmonicBondForceKernel {
public:
    CudaCalcHarmonicBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcHarmonicBondForceKernel(name, platform),
            hasInitializedKernel(false), cu(cu), system(system), params(NULL) {
    }
    ~CudaCalcHarmonicBondForceKernel();
    /**
     * 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;
    bool hasInitializedKernel;
    CudaContext& cu;
    System& system;
    CudaArray* params;
};

///**
// * This kernel is invoked by CustomBondForce to calculate the forces acting on the system and the energy of the system.
// */
//class CudaCalcCustomBondForceKernel : public CalcCustomBondForceKernel {
//public:
//    CudaCalcCustomBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcCustomBondForceKernel(name, platform),
//            hasInitializedKernel(false), cu(cu), system(system), params(NULL), globals(NULL) {
//    }
//    ~CudaCalcCustomBondForceKernel();
//    /**
//     * 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;
//    bool hasInitializedKernel;
//    CudaContext& cu;
//    System& system;
//    CudaParameterSet* params;
//    CudaArray<cl_float>* globals;
//    std::vector<std::string> globalParamNames;
//    std::vector<cl_float> globalParamValues;
//};
//
///**
// * This kernel is invoked by HarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
// */
//class CudaCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
//public:
//    CudaCalcHarmonicAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcHarmonicAngleForceKernel(name, platform),
//            hasInitializedKernel(false), cu(cu), system(system), params(NULL) {
//    }
//    ~CudaCalcHarmonicAngleForceKernel();
//    /**
//     * 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;
//    bool hasInitializedKernel;
//    CudaContext& cu;
//    System& system;
//    CudaArray<mm_float2>* params;
//};
//
///**
// * This kernel is invoked by CustomAngleForce to calculate the forces acting on the system and the energy of the system.
// */
//class CudaCalcCustomAngleForceKernel : public CalcCustomAngleForceKernel {
//public:
//    CudaCalcCustomAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcCustomAngleForceKernel(name, platform),
//            hasInitializedKernel(false), cu(cu), system(system), params(NULL), globals(NULL) {
//    }
//    ~CudaCalcCustomAngleForceKernel();
//    /**
//     * 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;
//    bool hasInitializedKernel;
//    CudaContext& cu;
//    System& system;
//    CudaParameterSet* params;
//    CudaArray<cl_float>* globals;
//    std::vector<std::string> globalParamNames;
//    std::vector<cl_float> globalParamValues;
//};
//
///**
// * This kernel is invoked by PeriodicTorsionForce to calculate the forces acting on the system and the energy of the system.
// */
//class CudaCalcPeriodicTorsionForceKernel : public CalcPeriodicTorsionForceKernel {
//public:
//    CudaCalcPeriodicTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcPeriodicTorsionForceKernel(name, platform),
//            hasInitializedKernel(false), cu(cu), system(system), params(NULL) {
//    }
//    ~CudaCalcPeriodicTorsionForceKernel();
//    /**
//     * 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;
//    bool hasInitializedKernel;
//    CudaContext& cu;
//    System& system;
//    CudaArray<mm_float4>* params;
//};
//
///**
// * This kernel is invoked by RBTorsionForce to calculate the forces acting on the system and the energy of the system.
// */
//class CudaCalcRBTorsionForceKernel : public CalcRBTorsionForceKernel {
//public:
//    CudaCalcRBTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcRBTorsionForceKernel(name, platform),
//            hasInitializedKernel(false), cu(cu), system(system), params(NULL) {
//    }
//    ~CudaCalcRBTorsionForceKernel();
//    /**
//     * 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;
//    bool hasInitializedKernel;
//    CudaContext& cu;
//    System& system;
//    CudaArray<mm_float8>* params;
//};
//
///**
// * This kernel is invoked by CMAPTorsionForce to calculate the forces acting on the system and the energy of the system.
// */
//class CudaCalcCMAPTorsionForceKernel : public CalcCMAPTorsionForceKernel {
//public:
//    CudaCalcCMAPTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcCMAPTorsionForceKernel(name, platform),
//            hasInitializedKernel(false), cu(cu), system(system), coefficients(NULL), mapPositions(NULL), torsionMaps(NULL) {
//    }
//    ~CudaCalcCMAPTorsionForceKernel();
//    /**
//     * 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:
//    int numTorsions;
//    bool hasInitializedKernel;
//    CudaContext& cu;
//    System& system;
//    CudaArray<mm_float4>* coefficients;
//    CudaArray<mm_int2>* mapPositions;
//    CudaArray<cl_int>* torsionMaps;
//};
//
///**
// * This kernel is invoked by CustomTorsionForce to calculate the forces acting on the system and the energy of the system.
// */
//class CudaCalcCustomTorsionForceKernel : public CalcCustomTorsionForceKernel {
//public:
//    CudaCalcCustomTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcCustomTorsionForceKernel(name, platform),
//            hasInitializedKernel(false), cu(cu), system(system), params(NULL), globals(NULL) {
//    }
//    ~CudaCalcCustomTorsionForceKernel();
//    /**
//     * 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;
//    bool hasInitializedKernel;
//    CudaContext& cu;
//    System& system;
//    CudaParameterSet* params;
//    CudaArray<cl_float>* globals;
//    std::vector<std::string> globalParamNames;
//    std::vector<cl_float> globalParamValues;
//};
//
///**
// * This kernel is invoked by NonbondedForce to calculate the forces acting on the system.
// */
//class CudaCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
//public:
//    CudaCalcNonbondedForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcNonbondedForceKernel(name, platform),
//            hasInitializedKernel(false), cu(cu), sigmaEpsilon(NULL), exceptionParams(NULL), cosSinSums(NULL), pmeGrid(NULL),
//            pmeGrid2(NULL), pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeBsplineTheta(NULL), pmeBsplineDTheta(NULL),
//            pmeAtomRange(NULL), pmeAtomGridIndex(NULL), sort(NULL), fft(NULL) {
//    }
//    ~CudaCalcNonbondedForceKernel();
//    /**
//     * 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 includeDirect  true if direct space interactions should be included
//     * @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:
//    struct SortTrait {
//        typedef mm_int2 DataType;
//        typedef cl_int KeyType;
//        static const char* clDataType() {return "int2";}
//        static const char* clKeyType() {return "int";}
//        static const char* clMinKey() {return "INT_MIN";}
//        static const char* clMaxKey() {return "INT_MAX";}
//        static const char* clMaxValue() {return "(int2) (INT_MAX, INT_MAX)";}
//        static const char* clSortKey() {return "value.y";}
//    };
//    CudaContext& cu;
//    bool hasInitializedKernel;
//    CudaArray<mm_float2>* sigmaEpsilon;
//    CudaArray<mm_float4>* exceptionParams;
//    CudaArray<mm_float2>* cosSinSums;
//    CudaArray<mm_float2>* pmeGrid;
//    CudaArray<mm_float2>* pmeGrid2;
//    CudaArray<cl_float>* pmeBsplineModuliX;
//    CudaArray<cl_float>* pmeBsplineModuliY;
//    CudaArray<cl_float>* pmeBsplineModuliZ;
//    CudaArray<mm_float4>* pmeBsplineTheta;
//    CudaArray<mm_float4>* pmeBsplineDTheta;
//    CudaArray<cl_int>* pmeAtomRange;
//    CudaArray<mm_int2>* pmeAtomGridIndex;
//    CudaSort<SortTrait>* sort;
//    CudaFFT3D* fft;
//    CUfunction ewaldSumsKernel;
//    CUfunction ewaldForcesKernel;
//    CUfunction pmeGridIndexKernel;
//    CUfunction pmeAtomRangeKernel;
//    CUfunction pmeZIndexKernel;
//    CUfunction pmeUpdateBsplinesKernel;
//    CUfunction pmeSpreadChargeKernel;
//    CUfunction pmeFinishSpreadChargeKernel;
//    CUfunction pmeConvolutionKernel;
//    CUfunction pmeInterpolateForceKernel;
//    std::map<std::string, std::string> pmeDefines;
//    double ewaldSelfEnergy, dispersionCoefficient, alpha;
//    int interpolateForceThreads;
//    bool hasCoulomb, hasLJ;
//    static const int PmeOrder = 5;
//};
//
///**
// * This kernel is invoked by CustomNonbondedForce to calculate the forces acting on the system.
// */
//class CudaCalcCustomNonbondedForceKernel : public CalcCustomNonbondedForceKernel {
//public:
//    CudaCalcCustomNonbondedForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcCustomNonbondedForceKernel(name, platform),
//            hasInitializedKernel(false), cu(cu), params(NULL), globals(NULL), tabulatedFunctionParams(NULL), system(system) {
//    }
//    ~CudaCalcCustomNonbondedForceKernel();
//    /**
//     * 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:
//    bool hasInitializedKernel;
//    CudaContext& cu;
//    CudaParameterSet* params;
//    CudaArray<cl_float>* globals;
//    CudaArray<mm_float4>* tabulatedFunctionParams;
//    std::vector<std::string> globalParamNames;
//    std::vector<cl_float> globalParamValues;
//    std::vector<CudaArray<mm_float4>*> tabulatedFunctions;
//    System& system;
//};
//
///**
// * This kernel is invoked by GBSAOBCForce to calculate the forces acting on the system.
// */
//class CudaCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
//public:
//    CudaCalcGBSAOBCForceKernel(std::string name, const Platform& platform, CudaContext& cu) : CalcGBSAOBCForceKernel(name, platform), cu(cu),
//            hasCreatedKernels(false), params(NULL), bornSum(NULL), longBornSum(NULL), bornRadii(NULL), bornForce(NULL),
//            longBornForce(NULL), obcChain(NULL) {
//    }
//    ~CudaCalcGBSAOBCForceKernel();
//    /**
//     * 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:
//    double prefactor;
//    bool hasCreatedKernels;
//    int maxTiles;
//    CudaContext& cu;
//    CudaArray<mm_float2>* params;
//    CudaArray<cl_float>* bornSum;
//    CudaArray<cl_long>* longBornSum;
//    CudaArray<cl_float>* bornRadii;
//    CudaArray<cl_float>* bornForce;
//    CudaArray<cl_long>* longBornForce;
//    CudaArray<cl_float>* obcChain;
//    CUfunction computeBornSumKernel;
//    CUfunction reduceBornSumKernel;
//    CUfunction force1Kernel;
//    CUfunction reduceBornForceKernel;
//};
//
///**
// * This kernel is invoked by CustomGBForce to calculate the forces acting on the system.
// */
//class CudaCalcCustomGBForceKernel : public CalcCustomGBForceKernel {
//public:
//    CudaCalcCustomGBForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcCustomGBForceKernel(name, platform),
//            hasInitializedKernels(false), cu(cu), params(NULL), computedValues(NULL), energyDerivs(NULL), longEnergyDerivs(NULL), globals(NULL),
//            valueBuffers(NULL), longValueBuffers(NULL), tabulatedFunctionParams(NULL), system(system) {
//    }
//    ~CudaCalcCustomGBForceKernel();
//    /**
//     * 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:
//    bool hasInitializedKernels, needParameterGradient;
//    int maxTiles, numComputedValues;
//    CudaContext& cu;
//    CudaParameterSet* params;
//    CudaParameterSet* computedValues;
//    CudaParameterSet* energyDerivs;
//    CudaArray<cl_long>* longEnergyDerivs;
//    CudaArray<cl_float>* globals;
//    CudaArray<cl_float>* valueBuffers;
//    CudaArray<cl_long>* longValueBuffers;
//    CudaArray<mm_float4>* tabulatedFunctionParams;
//    std::vector<std::string> globalParamNames;
//    std::vector<cl_float> globalParamValues;
//    std::vector<CudaArray<mm_float4>*> tabulatedFunctions;
//    std::vector<bool> pairValueUsesParam, pairEnergyUsesParam, pairEnergyUsesValue;
//    System& system;
//    CUfunction pairValueKernel, perParticleValueKernel, pairEnergyKernel, perParticleEnergyKernel, gradientChainRuleKernel;
//};
//
///**
// * This kernel is invoked by CustomExternalForce to calculate the forces acting on the system and the energy of the system.
// */
//class CudaCalcCustomExternalForceKernel : public CalcCustomExternalForceKernel {
//public:
//    CudaCalcCustomExternalForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcCustomExternalForceKernel(name, platform),
//            hasInitializedKernel(false), cu(cu), system(system), params(NULL), globals(NULL) {
//    }
//    ~CudaCalcCustomExternalForceKernel();
//    /**
//     * 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;
//    bool hasInitializedKernel;
//    CudaContext& cu;
//    System& system;
//    CudaParameterSet* params;
//    CudaArray<cl_float>* globals;
//    std::vector<std::string> globalParamNames;
//    std::vector<cl_float> globalParamValues;
//};
//
///**
// * This kernel is invoked by CustomHbondForce to calculate the forces acting on the system.
// */
//class CudaCalcCustomHbondForceKernel : public CalcCustomHbondForceKernel {
//public:
//    CudaCalcCustomHbondForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcCustomHbondForceKernel(name, platform),
//            hasInitializedKernel(false), cu(cu), donorParams(NULL), acceptorParams(NULL), donors(NULL), acceptors(NULL),
//            donorBufferIndices(NULL), acceptorBufferIndices(NULL), globals(NULL), donorExclusions(NULL), acceptorExclusions(NULL),
//            tabulatedFunctionParams(NULL), system(system) {
//    }
//    ~CudaCalcCustomHbondForceKernel();
//    /**
//     * 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;
//    bool hasInitializedKernel;
//    CudaContext& cu;
//    CudaParameterSet* donorParams;
//    CudaParameterSet* acceptorParams;
//    CudaArray<cl_float>* globals;
//    CudaArray<mm_int4>* donors;
//    CudaArray<mm_int4>* acceptors;
//    CudaArray<mm_int4>* donorBufferIndices;
//    CudaArray<mm_int4>* acceptorBufferIndices;
//    CudaArray<mm_int4>* donorExclusions;
//    CudaArray<mm_int4>* acceptorExclusions;
//    CudaArray<mm_float4>* tabulatedFunctionParams;
//    std::vector<std::string> globalParamNames;
//    std::vector<cl_float> globalParamValues;
//    std::vector<CudaArray<mm_float4>*> tabulatedFunctions;
//    System& system;
//    CUfunction donorKernel, acceptorKernel;
//};
//
///**
// * This kernel is invoked by CustomCompoundBondForce to calculate the forces acting on the system.
// */
//class CudaCalcCustomCompoundBondForceKernel : public CalcCustomCompoundBondForceKernel {
//public:
//    CudaCalcCustomCompoundBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) : CalcCustomCompoundBondForceKernel(name, platform),
//            cu(cu), params(NULL), globals(NULL), tabulatedFunctionParams(NULL), system(system) {
//    }
//    ~CudaCalcCustomCompoundBondForceKernel();
//    /**
//     * 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;
//    CudaContext& cu;
//    CudaParameterSet* params;
//    CudaArray<cl_float>* globals;
//    CudaArray<mm_float4>* tabulatedFunctionParams;
//    std::vector<std::string> globalParamNames;
//    std::vector<cl_float> globalParamValues;
//    std::vector<CudaArray<mm_float4>*> tabulatedFunctions;
//    System& system;
//};

/**
 * This kernel is invoked by VerletIntegrator to take one time step.
 */
class CudaIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
public:
    CudaIntegrateVerletStepKernel(std::string name, const Platform& platform, CudaContext& cu) : IntegrateVerletStepKernel(name, platform), cu(cu) {
    }
    ~CudaIntegrateVerletStepKernel();
    /**
     * 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:
    CudaContext& cu;
    double prevStepSize;
    CUfunction kernel1, kernel2;
};

///**
// * This kernel is invoked by LangevinIntegrator to take one time step.
// */
//class CudaIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
//public:
//    CudaIntegrateLangevinStepKernel(std::string name, const Platform& platform, CudaContext& cu) : IntegrateLangevinStepKernel(name, platform), cu(cu),
//            hasInitializedKernels(false), params(NULL) {
//    }
//    ~CudaIntegrateLangevinStepKernel();
//    /**
//     * 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:
//    CudaContext& cu;
//    double prevTemp, prevFriction, prevStepSize;
//    bool hasInitializedKernels;
//    CudaArray<cl_float>* params;
//    CUfunction kernel1, kernel2;
//};
//
///**
// * This kernel is invoked by BrownianIntegrator to take one time step.
// */
//class CudaIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
//public:
//    CudaIntegrateBrownianStepKernel(std::string name, const Platform& platform, CudaContext& cu) : IntegrateBrownianStepKernel(name, platform), cu(cu),
//            hasInitializedKernels(false), prevTemp(-1), prevFriction(-1), prevStepSize(-1) {
//    }
//    ~CudaIntegrateBrownianStepKernel();
//    /**
//     * 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:
//    CudaContext& cu;
//    double prevTemp, prevFriction, prevStepSize;
//    bool hasInitializedKernels;
//    CUfunction kernel1, kernel2;
//};
//
///**
// * This kernel is invoked by VariableVerletIntegrator to take one time step.
// */
//class CudaIntegrateVariableVerletStepKernel : public IntegrateVariableVerletStepKernel {
//public:
//    CudaIntegrateVariableVerletStepKernel(std::string name, const Platform& platform, CudaContext& cu) : IntegrateVariableVerletStepKernel(name, platform), cu(cu),
//            hasInitializedKernels(false) {
//    }
//    ~CudaIntegrateVariableVerletStepKernel();
//    /**
//     * 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:
//    CudaContext& cu;
//    bool hasInitializedKernels;
//    int blockSize;
//    CUfunction kernel1, kernel2, selectSizeKernel;
//};
//
///**
// * This kernel is invoked by VariableLangevinIntegrator to take one time step.
// */
//class CudaIntegrateVariableLangevinStepKernel : public IntegrateVariableLangevinStepKernel {
//public:
//    CudaIntegrateVariableLangevinStepKernel(std::string name, const Platform& platform, CudaContext& cu) : IntegrateVariableLangevinStepKernel(name, platform), cu(cu),
//            hasInitializedKernels(false), params(NULL) {
//    }
//    ~CudaIntegrateVariableLangevinStepKernel();
//    /**
//     * Initialize the kernel, setting up the particle masses.
//     *
//     * @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);
//private:
//    CudaContext& cu;
//    bool hasInitializedKernels;
//    int blockSize;
//    CudaArray<cl_float>* params;
//    CUfunction kernel1, kernel2, selectSizeKernel;
//    double prevTemp, prevFriction, prevErrorTol;
//};
//
///**
// * This kernel is invoked by CustomIntegrator to take one time step.
// */
//class CudaIntegrateCustomStepKernel : public IntegrateCustomStepKernel {
//public:
//    CudaIntegrateCustomStepKernel(std::string name, const Platform& platform, CudaContext& cu) : IntegrateCustomStepKernel(name, platform), cu(cu),
//            hasInitializedKernels(false), localValuesAreCurrent(false), globalValues(NULL), contextParameterValues(NULL), sumBuffer(NULL), energy(NULL),
//            uniformRandoms(NULL), randomSeed(NULL), perDofValues(NULL) {
//    }
//    ~CudaIntegrateCustomStepKernel();
//    /**
//     * 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:
//    class ReorderListener;
//    std::string createGlobalComputation(const std::string& variable, const Lepton::ParsedExpression& expr, CustomIntegrator& integrator, const std::string& energyName);
//    std::string createPerDofComputation(const std::string& variable, const Lepton::ParsedExpression& expr, int component, CustomIntegrator& integrator, const std::string& forceName, const std::string& energyName);
//    void recordChangedParameters(ContextImpl& context);
//    CudaContext& cu;
//    double prevStepSize;
//    int numGlobalVariables;
//    bool hasInitializedKernels, deviceValuesAreCurrent, modifiesParameters;
//    mutable bool localValuesAreCurrent;
//    CudaArray<cl_float>* globalValues;
//    CudaArray<cl_float>* contextParameterValues;
//    CudaArray<cl_float>* sumBuffer;
//    CudaArray<cl_float>* energy;
//    CudaArray<mm_float4>* uniformRandoms;
//    CudaArray<mm_int4>* randomSeed;
//    CudaParameterSet* perDofValues;
//    mutable std::vector<std::vector<cl_float> > localPerDofValues;
//    std::vector<std::vector<CUfunction> > kernels;
//    CUfunction sumEnergyKernel, randomKernel;
//    std::vector<CustomIntegrator::ComputationType> stepType;
//    std::vector<bool> needsForces;
//    std::vector<bool> needsEnergy;
//    std::vector<bool> invalidatesForces;
//    std::vector<bool> merged;
//    std::vector<int> forceGroup;
//    std::vector<int> requiredGaussian;
//    std::vector<int> requiredUniform;
//    std::vector<std::string> parameterNames;
//};
//
///**
// * This kernel is invoked by AndersenThermostat at the start of each time step to adjust the particle velocities.
// */
//class CudaApplyAndersenThermostatKernel : public ApplyAndersenThermostatKernel {
//public:
//    CudaApplyAndersenThermostatKernel(std::string name, const Platform& platform, CudaContext& cu) : ApplyAndersenThermostatKernel(name, platform), cu(cu),
//            hasInitializedKernels(false), atomGroups(NULL) {
//    }
//    ~CudaApplyAndersenThermostatKernel();
//    /**
//     * 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:
//    CudaContext& cu;
//    bool hasInitializedKernels;
//    int randomSeed;
//    CudaArray<cl_int>* atomGroups;
//    CUfunction kernel;
//};
//
///**
// * This kernel is invoked by MonteCarloBarostat to adjust the periodic box volume
// */
//class CudaApplyMonteCarloBarostatKernel : public ApplyMonteCarloBarostatKernel {
//public:
//    CudaApplyMonteCarloBarostatKernel(std::string name, const Platform& platform, CudaContext& cu) : ApplyMonteCarloBarostatKernel(name, platform), cu(cu),
//            hasInitializedKernels(false), savedPositions(NULL), moleculeAtoms(NULL), moleculeStartIndex(NULL) {
//    }
//    ~CudaApplyMonteCarloBarostatKernel();
//    /**
//     * 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:
//    CudaContext& cu;
//    bool hasInitializedKernels;
//    int numMolecules;
//    CudaArray<mm_float4>* savedPositions;
//    CudaArray<cl_int>* moleculeAtoms;
//    CudaArray<cl_int>* moleculeStartIndex;
//    CUfunction kernel;
//};

/**
 * This kernel is invoked to calculate the kinetic energy of the system.
 */
class CudaCalcKineticEnergyKernel : public CalcKineticEnergyKernel {
public:
    CudaCalcKineticEnergyKernel(std::string name, const Platform& platform, CudaContext& cu) : CalcKineticEnergyKernel(name, platform), cu(cu) {
    }
    /**
     * 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:
    CudaContext& cu;
    std::vector<double> masses;
};

///**
// * This kernel is invoked to remove center of mass motion from the system.
// */
//class CudaRemoveCMMotionKernel : public RemoveCMMotionKernel {
//public:
//    CudaRemoveCMMotionKernel(std::string name, const Platform& platform, CudaContext& cu) : RemoveCMMotionKernel(name, platform), cu(cu), cmMomentum(NULL) {
//    }
//    ~CudaRemoveCMMotionKernel();
//    /**
//     * 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:
//    CudaContext& cu;
//    int frequency;
//    CudaArray<mm_float4>* cmMomentum;
//    CUfunction kernel1, kernel2;
//};

} // namespace OpenMM

#endif /*OPENMM_CUDAKERNELS_H_*/