OpenCLKernels.h

#ifndef OPENMM_OPENCLKERNELS_H_
#define OPENMM_OPENCLKERNELS_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) 2008-2010 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 "OpenCLPlatform.h"
#include "OpenCLArray.h"
#include "OpenCLContext.h"
#include "OpenCLFFT3D.h"
#include "OpenCLParameterSet.h"
#include "OpenCLSort.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 OpenCLCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
public:
    OpenCLCalcForcesAndEnergyKernel(std::string name, const Platform& platform, OpenCLContext& cl) : CalcForcesAndEnergyKernel(name, platform), cl(cl) {
    }
    /**
     * 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:
   OpenCLContext& cl;
};

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

/**
 * This kernel modifies the positions of particles to enforce distance constraints.
 */
class OpenCLApplyConstraintsKernel : public ApplyConstraintsKernel {
public:
    OpenCLApplyConstraintsKernel(std::string name, const Platform& platform, OpenCLContext& cl) : ApplyConstraintsKernel(name, platform),
            cl(cl), 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:
    OpenCLContext& cl;
    bool hasInitializedKernel;
    cl::Kernel applyDeltasKernel;
};

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

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

/**
 * This kernel is invoked by CustomBondForce to calculate the forces acting on the system and the energy of the system.
 */
class OpenCLCalcCustomBondForceKernel : public CalcCustomBondForceKernel {
public:
    OpenCLCalcCustomBondForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomBondForceKernel(name, platform),
            hasInitializedKernel(false), cl(cl), system(system), params(NULL), globals(NULL) {
    }
    ~OpenCLCalcCustomBondForceKernel();
    /**
     * 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;
    OpenCLContext& cl;
    System& system;
    OpenCLParameterSet* params;
    OpenCLArray* 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 OpenCLCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
public:
    OpenCLCalcHarmonicAngleForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcHarmonicAngleForceKernel(name, platform),
            hasInitializedKernel(false), cl(cl), system(system), params(NULL) {
    }
    ~OpenCLCalcHarmonicAngleForceKernel();
    /**
     * 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;
    OpenCLContext& cl;
    System& system;
    OpenCLArray* params;
};

/**
 * This kernel is invoked by CustomAngleForce to calculate the forces acting on the system and the energy of the system.
 */
class OpenCLCalcCustomAngleForceKernel : public CalcCustomAngleForceKernel {
public:
    OpenCLCalcCustomAngleForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomAngleForceKernel(name, platform),
            hasInitializedKernel(false), cl(cl), system(system), params(NULL), globals(NULL) {
    }
    ~OpenCLCalcCustomAngleForceKernel();
    /**
     * 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;
    OpenCLContext& cl;
    System& system;
    OpenCLParameterSet* params;
    OpenCLArray* 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 OpenCLCalcPeriodicTorsionForceKernel : public CalcPeriodicTorsionForceKernel {
public:
    OpenCLCalcPeriodicTorsionForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcPeriodicTorsionForceKernel(name, platform),
            hasInitializedKernel(false), cl(cl), system(system), params(NULL) {
    }
    ~OpenCLCalcPeriodicTorsionForceKernel();
    /**
     * 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;
    OpenCLContext& cl;
    System& system;
    OpenCLArray* params;
};

/**
 * This kernel is invoked by RBTorsionForce to calculate the forces acting on the system and the energy of the system.
 */
class OpenCLCalcRBTorsionForceKernel : public CalcRBTorsionForceKernel {
public:
    OpenCLCalcRBTorsionForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcRBTorsionForceKernel(name, platform),
            hasInitializedKernel(false), cl(cl), system(system), params(NULL) {
    }
    ~OpenCLCalcRBTorsionForceKernel();
    /**
     * 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;
    OpenCLContext& cl;
    System& system;
    OpenCLArray* params;
};

/**
 * This kernel is invoked by CMAPTorsionForce to calculate the forces acting on the system and the energy of the system.
 */
class OpenCLCalcCMAPTorsionForceKernel : public CalcCMAPTorsionForceKernel {
public:
    OpenCLCalcCMAPTorsionForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCMAPTorsionForceKernel(name, platform),
            hasInitializedKernel(false), cl(cl), system(system), coefficients(NULL), mapPositions(NULL), torsionMaps(NULL) {
    }
    ~OpenCLCalcCMAPTorsionForceKernel();
    /**
     * 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;
    OpenCLContext& cl;
    System& system;
    OpenCLArray* coefficients;
    OpenCLArray* mapPositions;
    OpenCLArray* torsionMaps;
};

/**
 * This kernel is invoked by CustomTorsionForce to calculate the forces acting on the system and the energy of the system.
 */
class OpenCLCalcCustomTorsionForceKernel : public CalcCustomTorsionForceKernel {
public:
    OpenCLCalcCustomTorsionForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomTorsionForceKernel(name, platform),
            hasInitializedKernel(false), cl(cl), system(system), params(NULL), globals(NULL) {
    }
    ~OpenCLCalcCustomTorsionForceKernel();
    /**
     * 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;
    OpenCLContext& cl;
    System& system;
    OpenCLParameterSet* params;
    OpenCLArray* 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 OpenCLCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public:
    OpenCLCalcNonbondedForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcNonbondedForceKernel(name, platform),
            hasInitializedKernel(false), cl(cl), 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) {
    }
    ~OpenCLCalcNonbondedForceKernel();
    /**
     * 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";}
    };
    OpenCLContext& cl;
    bool hasInitializedKernel;
    OpenCLArray* sigmaEpsilon;
    OpenCLArray* exceptionParams;
    OpenCLArray* cosSinSums;
    OpenCLArray* pmeGrid;
    OpenCLArray* pmeGrid2;
    OpenCLArray* pmeBsplineModuliX;
    OpenCLArray* pmeBsplineModuliY;
    OpenCLArray* pmeBsplineModuliZ;
    OpenCLArray* pmeBsplineTheta;
    OpenCLArray* pmeBsplineDTheta;
    OpenCLArray* pmeAtomRange;
    OpenCLArray* pmeAtomGridIndex;
    OpenCLSort<SortTrait>* sort;
    OpenCLFFT3D* fft;
    cl::Kernel ewaldSumsKernel;
    cl::Kernel ewaldForcesKernel;
    cl::Kernel pmeGridIndexKernel;
    cl::Kernel pmeAtomRangeKernel;
    cl::Kernel pmeZIndexKernel;
    cl::Kernel pmeUpdateBsplinesKernel;
    cl::Kernel pmeSpreadChargeKernel;
    cl::Kernel pmeFinishSpreadChargeKernel;
    cl::Kernel pmeConvolutionKernel;
    cl::Kernel pmeInterpolateForceKernel;
    std::map<std::string, std::string> pmeDefines;
    std::vector<std::pair<int, int> > exceptionAtoms;
    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 OpenCLCalcCustomNonbondedForceKernel : public CalcCustomNonbondedForceKernel {
public:
    OpenCLCalcCustomNonbondedForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomNonbondedForceKernel(name, platform),
            cl(cl), params(NULL), globals(NULL), tabulatedFunctionParams(NULL), system(system) {
    }
    ~OpenCLCalcCustomNonbondedForceKernel();
    /**
     * 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:
    OpenCLContext& cl;
    OpenCLParameterSet* params;
    OpenCLArray* globals;
    OpenCLArray* tabulatedFunctionParams;
    std::vector<std::string> globalParamNames;
    std::vector<cl_float> globalParamValues;
    std::vector<OpenCLArray*> tabulatedFunctions;
    System& system;
};

/**
 * This kernel is invoked by GBSAOBCForce to calculate the forces acting on the system.
 */
class OpenCLCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
public:
    OpenCLCalcGBSAOBCForceKernel(std::string name, const Platform& platform, OpenCLContext& cl) : CalcGBSAOBCForceKernel(name, platform), cl(cl),
            hasCreatedKernels(false), params(NULL), bornSum(NULL), longBornSum(NULL), bornRadii(NULL), bornForce(NULL),
            longBornForce(NULL), obcChain(NULL) {
    }
    ~OpenCLCalcGBSAOBCForceKernel();
    /**
     * 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;
    OpenCLContext& cl;
    OpenCLArray* params;
    OpenCLArray* bornSum;
    OpenCLArray* longBornSum;
    OpenCLArray* bornRadii;
    OpenCLArray* bornForce;
    OpenCLArray* longBornForce;
    OpenCLArray* obcChain;
    cl::Kernel computeBornSumKernel;
    cl::Kernel reduceBornSumKernel;
    cl::Kernel force1Kernel;
    cl::Kernel reduceBornForceKernel;
};

/**
 * This kernel is invoked by CustomGBForce to calculate the forces acting on the system.
 */
class OpenCLCalcCustomGBForceKernel : public CalcCustomGBForceKernel {
public:
    OpenCLCalcCustomGBForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomGBForceKernel(name, platform),
            hasInitializedKernels(false), cl(cl), params(NULL), computedValues(NULL), energyDerivs(NULL), longEnergyDerivs(NULL), globals(NULL),
            valueBuffers(NULL), longValueBuffers(NULL), tabulatedFunctionParams(NULL), system(system) {
    }
    ~OpenCLCalcCustomGBForceKernel();
    /**
     * 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;
    OpenCLContext& cl;
    OpenCLParameterSet* params;
    OpenCLParameterSet* computedValues;
    OpenCLParameterSet* energyDerivs;
    OpenCLArray* longEnergyDerivs;
    OpenCLArray* globals;
    OpenCLArray* valueBuffers;
    OpenCLArray* longValueBuffers;
    OpenCLArray* tabulatedFunctionParams;
    std::vector<std::string> globalParamNames;
    std::vector<cl_float> globalParamValues;
    std::vector<OpenCLArray*> tabulatedFunctions;
    std::vector<bool> pairValueUsesParam, pairEnergyUsesParam, pairEnergyUsesValue;
    System& system;
    cl::Kernel 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 OpenCLCalcCustomExternalForceKernel : public CalcCustomExternalForceKernel {
public:
    OpenCLCalcCustomExternalForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomExternalForceKernel(name, platform),
            hasInitializedKernel(false), cl(cl), system(system), params(NULL), globals(NULL) {
    }
    ~OpenCLCalcCustomExternalForceKernel();
    /**
     * 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;
    OpenCLContext& cl;
    System& system;
    OpenCLParameterSet* params;
    OpenCLArray* 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 OpenCLCalcCustomHbondForceKernel : public CalcCustomHbondForceKernel {
public:
    OpenCLCalcCustomHbondForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomHbondForceKernel(name, platform),
            hasInitializedKernel(false), cl(cl), donorParams(NULL), acceptorParams(NULL), donors(NULL), acceptors(NULL),
            donorBufferIndices(NULL), acceptorBufferIndices(NULL), globals(NULL), donorExclusions(NULL), acceptorExclusions(NULL),
            tabulatedFunctionParams(NULL), system(system) {
    }
    ~OpenCLCalcCustomHbondForceKernel();
    /**
     * 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;
    OpenCLContext& cl;
    OpenCLParameterSet* donorParams;
    OpenCLParameterSet* acceptorParams;
    OpenCLArray* globals;
    OpenCLArray* donors;
    OpenCLArray* acceptors;
    OpenCLArray* donorBufferIndices;
    OpenCLArray* acceptorBufferIndices;
    OpenCLArray* donorExclusions;
    OpenCLArray* acceptorExclusions;
    OpenCLArray* tabulatedFunctionParams;
    std::vector<std::string> globalParamNames;
    std::vector<cl_float> globalParamValues;
    std::vector<OpenCLArray*> tabulatedFunctions;
    System& system;
    cl::Kernel donorKernel, acceptorKernel;
};

/**
 * This kernel is invoked by CustomCompoundBondForce to calculate the forces acting on the system.
 */
class OpenCLCalcCustomCompoundBondForceKernel : public CalcCustomCompoundBondForceKernel {
public:
    OpenCLCalcCustomCompoundBondForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomCompoundBondForceKernel(name, platform),
            cl(cl), params(NULL), globals(NULL), tabulatedFunctionParams(NULL), system(system) {
    }
    ~OpenCLCalcCustomCompoundBondForceKernel();
    /**
     * 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;
    OpenCLContext& cl;
    OpenCLParameterSet* params;
    OpenCLArray* globals;
    OpenCLArray* tabulatedFunctionParams;
    std::vector<std::string> globalParamNames;
    std::vector<cl_float> globalParamValues;
    std::vector<OpenCLArray*> tabulatedFunctions;
    System& system;
};

/**
 * This kernel is invoked by VerletIntegrator to take one time step.
 */
class OpenCLIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
public:
    OpenCLIntegrateVerletStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateVerletStepKernel(name, platform), cl(cl),
            hasInitializedKernels(false) {
    }
    ~OpenCLIntegrateVerletStepKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param integrator the VerletIntegrator this kernel will be used for
     */
    void initialize(const System& system, const VerletIntegrator& integrator);
    /**
     * Execute the kernel.
     *
     * @param context    the context in which to execute this kernel
     * @param integrator the VerletIntegrator this kernel is being used for
     */
    void execute(ContextImpl& context, const VerletIntegrator& integrator);
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the VerletIntegrator this kernel is being used for
     */
    double computeKineticEnergy(ContextImpl& context, const VerletIntegrator& integrator);
private:
    OpenCLContext& cl;
    double prevStepSize;
    bool hasInitializedKernels;
    cl::Kernel kernel1, kernel2;
};

/**
 * This kernel is invoked by LangevinIntegrator to take one time step.
 */
class OpenCLIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
public:
    OpenCLIntegrateLangevinStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateLangevinStepKernel(name, platform), cl(cl),
            hasInitializedKernels(false), params(NULL) {
    }
    ~OpenCLIntegrateLangevinStepKernel();
    /**
     * Initialize the kernel, setting up the particle masses.
     *
     * @param system     the System this kernel will be applied to
     * @param integrator the LangevinIntegrator this kernel will be used for
     */
    void initialize(const System& system, const LangevinIntegrator& integrator);
    /**
     * Execute the kernel.
     *
     * @param context    the context in which to execute this kernel
     * @param integrator the LangevinIntegrator this kernel is being used for
     */
    void execute(ContextImpl& context, const LangevinIntegrator& integrator);
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the LangevinIntegrator this kernel is being used for
     */
    double computeKineticEnergy(ContextImpl& context, const LangevinIntegrator& integrator);
private:
    OpenCLContext& cl;
    double prevTemp, prevFriction, prevStepSize;
    bool hasInitializedKernels;
    OpenCLArray* params;
    cl::Kernel kernel1, kernel2;
};

/**
 * This kernel is invoked by BrownianIntegrator to take one time step.
 */
class OpenCLIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
public:
    OpenCLIntegrateBrownianStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateBrownianStepKernel(name, platform), cl(cl),
            hasInitializedKernels(false), prevTemp(-1), prevFriction(-1), prevStepSize(-1) {
    }
    ~OpenCLIntegrateBrownianStepKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param integrator the BrownianIntegrator this kernel will be used for
     */
    void initialize(const System& system, const BrownianIntegrator& integrator);
    /**
     * Execute the kernel.
     *
     * @param context    the context in which to execute this kernel
     * @param integrator the BrownianIntegrator this kernel is being used for
     */
    void execute(ContextImpl& context, const BrownianIntegrator& integrator);
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the BrownianIntegrator this kernel is being used for
     */
    double computeKineticEnergy(ContextImpl& context, const BrownianIntegrator& integrator);
private:
    OpenCLContext& cl;
    double prevTemp, prevFriction, prevStepSize;
    bool hasInitializedKernels;
    cl::Kernel kernel1, kernel2;
};

/**
 * This kernel is invoked by VariableVerletIntegrator to take one time step.
 */
class OpenCLIntegrateVariableVerletStepKernel : public IntegrateVariableVerletStepKernel {
public:
    OpenCLIntegrateVariableVerletStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateVariableVerletStepKernel(name, platform), cl(cl),
            hasInitializedKernels(false) {
    }
    ~OpenCLIntegrateVariableVerletStepKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param integrator the VariableVerletIntegrator this kernel will be used for
     */
    void initialize(const System& system, const VariableVerletIntegrator& integrator);
    /**
     * Execute the kernel.
     *
     * @param context    the context in which to execute this kernel
     * @param integrator the VariableVerletIntegrator this kernel is being used for
     * @param maxTime    the maximum time beyond which the simulation should not be advanced
     * @return the size of the step that was taken
     */
    double execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime);
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the VariableVerletIntegrator this kernel is being used for
     */
    double computeKineticEnergy(ContextImpl& context, const VariableVerletIntegrator& integrator);
private:
    OpenCLContext& cl;
    bool hasInitializedKernels;
    int blockSize;
    cl::Kernel kernel1, kernel2, selectSizeKernel;
};

/**
 * This kernel is invoked by VariableLangevinIntegrator to take one time step.
 */
class OpenCLIntegrateVariableLangevinStepKernel : public IntegrateVariableLangevinStepKernel {
public:
    OpenCLIntegrateVariableLangevinStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateVariableLangevinStepKernel(name, platform), cl(cl),
            hasInitializedKernels(false), params(NULL) {
    }
    ~OpenCLIntegrateVariableLangevinStepKernel();
    /**
     * 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);
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the VariableLangevinIntegrator this kernel is being used for
     */
    double computeKineticEnergy(ContextImpl& context, const VariableLangevinIntegrator& integrator);
private:
    OpenCLContext& cl;
    bool hasInitializedKernels;
    int blockSize;
    OpenCLArray* params;
    cl::Kernel kernel1, kernel2, selectSizeKernel;
    double prevTemp, prevFriction, prevErrorTol;
};

/**
 * This kernel is invoked by CustomIntegrator to take one time step.
 */
class OpenCLIntegrateCustomStepKernel : public IntegrateCustomStepKernel {
public:
    OpenCLIntegrateCustomStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateCustomStepKernel(name, platform), cl(cl),
            hasInitializedKernels(false), localValuesAreCurrent(false), globalValues(NULL), contextParameterValues(NULL), sumBuffer(NULL), potentialEnergy(NULL),
            kineticEnergy(NULL), uniformRandoms(NULL), randomSeed(NULL), perDofValues(NULL) {
    }
    ~OpenCLIntegrateCustomStepKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param integrator the CustomIntegrator this kernel will be used for
     */
    void initialize(const System& system, const CustomIntegrator& integrator);
    /**
     * Execute the kernel.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the CustomIntegrator this kernel is being used for
     * @param forcesAreValid if the context has been modified since the last time step, this will be
     *                       false to show that cached forces are invalid and must be recalculated.
     *                       On exit, this should specify whether the cached forces are valid at the
     *                       end of the step.
     */
    void execute(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid);
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the CustomIntegrator this kernel is being used for
     * @param forcesAreValid if the context has been modified since the last time step, this will be
     *                       false to show that cached forces are invalid and must be recalculated.
     *                       On exit, this should specify whether the cached forces are valid at the
     *                       end of the step.
     */
    double computeKineticEnergy(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid);
    /**
     * Get the values of all global variables.
     *
     * @param context   the context in which to execute this kernel
     * @param values    on exit, this contains the values
     */
    void getGlobalVariables(ContextImpl& context, std::vector<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 prepareForComputation(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid);
    void recordChangedParameters(ContextImpl& context);
    OpenCLContext& cl;
    double prevStepSize;
    int numGlobalVariables;
    bool hasInitializedKernels, deviceValuesAreCurrent, modifiesParameters, keNeedsForce;
    mutable bool localValuesAreCurrent;
    OpenCLArray* globalValues;
    OpenCLArray* contextParameterValues;
    OpenCLArray* sumBuffer;
    OpenCLArray* potentialEnergy;
    OpenCLArray* kineticEnergy;
    OpenCLArray* uniformRandoms;
    OpenCLArray* randomSeed;
    OpenCLParameterSet* perDofValues;
    mutable std::vector<std::vector<cl_float> > localPerDofValuesFloat;
    mutable std::vector<std::vector<cl_double> > localPerDofValuesDouble;
    std::vector<float> contextValuesFloat;
    std::vector<double> contextValuesDouble;
    std::vector<float> contextValues;
    std::vector<std::vector<cl::Kernel> > kernels;
    cl::Kernel sumPotentialEnergyKernel, randomKernel, kineticEnergyKernel, sumKineticEnergyKernel;
    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 OpenCLApplyAndersenThermostatKernel : public ApplyAndersenThermostatKernel {
public:
    OpenCLApplyAndersenThermostatKernel(std::string name, const Platform& platform, OpenCLContext& cl) : ApplyAndersenThermostatKernel(name, platform), cl(cl),
            hasInitializedKernels(false), atomGroups(NULL) {
    }
    ~OpenCLApplyAndersenThermostatKernel();
    /**
     * 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:
    OpenCLContext& cl;
    bool hasInitializedKernels;
    int randomSeed;
    OpenCLArray* atomGroups;
    cl::Kernel kernel;
};

/**
 * This kernel is invoked by MonteCarloBarostat to adjust the periodic box volume
 */
class OpenCLApplyMonteCarloBarostatKernel : public ApplyMonteCarloBarostatKernel {
public:
    OpenCLApplyMonteCarloBarostatKernel(std::string name, const Platform& platform, OpenCLContext& cl) : ApplyMonteCarloBarostatKernel(name, platform), cl(cl),
            hasInitializedKernels(false), savedPositions(NULL), moleculeAtoms(NULL), moleculeStartIndex(NULL) {
    }
    ~OpenCLApplyMonteCarloBarostatKernel();
    /**
     * 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:
    OpenCLContext& cl;
    bool hasInitializedKernels;
    int numMolecules;
    OpenCLArray* savedPositions;
    OpenCLArray* moleculeAtoms;
    OpenCLArray* moleculeStartIndex;
    cl::Kernel kernel;
    std::vector<int> lastAtomOrder;
};

/**
 * This kernel is invoked to remove center of mass motion from the system.
 */
class OpenCLRemoveCMMotionKernel : public RemoveCMMotionKernel {
public:
    OpenCLRemoveCMMotionKernel(std::string name, const Platform& platform, OpenCLContext& cl) : RemoveCMMotionKernel(name, platform), cl(cl), cmMomentum(NULL) {
    }
    ~OpenCLRemoveCMMotionKernel();
    /**
     * 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:
    OpenCLContext& cl;
    int frequency;
    OpenCLArray* cmMomentum;
    cl::Kernel kernel1, kernel2;
};

} // namespace OpenMM

#endif /*OPENMM_OPENCLKERNELS_H_*/