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) 2008-2019 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/internal/CompiledExpressionSet.h"
#include "openmm/internal/CustomIntegratorUtilities.h"
#include "lepton/CompiledExpression.h"
#include "lepton/ExpressionProgram.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
     * @param valid         the method may set this to false to indicate the results are invalid and the force/energy
     *                      calculation should be repeated
     * @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, bool& valid);
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 derivatives of the energy with respect to context parameters.
     *
     * @param derivs  on exit, this contains the derivatives
     */
    void getEnergyParameterDerivatives(ContextImpl& context, std::map<std::string, double>& derivs);
    /**
     * 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);
    /**
     * 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);
    /**
     * Update particle velocities to enforce constraints.
     *
     * @param context    the context in which to execute this kernel
     * @param tol        the velocity tolerance within which constraints must be satisfied.
     */
    void applyToVelocities(ContextImpl& context, double tol);
private:
    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 NonbondedForce to calculate the forces acting on the system.
 */
class OpenCLCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public:
    OpenCLCalcNonbondedForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, const System& system) : CalcNonbondedForceKernel(name, platform),
            hasInitializedKernel(false), cl(cl), sort(NULL), fft(NULL), dispersionFft(NULL), pmeio(NULL), usePmeQueue(false) {
    }
    ~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);
    /**
     * Get the parameters being used for PME.
     *
     * @param alpha   the separation parameter
     * @param nx      the number of grid points along the X axis
     * @param ny      the number of grid points along the Y axis
     * @param nz      the number of grid points along the Z axis
     */
    void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
    /**
     * Get the parameters being used for the dispersion term in LJPME.
     *
     * @param alpha   the separation parameter
     * @param nx      the number of grid points along the X axis
     * @param ny      the number of grid points along the Y axis
     * @param nz      the number of grid points along the Z axis
     */
    void getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
private:
    class SortTrait : public OpenCLSort::SortTrait {
        int getDataSize() const {return 8;}
        int getKeySize() const {return 4;}
        const char* getDataType() const {return "int2";}
        const char* getKeyType() const {return "int";}
        const char* getMinKey() const {return "INT_MIN";}
        const char* getMaxKey() const {return "INT_MAX";}
        const char* getMaxValue() const {return "(int2) (INT_MAX, INT_MAX)";}
        const char* getSortKey() const {return "value.y";}
    };
    class ForceInfo;
    class PmeIO;
    class PmePreComputation;
    class PmePostComputation;
    class SyncQueuePreComputation;
    class SyncQueuePostComputation;
    OpenCLContext& cl;
    ForceInfo* info;
    bool hasInitializedKernel;
    OpenCLArray charges;
    OpenCLArray sigmaEpsilon;
    OpenCLArray exceptionParams;
    OpenCLArray exclusionAtoms;
    OpenCLArray exclusionParams;
    OpenCLArray baseParticleParams;
    OpenCLArray baseExceptionParams;
    OpenCLArray particleParamOffsets;
    OpenCLArray exceptionParamOffsets;
    OpenCLArray particleOffsetIndices;
    OpenCLArray exceptionOffsetIndices;
    OpenCLArray globalParams;
    OpenCLArray cosSinSums;
    OpenCLArray pmeGrid1;
    OpenCLArray pmeGrid2;
    OpenCLArray pmeBsplineModuliX;
    OpenCLArray pmeBsplineModuliY;
    OpenCLArray pmeBsplineModuliZ;
    OpenCLArray pmeDispersionBsplineModuliX;
    OpenCLArray pmeDispersionBsplineModuliY;
    OpenCLArray pmeDispersionBsplineModuliZ;
    OpenCLArray pmeBsplineTheta;
    OpenCLArray pmeAtomRange;
    OpenCLArray pmeAtomGridIndex;
    OpenCLArray pmeEnergyBuffer;
    OpenCLSort* sort;
    cl::CommandQueue pmeQueue;
    cl::Event pmeSyncEvent;
    OpenCLFFT3D* fft;
    OpenCLFFT3D* dispersionFft;
    Kernel cpuPme;
    PmeIO* pmeio;
    SyncQueuePostComputation* syncQueue;
    cl::Kernel computeParamsKernel, computeExclusionParamsKernel;
    cl::Kernel ewaldSumsKernel;
    cl::Kernel ewaldForcesKernel;
    cl::Kernel pmeAtomRangeKernel;
    cl::Kernel pmeDispersionAtomRangeKernel;
    cl::Kernel pmeZIndexKernel;
    cl::Kernel pmeDispersionZIndexKernel;
    cl::Kernel pmeUpdateBsplinesKernel;
    cl::Kernel pmeDispersionUpdateBsplinesKernel;
    cl::Kernel pmeSpreadChargeKernel;
    cl::Kernel pmeDispersionSpreadChargeKernel;
    cl::Kernel pmeFinishSpreadChargeKernel;
    cl::Kernel pmeDispersionFinishSpreadChargeKernel;
    cl::Kernel pmeConvolutionKernel;
    cl::Kernel pmeDispersionConvolutionKernel;
    cl::Kernel pmeEvalEnergyKernel;
    cl::Kernel pmeDispersionEvalEnergyKernel;
    cl::Kernel pmeInterpolateForceKernel;
    cl::Kernel pmeDispersionInterpolateForceKernel;
    std::map<std::string, std::string> pmeDefines;
    std::vector<std::pair<int, int> > exceptionAtoms;
    std::vector<std::string> paramNames;
    std::vector<double> paramValues;
    double ewaldSelfEnergy, dispersionCoefficient, alpha, dispersionAlpha;
    int gridSizeX, gridSizeY, gridSizeZ;
    int dispersionGridSizeX, dispersionGridSizeY, dispersionGridSizeZ;
    bool hasCoulomb, hasLJ, usePmeQueue, doLJPME, usePosqCharges, recomputeParams, hasOffsets;
    NonbondedMethod nonbondedMethod;
    static const int PmeOrder = 5;
};

/**
 * This kernel is invoked by CustomCVForce to calculate the forces acting on the system and the energy of the system.
 */
class OpenCLCalcCustomCVForceKernel : public CalcCustomCVForceKernel {
public:
    OpenCLCalcCustomCVForceKernel(std::string name, const Platform& platform, OpenCLContext& cl) : CalcCustomCVForceKernel(name, platform),
            cl(cl), hasInitializedKernels(false) {
    }
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the CustomCVForce this kernel will be used for
     * @param innerContext   the context created by the CustomCVForce for computing collective variables
     */
    void initialize(const System& system, const CustomCVForce& force, ContextImpl& innerContext);
    /**
     * Execute the kernel to calculate the forces and/or energy.
     *
     * @param context        the context in which to execute this kernel
     * @param innerContext   the context created by the CustomCVForce for computing collective variables
     * @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, ContextImpl& innerContext, bool includeForces, bool includeEnergy);
    /**
     * Copy state information to the inner context.
     *
     * @param context        the context in which to execute this kernel
     * @param innerContext   the context created by the CustomCVForce for computing collective variables
     */
    void copyState(ContextImpl& context, ContextImpl& innerContext);
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the CustomCVForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const CustomCVForce& force);
private:
    class ForceInfo;
    class ReorderListener;
    OpenCLContext& cl;
    bool hasInitializedKernels;
    Lepton::ExpressionProgram energyExpression;
    std::vector<std::string> variableNames, paramDerivNames, globalParameterNames;
    std::vector<Lepton::ExpressionProgram> variableDerivExpressions;
    std::vector<Lepton::ExpressionProgram> paramDerivExpressions;
    std::vector<OpenCLArray> cvForces;
    OpenCLArray invAtomOrder;
    OpenCLArray innerInvAtomOrder;
    cl::Kernel copyStateKernel, copyForcesKernel, addForcesKernel;
};

/*
 * This kernel is invoked by NoseHooverIntegrator to take one time step.
 */
class OpenCLIntegrateVelocityVerletStepKernel : public IntegrateVelocityVerletStepKernel {
public:
    OpenCLIntegrateVelocityVerletStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) :
                                  IntegrateVelocityVerletStepKernel(name, platform), cl(cl) { }
    ~OpenCLIntegrateVelocityVerletStepKernel() {}
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param integrator the NoseHooverIntegrator this kernel will be used for
     */
    void initialize(const System& system, const NoseHooverIntegrator& 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 forcesAreValid a reference to the parent integrator's boolean for keeping
     *                       track of the validity of the current forces.
     */
    void execute(ContextImpl& context, const NoseHooverIntegrator& integrator, bool &forcesAreValid);
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the NoseHooverIntegrator this kernel is being used for
     */
    double computeKineticEnergy(ContextImpl& context, const NoseHooverIntegrator& integrator);
private:
    OpenCLContext& cl;
    float prevMaxPairDistance;
    OpenCLArray maxPairDistanceBuffer, pairListBuffer, atomListBuffer, pairTemperatureBuffer; 
    cl::Kernel kernel1, kernel2, kernel3, kernelHardWall;
};

/**
 * This kernel is invoked by NoseHooverChain at the start of each time step to adjust the thermostat
 * and update the associated particle velocities.
 */
class OpenCLNoseHooverChainKernel : public NoseHooverChainKernel {
public:
    OpenCLNoseHooverChainKernel(std::string name, const Platform& platform, OpenCLContext& cl) : NoseHooverChainKernel(name, platform), cl(cl) {
    }
    ~OpenCLNoseHooverChainKernel() {}
    /**
     * Initialize the kernel.
     */
    void initialize();
    /**
     * Execute the kernel that propagates the Nose Hoover chain and determines the velocity scale factor.
     * 
     * @param context  the context in which to execute this kernel
     * @param noseHooverChain the object describing the chain to be propagated.
     * @param kineticEnergies the {absolute, relative} kineticEnergy of the particles being thermostated by this chain.
     * @param timeStep the time step used by the integrator.
     * @return the {absolute, relative} velocity scale factor to apply to the particles associated with this heat bath.
     */
    std::pair<double, double> propagateChain(ContextImpl& context, const NoseHooverChain &nhc, std::pair<double, double> kineticEnergies, double timeStep);
    /**
     * Execute the kernal that computes the total (kinetic + potential) heat bath energy.
     *
     * @param context the context in which to execute this kernel
     * @param noseHooverChain the chain whose energy is to be determined.
     * @return the total heat bath energy.
     */
    double computeHeatBathEnergy(ContextImpl& context, const NoseHooverChain &nhc);
    /**
     * Execute the kernel that computes the kinetic energy for a subset of atoms,
     * or the relative kinetic energy of Drude particles with respect to their parent atoms
     *
     * @param context the context in which to execute this kernel
     * @param noseHooverChain the chain whose energy is to be determined.
     * @param downloadValue whether the computed value should be downloaded and returned.
     *
     */
    std::pair<double,double> computeMaskedKineticEnergy(ContextImpl& context, const NoseHooverChain &noseHooverChain, bool downloadValue);

    /**
     * Execute the kernel that scales the velocities of particles associated with a nose hoover chain
     *
     * @param context the context in which to execute this kernel
     * @param noseHooverChain the chain whose energy is to be determined.
     * @param scaleFactors the {absolute, relative} multiplicative factor by which velocities are scaled.
     */
    void scaleVelocities(ContextImpl& context, const NoseHooverChain &noseHooverChain, std::pair<double, double> scaleFactors);

private:
    int sumWorkGroupSize;
    OpenCLContext& cl;
    OpenCLArray energyBuffer, scaleFactorBuffer, kineticEnergyBuffer, chainMasses, chainForces, heatBathEnergy;
    std::map<int, OpenCLArray> atomlists, pairlists;
    std::map<int, cl::Kernel> propagateKernels;
    cl::Kernel reduceEnergyKernel;
    cl::Kernel computeHeatBathEnergyKernel;
    cl::Kernel computeAtomsKineticEnergyKernel;
    cl::Kernel computePairsKineticEnergyKernel;
    cl::Kernel scaleAtomsVelocitiesKernel;
    cl::Kernel scalePairsVelocitiesKernel;
};

/**
 * 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) {
    }
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param barostat   the MonteCarloBarostat this kernel will be used for
     */
    void initialize(const System& system, const Force& barostat);
    /**
     * Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
     * This version scales the x, y, and z positions independently.
     * This is called BEFORE the periodic box size is modified.  It should begin by translating each particle
     * or cluster into the first periodic box, so that coordinates will still be correct after the box size
     * is changed.
     *
     * @param context    the context in which to execute this kernel
     * @param scaleX     the scale factor by which to multiply particle x-coordinate
     * @param scaleY     the scale factor by which to multiply particle y-coordinate
     * @param scaleZ     the scale factor by which to multiply particle z-coordinate
     */
    void scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ);
    /**
     * Reject the most recent Monte Carlo step, restoring the particle positions to where they were before
     * scaleCoordinates() was last called.
     *
     * @param context    the context in which to execute this kernel
     */
    void restoreCoordinates(ContextImpl& context);
private:
    OpenCLContext& cl;
    bool hasInitializedKernels;
    int numMolecules;
    OpenCLArray savedPositions;
    OpenCLArray savedForces;
    OpenCLArray moleculeAtoms;
    OpenCLArray moleculeStartIndex;
    cl::Kernel kernel;
    std::vector<int> lastAtomOrder;
};

} // namespace OpenMM

#endif /*OPENMM_OPENCLKERNELS_H_*/