AmoebaCudaKernels.h

#ifndef AMOEBA_OPENMM_CUDAKERNELS_H_
#define AMOEBA_OPENMM_CUDAKERNELS_H_

/* -------------------------------------------------------------------------- *
 *                              OpenMMAmoeba                                  *
 * -------------------------------------------------------------------------- *
 * 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: Mark Friedrichs, 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 "openmm/amoebaKernels.h"
#include "openmm/kernels.h"
#include "openmm/System.h"
#include "CudaArray.h"
#include "CudaContext.h"
#include "CudaSort.h"
#include <cufft.h>

namespace OpenMM {

class CudaCalcAmoebaGeneralizedKirkwoodForceKernel;

/**
 * This kernel is invoked by AmoebaHarmonicBondForce to calculate the forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaHarmonicBondForceKernel : public CalcAmoebaHarmonicBondForceKernel {
public:
    CudaCalcAmoebaHarmonicBondForceKernel(std::string name, 
                                          const Platform& platform,
                                          CudaContext& cu,
                                          System& system);
    ~CudaCalcAmoebaHarmonicBondForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaHarmonicBondForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaHarmonicBondForce& 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:
    class ForceInfo;
    int numBonds;
    CudaContext& cu;
    System& system;
    CudaArray* params;
};

/**
 * This kernel is invoked by AmoebaUreyBradleyForce to calculate the forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaUreyBradleyForceKernel : public CalcAmoebaUreyBradleyForceKernel {
public:
    CudaCalcAmoebaUreyBradleyForceKernel(std::string name, 
                                         const Platform& platform,
                                         CudaContext& cu,
                                         System& system);
    ~CudaCalcAmoebaUreyBradleyForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaUreyBradleyForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaUreyBradleyForce& 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:
    class ForceInfo;
    int numInteractions;
    CudaContext& cu;
    System& system;
};

/**
 * This kernel is invoked by AmoebaHarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaHarmonicAngleForceKernel : public CalcAmoebaHarmonicAngleForceKernel {
public:
    CudaCalcAmoebaHarmonicAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
    ~CudaCalcAmoebaHarmonicAngleForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaHarmonicAngleForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaHarmonicAngleForce& 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:
    class ForceInfo;
    int numAngles;
    CudaContext& cu;
    System& system;
    CudaArray* params;
};

/**
 * This kernel is invoked by AmoebaHarmonicInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaHarmonicInPlaneAngleForceKernel : public CalcAmoebaHarmonicInPlaneAngleForceKernel {
public:
    CudaCalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
    ~CudaCalcAmoebaHarmonicInPlaneAngleForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaHarmonicInPlaneAngleForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& 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:
    class ForceInfo;
    int numAngles;
    CudaContext& cu;
    System& system;
    CudaArray* params;
};

/**
 * This kernel is invoked by AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaTorsionForceKernel : public CalcAmoebaTorsionForceKernel {
public:
    CudaCalcAmoebaTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
    ~CudaCalcAmoebaTorsionForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaTorsionForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaTorsionForce& 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:
    class ForceInfo;
    int numTorsions;
    CudaContext& cu;
    System& system;
};

/**
 * This kernel is invoked by AmoebaPiTorsionForce to calculate the forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaPiTorsionForceKernel : public CalcAmoebaPiTorsionForceKernel {
public:
    CudaCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
    ~CudaCalcAmoebaPiTorsionForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaPiTorsionForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaPiTorsionForce& 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:
    class ForceInfo;
    int numPiTorsions;
    CudaContext& cu;
    System& system;
    CudaArray* params;
};

/**
 * This kernel is invoked by AmoebaStretchBendForce to calculate the forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaStretchBendForceKernel : public CalcAmoebaStretchBendForceKernel {
public:
    CudaCalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
    ~CudaCalcAmoebaStretchBendForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaStretchBendForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaStretchBendForce& 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:
    class ForceInfo;
    int numStretchBends;
    CudaContext& cu;
    System& system;
    CudaArray* params;
};

/**
 * This kernel is invoked by AmoebaOutOfPlaneBendForce to calculate the forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaOutOfPlaneBendForceKernel : public CalcAmoebaOutOfPlaneBendForceKernel {
public:
    CudaCalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
    ~CudaCalcAmoebaOutOfPlaneBendForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaOutOfPlaneBendForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaOutOfPlaneBendForce& 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:
    class ForceInfo;
    int numOutOfPlaneBends;
    CudaContext& cu;
    System& system;
    CudaArray* params;
};

/**
 * This kernel is invoked by AmoebaTorsionTorsionForce to calculate the forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaTorsionTorsionForceKernel : public CalcAmoebaTorsionTorsionForceKernel {
public:
    CudaCalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
    ~CudaCalcAmoebaTorsionTorsionForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaTorsionTorsionForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaTorsionTorsionForce& 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:
    class ForceInfo;
    int numTorsionTorsions;
    int numTorsionTorsionGrids;
    CudaContext& cu;
    System& system;
    CudaArray* gridValues;
    CudaArray* gridParams;
    CudaArray* torsionParams;
};

/**
 * This kernel is invoked by AmoebaMultipoleForce to calculate the forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaMultipoleForceKernel : public CalcAmoebaMultipoleForceKernel {
public:
    CudaCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
    ~CudaCalcAmoebaMultipoleForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaMultipoleForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaMultipoleForce& 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);
    /**
     * Execute the kernel to calculate the electrostatic potential
     *
     * @param context        the context in which to execute this kernel
     * @param inputGrid      input grid coordinates
     * @param outputElectrostaticPotential output potential 
     */
    void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
                                   std::vector< double >& outputElectrostaticPotential );

   /** 
     * Get the system multipole moments
     *
     * @param origin       origin
     * @param context      context
     * @param outputMultipoleMoments (charge,
     *                                dipole_x, dipole_y, dipole_z,
     *                                quadrupole_xx, quadrupole_xy, quadrupole_xz,
     *                                quadrupole_yx, quadrupole_yy, quadrupole_yz,
     *                                quadrupole_zx, quadrupole_zy, quadrupole_zz )
     */
    void getSystemMultipoleMoments(ContextImpl& context, const Vec3& origin, std::vector<double>& outputMultipoleMoments);


private:
    class ForceInfo;
    class SortTrait : public CudaSort::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 "make_int2(INT_MAX, INT_MAX)";}
        const char* getSortKey() const {return "value.y";}
    };
    void initializeScaleFactors();
    template <class T, class T4> void computeSystemMultipoleMoments(ContextImpl& context, const Vec3& origin, std::vector<double>& outputMultipoleMoments);
    int numMultipoles, maxInducedIterations;
    double inducedEpsilon;
    bool hasInitializedScaleFactors, hasInitializedFFT;
    CudaContext& cu;
    System& system;
    std::vector<int3> covalentFlagValues;
    std::vector<int2> polarizationFlagValues;
    CudaArray* multipoleParticles;
    CudaArray* molecularDipoles;
    CudaArray* molecularQuadrupoles;
    CudaArray* labFrameDipoles;
    CudaArray* labFrameQuadrupoles;
    CudaArray* field;
    CudaArray* fieldPolar;
    CudaArray* inducedField;
    CudaArray* inducedFieldPolar;
    CudaArray* torque;
    CudaArray* dampingAndThole;
    CudaArray* inducedDipole;
    CudaArray* inducedDipolePolar;
    CudaArray* inducedDipoleErrors;
    CudaArray* polarizability;
    CudaArray* covalentFlags;
    CudaArray* polarizationGroupFlags;
    CudaArray* pmeGrid;
    CudaArray* pmeBsplineModuliX;
    CudaArray* pmeBsplineModuliY;
    CudaArray* pmeBsplineModuliZ;
    CudaArray* pmeTheta1;
    CudaArray* pmeTheta2;
    CudaArray* pmeTheta3;
    CudaArray* pmeIgrid;
    CudaArray* pmePhi;
    CudaArray* pmePhid;
    CudaArray* pmePhip;
    CudaArray* pmePhidp;
    CudaArray* pmeAtomRange;
    CudaArray* pmeAtomGridIndex;
    CudaSort* sort;
    cufftHandle fft;
    CUfunction computeMomentsKernel, recordInducedDipolesKernel, computeFixedFieldKernel, computeInducedFieldKernel, updateInducedFieldKernel, electrostaticsKernel, mapTorqueKernel;
    CUfunction pmeUpdateBsplinesKernel, pmeAtomRangeKernel, pmeZIndexKernel, pmeSpreadFixedMultipolesKernel, pmeSpreadInducedDipolesKernel, pmeConvolutionKernel, pmeFixedPotentialKernel, pmeInducedPotentialKernel;
    CUfunction pmeFixedForceKernel, pmeInducedForceKernel, pmeRecordInducedFieldDipolesKernel, computePotentialKernel;
    CudaCalcAmoebaGeneralizedKirkwoodForceKernel* gkKernel;
    static const int PmeOrder = 5;
};

/**
 * This kernel is invoked by AmoebaMultipoleForce to calculate the forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaGeneralizedKirkwoodForceKernel : public CalcAmoebaGeneralizedKirkwoodForceKernel {
public:
    CudaCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
    ~CudaCalcAmoebaGeneralizedKirkwoodForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaMultipoleForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaGeneralizedKirkwoodForce& 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);
    /**
     * Perform the computation of Born radii.
     */
    void computeBornRadii();
    /**
     * Perform the final parts of the force/energy computation.
     */
    void finishComputation(CudaArray& torque, CudaArray& labFrameDipoles, CudaArray& labFrameQuadrupoles, CudaArray& inducedDipole, CudaArray& inducedDipolePolar, CudaArray& dampingAndThole, CudaArray& covalentFlags, CudaArray& polarizationGroupFlags);
    CudaArray* getBornRadii() {
        return bornRadii;
    }
    CudaArray* getField() {
        return field;
    }
    CudaArray* getInducedField() {
        return inducedField;
    }
    CudaArray* getInducedFieldPolar() {
        return inducedFieldPolar;
    }
    CudaArray* getInducedDipoles() {
        return inducedDipoleS;
    }
    CudaArray* getInducedDipolesPolar() {
        return inducedDipolePolarS;
    }
private:
    class ForceInfo;
    CudaContext& cu;
    System& system;
    CudaArray* params;
    CudaArray* bornSum;
    CudaArray* bornRadii;
    CudaArray* bornForce;
    CudaArray* field;
    CudaArray* inducedField;
    CudaArray* inducedFieldPolar;
    CudaArray* inducedDipoleS;
    CudaArray* inducedDipolePolarS;
    CUfunction computeBornSumKernel, reduceBornSumKernel, gkForceKernel, chainRuleKernel, ediffKernel;
};

/**
 * This kernel is invoked to calculate the vdw forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaVdwForceKernel : public CalcAmoebaVdwForceKernel {
public:
    CudaCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
    ~CudaCalcAmoebaVdwForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaMultipoleForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaVdwForce& 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:
    class ForceInfo;
    CudaContext& cu;
    System& system;
    bool hasInitializedNonbonded;
    double dispersionCoefficient;
    CudaArray* sigmaEpsilon;
    CudaArray* bondReductionAtoms;
    CudaArray* bondReductionFactors;
    CudaArray* tempPosq;
    CudaArray* tempForces;
    CudaNonbondedUtilities* nonbonded;
    CUfunction prepareKernel, spreadKernel;
};

/**
 * This kernel is invoked to calculate the WCA dispersion forces acting on the system and the energy of the system.
 */
class CudaCalcAmoebaWcaDispersionForceKernel : public CalcAmoebaWcaDispersionForceKernel {
public:
    CudaCalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
    ~CudaCalcAmoebaWcaDispersionForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the AmoebaMultipoleForce this kernel will be used for
     */
    void initialize(const System& system, const AmoebaWcaDispersionForce& 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:
    class ForceInfo;
    CudaContext& cu;
    System& system;
    double totalMaximumDispersionEnergy;
    CudaArray* radiusEpsilon;
    CUfunction forceKernel;
};

} // namespace OpenMM

#endif /*AMOEBA_OPENMM_CUDAKERNELS_H*/