[alexxy/gromacs.git] / src / gromacs / nbnxm / nbnxm.h

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
 * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS 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 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS 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 GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */

// FIXME: remove the "__" prefix in front of the group def when we move the
//        nonbonded code into separate dir.

/*! \libinternal \defgroup __module_nbnxm Short-range non-bonded interaction module
 * \ingroup group_mdrun
 *
 * \brief Computes forces and energies for short-range pair-interactions
 * based on the Verlet algorithm. The algorithm uses pair-lists generated
 * at fixed intervals as well as various flavors of pair interaction kernels
 * implemented for a wide range of CPU and GPU architectures.
 *
 * The module includes support for flavors of Coulomb and Lennard-Jones interaction
 * treatment implemented for a large range of SIMD instruction sets for CPU
 * architectures as well as in CUDA and OpenCL for GPU architectures.
 * Additionally there is a reference CPU non-SIMD and a reference CPU
 * for GPU pair-list setup interaction kernel.
 *
 * The implementation of the kernels is based on the cluster non-bonded algorithm
 * which in the code is referred to as the NxM algorithms ("nbnxm_" prefix);
 * for details of the algorithm see DOI:10.1016/j.cpc.2013.06.003.
 *
 * Algorithmically, the non-bonded computation has two different modes:
 * A "classical" mode: generate a list every nstlist steps containing at least
 * all atom pairs up to a distance of rlistOuter and compute pair interactions
 * for all pairs that are within the interaction cut-off.
 * A "dynamic pruning" mode: generate an "outer-list" up to cut-off rlistOuter
 * every nstlist steps and prune the outer-list using a cut-off of rlistInner
 * every nstlistPrune steps to obtain a, smaller, "inner-list". This
 * results in fewer interaction computations and allows for a larger nstlist.
 * On a GPU, this dynamic pruning is performed in a rolling fashion, pruning
 * only a sub-part of the list each (second) step. This way it can often
 * overlap with integration and constraints on the CPU.
 * Currently a simple heuristic determines which mode will be used.
 *
 * TODO: add a summary list and brief descriptions of the different submodules:
 * search, CPU kernels, GPU glue code + kernels.
 *
 * \author Berk Hess <hess@kth.se>
 * \author Szilárd Páll <pall.szilard@gmail.com>
 * \author Mark Abraham <mark.j.abraham@gmail.com>
 * \author Anca Hamuraru <anca@streamcomputing.eu>
 * \author Teemu Virolainen <teemu@streamcomputing.eu>
 * \author Dimitrios Karkoulis <dimitris.karkoulis@gmail.com>
 *
 * TODO: add more authors!
 */

/*! \libinternal
 * \defgroup module_nbnxm Non-bonded pair interactions
 * \ingroup group_mdrun
 * \brief
 * Implements non-bonded pair interaction functionality for NxM atom clusters.
 *
 * This module provides methods to, very efficiently, compute non-bonded
 * pair interactions on CPUs as well as accelerators. It also provides
 * a method to construct the NxM atom-cluster pair-list required for
 * computing these non-bonded iteractions.
 */

/*! \libinternal \file
 *
 * \brief This file contains the public interface of the nbnxm module
 * that implements the NxM atom cluster non-bonded algorithm to efficiently
 * compute pair forces.
 *
 *
 * \author Berk Hess <hess@kth.se>
 * \author Szilárd Páll <pall.szilard@gmail.com>
 *
 * \inlibraryapi
 * \ingroup module_nbnxm
 */


#ifndef GMX_NBNXM_NBNXM_H
#define GMX_NBNXM_NBNXM_H

#include <memory>

#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/locality.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"

struct DeviceInformation;
class FreeEnergyDispatch;
struct gmx_domdec_zones_t;
struct gmx_enerdata_t;
struct gmx_hw_info_t;
struct gmx_mtop_t;
struct NbnxmGpu;
struct gmx_wallcycle;
struct interaction_const_t;
enum class LJCombinationRule;
struct nbnxn_atomdata_t;
struct nonbonded_verlet_t;
class PairSearch;
class PairlistSets;
struct t_commrec;
struct t_lambda;
struct t_nrnb;
struct t_forcerec;
struct t_inputrec;
struct gmx_grppairener_t;

class GpuEventSynchronizer;

namespace gmx
{
template<typename>
class ArrayRefWithPadding;
class DeviceStreamManager;
class ForceWithShiftForces;
class ListedForcesGpu;
template<typename>
class ListOfLists;
class MDLogger;
template<typename>
class Range;
class StepWorkload;
class UpdateGroupsCog;
} // namespace gmx

//! Namespace for non-bonded kernels
namespace Nbnxm
{
enum class KernelType;

/*! \brief Nbnxm electrostatic GPU kernel flavors.
 *
 *  Types of electrostatics implementations available in the GPU non-bonded
 *  force kernels. These represent both the electrostatics types implemented
 *  by the kernels (cut-off, RF, and Ewald - a subset of what's defined in
 *  enums.h) as well as encode implementation details analytical/tabulated
 *  and single or twin cut-off (for Ewald kernels).
 *  Note that the cut-off and RF kernels have only analytical flavor and unlike
 *  in the CPU kernels, the tabulated kernels are ATM Ewald-only.
 *
 *  The row-order of pointers to different electrostatic kernels defined in
 *  nbnxn_cuda.cu by the nb_*_kfunc_ptr function pointer table
 *  should match the order of enumerated types below.
 */
enum class ElecType : int
{
    Cut,          //!< Plain cut-off
    RF,           //!< Reaction field
    EwaldTab,     //!< Tabulated Ewald with single cut-off
    EwaldTabTwin, //!< Tabulated Ewald with twin cut-off
    EwaldAna,     //!< Analytical Ewald with single cut-off
    EwaldAnaTwin, //!< Analytical Ewald with twin cut-off
    Count         //!< Number of valid values
};

//! Number of possible \ref ElecType values.
constexpr int c_numElecTypes = static_cast<int>(ElecType::Count);

/*! \brief Nbnxm VdW GPU kernel flavors.
 *
 * The enumerates values correspond to the LJ implementations in the GPU non-bonded
 * kernels.
 *
 * The column-order of pointers to different electrostatic kernels defined in
 * nbnxn_cuda_ocl.cpp/.cu by the nb_*_kfunc_ptr function pointer table
 * should match the order of enumerated types below.
 */
enum class VdwType : int
{
    Cut,         //!< Plain cut-off
    CutCombGeom, //!< Cut-off with geometric combination rules
    CutCombLB,   //!< Cut-off with Lorentz-Berthelot combination rules
    FSwitch,     //!< Smooth force switch
    PSwitch,     //!< Smooth potential switch
    EwaldGeom,   //!< Ewald with geometric combination rules
    EwaldLB,     //!< Ewald with Lorentz-Berthelot combination rules
    Count        //!< Number of valid values
};

//! Number of possible \ref VdwType values.
constexpr int c_numVdwTypes = static_cast<int>(VdwType::Count);

/*! \brief Nonbonded NxN kernel types: plain C, CPU SIMD, GPU, GPU emulation */
enum class KernelType : int
{
    NotSet = 0,
    Cpu4x4_PlainC,
    Cpu4xN_Simd_4xN,
    Cpu4xN_Simd_2xNN,
    Gpu8x8x8,
    Cpu8x8x8_PlainC,
    Count
};

/*! \brief Ewald exclusion types */
enum class EwaldExclusionType : int
{
    NotSet = 0,
    Table,
    Analytical,
    DecidedByGpuModule
};

/* \brief The non-bonded setup, also affects the pairlist construction kernel */
struct KernelSetup
{
    //! The non-bonded type, also affects the pairlist construction kernel
    KernelType kernelType = KernelType::NotSet;
    //! Ewald exclusion computation handling type, currently only used for CPU
    EwaldExclusionType ewaldExclusionType = EwaldExclusionType::NotSet;
};

/*! \brief Return a string identifying the kernel type.
 *
 * \param [in] kernelType   nonbonded kernel type, takes values from the nbnxn_kernel_type enum
 * \returns                 a string identifying the kernel corresponding to the type passed as argument
 */
const char* lookup_kernel_name(Nbnxm::KernelType kernelType);

} // namespace Nbnxm

/*! \brief Flag to tell the nonbonded kernels whether to clear the force output buffers */
enum
{
    enbvClearFNo,
    enbvClearFYes
};

/*! \libinternal
 *  \brief Top-level non-bonded data structure for the Verlet-type cut-off scheme. */
struct nonbonded_verlet_t
{
public:
    //! Constructs an object from its components
    nonbonded_verlet_t(std::unique_ptr<PairlistSets>     pairlistSets,
                       std::unique_ptr<PairSearch>       pairSearch,
                       std::unique_ptr<nbnxn_atomdata_t> nbat,
                       const Nbnxm::KernelSetup&         kernelSetup,
                       NbnxmGpu*                         gpu_nbv,
                       gmx_wallcycle*                    wcycle);

    ~nonbonded_verlet_t();

    //! Returns whether a GPU is use for the non-bonded calculations
    bool useGpu() const { return kernelSetup_.kernelType == Nbnxm::KernelType::Gpu8x8x8; }

    //! Returns whether a GPU is emulated for the non-bonded calculations
    bool emulateGpu() const
    {
        return kernelSetup_.kernelType == Nbnxm::KernelType::Cpu8x8x8_PlainC;
    }

    //! Return whether the pairlist is of simple, CPU type
    bool pairlistIsSimple() const { return !useGpu() && !emulateGpu(); }


    //! Returns the order of the local atoms on the grid
    gmx::ArrayRef<const int> getLocalAtomOrder() const;

    //! Sets the order of the local atoms to the order grid atom ordering
    void setLocalAtomOrder() const;

    //! Returns the index position of the atoms on the search grid
    gmx::ArrayRef<const int> getGridIndices() const;

    /*! \brief Constructs the pairlist for the given locality
     *
     * When there are no non-self exclusions, \p exclusions can be empty.
     * Otherwise the number of lists in \p exclusions should match the number
     * of atoms when not using DD, or the total number of atoms in the i-zones
     * when using DD.
     *
     * \param[in] iLocality   The interaction locality: local or non-local
     * \param[in] exclusions  Lists of exclusions for every atom.
     * \param[in] step        Used to set the list creation step
     * \param[in,out] nrnb    Flop accounting struct, can be nullptr
     */
    void constructPairlist(gmx::InteractionLocality     iLocality,
                           const gmx::ListOfLists<int>& exclusions,
                           int64_t                      step,
                           t_nrnb*                      nrnb) const;

    //! Updates all the atom properties in Nbnxm
    void setAtomProperties(gmx::ArrayRef<const int>     atomTypes,
                           gmx::ArrayRef<const real>    atomCharges,
                           gmx::ArrayRef<const int64_t> atomInfo) const;

    /*!\brief Convert the coordinates to NBNXM format for the given locality.
     *
     * The API function for the transformation of the coordinates from one layout to another.
     *
     * \param[in] locality     Whether coordinates for local or non-local atoms should be
     * transformed. \param[in] coordinates  Coordinates in plain rvec format to be transformed.
     */
    void convertCoordinates(gmx::AtomLocality locality, gmx::ArrayRef<const gmx::RVec> coordinates);

    /*!\brief Convert the coordinates to NBNXM format on the GPU for the given locality
     *
     * The API function for the transformation of the coordinates from one layout to another in the GPU memory.
     *
     * \param[in] locality        Whether coordinates for local or non-local atoms should be transformed.
     * \param[in] d_x             GPU coordinates buffer in plain rvec format to be transformed.
     * \param[in] xReadyOnDevice  Event synchronizer indicating that the coordinates are ready in the device memory.
     */
    void convertCoordinatesGpu(gmx::AtomLocality       locality,
                               DeviceBuffer<gmx::RVec> d_x,
                               GpuEventSynchronizer*   xReadyOnDevice);

    //! Init for GPU version of setup coordinates in Nbnxm
    void atomdata_init_copy_x_to_nbat_x_gpu() const;

    //! Returns a reference to the pairlist sets
    const PairlistSets& pairlistSets() const { return *pairlistSets_; }

    //! Returns whether step is a dynamic list pruning step, for CPU lists
    bool isDynamicPruningStepCpu(int64_t step) const;

    //! Returns whether step is a dynamic list pruning step, for GPU lists
    bool isDynamicPruningStepGpu(int64_t step) const;

    //! Dispatches the dynamic pruning kernel for the given locality, for CPU lists
    void dispatchPruneKernelCpu(gmx::InteractionLocality       iLocality,
                                gmx::ArrayRef<const gmx::RVec> shift_vec) const;

    //! Dispatches the dynamic pruning kernel for GPU lists
    void dispatchPruneKernelGpu(int64_t step);

    //! \brief Executes the non-bonded kernel of the GPU or launches it on the GPU
    void dispatchNonbondedKernel(gmx::InteractionLocality       iLocality,
                                 const interaction_const_t&     ic,
                                 const gmx::StepWorkload&       stepWork,
                                 int                            clearF,
                                 gmx::ArrayRef<const gmx::RVec> shiftvec,
                                 gmx::ArrayRef<real>            repulsionDispersionSR,
                                 gmx::ArrayRef<real>            CoulombSR,
                                 t_nrnb*                        nrnb) const;

    //! Executes the non-bonded free-energy kernels, local + non-local, always runs on the CPU
    void dispatchFreeEnergyKernels(const gmx::ArrayRefWithPadding<const gmx::RVec>& coords,
                                   gmx::ForceWithShiftForces*                forceWithShiftForces,
                                   bool                                      useSimd,
                                   int                                       ntype,
                                   real                                      rlist,
                                   const interaction_const_t&                ic,
                                   gmx::ArrayRef<const gmx::RVec>            shiftvec,
                                   gmx::ArrayRef<const real>                 nbfp,
                                   gmx::ArrayRef<const real>                 nbfp_grid,
                                   gmx::ArrayRef<const real>                 chargeA,
                                   gmx::ArrayRef<const real>                 chargeB,
                                   gmx::ArrayRef<const int>                  typeA,
                                   gmx::ArrayRef<const int>                  typeB,
                                   t_lambda*                                 fepvals,
                                   gmx::ArrayRef<const real>                 lambda,
                                   gmx_enerdata_t*                           enerd,
                                   const gmx::StepWorkload&                  stepWork,
                                   t_nrnb*                                   nrnb);

    /*! \brief Add the forces stored in nbat to f, zeros the forces in nbat
     * \param [in] locality         Local or non-local
     * \param [inout] force         Force to be added to
     */
    void atomdata_add_nbat_f_to_f(gmx::AtomLocality locality, gmx::ArrayRef<gmx::RVec> force);

    /*! \brief Get the number of atoms for a given locality
     *
     * \param [in] locality   Local or non-local
     * \returns               The number of atoms for given locality
     */
    int getNumAtoms(gmx::AtomLocality locality) const;

    //! Return the kernel setup
    const Nbnxm::KernelSetup& kernelSetup() const { return kernelSetup_; }

    //! Returns the outer radius for the pair list
    real pairlistInnerRadius() const;

    //! Returns the outer radius for the pair list
    real pairlistOuterRadius() const;

    //! Changes the pair-list outer and inner radius
    void changePairlistRadii(real rlistOuter, real rlistInner) const;

    //! Set up internal flags that indicate what type of short-range work there is.
    void setupGpuShortRangeWork(const gmx::ListedForcesGpu* listedForcesGpu,
                                gmx::InteractionLocality    iLocality) const;

    void setupFepThreadedForceBuffer(int numAtomsForce);

    // TODO: Make all data members private
    //! All data related to the pair lists
    std::unique_ptr<PairlistSets> pairlistSets_;
    //! Working data for constructing the pairlists
    std::unique_ptr<PairSearch> pairSearch_;
    //! Atom data
    std::unique_ptr<nbnxn_atomdata_t> nbat;

private:
    //! The non-bonded setup, also affects the pairlist construction kernel
    Nbnxm::KernelSetup kernelSetup_;

    //! \brief Pointer to wallcycle structure.
    gmx_wallcycle* wcycle_;

    //! \brief The non-bonded free-energy kernel dispatcher
    std::unique_ptr<FreeEnergyDispatch> freeEnergyDispatch_;

public:
    //! GPU Nbnxm data, only used with a physical GPU (TODO: use unique_ptr)
    NbnxmGpu* gpu_nbv;
};

namespace Nbnxm
{

/*! \brief Creates an Nbnxm object */
std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger& mdlog,
                                                   const t_inputrec&    inputrec,
                                                   const t_forcerec&    forcerec,
                                                   const t_commrec*     commrec,
                                                   const gmx_hw_info_t& hardwareInfo,
                                                   bool                 useGpuForNonbonded,
                                                   const gmx::DeviceStreamManager* deviceStreamManager,
                                                   const gmx_mtop_t&               mtop,
                                                   matrix                          box,
                                                   gmx_wallcycle*                  wcycle);

} // namespace Nbnxm

/*! \brief Put the atoms on the pair search grid.
 *
 * Only atoms with indices wihtin \p atomRange in x are put on the grid.
 * When \p updateGroupsCog != nullptr, atoms are put on the grid
 * based on the center of geometry of the group they belong to.
 * Atoms or COGs of groups should be within the bounding box provided,
 * this is checked in debug builds when not using update groups.
 * The atom density is used to determine the grid size when \p gridIndex = 0.
 * When \p atomDensity <= 0, the density is determined from atomEnd-atomStart
 * and the bounding box corners.
 * With domain decomposition, part of the atoms might have migrated,
 * but have not been removed yet. This count is given by \p numAtomsMoved.
 * When \p move[i] < 0 particle i has migrated and will not be put on the grid.
 *
 * \param[in,out] nb_verlet    The non-bonded object
 * \param[in]     box          Box used for periodic distance calculations
 * \param[in]     gridIndex    The index of the grid to spread to, always 0 except with test particle insertion
 * \param[in]     lowerCorner  Atom groups to be gridded should have coordinates >= this corner
 * \param[in]     upperCorner  Atom groups to be gridded should have coordinates <= this corner
 * \param[in]     updateGroupsCog  Centers of geometry for update groups, pass nullptr when not using update groups
 * \param[in]     atomRange    Range of atoms to grid
 * \param[in]     atomDensity  An estimate of the atom density, used for peformance optimization and only with \p gridIndex = 0
 * \param[in]     atomInfo     Atom information flags
 * \param[in]     x            Coordinates for atoms to grid
 * \param[in]     numAtomsMoved  The number of atoms that will move to another domain, pass 0 without DD
 * \param[in]     move         Move flags for atoms, pass nullptr without DD
 */
void nbnxn_put_on_grid(nonbonded_verlet_t*            nb_verlet,
                       const matrix                   box,
                       int                            gridIndex,
                       const rvec                     lowerCorner,
                       const rvec                     upperCorner,
                       const gmx::UpdateGroupsCog*    updateGroupsCog,
                       gmx::Range<int>                atomRange,
                       real                           atomDensity,
                       gmx::ArrayRef<const int64_t>   atomInfo,
                       gmx::ArrayRef<const gmx::RVec> x,
                       int                            numAtomsMoved,
                       const int*                     move);

/*! \brief As nbnxn_put_on_grid, but for the non-local atoms
 *
 * with domain decomposition. Should be called after calling
 * nbnxn_search_put_on_grid for the local atoms / home zone.
 */
void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*              nb_verlet,
                                const struct gmx_domdec_zones_t* zones,
                                gmx::ArrayRef<const int64_t>     atomInfo,
                                gmx::ArrayRef<const gmx::RVec>   x);

/*! \brief Check if GROMACS has been built with GPU support.
 *
 * \param[in] error Pointer to error string or nullptr.
 * \todo Move this to NB module once it exists.
 */
bool buildSupportsNonbondedOnGpu(std::string* error);

#endif // GMX_NBNXN_NBNXM_H