#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/nblist.h"
#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/bitmask.h"
#include "gromacs/utility/defaultinitializationallocator.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
struct NbnxnListParameters;
struct NbnxnPairlistCpuWork;
struct NbnxnPairlistGpuWork;
-struct tMPI_Atomic;
namespace Nbnxm
{
std::vector<t_nblist *> nbl_fep; /* List of free-energy atom pair interactions */
};
-enum {
- nbatXYZ, nbatXYZQ, nbatX4, nbatX8
-};
-
-// Struct that holds force and energy output buffers
-struct nbnxn_atomdata_output_t
-{
- /* Constructor
- *
- * \param[in] kernelType Type of non-bonded kernel
- * \param[in] numEnergyGroups The number of energy groups
- * \param[in] simdEnergyBufferStride Stride for entries in the energy buffers for SIMD kernels
- * \param[in] pinningPolicy Sets the pinning policy for all buffers used on the GPU
- */
- nbnxn_atomdata_output_t(Nbnxm::KernelType kernelType,
- int numEnergyGroups,
- int simdEnergyBUfferStride,
- gmx::PinningPolicy pinningPolicy);
-
- gmx::HostVector<real> f; // f, size natoms*fstride
- gmx::HostVector<real> fshift; // Shift force array, size SHIFTS*DIM
- gmx::HostVector<real> Vvdw; // Temporary Van der Waals group energy storage
- gmx::HostVector<real> Vc; // Temporary Coulomb group energy storage
- AlignedVector<real> VSvdw; // Temporary SIMD Van der Waals group energy storage
- AlignedVector<real> VSc; // Temporary SIMD Coulomb group energy storage
-};
-
-/* Block size in atoms for the non-bonded thread force-buffer reduction,
- * should be a multiple of all cell and x86 SIMD sizes (i.e. 2, 4 and 8).
- * Should be small to reduce the reduction and zeroing cost,
- * but too small will result in overhead.
- * Currently the block size is NBNXN_BUFFERFLAG_SIZE*3*sizeof(real)=192 bytes.
- */
-#if GMX_DOUBLE
-#define NBNXN_BUFFERFLAG_SIZE 8
-#else
-#define NBNXN_BUFFERFLAG_SIZE 16
-#endif
-
-/* We store the reduction flags as gmx_bitmask_t.
- * This limits the number of flags to BITMASK_SIZE.
- */
-#define NBNXN_BUFFERFLAG_MAX_THREADS (BITMASK_SIZE)
-
-/* Flags for telling if threads write to force output buffers */
-typedef struct {
- int nflag; /* The number of flag blocks */
- gmx_bitmask_t *flag; /* Bit i is set when thread i writes to a cell-block */
- int flag_nalloc; /* Allocation size of cxy_flag */
-} nbnxn_buffer_flags_t;
-
-/* LJ combination rules: geometric, Lorentz-Berthelot, none */
-enum {
- ljcrGEOM, ljcrLB, ljcrNONE, ljcrNR
-};
-
-/* Struct that stores atom related data for the nbnxn module
- *
- * Note: performance would improve slightly when all std::vector containers
- * in this struct would not initialize during resize().
- */
-struct nbnxn_atomdata_t
-{ //NOLINT(clang-analyzer-optin.performance.Padding)
- struct Params
- {
- /* Constructor
- *
- * \param[in] pinningPolicy Sets the pinning policy for all data that might be transfered to a GPU
- */
- Params(gmx::PinningPolicy pinningPolicy);
-
- // The number of different atom types
- int numTypes;
- // Lennard-Jone 6*C6 and 12*C12 parameters, size numTypes*2*2
- gmx::HostVector<real> nbfp;
- // Combination rule, see enum defined above
- int comb_rule;
- // LJ parameters per atom type, size numTypes*2
- gmx::HostVector<real> nbfp_comb;
- // As nbfp, but with a stride for the present SIMD architecture
- AlignedVector<real> nbfp_aligned;
- // Atom types per atom
- gmx::HostVector<int> type;
- // LJ parameters per atom for fast SIMD loading
- gmx::HostVector<real> lj_comb;
- // Charges per atom, not set with format nbatXYZQ
- gmx::HostVector<real> q;
- // The number of energy groups
- int nenergrp;
- // 2log(nenergrp)
- int neg_2log;
- // The energy groups, one int entry per cluster, only set when needed
- gmx::HostVector<int> energrp;
- };
-
- // Diagonal and topology exclusion helper data for all SIMD kernels
- struct SimdMasks
- {
- SimdMasks();
-
- // Helper data for setting up diagonal exclusion masks in the SIMD 4xN kernels
- AlignedVector<real> diagonal_4xn_j_minus_i;
- // Helper data for setting up diaginal exclusion masks in the SIMD 2xNN kernels
- AlignedVector<real> diagonal_2xnn_j_minus_i;
- // Filters for topology exclusion masks for the SIMD kernels
- AlignedVector<uint32_t> exclusion_filter;
- // Filters for topology exclusion masks for double SIMD kernels without SIMD int32 logical support
- AlignedVector<uint64_t> exclusion_filter64;
- // Array of masks needed for exclusions
- AlignedVector<real> interaction_array;
- };
-
- /* Constructor
- *
- * \param[in] pinningPolicy Sets the pinning policy for all data that might be transfered to a GPU
- */
- nbnxn_atomdata_t(gmx::PinningPolicy pinningPolicy);
-
- /* Returns a const reference to the parameters */
- const Params ¶ms() const
- {
- return params_;
- }
-
- /* Returns a non-const reference to the parameters */
- Params ¶msDeprecated()
- {
- return params_;
- }
-
- /* Returns the current total number of atoms stored */
- int numAtoms() const
- {
- return numAtoms_;
- }
-
- /* Return the coordinate buffer, and q with xFormat==nbatXYZQ */
- gmx::ArrayRef<const real> x() const
- {
- return x_;
- }
-
- /* Return the coordinate buffer, and q with xFormat==nbatXYZQ */
- gmx::ArrayRef<real> x()
- {
- return x_;
- }
-
- /* Resizes the coordinate buffer and sets the number of atoms */
- void resizeCoordinateBuffer(int numAtoms);
-
- /* Resizes the force buffers for the current number of atoms */
- void resizeForceBuffers();
-
- private:
- // The LJ and charge parameters
- Params params_;
- // The total number of atoms currently stored
- int numAtoms_;
- public:
- int natoms_local; /* Number of local atoms */
- int XFormat; /* The format of x (and q), enum */
- int FFormat; /* The format of f, enum */
- gmx_bool bDynamicBox; /* Do we need to update shift_vec every step? */
- gmx::HostVector<gmx::RVec> shift_vec; /* Shift vectors, copied from t_forcerec */
- int xstride; /* stride for a coordinate in x (usually 3 or 4) */
- int fstride; /* stride for a coordinate in f (usually 3 or 4) */
- private:
- gmx::HostVector<real> x_; /* x and possibly q, size natoms*xstride */
-
- public:
- // Masks for handling exclusions in the SIMD kernels
- const SimdMasks simdMasks;
-
- /* Output data */
- std::vector<nbnxn_atomdata_output_t> out; /* Output data structures, 1 per thread */
-
- /* Reduction related data */
- gmx_bool bUseBufferFlags; /* Use the flags or operate on all atoms */
- nbnxn_buffer_flags_t buffer_flags; /* Flags for buffer zeroing+reduc. */
- gmx_bool bUseTreeReduce; /* Use tree for force reduction */
- tMPI_Atomic *syncStep; /* Synchronization step for tree reduce */
-};
-
#endif
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