{
class GridSet;
enum class KernelType;
-}
+} // namespace Nbnxm
/* Convenience type for vector with aligned memory */
template<typename T>
-using AlignedVector = std::vector < T, gmx::AlignedAllocator < T>>;
+using AlignedVector = std::vector<T, gmx::AlignedAllocator<T>>;
-enum {
- nbatXYZ, nbatXYZQ, nbatX4, nbatX8
+enum
+{
+ nbatXYZ,
+ nbatXYZQ,
+ nbatX4,
+ nbatX8
};
//! Stride for coordinate/force arrays with xyz coordinate storage
-static constexpr int STRIDE_XYZ = 3;
+static constexpr int STRIDE_XYZ = 3;
//! Stride for coordinate/force arrays with xyzq coordinate storage
static constexpr int STRIDE_XYZQ = 4;
//! Size of packs of x, y or z with SIMD 4-grouped packed coordinates/forces
-static constexpr int c_packX4 = 4;
+static constexpr int c_packX4 = 4;
//! Size of packs of x, y or z with SIMD 8-grouped packed coordinates/forces
-static constexpr int c_packX8 = 8;
+static constexpr int c_packX8 = 8;
//! Stridefor a pack of 4 coordinates/forces
-static constexpr int STRIDE_P4 = DIM*c_packX4;
+static constexpr int STRIDE_P4 = DIM * c_packX4;
//! Stridefor a pack of 8 coordinates/forces
-static constexpr int STRIDE_P8 = DIM*c_packX8;
+static constexpr int STRIDE_P8 = DIM * c_packX8;
//! Returns the index in a coordinate array corresponding to atom a
-template<int packSize> static inline int atom_to_x_index(int a)
+template<int packSize>
+static inline int atom_to_x_index(int a)
{
- return DIM*(a & ~(packSize - 1)) + (a & (packSize - 1));
+ return DIM * (a & ~(packSize - 1)) + (a & (packSize - 1));
}
// Struct that holds force and energy output buffers
* Currently the block size is NBNXN_BUFFERFLAG_SIZE*3*sizeof(real)=192 bytes.
*/
#if GMX_DOUBLE
-#define NBNXN_BUFFERFLAG_SIZE 8
+# define NBNXN_BUFFERFLAG_SIZE 8
#else
-#define NBNXN_BUFFERFLAG_SIZE 16
+# 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)
+#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 */
+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
+enum
+{
+ ljcrGEOM,
+ ljcrLB,
+ ljcrNONE,
+ ljcrNR
};
/* Struct that stores atom related data for the nbnxn module
* in this struct would not initialize during resize().
*/
struct nbnxn_atomdata_t
-{ //NOLINT(clang-analyzer-optin.performance.Padding)
+{ //NOLINT(clang-analyzer-optin.performance.Padding)
struct Params
{
/* Constructor
Params(gmx::PinningPolicy pinningPolicy);
// The number of different atom types
- int numTypes;
+ 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;
+ 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;
+ AlignedVector<real> nbfp_aligned;
// Atom types per atom
- gmx::HostVector<int> type;
+ 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;
+ int nenergrp;
// 2log(nenergrp)
- int neg_2log;
+ int neg_2log;
// The energy groups, one int entry per cluster, only set when needed
- gmx::HostVector<int> energrp;
+ gmx::HostVector<int> energrp;
};
// Diagonal and topology exclusion helper data for all SIMD kernels
SimdMasks();
// Helper data for setting up diagonal exclusion masks in the SIMD 4xN kernels
- AlignedVector<real> diagonal_4xn_j_minus_i;
+ 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;
+ 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;
+ AlignedVector<real> interaction_array;
};
/* Constructor
nbnxn_atomdata_t(gmx::PinningPolicy pinningPolicy);
/* Returns a const reference to the parameters */
- const Params ¶ms() const
- {
- return params_;
- }
+ const Params& params() const { return params_; }
/* Returns a non-const reference to the parameters */
- Params ¶msDeprecated()
- {
- return params_;
- }
+ Params& paramsDeprecated() { return params_; }
/* Returns the current total number of atoms stored */
- int numAtoms() const
- {
- return numAtoms_;
- }
+ int numAtoms() const { return numAtoms_; }
/* Return the coordinate buffer, and q with xFormat==nbatXYZQ */
- gmx::ArrayRef<const real> x() const
- {
- return x_;
- }
+ gmx::ArrayRef<const real> x() const { return x_; }
/* Return the coordinate buffer, and q with xFormat==nbatXYZQ */
- gmx::ArrayRef<real> x()
- {
- return x_;
- }
+ 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 */
+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 */
};
/* Copy na rvec elements from x to xnb using nbatFormat, start dest a0,
* and fills up to na_round with coordinates that are far away.
*/
-void copy_rvec_to_nbat_real(const int *a, int na, int na_round,
- const rvec *x, int nbatFormat,
- real *xnb, int a0);
+void copy_rvec_to_nbat_real(const int* a, int na, int na_round, const rvec* x, int nbatFormat, real* xnb, int a0);
-enum {
- enbnxninitcombruleDETECT, enbnxninitcombruleGEOM, enbnxninitcombruleLB, enbnxninitcombruleNONE
+enum
+{
+ enbnxninitcombruleDETECT,
+ enbnxninitcombruleGEOM,
+ enbnxninitcombruleLB,
+ enbnxninitcombruleNONE
};
/* Initialize the non-bonded atom data structure.
* to the atom data structure.
* enbnxninitcombrule sets what combination rule data gets stored in nbat.
*/
-void nbnxn_atomdata_init(const gmx::MDLogger &mdlog,
- nbnxn_atomdata_t *nbat,
- Nbnxm::KernelType kernelType,
- int enbnxninitcombrule,
- int ntype, const real *nbfp,
- int n_energygroups,
- int nout);
-
-void nbnxn_atomdata_set(nbnxn_atomdata_t *nbat,
- const Nbnxm::GridSet &gridSet,
- const t_mdatoms *mdatoms,
- const int *atinfo);
+void nbnxn_atomdata_init(const gmx::MDLogger& mdlog,
+ nbnxn_atomdata_t* nbat,
+ Nbnxm::KernelType kernelType,
+ int enbnxninitcombrule,
+ int ntype,
+ const real* nbfp,
+ int n_energygroups,
+ int nout);
+
+void nbnxn_atomdata_set(nbnxn_atomdata_t* nbat,
+ const Nbnxm::GridSet& gridSet,
+ const t_mdatoms* mdatoms,
+ const int* atinfo);
/* Copy the shift vectors to nbat */
-void nbnxn_atomdata_copy_shiftvec(gmx_bool dynamic_box,
- rvec *shift_vec,
- nbnxn_atomdata_t *nbat);
+void nbnxn_atomdata_copy_shiftvec(gmx_bool dynamic_box, rvec* shift_vec, nbnxn_atomdata_t* nbat);
/*! \brief Transform coordinates to xbat layout
*
* \param[in] coordinates Coordinates in plain rvec format.
* \param[in,out] nbat Data in NBNXM format, used for mapping formats and to locate the output buffer.
*/
-void nbnxn_atomdata_copy_x_to_nbat_x(const Nbnxm::GridSet &gridSet,
- gmx::AtomLocality locality,
- bool fillLocal,
- const rvec *coordinates,
- nbnxn_atomdata_t *nbat);
+void nbnxn_atomdata_copy_x_to_nbat_x(const Nbnxm::GridSet& gridSet,
+ gmx::AtomLocality locality,
+ bool fillLocal,
+ const rvec* coordinates,
+ nbnxn_atomdata_t* nbat);
/*! \brief Transform coordinates to xbat layout on GPU
*
* \param[in] d_x Coordinates to be copied (in plain rvec format).
* \param[in] xReadyOnDevice Event synchronizer indicating that the coordinates are ready in the device memory.
*/
-void nbnxn_atomdata_x_to_nbat_x_gpu(const Nbnxm::GridSet &gridSet,
- gmx::AtomLocality locality,
- bool fillLocal,
- gmx_nbnxn_gpu_t *gpu_nbv,
- DeviceBuffer<float> d_x,
- GpuEventSynchronizer *xReadyOnDevice);
+void nbnxn_atomdata_x_to_nbat_x_gpu(const Nbnxm::GridSet& gridSet,
+ gmx::AtomLocality locality,
+ bool fillLocal,
+ gmx_nbnxn_gpu_t* gpu_nbv,
+ DeviceBuffer<float> d_x,
+ GpuEventSynchronizer* xReadyOnDevice);
/*! \brief Add the computed forces to \p f, an internal reduction might be performed as well
*
* \param[in] gridSet The grids data.
* \param[out] totalForce Buffer to accumulate resulting force
*/
-void reduceForces(nbnxn_atomdata_t *nbat,
- gmx::AtomLocality locality,
- const Nbnxm::GridSet &gridSet,
- rvec *totalForce);
+void reduceForces(nbnxn_atomdata_t* nbat, gmx::AtomLocality locality, const Nbnxm::GridSet& gridSet, rvec* totalForce);
/*! \brief Reduce forces on the GPU
*
* \param[in] useGpuFPmeReduction Whether PME forces should be added.
* \param[in] accumulateForce Whether there are usefull data already in the total force buffer.
*/
-void reduceForcesGpu(gmx::AtomLocality locality,
- DeviceBuffer<float> totalForcesDevice,
- const Nbnxm::GridSet &gridSet,
- void *pmeForcesDevice,
- gmx::ArrayRef<GpuEventSynchronizer* const> dependencyList,
- gmx_nbnxn_gpu_t *gpu_nbv,
- bool useGpuFPmeReduction,
- bool accumulateForce);
+void reduceForcesGpu(gmx::AtomLocality locality,
+ DeviceBuffer<float> totalForcesDevice,
+ const Nbnxm::GridSet& gridSet,
+ void* pmeForcesDevice,
+ gmx::ArrayRef<GpuEventSynchronizer* const> dependencyList,
+ gmx_nbnxn_gpu_t* gpu_nbv,
+ bool useGpuFPmeReduction,
+ bool accumulateForce);
/* Add the fshift force stored in nbat to fshift */
-void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t &nbat,
- gmx::ArrayRef<gmx::RVec> fshift);
+void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift);
/* Get the atom start index and number of atoms for a given locality */
-void nbnxn_get_atom_range(gmx::AtomLocality atomLocality,
- const Nbnxm::GridSet &gridSet,
- int *atomStart,
- int *nAtoms);
+void nbnxn_get_atom_range(gmx::AtomLocality atomLocality,
+ const Nbnxm::GridSet& gridSet,
+ int* atomStart,
+ int* nAtoms);
#endif
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