atomdata.h File Reference

#include <cstdint>
#include <cstdio>
#include <memory>
#include <optional>
#include <vector>
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/gpu_utils/hostallocator.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/locality.h"
#include "gromacs/nbnxm/nbnxm_enums.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/bitmask.h"
#include "gromacs/utility/real.h"

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Description

Functionality for per-atom data in the nbnxm module.

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Classes
class	gmx::EnergyAccumulator< bool, bool >
	Base energy accumulator class, only specializations are used. More...
struct	gmx::nbnxn_atomdata_output_t
	Struct that holds force and energy output buffers. More...
struct	gmx::nbnxn_atomdata_t
	Struct that stores atom related data for the nbnxn module. More...
struct	gmx::nbnxn_atomdata_t::Params
	The actual atom data parameter values. More...
struct	gmx::nbnxn_atomdata_t::SimdMasks
	Diagonal and topology exclusion helper data for all SIMD kernels. More...

Macros
#define	NBNXN_BUFFERFLAG_SIZE   16
	Block size in atoms for the non-bonded thread force-buffer reduction. More...
#define	NBNXN_BUFFERFLAG_MAX_THREADS   (BITMASK_SIZE)
	We store the reduction flags as gmx_bitmask_t. This limits the number of flags to BITMASK_SIZE.

Enumerations
enum	{ nbatXYZ, nbatXYZQ, nbatX4, nbatX8 }
enum	gmx::LJCombinationRule : int { gmx::LJCombinationRule::Geometric, gmx::LJCombinationRule::LorentzBerthelot, gmx::LJCombinationRule::None, gmx::LJCombinationRule::Count }
	LJ combination rules. More...

Functions
template<int packSize>
static int	gmx::atom_to_x_index (int a)
	Returns the index in a coordinate array corresponding to atom a.
const char *	gmx::enumValueToString (LJCombinationRule enumValue)
	String corresponding to LJ combination rule.
void	gmx::copy_rvec_to_nbat_real (const int *a, int na, int na_round, const rvec *x, int nbatFormat, real *xnb, int a0)
	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	gmx::nbnxn_atomdata_set (nbnxn_atomdata_t *nbat, const GridSet &gridSet, ArrayRef< const int > atomTypes, ArrayRef< const real > atomCharges, ArrayRef< const int32_t > atomInfo)
	Sets the atomdata after pair search.
void	gmx::nbnxn_atomdata_copy_shiftvec (bool dynamic_box, ArrayRef< RVec > shift_vec, nbnxn_atomdata_t *nbat)
	Copy the shift vectors to nbat.
void	gmx::nbnxn_atomdata_copy_x_to_nbat_x (const GridSet &gridSet, AtomLocality locality, const rvec *coordinates, nbnxn_atomdata_t *nbat)
	Transform coordinates to xbat layout. More...
void	gmx::nbnxn_atomdata_x_to_nbat_x_gpu (const GridSet &gridSet, AtomLocality locality, NbnxmGpu *gpu_nbv, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice)
	Transform coordinates to xbat layout on GPU. More...
void	gmx::nbnxn_atomdata_add_nbat_fshift_to_fshift (const nbnxn_atomdata_t &nbat, ArrayRef< RVec > fshift)
	Add the fshift force stored in nbat to fshift.

Variables
static constexpr int	gmx::STRIDE_XYZ = 3
	Stride for coordinate/force arrays with xyz coordinate storage.
static constexpr int	gmx::STRIDE_XYZQ = 4
	Stride for coordinate/force arrays with xyzq coordinate storage.
static constexpr int	gmx::c_packX4 = 4
	Size of packs of x, y or z with SIMD 4-grouped packed coordinates/forces.
static constexpr int	gmx::c_packX8 = 8
	Size of packs of x, y or z with SIMD 8-grouped packed coordinates/forces.
static constexpr int	gmx::STRIDE_P4 = DIM * c_packX4
	Stridefor a pack of 4 coordinates/forces.
static constexpr int	gmx::STRIDE_P8 = DIM * c_packX8
	Stridefor a pack of 8 coordinates/forces.

Macro Definition Documentation

#define NBNXN_BUFFERFLAG_SIZE   16

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.