atomdata.h File Reference

#include <cstdio>
#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/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
struct	nbnxn_atomdata_output_t
	Struct that holds force and energy output buffers. More...
struct	nbnxn_atomdata_t
	Struct that stores atom related data for the nbnxn module. More...
struct	nbnxn_atomdata_t::Params
	The actual atom data parameter values. More...
struct	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.

Typedefs
template<typename T >
using	AlignedVector = std::vector< T, gmx::AlignedAllocator< T >>
	Convenience type for vector with aligned memory.

Enumerations
enum	{ nbatXYZ, nbatXYZQ, nbatX4, nbatX8 }
enum	LJCombinationRule : int { LJCombinationRule::Geometric, LJCombinationRule::LorentzBerthelot, LJCombinationRule::None, LJCombinationRule::Count }
	LJ combination rules. More...
enum	{ enbnxninitcombruleDETECT, enbnxninitcombruleGEOM, enbnxninitcombruleLB, enbnxninitcombruleNONE }
	Describes the combination rule in use by this force field.

Functions
template<int packSize>
static int	atom_to_x_index (int a)
	Returns the index in a coordinate array corresponding to atom a.
const char *	enumValueToString (LJCombinationRule enumValue)
	String corresponding to LJ combination rule.
void	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	nbnxn_atomdata_set (nbnxn_atomdata_t *nbat, const Nbnxm::GridSet &gridSet, gmx::ArrayRef< const int > atomTypes, gmx::ArrayRef< const real > atomCharges, gmx::ArrayRef< const int64_t > atomInfo)
	Sets the atomdata after pair search.
void	nbnxn_atomdata_copy_shiftvec (bool dynamic_box, gmx::ArrayRef< gmx::RVec > shift_vec, nbnxn_atomdata_t *nbat)
	Copy the shift vectors to nbat.
void	nbnxn_atomdata_copy_x_to_nbat_x (const Nbnxm::GridSet &gridSet, gmx::AtomLocality locality, const rvec *coordinates, nbnxn_atomdata_t *nbat)
	Transform coordinates to xbat layout. More...
void	nbnxn_atomdata_x_to_nbat_x_gpu (const Nbnxm::GridSet &gridSet, gmx::AtomLocality locality, NbnxmGpu *gpu_nbv, DeviceBuffer< gmx::RVec > d_x, GpuEventSynchronizer *xReadyOnDevice)
	Transform coordinates to xbat layout on GPU. More...
void	reduceForces (nbnxn_atomdata_t *nbat, gmx::AtomLocality locality, const Nbnxm::GridSet &gridSet, rvec *totalForce)
	Add the computed forces to f, an internal reduction might be performed as well. More...
void	nbnxn_atomdata_add_nbat_fshift_to_fshift (const nbnxn_atomdata_t &nbat, gmx::ArrayRef< gmx::RVec > fshift)
	Add the fshift force stored in nbat to fshift.

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

Enumeration Type Documentation

enum LJCombinationRule : int

strong

LJ combination rules.

Enumerator
Geometric	Geometric.
LorentzBerthelot	Lorentz-Berthelot.
None	No rule.
Count	Size of the enum.

Function Documentation

void nbnxn_atomdata_copy_x_to_nbat_x	(	const Nbnxm::GridSet &	gridSet,
		gmx::AtomLocality	locality,
		const rvec *	coordinates,
		nbnxn_atomdata_t *	nbat
	)

Transform coordinates to xbat layout.

Creates a copy of the coordinates buffer using short-range ordering.

Parameters

[in]	gridSet	The grids data.
[in]	locality	If the transformation should be applied to local or non local coordinates.
[in]	coordinates	Coordinates in plain rvec format.
[in,out]	nbat	Data in NBNXM format, used for mapping formats and to locate the output buffer.

void nbnxn_atomdata_x_to_nbat_x_gpu	(	const Nbnxm::GridSet &	gridSet,
		gmx::AtomLocality	locality,
		NbnxmGpu *	gpu_nbv,
		DeviceBuffer< gmx::RVec >	d_x,
		GpuEventSynchronizer *	xReadyOnDevice
	)

Transform coordinates to xbat layout on GPU.

Creates a GPU copy of the coordinates buffer using short-range ordering. As input, uses coordinates in plain rvec format in GPU memory.

Parameters

[in]	gridSet	The grids data.
[in]	locality	If the transformation should be applied to local or non local coordinates.
[in,out]	gpu_nbv	The NBNXM GPU data structure.
[in]	d_x	Coordinates to be copied (in plain rvec format).
[in]	xReadyOnDevice	Event synchronizer indicating that the coordinates are ready in the device memory. If there is no need to wait for any event (e.g., the wait has already been enqueued into the appropriate stream), it can be nullptr.

void reduceForces	(	nbnxn_atomdata_t *	nbat,
		gmx::AtomLocality	locality,
		const Nbnxm::GridSet &	gridSet,
		rvec *	totalForce
	)

Add the computed forces to f, an internal reduction might be performed as well.

Parameters

[in]	nbat	Atom data in NBNXM format.
[in]	locality	If the reduction should be performed on local or non-local atoms.
[in]	gridSet	The grids data.
[out]	totalForce	Buffer to accumulate resulting force