#include <gromacs/nbnxm/nbnxm.h>

Description

Top-level non-bonded data structure for the Verlet-type cut-off scheme.

Public Member Functions
	nonbonded_verlet_t (std::unique_ptr< PairlistSets > pairlistSets, std::unique_ptr< PairSearch > pairSearch, std::unique_ptr< nbnxn_atomdata_t > nbat, const Nbnxm::KernelSetup &kernelSetup, std::unique_ptr< ExclusionChecker > exclusionChecker, NbnxmGpu gpu_nbv, gmx_wallcycle wcycle)
	Constructs an object from its components. More...

	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)
	Constructs an object from its, minimal, components. More...

bool	useGpu () const
	Returns whether a GPU is use for the non-bonded calculations.

bool	emulateGpu () const
	Returns whether a GPU is emulated for the non-bonded calculations.

bool	pairlistIsSimple () const
	Return whether the pairlist is of simple, CPU type.

void	putAtomsOnGrid (const matrix box, int gridIndex, const gmx::RVec &lowerCorner, const gmx::RVec &upperCorner, const gmx::UpdateGroupsCog updateGroupsCog, gmx::Range< int > atomRange, real atomDensity, gmx::ArrayRef< const int32_t > atomInfo, gmx::ArrayRef< const gmx::RVec > x, int numAtomsMoved, const int move)
	Put the atoms on the pair search grid. More...

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

void	setLocalAtomOrder () const
	Sets the order of the local atoms to the order grid atom ordering.

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

void	constructPairlist (gmx::InteractionLocality iLocality, const gmx::ListOfLists< int > &exclusions, int64_t step, t_nrnb *nrnb) const
	Constructs the pairlist for the given locality. More...

void	setAtomProperties (gmx::ArrayRef< const int > atomTypes, gmx::ArrayRef< const real > atomCharges, gmx::ArrayRef< const int32_t > atomInfo) const
	Updates all the atom properties in Nbnxm.

void	convertCoordinates (gmx::AtomLocality locality, gmx::ArrayRef< const gmx::RVec > coordinates)
	Convert the coordinates to NBNXM format for the given locality. More...

void	convertCoordinatesGpu (gmx::AtomLocality locality, DeviceBuffer< gmx::RVec > d_x, GpuEventSynchronizer *xReadyOnDevice)
	Convert the coordinates to NBNXM format on the GPU for the given locality. More...

void	atomdata_init_copy_x_to_nbat_x_gpu () const
	Init for GPU version of setup coordinates in Nbnxm.

const PairlistSets &	pairlistSets () const
	Returns a reference to the pairlist sets.

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

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

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

void	dispatchPruneKernelGpu (int64_t step)
	Dispatches the dynamic pruning kernel for GPU lists.

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 kernel of the GPU or launches it on the GPU.

void	dispatchFreeEnergyKernels (const gmx::ArrayRefWithPadding< const gmx::RVec > &coords, gmx::ForceWithShiftForces forceWithShiftForces, bool useSimd, int ntype, 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, gmx::ArrayRef< const real > lambda, gmx_enerdata_t enerd, const gmx::StepWorkload &stepWork, t_nrnb *nrnb)
	Executes the non-bonded free-energy kernels, local + non-local, always runs on the CPU.

void	atomdata_add_nbat_f_to_f (gmx::AtomLocality locality, gmx::ArrayRef< gmx::RVec > force)
	Add the forces stored in nbat to f, zeros the forces in nbat. More...

int	getNumAtoms (gmx::AtomLocality locality) const
	Get the number of atoms for a given locality. More...

const Nbnxm::KernelSetup &	kernelSetup () const
	Return the kernel setup.

real	pairlistInnerRadius () const
	Returns the outer radius for the pair list.

real	pairlistOuterRadius () const
	Returns the outer radius for the pair list.

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

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

void	setupFepThreadedForceBuffer (int numAtomsForce)

nbnxn_atomdata_t &	nbat ()
	Returns a reference to the nbnxn_atomdata_t object.

const NbnxmGpu *	gpuNbv () const
	Returns a pointer to the NbnxmGpu object, can return nullptr.

NbnxmGpu *	gpuNbv ()
	Returns a pointer to the NbnxmGpu object, can return nullptr.

Constructor & Destructor Documentation

nonbonded_verlet_t::nonbonded_verlet_t	(	std::unique_ptr< PairlistSets >	pairlistSets,
		std::unique_ptr< PairSearch >	pairSearch,
		std::unique_ptr< nbnxn_atomdata_t >	nbat,
		const Nbnxm::KernelSetup &	kernelSetup,
		std::unique_ptr< ExclusionChecker >	exclusionChecker,
		NbnxmGpu *	gpu_nbv,
		gmx_wallcycle *	wcycle
	)

Constructs an object from its components.

Parameters

[in]	pairlistSets	The pairlist sets, is consumed
[in]	pairSearch	The pairsearch setup, is consumed
[in]	nbat	The atom data, is consumed
[in]	kernelSetup	The non-bonded kernel setup
[in]	exclusionChecker	The FEP exclusion checker, is consumed, can be nullptr
[in]	gpu_nbv	The GPU non-bonded setup, ownership is transferred, can be nullptr
[in]	wcycle	Pointer to wallcycle counters, can be nullptr

nonbonded_verlet_t::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
	)

Constructs an object from its, minimal, components.

Parameters

[in]	pairlistSets	The pairlist sets, is consumed
[in]	pairSearch	The pairsearch setup, is consumed
[in]	nbat	The atom data, is consumed
[in]	kernelSetup	The non-bonded kernel setup
[in]	gpu_nbv	The GPU non-bonded setup, ownership is transferred, can be nullptr

Member Function Documentation

void nonbonded_verlet_t::atomdata_add_nbat_f_to_f	(	gmx::AtomLocality	locality,
		gmx::ArrayRef< gmx::RVec >	force
	)

Add the forces stored in nbat to f, zeros the forces in nbat.

Parameters

[in]	locality	Local or non-local
[in,out]	force	Force to be added to

void nonbonded_verlet_t::constructPairlist	(	gmx::InteractionLocality	iLocality,
		const gmx::ListOfLists< int > &	exclusions,
		int64_t	step,
		t_nrnb *	nrnb
	)		const

Constructs the pairlist for the given locality.

When there are no non-self exclusions, exclusions can be empty. Otherwise the number of lists in exclusions should match the number of atoms when not using DD, or the total number of atoms in the i-zones when using DD.

Parameters

[in]	iLocality	The interaction locality: local or non-local
[in]	exclusions	Lists of exclusions for every atom.
[in]	step	Used to set the list creation step
[in,out]	nrnb	Flop accounting struct, can be nullptr

void nonbonded_verlet_t::convertCoordinates	(	gmx::AtomLocality	locality,
		gmx::ArrayRef< const gmx::RVec >	coordinates
	)

Convert the coordinates to NBNXM format for the given locality.

The API function for the transformation of the coordinates from one layout to another.

Parameters

[in]	locality	Whether coordinates for local or non-local atoms should be transformed.
[in]	coordinates	Coordinates in plain rvec format to be transformed.

void nonbonded_verlet_t::convertCoordinatesGpu	(	gmx::AtomLocality	locality,
		DeviceBuffer< gmx::RVec >	d_x,
		GpuEventSynchronizer *	xReadyOnDevice
	)

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.

Parameters

[in]	locality	Whether coordinates for local or non-local atoms should be transformed.
[in]	d_x	GPU coordinates buffer in plain rvec format to be transformed.
[in]	xReadyOnDevice	Event synchronizer indicating that the coordinates are ready in the device memory.

int nonbonded_verlet_t::getNumAtoms ( gmx::AtomLocality locality ) const

Get the number of atoms for a given locality.

Parameters

[in] locality Local or non-local

Returns: The number of atoms for given locality

void nonbonded_verlet_t::putAtomsOnGrid	(	const matrix	box,
		int	gridIndex,
		const gmx::RVec &	lowerCorner,
		const gmx::RVec &	upperCorner,
		const gmx::UpdateGroupsCog *	updateGroupsCog,
		gmx::Range< int >	atomRange,
		real	atomDensity,
		gmx::ArrayRef< const int32_t >	atomInfo,
		gmx::ArrayRef< const gmx::RVec >	x,
		int	numAtomsMoved,
		const int *	move
	)

Put the atoms on the pair search grid.

Only atoms with indices wihtin atomRange in x are put on the grid. When 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 gridIndex = 0. When 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 numAtomsMoved. When move[i] < 0 particle i has migrated and will not be put on the grid.

Parameters

[in]	box	Box used for periodic distance calculations
[in]	gridIndex	The index of the grid to spread to, always 0 except with test particle insertion
[in]	lowerCorner	Atom groups to be gridded should have coordinates >= this corner
[in]	upperCorner	Atom groups to be gridded should have coordinates <= this corner
[in]	updateGroupsCog	Centers of geometry for update groups, pass nullptr when not using update groups
[in]	atomRange	Range of atoms to grid
[in]	atomDensity	An estimate of the atom density, used for peformance optimization and only with `gridIndex` = 0
[in]	atomInfo	Atom information flags
[in]	x	Coordinates for atoms to grid
[in]	numAtomsMoved	The number of atoms that will move to another domain, pass 0 without DD
[in]	move	Move flags for atoms, pass nullptr without DD

The documentation for this struct was generated from the following files:

src/gromacs/nbnxm/nbnxm.h
src/gromacs/nbnxm/freeenergydispatch.cpp
src/gromacs/nbnxm/kerneldispatch.cpp
src/gromacs/nbnxm/nbnxm_setup.cpp
src/gromacs/nbnxm/pairlist.cpp
src/gromacs/nbnxm/prunekerneldispatch.cpp

Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation