gmx::nbnxn_atomdata_t Struct Reference

#include <gromacs/nbnxm/atomdata.h>

Description

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().

Classes
struct	Params
	The actual atom data parameter values. More...
struct	SimdMasks
	Diagonal and topology exclusion helper data for all SIMD kernels. More...

Public Member Functions
	nbnxn_atomdata_t (PinningPolicy pinningPolicy)
	nbnxn_atomdata_t (PinningPolicy pinningPolicy, const MDLogger &mdlog, NbnxmKernelType kernelType, const std::optional< LJCombinationRule > &ljCombinationRule, LJCombinationRule pmeLJCombinationRule, ArrayRef< const real > nbfp, bool addFillerAtomType, int numEnergyGroups, int numOutputBuffers)
	Constructor. More...
const Params &	params () const
	Returns a const reference to the parameters.
Params &	paramsDeprecated ()
	Returns a non-const reference to the parameters.
int	numAtoms () const
	Returns the current total number of atoms stored.
int	numLocalAtoms () const
	Returns the number of local atoms.
ArrayRef< const real >	x () const
	Return the coordinate buffer, and q with xFormat==nbatXYZQ.
ArrayRef< real >	x ()
	Return the coordinate buffer, and q with xFormat==nbatXYZQ.
const SimdMasks &	simdMasks () const
	Masks for handling exclusions in the SIMD kernels.
void	resizeCoordinateBuffer (int numAtoms, int domainDecompositionZone)
	Resizes the coordinate buffer and sets the number of atoms. More...
void	resizeForceBuffers ()
	Resizes the force buffers for the current number of atoms.
nbnxn_atomdata_output_t &	outputBuffer (int thread)
	Returns the output buffer for the given thread.
const nbnxn_atomdata_output_t &	outputBuffer (int thread) const
	Returns the output buffer for the given thread.
ArrayRef< const nbnxn_atomdata_output_t >	outputBuffers () const
	Returns the list of output buffers.
bool	useBufferFlags () const
	Returns whether buffer flags are used.
std::vector< gmx_bitmask_t > &	bufferFlags ()
	Returns the vector of buffer flags.
void	reduceForces (AtomLocality locality, const GridSet &gridSet, ArrayRef< RVec > totalForce)
	Add the computed forces to f, an internal reduction might be performed as well. More...
void	clearForceBuffer (int outputIndex)
	Clears the force buffer. More...

Public Attributes
int	XFormat
	The format of x (and q), enum.
int	FFormat
	The format of f, enum.
bool	bDynamicBox
	Do we need to update shift_vec every step?
HostVector< 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)

Constructor & Destructor Documentation

gmx::nbnxn_atomdata_t::nbnxn_atomdata_t	(	PinningPolicy	pinningPolicy,
		const MDLogger &	mdlog,
		NbnxmKernelType	kernelType,
		const std::optional< LJCombinationRule > &	ljCombinationRule,
		LJCombinationRule	pmeLJCombinationRule,
		ArrayRef< const real >	nbfp,
		bool	addFillerAtomType,
		int	numEnergyGroups,
		int	numOutputBuffers
	)

Constructor.

This class only stores one, or no, LJ combination rule parameter list. With LJ-PME the rule for the LJ PME-grid must match the PME grid combination rule and there can be no combination rule for the LJ pair parameters. Without LJ-PME the combination rule should match the combination rule for the LJ parameters. An (release) assertion failure will occur when these conditions are not met.

The non-bonded force parameter matrix nbfp is a serialized version of a square parameter matrix with a pair of parameters 6*C6, 12*C12 for every atom type pair.

Parameters

[in]	pinningPolicy	Sets the pinning policy for all data that might be transferred to a GPU
[in]	mdlog	The logger
[in]	kernelType	Nonbonded NxN kernel type
[in]	ljCombinationRule	The LJ combination rule parameters to generate, empty is detect from the LJ parameters
[in]	pmeLJCombinationRule	The LJ combination rule parameters to generate for the LJ PME-grid part
[in]	nbfp	Non-bonded force parameter matrix
[in]	addFillerAtomType	When true, add a filler atom type, when false, nbfp should have atom-type with index numTypes-1 with all parameters zero so that that row and column have only zero values.
[in]	numEnergyGroups	Number of energy groups
[in]	numOutputBuffers	Number of output data structures

Member Function Documentation

void gmx::nbnxn_atomdata_t::clearForceBuffer

(

int

outputIndex

)

Clears the force buffer.

Either the whole buffer is cleared or only the parts used by thread/task outputIndex when useBufferFlags() returns true.

Parameters

[in]

outputIndex

The index of the output object to clear

void gmx::nbnxn_atomdata_t::reduceForces	(	AtomLocality	locality,
		const GridSet &	gridSet,
		ArrayRef< RVec >	totalForce
	)

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

Parameters

[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

void gmx::nbnxn_atomdata_t::resizeCoordinateBuffer	(	int	numAtoms,
		int	domainDecompositionZone
	)

Resizes the coordinate buffer and sets the number of atoms.

Parameters

numAtoms	The new number of atoms
domainDecompositionZone	The domain decomposition zone index

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

• src/gromacs/nbnxm/atomdata.h
• src/gromacs/nbnxm/atomdata.cpp