gmx::LincsGpu Class Reference

#include <gromacs/mdlib/lincs_gpu.h>

Description

Class with interfaces and data for GPU version of LINCS.

Public Member Functions
	LincsGpu (int numIterations, int expansionOrder, const DeviceContext &deviceContext, const DeviceStream &deviceStream)
	Constructor. More...
	~LincsGpu ()
	Destructor.
void	apply (const DeviceBuffer< Float3 > &d_x, DeviceBuffer< Float3 > d_xp, bool updateVelocities, DeviceBuffer< Float3 > d_v, real invdt, bool computeVirial, tensor virialScaled, const PbcAiuc &pbcAiuc)
	Apply LINCS. More...
void	set (const InteractionDefinitions &idef, int numAtoms, ArrayRef< const real > invmass)
	Update data-structures (e.g. after NB search step). More...

Static Public Member Functions
static bool	isNumCoupledConstraintsSupported (const gmx_mtop_t &mtop)
	Returns whether the maximum number of coupled constraints is supported by the GPU LINCS code. More...

Constructor & Destructor Documentation

gmx::LincsGpu::LincsGpu	(	int	numIterations,
		int	expansionOrder,
		const DeviceContext &	deviceContext,
		const DeviceStream &	deviceStream
	)

Constructor.

Parameters

[in]	numIterations	Number of iteration for the correction of the projection.
[in]	expansionOrder	Order of the matrix inversion algorithm.
[in]	deviceContext	Device context (dummy in CUDA).
[in]	deviceStream	Device command stream.

Member Function Documentation

void gmx::LincsGpu::apply	(	const DeviceBuffer< Float3 > &	d_x,
		DeviceBuffer< Float3 >	d_xp,
		bool	updateVelocities,
		DeviceBuffer< Float3 >	d_v,
		real	invdt,
		bool	computeVirial,
		tensor	virialScaled,
		const PbcAiuc &	pbcAiuc
	)

Apply LINCS.

Applies LINCS to coordinates and velocities, stored on GPU. The results are not automatically copied back to the CPU memory. Method uses this class data structures which should be updated when needed using set() method.

Parameters

[in]	d_x	Coordinates before timestep (in GPU memory)
[in,out]	d_xp	Coordinates after timestep (in GPU memory). The resulting constrained coordinates will be saved here.
[in]	updateVelocities	If the velocities should be updated.
[in,out]	d_v	Velocities to update (in GPU memory, can be nullptr if not updated)
[in]	invdt	Reciprocal timestep (to scale Lagrange multipliers when velocities are updated)
[in]	computeVirial	If virial should be updated.
[in,out]	virialScaled	Scaled virial tensor to be updated.
[in]	pbcAiuc	PBC data.

bool gmx::LincsGpu::isNumCoupledConstraintsSupported ( const gmx_mtop_t &  mtop )

static

Returns whether the maximum number of coupled constraints is supported by the GPU LINCS code.

Parameters

[in]

mtop

The molecular topology

void gmx::LincsGpu::set	(	const InteractionDefinitions &	idef,
		int	numAtoms,
		ArrayRef< const real >	invmass
	)

Update data-structures (e.g. after NB search step).

Updates the constraints data and copies it to the GPU. Should be called if the particles were sorted, redistributed between domains, etc. This version uses common data formats so it can be called from anywhere in the code. Does not recycle the data preparation routines from the CPU version. Works only with simple case when all the constraints in idef are are handled by a single GPU. Triangles are not handled as special case.

Information about constraints is taken from: idef.il[F_CONSTR].iatoms — type (T) of constraint and two atom indexes (i1, i2) idef.iparams[T].constr.dA — target length for constraint of type T

Parameters

[in]	idef	Local topology data to get information on constraints from.
[in]	numAtoms	Number of atoms.
[in]	invmass	Inverse masses of atoms.

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

• src/gromacs/mdlib/lincs_gpu.h
• src/gromacs/mdlib/lincs_gpu.cpp