gmx::Lincs Class Reference

Collaboration diagram for gmx::Lincs:

Description

Data for LINCS algorithm.

Public Attributes
int	ncg = 0
	The global number of constraints.
int	ncg_flex = 0
	The global number of flexible constraints.
int	ncg_triangle = 0
	The global number of constraints in triangles.
int	nIter = 0
	The number of iterations.
int	nOrder = 0
	The order of the matrix expansion.
int	max_connect = 0
	The maximum number of constraints connected to a single atom.
int	nc_real = 0
	The number of real constraints.
int	nc = 0
	The number of constraints including padding for SIMD.
int	ncc = 0
	The number of constraint connections.
real	matlam = 0
	The FE lambda value used for filling blc and blmf.
std::vector< int >	con_index
	mapping from topology to LINCS constraints.
std::vector< real, AlignedAllocator< real > >	bllen0
	The reference distance in topology A.
std::vector< real, AlignedAllocator< real > >	ddist
	The reference distance in top B - the r.d. in top A.
std::vector< AtomPair >	atoms
	The atom pairs involved in the constraints.
std::vector< real, AlignedAllocator< real > >	blc
	1/sqrt(invmass1 invmass2).
std::vector< real, AlignedAllocator< real > >	blc1
	As blc, but with all masses 1.
std::vector< int >	blnr
	Index into blbnb and blmf.
std::vector< int >	blbnb
	List of constraint connections.
int	ntriangle = 0
	The local number of constraints in triangles.
int	ncc_triangle = 0
	The number of constraint connections in triangles.
bool	bCommIter = false
	Communicate before each LINCS interation.
std::vector< real >	blmf
	Matrix of mass factors for constraint connections.
std::vector< real >	blmf1
	As blmf, but with all masses 1.
std::vector< real, AlignedAllocator< real > >	bllen
	The reference bond length.
std::vector< int >	nlocat
	The local atom count per constraint, can be NULL.
int	ntask = 0
	The number of tasks used for LINCS work. More...
std::vector< Task >	task
	LINCS thread division.
std::vector< gmx_bitmask_t >	atf
	Atom flags for thread parallelization.
bool	bTaskDep = false
	Are the LINCS tasks interdependent?
bool	bTaskDepTri = false
	Are there triangle constraints that cross task borders?
bool	haveSecondUpdateTask = false
	Whether any task has constraints in the second update list.
std::vector< real, AlignedAllocator< real > >	mlambda
	The Lagrange multipliers times -1.
std::optional < ObservablesReducerBuilder::CallbackToRequireReduction >	callbackToRequireReduction
	Callback used after constraining to require reduction of values later used to compute the constraint RMS relative deviation, so the latter can be output.
ArrayRef< double >	rmsdReductionBuffer
	View used for reducing the components of the global relative RMS constraint deviation. More...
std::optional< double >	constraintRmsDeviation
	The value of the constraint RMS deviation after it has been computed. More...
PaddedVector< gmx::RVec >	tmpv
	Arrays for temporary storage in the LINCS algorithm.
std::vector< real >	tmpncc
std::vector< real, AlignedAllocator< real > >	tmp1
std::vector< real, AlignedAllocator< real > >	tmp2
std::vector< real, AlignedAllocator< real > >	tmp3
std::vector< real, AlignedAllocator< real > >	tmp4

Member Data Documentation

std::optional<double> gmx::Lincs::constraintRmsDeviation

The value of the constraint RMS deviation after it has been computed.

When DD is active, filled by the ObservablesReducer, otherwise filled directly here.

int gmx::Lincs::ntask = 0

The number of tasks used for LINCS work.

Todo:

This is mostly used to loop over task, which would be nicer to do with range-based for loops, but the thread index is used for constructing bit masks and organizing the virial output buffer, so other things need to change, first.

ArrayRef<double> gmx::Lincs::rmsdReductionBuffer

View used for reducing the components of the global relative RMS constraint deviation.

Can be written any time, but that is only useful when followed by a call of the callbackToRequireReduction. Useful to read only from the callback that the ObservablesReducer will later make after reduction.

---

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

• src/gromacs/mdlib/lincs.cpp