Namespace for SBP operators and associated data structures. More...

Detailed Description

Namespace for SBP operators and associated data structures.

Typedefs
typedef stencilset	base
	The sbp::base is an SBP-specific stencilset. More...

Functions
bool	IsValidOrder (int overallOrder)

int	Initialize (base &stencilSet, int interiorOrder)
	Initialize the sbp::base stencilset with the SBP operator of given order. More...

void	OperatorSetup (base &stencilSet, int interiorOrder, int boundaryDepth, int boundaryWidth, double boundaryWeight, std::vector< double > centralWeightsRight, std::vector< std::vector< double > > leftWeights, std::vector< int > leftOrders)
	Setup the SBP operator given the appropriate coefficients – called from Initialize. More...

int	BruteTest1 (base &inOperator, int interiorOrder, int numDim, int numComponents, int numTrials, std::vector< bool > &testResults)
	Brute-force accuracy test for SBP operators. More...

int	CreateStencilConnectivity (int numDim, size_t dimSizes, size_t opInterval, int boundaryDepth, int *stencilID, bool fortranInterval=false)
	Creates simple stencil connectivity assuming all domain boundaries are physical boundaries. More...

int	CreateStencilConnectivity (int numDim, size_t dimSizes, size_t opInterval, int boundaryDepth, int periodicDirs, int stencilID, bool fortranInterval=false)
	Creates simple stencil connectivity assuming all domain boundaries are either periodic or physical boundaries. More...

int	InvertStencilConnectivity (int numDim, size_t dimSizes, size_t opInterval, int numStencils, int stencilID, size_t dualStencilConn, size_t *numPointsStencil, bool fortranInterval=false)
	Inverts stencil connectivity to populate the so-called dual stencil connectivity More...

int	BoundaryStencilConnectivity (std::vector< size_t > &bufferSizes, pcpp::IndexIntervalType &partitionInterval, pcpp::IndexIntervalType &partitionBufferInterval, pcpp::IndexIntervalType &boundaryInterval, int boundaryDepth, int boundaryDirection, int *stencilConnectivity)
	Update a stencil connectivity with a boundary. More...

int	HoleStencilConnectivity (std::vector< size_t > &bufferSizes, pcpp::IndexIntervalType &partitionInterval, pcpp::IndexIntervalType &partitionBufferInterval, pcpp::IndexIntervalType &holeInterval, int holeStencil, int *stencilConnectivity)
	Update a stencil connectivity with a hole. More...

int	MaskStencilConnectivity (int numDim, size_t dimSizes, size_t opInterval, int boundaryDepth, int boundaryStart, int holeBit, int inMask, int stencilID)

int	DetectHoles (int numDim, size_t dimSizes, size_t opInterval, int boundaryDepth, int holeBit, int inMask, int stencilID)
	Detect unstructured holes and set up boundary stencil id's accordingly. More...

size_t	IntervalSize (int numDim, size_t *opInterval)

size_t	BufferSize (int numDim, size_t *dimSize)

int	StructuredHole (int numDim, size_t dimSizes, size_t opInterval, size_t holeInterval, int boundaryDepth, int boundaryStart, int holeBit, int inMask, int *stencilID)

Typedef Documentation

◆ base

typedef stencilset base

The sbp::base is an SBP-specific stencilset.

The sbp::base stencilset

The SBP stencilset (i.e. sbp::base) is a plascom2::operator::stencilset that contains all of the stencils implementing an SBP scheme of a given spatial order N_M (e.g. 1_2, 2_4, 4_8, etc), where N is the order of the boundary stencil and M the interior spatial order. Each scheme has an internal stencil (I) implementing an M-order finite difference (FD) operator, and some number $N_b$ of biased boundary stencils of order N for each of the left and right boundaries ( $B_l$ and $B_r$ , resp), where $N_b$ is the so-called boundary depth.

The total number of stencils in the SBP stencilset is $2N_b + 1$ , and they are arranged in the data structures in the following order:

{Interior, $B_l$ , $B_l+1$ , $B_l+2$ ,..., $B_l + (N_b-1)$ , $R_b$ , $R_b-1$ , $R_b-2$ ,..., $R_b-(N_b-1)$ }.

Definition at line 141 of file Stencil.H.

Function Documentation

◆ BoundaryStencilConnectivity()

int BoundaryStencilConnectivity	(	std::vector< size_t > &	bufferSizes,
		pcpp::IndexIntervalType &	partitionInterval,
		pcpp::IndexIntervalType &	partitionBufferInterval,
		pcpp::IndexIntervalType &	boundaryInterval,
		int	boundaryDepth,
		int	boundaryDirection,
		int *	stencilConnectivity
	)

Update a stencil connectivity with a boundary.

Given a stencil connectivity, boundary interval, depth, and direction, this function populates the stencil connectivity with the stencil id that corresponds to the SBP biased boundary stencils needed to respect the specified boundary. This routine is not (yet) thread-safe.

Parameters

[in]	bufferSizes	std::vector<size_t> that indicates the number of points in each dimension
[in]	partitionInterval	pcpp::IndexIntervalType that indicates the local partition
[in]	partitionBufferInterval	pcpp::IndexIntervalType that indicates the buffer interval for the lcoal partition
[in]	boundaryInterval	pcpp::IndexIntervalType that indicates the boundary interval (wrt the global grid size)
[in]	boundaryDepth	integer indicating the boundary depth for this SBP operator
[in]	boundaryDirection	direction points into the domain from the boundary
[out]	stencilConnectivity	the stencil connectivity that is update with the boundary stencils on return

Returns: 0 on success, non-zero otherwise

Definition at line 1114 of file Stencil.C.

References bufferInterval, sizeextent::GetFlatIndices(), sizeextent::InitSimple(), sizeextent::NNodes(), numPointsBuffer, and sizeextent::Overlap().

Referenced by rhs< GridT, StateT, OperatorT >::SetDomainBoundaries().

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◆ BruteTest1()

int BruteTest1	(	base &	inOperator,
		int	interiorOrder,
		int	numDim,
		int	numComponents,
		int	numTrials,
		std::vector< bool > &	testResults
	)

Brute-force accuracy test for SBP operators.

This test uses the brute force ApplyOperator kernel to test the accuracy of SBP finite difference operators. It applies the indicated operator of interior order M to the N-dimensional domain $[.5,1.5]^N$ , with test functions $F(x^n)$ with $0 \leq n \leq (M+1)$ . The operator is applied in each dimension using numTrials grid refinements with $\Delta{x}_t = \frac{1.0}{(2^t)20} | 0 \leq t \leq (numTrials-1)$ to ensure that the truncation error has the proper order dependence on $\Delta{x}$ .

The test results are as follows:

Interior stencil in dimension 1 (I1) [A := (accurate/exact?)] (pass/fail)
Interior stencil in dimension 2 (I2) [O := (order == interior order?)] (pass/fail)
(I3) [A] (pass/fail)
(I3) [O] (pass/fail)
Left boundary stencil in dimension 1 ( $B1_{l}$ ) [A] (pass/fail)
( $B1_{l}$ ) [O] (pass/fail)
First biased stencil for left boundary
( $B1_{(l+1)}$ ) [A] (pass/fail)
( $B1_{(l+1)}$ ) [O] (pass/fail)
Left boundary stencil in dimension 2 ( $B2_{(l+1)}$ ) [A] (pass/fail)
(....)
( $B(nDim)_{(l+(N_b-1))}$ ) [A][O] (pass/fail)
Right boundary stencils results
( $B1_{r}$ ) - ( $B(nDim)_{(r-(N_b-1))}$ ) [A][O] (pass/fail)

In short, testResults contains: for each stencil, for each dimension, for each test (i.e. accuracy + order) the test results.

Parameters

[in]	inOperator	plascom2::operator::sbp::base stencilset encapsulating the operator
[in]	interiorOrder	indicates the order of accuracy for the interior stencil
[in]	numDim	indicates the number of dimensions in which to test
[in]	numComponents	indicates the number of vector components for the test function
[in]	numTrials	indicates the number of successive grid refinements to use in the test
[out]	testResults	a vector of boolean test results (true for pass, false for fail)

Definition at line 625 of file Stencil.C.

References operators::applyoperator(), stencilset::boundaryDepth, stencilset::boundaryWidth, CreateStencilConnectivity(), FC_MODULE(), GetFunctionOrder(), numComponents, numPoints, numStencils, stencilset::numStencils, stencilset::numValues, opDir, opInterval, stencilID, stencilset::stencilOffsets, stencilset::stencilOrders, stencilset::stencilSizes, stencilset::stencilStarts, and stencilset::stencilWeights.

Referenced by TestOperatorSBP12(), TestOperatorSBP24(), and TestOperatorSBP36().

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◆ BufferSize()

size_t plascom2::operators::sbp::BufferSize	(	int	numDim,
		size_t *	dimSize
	)

Definition at line 1300 of file Stencil.C.

Referenced by parallel_blockstructured::FlagData(), and InvertStencilConnectivity().

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◆ CreateStencilConnectivity() [1/2]

int CreateStencilConnectivity	(	int	numDim,
		size_t *	dimSizes,
		size_t *	opInterval,
		int	boundaryDepth,
		int *	stencilID,
		bool	fortranInterval = `false`
	)

Creates simple stencil connectivity assuming all domain boundaries are physical boundaries.

This function populates the stencilID with the ID (1-numStencils) assuming an SBP operator stencilset. An example SBP stencilset with boundaryDepth=4 has the stencil ID's arranged as follows:

1: Interior stencil
2: Left boundary stencil
3: Left boundary + 1 biased stencil
4: Left boundary + 2 biased stencil
5: Left boundary + 3 biased stencil
6: Right boundary stencil
7: Right boundary - 1 biased stencil
8: Right boundary - 2 biased stencil
9: Right boundary - 3 biased stencil

Parameters

[in]	numDim	indicates the number of spatial dimensions
[in]	dimSizes	array of size (numDim) that indicates the number of points in each dimension [Nx Ny Nz]
[in]	opInterval	array of size (2*numDim) indicating the range of indices over which to determine stencilIDs
[in]	boundaryDepth	indicates the boundary depth as described above
[out]	stencilID	array of pre-sized to (numDim*numPoints) which on output contains the determined stencil IDs for each dimension
[in]	fortranInterval	indicates whether the opInterval is 1-based (true) or not (false). DEFAULT=false

Returns: 0 on success, non-zero otherwise

Note: Holes and other non-domain boundaries not yet supported - but support will be added here (or similar)

Definition at line 840 of file Stencil.C.

References numPoints.

Referenced by BruteTest1(), rhs< GridT, StateT, OperatorT >::SetupStencilConnectivities(), TestApplyOperatorAppl(), TestApplyOperatorBlobs(), TestCurlOperator(), TestEulerKernels(), TestGrid_CurvilinearMetric(), TestGrid_CurvilinearVGWavy(), TestGrid_RectilinearMetric(), TestHoleDetection(), TestMaxwellRHS_Bfield(), and TestMaxwellRHS_Dfield().

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◆ CreateStencilConnectivity() [2/2]

int CreateStencilConnectivity	(	int	numDim,
		size_t *	dimSizes,
		size_t *	opInterval,
		int	boundaryDepth,
		int *	periodicDirs,
		int *	stencilID,
		bool	fortranInterval = `false`
	)

Creates simple stencil connectivity assuming all domain boundaries are either periodic or physical boundaries.

This function populates the stencilID with the ID (1-numStencils) assuming an SBP operator stencilset. An example SBP stencilset with boundaryDepth=4 has the stencil ID's arranged as follows:

1: Interior stencil
2: Left boundary stencil
3: Left boundary + 1 biased stencil
4: Left boundary + 2 biased stencil
5: Left boundary + 3 biased stencil
6: Right boundary stencil
7: Right boundary - 1 biased stencil
8: Right boundary - 2 biased stencil
9: Right boundary - 3 biased stencil

Parameters

[in]	numDim	indicates the number of spatial dimensions
[in]	dimSizes	array of size (numDim) that indicates the number of points in each dimension [Nx Ny Nz]
[in]	opInterval	array of size (2*numDim) indicating the range of indices over which to determine stencilIDs
[in]	boundaryDepth	indicates the boundary depth as described above
[in]	periodicDirs	indicates the periodic directions
[out]	stencilID	array of pre-sized to (numDim*numPoints) which on output contains the determined stencil IDs for each dimension
[in]	fortranInterval	indicates whether the opInterval is 1-based (true) or not (false). DEFAULT=false

Returns: 0 on success, non-zero otherwise

Note: Holes and other non-domain boundaries (besides periodic) not yet supported - but support will be added here (or similar)

Definition at line 968 of file Stencil.C.

References numPoints.

◆ DetectHoles()

int DetectHoles	(	int	numDim,
		size_t *	dimSizes,
		size_t *	opInterval,
		int	boundaryDepth,
		int	holeBit,
		int *	inMask,
		int *	stencilID
	)

Detect unstructured holes and set up boundary stencil id's accordingly.

Definition at line 1454 of file Stencil.C.

References bufferInterval, sizeextent::GetFlatIndices(), numPointsBuffer, numStencils, and opInterval.

Referenced by rhs< GridT, StateT, OperatorT >::SetDomainBCs(), and TestHoleDetection().

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◆ HoleStencilConnectivity()

int HoleStencilConnectivity	(	std::vector< size_t > &	bufferSizes,
		pcpp::IndexIntervalType &	partitionInterval,
		pcpp::IndexIntervalType &	partitionBufferInterval,
		pcpp::IndexIntervalType &	holeInterval,
		int	holeStencil,
		int *	stencilConnectivity
	)

Update a stencil connectivity with a hole.

Sets stencil connectivity for all points inside a "hole" or iblanked region.

Given a stencil connectivity, and a hole interval, this function populates the stencil connectivity with the stencil id that corresponds to the specified hole stencil which is usually the number of SBP stencils + 1. This routine is not (yet) thread-safe.

Parameters

[in]	bufferSizes	std::vector<size_t> that indicates the number of points in each dimension
[in]	partitionInterval	pcpp::IndexIntervalType that indicates the local partition
[in]	partitionBufferInterval	pcpp::IndexIntervalType that indicates the buffer interval for the lcoal partition
[in]	holeInterval	pcpp::IndexIntervalType that indicates the interval of the hole (wrt the global grid size)
[in]	holeStencil	integer to which to set the stencil connectivity
[out]	stencilConnectivity	the stencil connectivity that is update with the boundary stencils on return

Returns: 0 on success, non-zero otherwise

This routine takes the partition and hole global intervals and sets a hole stencil on every point inside the hole.

Definition at line 1230 of file Stencil.C.

References bufferInterval, sizeextent::GetFlatIndices(), sizeextent::InitSimple(), sizeextent::NNodes(), numPointsBuffer, and sizeextent::Overlap().

Referenced by rhs< GridT, StateT, OperatorT >::SetDomainBoundaries().

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◆ Initialize()

int Initialize	(	base &	stencilSet,
		int	interiorOrder
	)

Initialize the sbp::base stencilset with the SBP operator of given order.

Definition at line 360 of file Stencil.C.

References stencilset::Destroy(), and OperatorSetup().

Referenced by base< GridT, StateT >::ConfigureDomain(), application::ConfigureSimulation(), testfixtures::CreateSerialSimulationFixtures(), testfixtures::CreateSimulationFixtures(), euler::util::CreateSimulationFixtures(), eos::eos(), testing_parallel_program::Initialize(), euler::util::InitializeSimulationFixtures(), CommunicatorObject::NOpenRequests(), TestApplyOperatorAppl(), TestApplyOperatorBlobs(), TestCurlOperator(), TestEulerKernels(), TestGrid_CurvilinearMetric(), TestGrid_CurvilinearVGWavy(), TestGrid_PBS_IntegratedHalo(), TestGrid_RectilinearMetric(), TestHDF5PBSGridIO(), TestHoleDetection(), TestMaxwellRHS(), TestMaxwellRHS_Bfield(), TestMaxwellRHS_Dfield(), TestOperatorSBP12(), TestOperatorSBP24(), TestOperatorSBP36(), TestPlasCom2Output(), and TestSBPInitialize().

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◆ IntervalSize()

size_t plascom2::operators::sbp::IntervalSize	(	int	numDim,
		size_t *	opInterval
	)

Definition at line 1293 of file Stencil.C.

Referenced by InvertStencilConnectivity().

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◆ InvertStencilConnectivity()

int InvertStencilConnectivity	(	int	numDim,
		size_t *	dimSizes,
		size_t *	opInterval,
		int	numStencils,
		int *	stencilID,
		size_t *	dualStencilConn,
		size_t *	numPointsStencil,
		bool	fortranInterval = `false`
	)

Inverts stencil connectivity to populate the so-called dual stencil connectivity

Given a whole stencil connectivity (i.e. wrt all partition points), this function populates the dual stencil connectivity with the points to which each stencil should be applied. The dual stencil connectivity array (dualStencilConn) must have size numDim*numPointsInterval, where numPointsInterval is inferred from the opInterval argument. The numPointsStencil array must be of size (numDim*numStencils). On output, the dualStencilConn contains a list of point id's for each stencil for each dimension.

Parameters

[in]	numDim	indicates the number of spatial dimensions
[in]	dimSizes	array of size (numDim) that indicates the number of points in each dimension [Nx Ny Nz]
[in]	opInterval	array of size (2*numDim) indicating the range of indices over which to determine stencilIDs
[in]	numStencils	indicates the number of stencils represented in the stencilID
[in]	stencilID	array of (numDimnumPoints) elements where numPoints = dimSize[0]dimSize[1]....*dimSize[nDim-1]
[out]	dualStencilConn	array of size (numDim*numPointsInterval) to store dual stencil connectivity on output
[out]	numPointsStencil	array of size (numDim*numStencils) to store the number of points for each stencil in each dimension
[in]	fortranInterval	indicates whether the opInterval is 1-based (true) or not (false). DEFAULT=false

Returns: 0 on success, non-zero otherwise

Definition at line 1739 of file Stencil.C.

References BufferSize(), IntervalSize(), numPointsBuffer, numStencils, and opInterval.

Referenced by TestApplyOperatorBlobs().

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◆ IsValidOrder()

bool IsValidOrder ( int overallOrder )

Definition at line 352 of file Stencil.C.

Referenced by application::ConfigureSimulation().

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◆ MaskStencilConnectivity()

int MaskStencilConnectivity	(	int	numDim,
		size_t *	dimSizes,
		size_t *	opInterval,
		int	boundaryDepth,
		int	boundaryStart,
		int	holeBit,
		int *	inMask,
		int *	stencilID
	)

Definition at line 1381 of file Stencil.C.

References sizeextent::GetFlatIndices(), and numPoints.

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◆ OperatorSetup()

void OperatorSetup	(	base &	stencilSet,
		int	interiorOrder,
		int	boundaryDepth,
		int	boundaryWidth,
		double	boundaryWeight,
		std::vector< double >	centralWeightsRight,
		std::vector< std::vector< double > >	leftWeights,
		std::vector< int >	leftOrders
	)

Setup the SBP operator given the appropriate coefficients – called from Initialize.

Definition at line 485 of file Stencil.C.

References stencilset::boundaryDepth, stencilset::boundaryWeight, stencilset::boundaryWidth, stencilset::numStencils, stencilset::numValues, stencilset::overallOrder, stencilset::ownData, stencilset::stencilOffsets, stencilset::stencilOrders, stencilset::stencilSizes, stencilset::stencilStarts, and stencilset::stencilWeights.

Referenced by Initialize().

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◆ StructuredHole()

int plascom2::operators::sbp::StructuredHole	(	int	numDim,
		size_t *	dimSizes,
		size_t *	opInterval,
		size_t *	holeInterval,
		int	boundaryDepth,
		int	boundaryStart,
		int	holeBit,
		int *	inMask,
		int *	stencilID
	)

Definition at line 1307 of file Stencil.C.

References sizeextent::GetFlatIndices(), numPoints, and sizeextent::Overlap().

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Detailed Description

Typedefs

Functions

Typedef Documentation

◆ base

Function Documentation

◆ BoundaryStencilConnectivity()

◆ BruteTest1()

◆ BufferSize()

◆ CreateStencilConnectivity() [1/2]

◆ CreateStencilConnectivity() [2/2]

◆ DetectHoles()

◆ HoleStencilConnectivity()

◆ Initialize()

◆ IntervalSize()

◆ InvertStencilConnectivity()

◆ IsValidOrder()

◆ MaskStencilConnectivity()

◆ OperatorSetup()

◆ StructuredHole()