mesh/testMesh.cpp File Reference

#include "header.h"
#include "SparseMatrix.h"
#include "../shell/Shell.h"
#include "Boundary.h"
#include "MeshEntry.h"
#include "ChemCompt.h"
#include "MeshCompt.h"
#include "CubeMesh.h"
#include "CylBase.h"
#include "NeuroNode.h"
#include "NeuroMesh.h"
#include "../utility/Vec.h"
#include "CylMesh.h"
#include "SpineEntry.h"
#include "SpineMesh.h"
#include "PsdMesh.h"

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Typedefs
typedef pair< unsigned int, unsigned int >	PII
Functions
void	testVolScaling ()
void	testCubeMesh ()
void	testCubeMeshExtendStencil ()
void	testReMesh ()
Id	makeCompt (Id parentCompt, Id parentObj, string name, double len, double dia, double theta)
void	setIntersectVoxel (vector< PII > &intersect, unsigned int ix, unsigned int iy, unsigned int iz, unsigned int nx, unsigned int ny, unsigned int nz, unsigned int meshIndex)
void	checkAbut (const vector< PII > &intersect, unsigned int ix, unsigned int iy, unsigned int iz, unsigned int nx, unsigned int ny, unsigned int nz, unsigned int meshIndex, vector< VoxelJunction > &ret)
void	testIntersectVoxel ()
void	testCubeMeshFillTwoDimSurface ()
void	testCubeMeshFillThreeDimSurface ()
void	testCubeMeshJunctionTwoDimSurface ()
void	testCubeMeshJunctionDiffSizeMesh ()
void	testCubeMeshJunctionThreeDimSurface ()
void	testCubeMeshMultiJunctionTwoD ()
void	testVec ()
void	testMesh ()

Typedef Documentation

typedef pair< unsigned int, unsigned int > PII

Function Documentation

void checkAbut	(	const vector< PII > &	intersect,
		unsigned int	ix,
		unsigned int	iy,
		unsigned int	iz,
		unsigned int	nx,
		unsigned int	ny,
		unsigned int	nz,
		unsigned int	meshIndex,
		vector< VoxelJunction > &	ret
	)

checkAbut checks the intersect vector for the current position ix, iy, iz, to determine how many diffusion terms to extract. It then puts each of the extracted terms into the ret vector. There is a minor efficiency for one and two diffusion terms as they are encoded within the intersect vector. Higher-order surface alignments require an in-line scan of neighboring voxels. In all casesl the function inserts a flag indicating surface direction into the diffScale field of the VoxelJunction. 0 = x; 1 = y; 2 = z.

References CubeMesh::ABUTX, CubeMesh::ABUTY, CubeMesh::ABUTZ, CubeMesh::EMPTY, CubeMesh::MULTI, and CubeMesh::SURFACE.

Referenced by testIntersectVoxel().

Id makeCompt	(	Id	parentCompt,
		Id	parentObj,
		string	name,
		double	len,
		double	dia,
		double	theta
	)

theta in degrees len and dia in metres as usual

References Shell::doAddMsg(), Shell::doCreate(), Field< A >::get(), PI, and Field< A >::set().

Referenced by ReadSwc::build().

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void setIntersectVoxel	(	vector< PII > &	intersect,
		unsigned int	ix,
		unsigned int	iy,
		unsigned int	iz,
		unsigned int	nx,
		unsigned int	ny,
		unsigned int	nz,
		unsigned int	meshIndex
	)

References CubeMesh::ABUTX, CubeMesh::ABUTY, CubeMesh::ABUTZ, setAbut(), and CubeMesh::SURFACE.

Referenced by testIntersectVoxel().

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void testCubeMesh ( )

Low-level tests for the CubeMesh object: No MOOSE calls involved.

References CUBOID, doubleEq(), CubeMesh::getCoords(), ChemCompt::getDimensions(), CubeMesh::getDx(), CubeMesh::getDy(), CubeMesh::getDz(), CubeMesh::getMeshDimensions(), CubeMesh::getMeshType(), MeshCompt::getNeighbors(), CubeMesh::getNx(), CubeMesh::getNy(), CubeMesh::getNz(), CubeMesh::getX0(), CubeMesh::getX1(), CubeMesh::getY0(), CubeMesh::getY1(), CubeMesh::getZ0(), CubeMesh::getZ1(), CubeMesh::innerGetNumEntries(), CubeMesh::innerSetCoords(), CubeMesh::setPreserveNumEntries(), CubeMesh::setX0(), CubeMesh::setX1(), CubeMesh::setY0(), CubeMesh::setY1(), CubeMesh::setZ0(), and CubeMesh::setZ1().

Referenced by testMesh().

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void testCubeMeshExtendStencil ( )

References CUBOID, MeshCompt::extendStencil(), ChemCompt::getDimensions(), CubeMesh::getMeshDimensions(), CubeMesh::getMeshType(), MeshCompt::getStencilRow(), CubeMesh::innerSetCoords(), and CubeMesh::setPreserveNumEntries().

Referenced by testMesh().

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void testCubeMeshFillThreeDimSurface ( )

Referenced by testMesh().

void testCubeMeshFillTwoDimSurface ( )

References CubeMesh::innerSetCoords(), CubeMesh::numDims(), CubeMesh::setPreserveNumEntries(), and CubeMesh::surface().

Referenced by testMesh().

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void testCubeMeshJunctionDiffSizeMesh ( )

14 15 12 13 10 11 12 13 14 10 11 8 9 5 6 7 8 9 6 7 4 5 0 1 2 3 4 2 3 0 1

So, junction should be (4,2)(4,4),(9,6),(9,8),(14,10),(14,12)

References CylMesh::innerSetCoords(), CubeMesh::innerSetCoords(), CubeMesh::matchCubeMeshEntries(), CubeMesh::setPreserveNumEntries(), and CubeMesh::surface().

Referenced by testMesh().

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void testCubeMeshJunctionThreeDimSurface ( )

Referenced by testMesh().

void testCubeMeshJunctionTwoDimSurface ( )

8 9 10 11 12 13 14 6 7 5 6 7 8 9 4 5 0 1 2 3 4 2 3 0 1

So, junction should be (4,2),(9,4),(14,6)

That was too easy, since the spatial and meshIndices were identical. Now trim the geometries a bit to look like: 6 7 10 11 12 13 - 4 5 5 6 7 8 9 2 3 0 1 2 3 4 - 1

0

So, junction should be (9,2) only.

References CubeMesh::getMeshToSpace(), CubeMesh::getSpaceToMesh(), CylMesh::innerSetCoords(), CubeMesh::innerSetCoords(), CubeMesh::matchCubeMeshEntries(), CubeMesh::setMeshToSpace(), CubeMesh::setPreserveNumEntries(), CubeMesh::setSpaceToMesh(), CubeMesh::setSurface(), and CubeMesh::surface().

Referenced by testMesh().

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void testCubeMeshMultiJunctionTwoD ( )

The simulated geometry is: D D BBBA CCCCC Here, A is at (0,0,0) to (10,10,10) microns. B is then (-30,0,0) to (0,10,10) microns C is (-30,-10,0) to (20,0,10) microns D is (0,10,0) to (10,30,10) microns.

References CubeMesh::innerSetCoords(), CubeMesh::setPreserveNumEntries(), and CubeMesh::surface().

Referenced by testMesh().

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