#include <FineCoarseMeshPair.hpp>
Collaboration diagram for FineCoarseMeshPair< DIM >:
Detailed Description
template<unsigned DIM>
class FineCoarseMeshPair< DIM >
Class for a pair of meshes, one fine, one coarse, which should cover the same domain (or very nearly match). This class is used to set up interpolation information from one mesh to the other.
At the moment the functionality is very much based on the four information-transfers required in cardiac electro-mechanics problems
(i) Calcium (or voltage) to induce deformation: FINE(electrics) MESH NODEs ---> COARSE(mechanics) MESH QUADRATURE POINTS (ii) Deformation gradient (assume constant in any coarse element) for altering conductivities: COARSE ELEMENTS ---> FINE ELEMENTS (iii) Deformation gradient/fibre-stretch (assume constant in any coarse element) for cell-model stretch activated channels COARSE ELEMENTS ---> FINE NODES (iv) Voltage visualisation on coarse mesh FINE NODES ---> COARSE NODES
The usage of this class for each of these tasks is:
(i) FINE NODEs ---> COARSE QUADRATURE POINTS FineCoarseMeshPair<2> mesh_pair(fine_mesh,coarse_mesh); mesh_pair.SetUpBoxesOnFineMesh(); mesh_pair.ComputeFineElementsAndWeightsForCoarseQuadPoints(quad_rule, false); mesh_pair.rGetElementsAndWeights(); (ii) COARSE ELEMENTS ---> FINE ELEMENTS FineCoarseMeshPair<2> mesh_pair(fine_mesh,coarse_mesh); mesh_pair.SetUpBoxesOnCoarseMesh(); mesh_pair.ComputeCoarseElementsForFineElementCentroids(); mesh_pair.rGetCoarseElementsForFineElementCentroids(); (iii) COARSE ELEMENTS ---> FINE NODES FineCoarseMeshPair<2> mesh_pair(fine_mesh,coarse_mesh); mesh_pair.SetUpBoxesOnCoarseMesh(); mesh_pair.ComputeCoarseElementsForFineNodes(); mesh_pair.rGetCoarseElementsForFineNodes();
Note the following should not be done at the same time as (i), as the results are stored in the same place (iv) FINE NODES ---> COARSE NODES FineCoarseMeshPair<2> mesh_pair(fine_mesh,coarse_mesh); mesh_pair.SetUpBoxesOnFineMesh(); mesh_pair.ComputeFineElementsAndWeightsForCoarseNodes(false); mesh_pair.rGetElementsAndWeights();
To see progression for any of these methods, run test from the command line with '-mesh_pair_verbose' as a command line parameter
Definition at line 108 of file FineCoarseMeshPair.hpp.
Constructor & Destructor Documentation
| FineCoarseMeshPair< DIM >::FineCoarseMeshPair | ( | TetrahedralMesh< DIM, DIM > & | rFineMesh, |
| TetrahedralMesh< DIM, DIM > & | rCoarseMesh | ||
| ) |
Constructor sets up domain size.
- Parameters:
-
rFineMesh Fine mesh (reference) rCoarseMesh Coarse mesh (reference)
Definition at line 39 of file FineCoarseMeshPair.cpp.
References FineCoarseMeshPair< DIM >::mpCoarseMeshBoxCollection, FineCoarseMeshPair< DIM >::mpFineMeshBoxCollection, and FineCoarseMeshPair< DIM >::ResetStatisticsVariables().
| FineCoarseMeshPair< DIM >::~FineCoarseMeshPair | ( | ) |
Destructor just deletes the box collection.
Definition at line 61 of file FineCoarseMeshPair.cpp.
Member Function Documentation
| void FineCoarseMeshPair< DIM >::CollectElementsInContainingBox | ( | BoxCollection< DIM > *& | rpBoxCollection, |
| unsigned | boxIndex, | ||
| std::set< unsigned > & | rElementIndices | ||
| ) | [private] |
Helper method. Gets all the elements in the given box, in the given box collection and puts them in the returned std::vector.
- Parameters:
-
rpBoxCollection Reference to the box collection to use (either mpFineBoxCollection or mpCoarseBoxCollection) boxIndex box index rElementIndices The returned vector of element indices in that box of the box collection. Not cleared before use.
Definition at line 540 of file FineCoarseMeshPair.cpp.
References BoxCollection< DIM >::rGetBox().
| void FineCoarseMeshPair< DIM >::CollectElementsInLocalBoxes | ( | BoxCollection< DIM > *& | rpBoxCollection, |
| unsigned | boxIndex, | ||
| std::set< unsigned > & | rElementIndices | ||
| ) | [private] |
Helper method. Gets all the elements in the given box, or in a box local to the given box, in the given box collection, and puts them in the returned std::vector.
- Parameters:
-
rpBoxCollection Reference to the box collection to use (either mpFineBoxCollection or mpCoarseBoxCollection) boxIndex box index rElementIndices The returned vector of element indices in that box or a local box. Not cleared before use.
Definition at line 553 of file FineCoarseMeshPair.cpp.
References BoxCollection< DIM >::GetLocalBoxes(), and BoxCollection< DIM >::rGetBox().
| unsigned FineCoarseMeshPair< DIM >::ComputeCoarseElementForGivenPoint | ( | ChastePoint< DIM > & | rPoint, |
| bool | safeMode, | ||
| unsigned | boxForThisPoint | ||
| ) | [private] |
For a given point, compute the containing element in the coarse mesh (returned).
- Parameters:
-
rPoint The point safeMode See documentation in ComputeCoarseElementsForFineNodes boxForThisPoint The box in coarse box collection containing this point
- Todo:
- : could possibly merge with ComputeFineElementAndWeightForGivenPoint(). Differences between the methods are: the other method uses fine mesh and fine mesh box, computes weights as well (and sets the element and weight in the vec), rather than returning the element, and that method saves information in mStatisticsCounters.
Definition at line 470 of file FineCoarseMeshPair.cpp.
| void FineCoarseMeshPair< DIM >::ComputeCoarseElementsForFineElementCentroids | ( | bool | safeMode | ) |
Compute the element in the coarse mesh that each fine element centroid is contained in (or nearest to). Call SetUpBoxesOnCoarseMesh() before, and rGetCoarseElementsForFineElementCentroids() afterwards.
- Parameters:
-
safeMode This method uses the elements in the boxes to guess which element a point is in. If a point is in none of these elements, then if safeMode==true, it will then search the whole mesh. If safeMode==false it will assume immediately the point isn't in the coarse mesh at all. safeMode=false is will far more efficient with big meshes. It should be fine to use safeMode=false if SetUpBoxesOnFineMesh() is called with default values.
Definition at line 427 of file FineCoarseMeshPair.cpp.
References EXCEPTION, CommandLineArguments::Instance(), and CommandLineArguments::OptionExists().
| void FineCoarseMeshPair< DIM >::ComputeCoarseElementsForFineNodes | ( | bool | safeMode | ) |
Compute the element in the coarse mesh that each fine mesh node is contained in (or nearest to). Call SetUpBoxesOnCoarseMesh() before, and rGetCoarseElementsForFineNodes() afterwards.
- Parameters:
-
safeMode This method uses the elements in the boxes to guess which element a point is in. If a point is in none of these elements, then if safeMode==true, it will then search the whole mesh. If safeMode==false it will assume immediately the point isn't in the coarse mesh at all. safeMode=false is will far more efficient with big meshes. It should be fine to use safeMode=false if SetUpBoxesOnFineMesh() is called with default values.
Definition at line 391 of file FineCoarseMeshPair.cpp.
References EXCEPTION, CommandLineArguments::Instance(), and CommandLineArguments::OptionExists().
| void FineCoarseMeshPair< DIM >::ComputeFineElementAndWeightForGivenPoint | ( | ChastePoint< DIM > & | rPoint, |
| bool | safeMode, | ||
| unsigned | boxForThisPoint, | ||
| unsigned | index | ||
| ) | [private] |
For a given point, compute the containing element and corresponding weight in the fine mesh.
- Parameters:
-
rPoint The point safeMode See documentation for ComputeFineElementsAndWeightsForCoarseQuadPoints() boxForThisPoint The box in the fine box collection containing this point index The index into the mFineMeshElementsAndWeights std::vector
- Todo:
- : could possibly merge with ComputeCoarseElementForGivenPoint(). Difference between the methods are: this uses fine mesh and fine mesh box, computes weights as well (and sets the element and weight in the vec), rather than returning the element, and this method saves information in mStatisticsCounters.
Definition at line 293 of file FineCoarseMeshPair.cpp.
| void FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseNodes | ( | bool | safeMode | ) |
Set up the containing (fine) elements and corresponding weights for all the nodes in the coarse mesh. Call GetElementsAndWeights() after calling this with the index of the nodes.
If calling this DO NOT call ComputeFineElementsAndWeightsForCoarseQuadPoints until you do done with this data.
- Parameters:
-
safeMode This method uses the elements in the boxes to guess which element a point is in. If a point is in none of these elements, then if safeMode==true, it will then search the whole mesh. If safeMode==false it will assume immediately the point isn't in the coarse mesh at all. safeMode=false is will far more efficient with big meshes. It should be fine to use safeMode=false if SetUpBoxesOnFineMesh() is called with default values.
Definition at line 246 of file FineCoarseMeshPair.cpp.
References EXCEPTION, CommandLineArguments::Instance(), CommandLineArguments::OptionExists(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().
Referenced by VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().
| void FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseQuadPoints | ( | GaussianQuadratureRule< DIM > & | rQuadRule, |
| bool | safeMode | ||
| ) |
Set up the containing (fine) elements and corresponding weights for all the quadrature points in the coarse mesh. Call GetElementsAndWeights() after calling this with the index of the quad point (=the index of the quad point in a QuadraturePointsGroup= the index if the quad points were listed by looping over all the element and then looping over all the quad points).
If calling this DO NOT call ComputeFineElementsAndWeightsForCoarseNodes until you do done with this data
- Parameters:
-
rQuadRule The quadrature rule, used to determine the number of quadrature points per element. safeMode This method uses the elements in the boxes to guess which element a quad point is in. If a quad point is in none of these elements, then if safeMode==true, it will then search the whole mesh. If safeMode==false it will assume immediately the quad point isn't in the mesh at all. safeMode=false is will far more efficient with big meshes. It should be fine to use safeMode=false if SetUpBoxesOnFineMesh() is called with default values.
Definition at line 198 of file FineCoarseMeshPair.cpp.
References EXCEPTION, QuadraturePointsGroup< DIM >::Get(), CommandLineArguments::Instance(), CommandLineArguments::OptionExists(), and QuadraturePointsGroup< DIM >::Size().
| void FineCoarseMeshPair< DIM >::DeleteCoarseBoxCollection | ( | ) |
Destroy the box collection for the coarse mesh - can be used to free memory once ComputeCoarseElementsForFineNodes (etc) has been called.
Definition at line 78 of file FineCoarseMeshPair.cpp.
| void FineCoarseMeshPair< DIM >::DeleteFineBoxCollection | ( | ) |
Destroy the box collection for the fine mesh - can be used to free memory once ComputeFineElementsAndWeightsForCoarseQuadPoints (etc) has been called.
Definition at line 68 of file FineCoarseMeshPair.cpp.
| const TetrahedralMesh< DIM, DIM > & FineCoarseMeshPair< DIM >::GetCoarseMesh | ( | ) | const |
Access the coarse mesh of this mesh pair
- Returns:
- the coarse mesh
Definition at line 55 of file FineCoarseMeshPair.cpp.
Referenced by AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetFineCoarseMeshPair().
| const TetrahedralMesh< DIM, DIM > & FineCoarseMeshPair< DIM >::GetFineMesh | ( | ) | const |
Access the fine mesh of this mesh pair
- Returns:
- the fine mesh
Definition at line 49 of file FineCoarseMeshPair.cpp.
| void FineCoarseMeshPair< DIM >::PrintStatistics | ( | ) |
Print information about the number of points found in the searched mesh. What the points are and which mesh was searched depends on whichever of the main Compute methods was last called.
If ComputeFineElementsAndWeightsForCoarseQuadPoints() or ComputeFineElementsAndWeightsForCoarseNodes() were last called, the indices of the points that were not found to be contained in the searched mesh are also printed, along with the weights for that point in the nearest element (which indicates how far from the mesh the points are).
Definition at line 584 of file FineCoarseMeshPair.cpp.
| void FineCoarseMeshPair< DIM >::ResetStatisticsVariables | ( | ) | [private] |
Resets mNotInMesh, mNotInMeshNearestElementWeights and mStatisticsCounters.
Definition at line 576 of file FineCoarseMeshPair.cpp.
Referenced by FineCoarseMeshPair< DIM >::FineCoarseMeshPair().
| std::vector<unsigned>& FineCoarseMeshPair< DIM >::rGetCoarseElementsForFineElementCentroids | ( | ) | [inline] |
Get the elements in the coarse mesh that each fine mesh element centroid is contained in (or nearest to). ComputeCoarseElementsForFineElementCentroids() needs to be called before calling this.
Definition at line 384 of file FineCoarseMeshPair.hpp.
References FineCoarseMeshPair< DIM >::mCoarseElementsForFineElementCentroids.
| std::vector<unsigned>& FineCoarseMeshPair< DIM >::rGetCoarseElementsForFineNodes | ( | ) | [inline] |
Get the elements in the coarse mesh that each fine mesh node is contained in (or nearest to). ComputeCoarseElementsForFineNodes() needs to be called before calling this.
Definition at line 374 of file FineCoarseMeshPair.hpp.
References FineCoarseMeshPair< DIM >::mCoarseElementsForFineNodes.
| std::vector<ElementAndWeights<DIM> >& FineCoarseMeshPair< DIM >::rGetElementsAndWeights | ( | ) | [inline] |
- Returns:
- A reference to the elements/weights information
Definition at line 365 of file FineCoarseMeshPair.hpp.
References FineCoarseMeshPair< DIM >::mFineMeshElementsAndWeights.
Referenced by VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().
| void FineCoarseMeshPair< DIM >::SetUpBoxes | ( | TetrahedralMesh< DIM, DIM > & | rMesh, |
| double | boxWidth, | ||
| BoxCollection< DIM > *& | rpBoxCollection | ||
| ) | [private] |
Set up a box collection on the given mesh. Should only be called using either SetUpBoxes(*mpFineMesh, boxWidth, mpFineBoxCollection) (from SetUpBoxesOnFineMesh) or SetUpBoxes(*mpCoarseMesh, boxWidth, mpCoarseBoxCollection) (from SetUpBoxesOnCoarseMesh)
- Parameters:
-
rMesh The mesh, either *mpFineMesh or *mpCoarseMesh) boxWidth box width (see SetUpBoxesOnCoarseMesh() dox) rpBoxCollection reference to either mpFineBoxCollection or mpCoarseBoxCollection
Definition at line 104 of file FineCoarseMeshPair.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox(), BoxCollection< DIM >::CalculateContainingBox(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesBegin(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesEnd(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), ChasteCuboid< SPACE_DIM >::GetWidth(), BoxCollection< DIM >::rGetBox(), ChasteCuboid< SPACE_DIM >::rGetLowerCorner(), ChasteCuboid< SPACE_DIM >::rGetUpperCorner(), and BoxCollection< DIM >::SetupAllLocalBoxes().
| void FineCoarseMeshPair< DIM >::SetUpBoxesOnCoarseMesh | ( | double | boxWidth = -1 | ) |
Set up boxes on coarse mesh. The elements contained in each box is stored, which makes finding the containing element for a given point much faster. This should be called before ComputeCoarseElementsForFineNodes() or ComputeCoarseElementsForFineElementCentroids()
- Parameters:
-
boxWidth width to use for the boxes (which will be cubes). Note that a domain which is a touch larger than the smallest containing cuboid of the fine mesh is used. boxWidth defaults to a negative value, in which case a box width such that there are approximately 20 boxes in the x-direction, unless this width is less than maximum (fine mesh edge length), in which case it is chosen accordingly.
Definition at line 98 of file FineCoarseMeshPair.cpp.
| void FineCoarseMeshPair< DIM >::SetUpBoxesOnFineMesh | ( | double | boxWidth = -1 | ) |
Set up boxes on fine mesh. The elements contained in each box is stored, which makes finding the containing element for a given point much faster. This should be called before ComputeFineElementsAndWeightsForCoarseQuadPoints() or ComputeFineElementsAndWeightsForCoarseNodes().
- Parameters:
-
boxWidth width to use for the boxes (which will be cubes). Note that a domain which is a touch larger than the smallest containing cuboid of the fine mesh is used. boxWidth defaults to a negative value, in which case a box width such that there are approximately 20 boxes in the x-direction, unless this width is less than maximum (fine mesh edge length), in which case it is chosen accordingly.
Definition at line 92 of file FineCoarseMeshPair.cpp.
Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Initialise(), and VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().
Member Data Documentation
std::vector<unsigned> FineCoarseMeshPair< DIM >::mCoarseElementsForFineElementCentroids [private] |
The element in the coarse mesh that each fine element centroid is contained in (or nearest to). ComputeCoarseElementsForFineElementCentroids() needs to be called for this to be set up.
Definition at line 170 of file FineCoarseMeshPair.hpp.
Referenced by FineCoarseMeshPair< DIM >::rGetCoarseElementsForFineElementCentroids().
std::vector<unsigned> FineCoarseMeshPair< DIM >::mCoarseElementsForFineNodes [private] |
The element in the coarse mesh that each fine mesh node is contained in (or nearest to). ComputeCoarseElementsForFineNodes() needs to be called for this to be set up.
Definition at line 163 of file FineCoarseMeshPair.hpp.
Referenced by FineCoarseMeshPair< DIM >::rGetCoarseElementsForFineNodes().
std::vector<ElementAndWeights<DIM> > FineCoarseMeshPair< DIM >::mFineMeshElementsAndWeights [private] |
The containing elements and corresponding weights in the fine mesh for the set of points given. The points may have been quadrature points in the coarse mesh, or nodes in coarse mesh, etc.
Definition at line 136 of file FineCoarseMeshPair.hpp.
Referenced by FineCoarseMeshPair< DIM >::rGetElementsAndWeights().
std::vector<unsigned> FineCoarseMeshPair< DIM >::mNotInMesh [private] |
Indices of the points which were found to be outside the fine mesh.
Definition at line 139 of file FineCoarseMeshPair.hpp.
std::vector<c_vector<double,DIM+1> > FineCoarseMeshPair< DIM >::mNotInMeshNearestElementWeights [private] |
The corresponding weights, for the nearest elements, of the points which were found to be outside the fine mesh.
Definition at line 145 of file FineCoarseMeshPair.hpp.
BoxCollection<DIM>* FineCoarseMeshPair< DIM >::mpCoarseMeshBoxCollection [private] |
Boxes on the coarse mesh domain, for easier determination of containing element for a given point.
Definition at line 129 of file FineCoarseMeshPair.hpp.
Referenced by FineCoarseMeshPair< DIM >::FineCoarseMeshPair().
BoxCollection<DIM>* FineCoarseMeshPair< DIM >::mpFineMeshBoxCollection [private] |
Boxes on the fine mesh domain, for easier determination of containingelement for a given point.
Definition at line 123 of file FineCoarseMeshPair.hpp.
Referenced by FineCoarseMeshPair< DIM >::FineCoarseMeshPair().
TetrahedralMesh<DIM,DIM>& FineCoarseMeshPair< DIM >::mrCoarseMesh [private] |
Coarse mesh (often be a quadratic mesh).
Definition at line 118 of file FineCoarseMeshPair.hpp.
TetrahedralMesh<DIM,DIM>& FineCoarseMeshPair< DIM >::mrFineMesh [private] |
Fine mesh.
Definition at line 115 of file FineCoarseMeshPair.hpp.
std::vector<unsigned> FineCoarseMeshPair< DIM >::mStatisticsCounters [private] |
2 values, [0] number of points for which the containing element was found [1] num points not in the searched mesh at all
Note, after ComputeFineElementsAndWeightsForCoarseQuadPoints() or ComputeFineElementsAndWeightsForCoarseNodes(), then mCounters[1] = mNotInMesh.size() = mNotInMeshNearestElementWeights.size();
Definition at line 156 of file FineCoarseMeshPair.hpp.
The documentation for this class was generated from the following files:
- pde/src/common/FineCoarseMeshPair.hpp
- pde/src/common/FineCoarseMeshPair.cpp
