Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
ImmersedBoundaryMeshWriter.hpp
1/*
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3Copyright (c) 2005-2024, University of Oxford.
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34*/
35
36#ifndef IMMERSEDBOUNDARYMESHWRITER_HPP_
37#define IMMERSEDBOUNDARYMESHWRITER_HPP_
38
39// Forward declaration prevents circular include chain
40template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
42
43#ifdef CHASTE_VTK
44// Requires "sudo aptitude install libvtk5-dev" or similar
45#define _BACKWARD_BACKWARD_WARNING_H 1 // Cut out the strstream deprecated warning for now (gcc4.3)
46#include <vtkDoubleArray.h>
47#include <vtkCellData.h>
48#include <vtkPointData.h>
49#include <vtkConvexPointSet.h>
50#include <vtkPolygon.h>
51#include <vtkUnstructuredGrid.h>
52#include <vtkUnstructuredGridWriter.h>
53#include <vtkXMLUnstructuredGridWriter.h>
54#include <vtkDataCompressor.h>
55#endif //CHASTE_VTK
56
57#include "AbstractMeshWriter.hpp"
58#include "ImmersedBoundaryMesh.hpp"
59
60#include <boost/geometry.hpp>
61#include <boost/geometry/geometries/segment.hpp>
62#include <boost/geometry/geometries/point.hpp>
63
64
65// Forward declaration prevents circular include chain
66template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
68
69template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
71
75template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
76class ImmersedBoundaryMeshWriter : public AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>
77{
78private:
84
87
89 unsigned mNumLaminas;
90
92 std::vector<std::vector<unsigned>> mElementParts;
93
94 // Node that this assumes SPACE_DIM == 2
96 using geom_point = boost::geometry::model::point<double, 2, boost::geometry::cs::cartesian>;
97
99 using geom_segment = boost::geometry::model::segment<geom_point>;
100
102 std::array<geom_segment, 4> mBoundaryEdges;
103
114 c_vector<double, SPACE_DIM> GetIntersectionOfEdgeWithBoundary(const c_vector<double, SPACE_DIM>& rStart,
115 const c_vector<double, SPACE_DIM>& rEnd);
116
123 c_vector<double, SPACE_DIM> GetNearestCorner(const c_vector<double, SPACE_DIM>& rA,
124 const c_vector<double, SPACE_DIM>& rB) const;
125
126#ifdef CHASTE_VTK
127//Requires "sudo aptitude install libvtk5-dev" or similar
129 vtkUnstructuredGrid* mpVtkUnstructedMesh;
130#endif //CHASTE_VTK
131
132public:
133
141 ImmersedBoundaryMeshWriter(const std::string& rDirectory,
142 const std::string& rBaseName,
143 bool clearOutputDir=true);
144
149
156
163 void WriteVtkUsingMesh(ImmersedBoundaryMesh<ELEMENT_DIM, SPACE_DIM>& rMesh, std::string stamp="");
164
172
179 void AddCellData(std::string dataName, std::vector<double> dataPayload);
180
187 void AddPointData(std::string dataName, std::vector<double> dataPayload);
188
192 std::vector<double> GetNextNode();
193
198
203
208 void WriteFiles();
209
216
218 const std::vector<std::vector<unsigned>>& rGetElementParts() const;
219};
220
221#endif /*IMMERSEDBOUNDARYMESHWRITER_HPP_*/
boost::geometry::model::point< double, 2, boost::geometry::cs::cartesian > geom_point
void FindElementOverlaps(ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
ImmersedBoundaryElementData GetNextImmersedBoundaryElement()
c_vector< double, SPACE_DIM > GetNearestCorner(const c_vector< double, SPACE_DIM > &rA, const c_vector< double, SPACE_DIM > &rB) const
ImmersedBoundaryElementData GetNextImmersedBoundaryLamina()
const std::vector< std::vector< unsigned > > & rGetElementParts() const
void WriteVtkUsingMesh(ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::string stamp="")
void AddPointData(std::string dataName, std::vector< double > dataPayload)
void MakeVtkMesh(ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
std::array< geom_segment, 4 > mBoundaryEdges
std::vector< std::vector< unsigned > > mElementParts
void WriteFilesUsingMesh(ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
boost::geometry::model::segment< geom_point > geom_segment
c_vector< double, SPACE_DIM > GetIntersectionOfEdgeWithBoundary(const c_vector< double, SPACE_DIM > &rStart, const c_vector< double, SPACE_DIM > &rEnd)
void AddCellData(std::string dataName, std::vector< double > dataPayload)
ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM > * mpMesh
MeshWriterIterators< ELEMENT_DIM, SPACE_DIM > * mpIters