Chaste  Release::2018.1
CellPopulationElementWriter.cpp
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35 
36 #include "CellPopulationElementWriter.hpp"
37 #include "AbstractCellPopulation.hpp"
38 #include "MeshBasedCellPopulation.hpp"
39 #include "CaBasedCellPopulation.hpp"
40 #include "NodeBasedCellPopulation.hpp"
41 #include "PottsBasedCellPopulation.hpp"
42 #include "VertexBasedCellPopulation.hpp"
43 
44 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
46  : AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM>("results.vizelements")
47 {
48 }
49 
50 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
52 {
54  elem_iter != static_cast<MutableMesh<ELEMENT_DIM,SPACE_DIM>&>((pCellPopulation->rGetMesh())).GetElementIteratorEnd();
55  ++elem_iter)
56  {
57  bool element_contains_dead_cells_or_deleted_nodes = false;
58 
59  // Hack that covers the case where the element contains a node that is associated with a cell that has just been killed (#1129)
60  for (unsigned i=0; i<ELEMENT_DIM+1; i++)
61  {
62  unsigned node_index = elem_iter->GetNodeGlobalIndex(i);
63 
64  if (pCellPopulation->GetNode(node_index)->IsDeleted())
65  {
66  element_contains_dead_cells_or_deleted_nodes = true;
67  break;
68  }
69  else if (pCellPopulation->IsCellAttachedToLocationIndex(node_index))
70  {
71  if (pCellPopulation->GetCellUsingLocationIndex(node_index)->IsDead())
72  {
73  element_contains_dead_cells_or_deleted_nodes = true;
74  break;
75  }
76  }
77  }
78  if (!element_contains_dead_cells_or_deleted_nodes)
79  {
80  for (unsigned i=0; i<ELEMENT_DIM+1; i++)
81  {
82  *this->mpOutStream << elem_iter->GetNodeGlobalIndex(i) << " ";
83  }
84  }
85  }
86 }
87 
88 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
90 {
91  EXCEPTION("CellPopulationElementWriter cannot be used with a CaBasedCellPopulation");
92 }
93 
94 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
96 {
97  EXCEPTION("CellPopulationElementWriter cannot be used with a NodeBasedCellPopulation");
98 }
99 
100 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
102 {
103  // Loop over cells and find associated elements so in the same order as the cells in output files
104  for (typename AbstractCellPopulation<SPACE_DIM, SPACE_DIM>::Iterator cell_iter = pCellPopulation->Begin();
105  cell_iter != pCellPopulation->End();
106  ++cell_iter)
107  {
108  unsigned elem_index = pCellPopulation->GetLocationIndexUsingCell(*cell_iter);
109 
110  // Hack that covers the case where the element is associated with a cell that has just been killed (#1129)
111  bool elem_corresponds_to_dead_cell = false;
112 
113  if (pCellPopulation->IsCellAttachedToLocationIndex(elem_index))
114  {
115  elem_corresponds_to_dead_cell = pCellPopulation->GetCellUsingLocationIndex(elem_index)->IsDead();
116  }
117 
118  // Write element data to file
119  if (!(pCellPopulation->GetElement(elem_index)->IsDeleted()) && !elem_corresponds_to_dead_cell)
120  {
121  PottsElement<SPACE_DIM>* p_element = pCellPopulation->rGetMesh().GetElement(elem_index);
122  unsigned num_nodes_in_element = p_element->GetNumNodes();
123 
124  // First write the number of Nodes belonging to this VertexElement
125  *this->mpOutStream << num_nodes_in_element << " ";
126 
127  // Then write the global index of each Node in this element
128  for (unsigned i=0; i<num_nodes_in_element; i++)
129  {
130  *this->mpOutStream << p_element->GetNodeGlobalIndex(i) << " ";
131  }
132  }
133  }
134 }
135 
136 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
138 {
139  // Loop over cells and find associated elements so in the same order as the cells in output files
140  for (typename AbstractCellPopulation<SPACE_DIM, SPACE_DIM>::Iterator cell_iter = pCellPopulation->Begin();
141  cell_iter != pCellPopulation->End();
142  ++cell_iter)
143  {
144  unsigned elem_index = pCellPopulation->GetLocationIndexUsingCell(*cell_iter);
145 
146  // Hack that covers the case where the element is associated with a cell that has just been killed (#1129)
147  bool elem_corresponds_to_dead_cell = false;
148 
149  if (pCellPopulation->IsCellAttachedToLocationIndex(elem_index))
150  {
151  elem_corresponds_to_dead_cell = pCellPopulation->GetCellUsingLocationIndex(elem_index)->IsDead();
152  }
153 
154  // Write element data to file
155  if (!(pCellPopulation->GetElement(elem_index)->IsDeleted()) && !elem_corresponds_to_dead_cell)
156  {
157  VertexElement<SPACE_DIM, SPACE_DIM>* p_element = pCellPopulation->rGetMesh().GetElement(elem_index);
158  unsigned num_nodes_in_element = p_element->GetNumNodes();
159 
160  // First write the number of Nodes belonging to this VertexElement
161  *this->mpOutStream << num_nodes_in_element << " ";
162 
163  // Then write the global index of each Node in this element
164  for (unsigned i=0; i<num_nodes_in_element; i++)
165  {
166  *this->mpOutStream << p_element->GetNodeGlobalIndex(i) << " ";
167  }
168  }
169  }
170 }
171 
172 // Explicit instantiation
173 template class CellPopulationElementWriter<1,1>;
174 template class CellPopulationElementWriter<1,2>;
175 template class CellPopulationElementWriter<2,2>;
176 template class CellPopulationElementWriter<1,3>;
177 template class CellPopulationElementWriter<2,3>;
178 template class CellPopulationElementWriter<3,3>;
179 
181 // Declare identifier for the serializer
ElementIterator GetElementIteratorBegin(bool skipDeletedElements=true)
virtual void Visit(MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)
virtual CellPtr GetCellUsingLocationIndex(unsigned index)
unsigned GetLocationIndexUsingCell(CellPtr pCell)
unsigned GetNodeGlobalIndex(unsigned localIndex) const
#define EXCEPTION(message)
Definition: Exception.hpp:143
virtual bool IsCellAttachedToLocationIndex(unsigned index)
VertexElement< ELEMENT_DIM, SPACE_DIM > * GetElement(unsigned index) const
Definition: VertexMesh.cpp:628
MutableMesh< ELEMENT_DIM, SPACE_DIM > & rGetMesh()
MutableVertexMesh< DIM, DIM > & rGetMesh()
unsigned GetNumNodes() const
#define EXPORT_TEMPLATE_CLASS_ALL_DIMS(CLASS)
Node< SPACE_DIM > * GetNode(unsigned index)
PottsElement< DIM > * GetElement(unsigned elementIndex)
VertexElement< DIM, DIM > * GetElement(unsigned elementIndex)