Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
AbstractGrowingDomainPdeModifier.cpp
1/*
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34*/
35
36#include "AbstractGrowingDomainPdeModifier.hpp"
37#include "VertexBasedCellPopulation.hpp"
38#include "MeshBasedCellPopulation.hpp"
39#include "CaBasedCellPopulation.hpp"
40#include "NodeBasedCellPopulation.hpp"
41#include "ReplicatableVector.hpp"
42#include "LinearBasisFunction.hpp"
43
44template <unsigned DIM>
46 boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition,
47 bool isNeumannBoundaryCondition,
48 Vec solution)
49 : AbstractPdeModifier<DIM>(pPde,
50 pBoundaryCondition,
51 isNeumannBoundaryCondition,
52 solution)
53{
54}
55
56template<unsigned DIM>
60
61template<unsigned DIM>
63{
64 if (this->mDeleteFeMesh)
65 {
66 // If a mesh has been created on a previous time step then we need to tidy it up
67 assert(this->mpFeMesh != nullptr);
68 delete this->mpFeMesh;
69 }
70 else
71 {
73 // This placement assumes that if this->mDeleteFeMesh is false it is uninitialised and needs to
74 // be checked. If true, it has been checked elsewhere.
75 this->mDeleteFeMesh = (dynamic_cast<MeshBasedCellPopulation<DIM>*>(&rCellPopulation) == nullptr);
76 }
77
78 // Get the finite element mesh via the cell population. Set to NULL first in case mesh generation fails.
79 this->mpFeMesh = nullptr;
80 this->mpFeMesh = rCellPopulation.GetTetrahedralMeshForPdeModifier();
81}
82
83template<unsigned DIM>
85{
86 // Store the PDE solution in an accessible form
87 ReplicatableVector solution_repl(this->mSolution);
88
89 // Local cell index used by the CA simulation
90 unsigned cell_index = 0;
91
92 unsigned index_in_solution_repl = 0;
93 for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
94 cell_iter != rCellPopulation.End();
95 ++cell_iter)
96 {
97 unsigned tet_node_index = rCellPopulation.GetLocationIndexUsingCell(*cell_iter);
98
100 if (dynamic_cast<VertexBasedCellPopulation<DIM>*>(&rCellPopulation) != nullptr)
101 {
102 // Offset to relate elements in vertex mesh to nodes in tetrahedral mesh
103 tet_node_index += rCellPopulation.GetNumNodes();
104 }
105 else if (dynamic_cast<CaBasedCellPopulation<DIM>*>(&rCellPopulation) != nullptr)
106 {
107 // Here local cell index corresponds to tet node
108 tet_node_index = cell_index;
109 cell_index++;
110 }
111 else if (dynamic_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation) != nullptr)
112 {
113 tet_node_index = index_in_solution_repl;
114 index_in_solution_repl++;
115 }
116
117 double solution_at_node = solution_repl[tet_node_index];
118
119 cell_iter->GetCellData()->SetItem(this->mDependentVariableName, solution_at_node);
120
121 if (this->mOutputGradient)
122 {
123 // Now calculate the gradient of the solution and store this in CellVecData
124 c_vector<double, DIM> solution_gradient = zero_vector<double>(DIM);
125
126 Node<DIM>* p_tet_node = this->mpFeMesh->GetNode(tet_node_index);
127
128 // Get the containing elements and average the contribution from each one
129 for (typename Node<DIM>::ContainingElementIterator element_iter = p_tet_node->ContainingElementsBegin();
130 element_iter != p_tet_node->ContainingElementsEnd();
131 ++element_iter)
132 {
133 // Calculate the basis functions at any point (eg zero) in the element
134 c_matrix<double, DIM, DIM> jacobian, inverse_jacobian;
135 double jacobian_det;
136 this->mpFeMesh->GetInverseJacobianForElement(*element_iter, jacobian, jacobian_det, inverse_jacobian);
137 const ChastePoint<DIM> zero_point;
138 c_matrix<double, DIM, DIM+1> grad_phi;
139 LinearBasisFunction<DIM>::ComputeTransformedBasisFunctionDerivatives(zero_point, inverse_jacobian, grad_phi);
140
141 // Add the contribution from this element
142 for (unsigned node_index=0; node_index<DIM+1; node_index++)
143 {
144 double nodal_value = solution_repl[this->mpFeMesh->GetElement(*element_iter)->GetNodeGlobalIndex(node_index)];
145
146 for (unsigned j=0; j<DIM; j++)
147 {
148 solution_gradient(j) += nodal_value* grad_phi(j, node_index);
149 }
150 }
151 }
152
153 // Divide by number of containing elements
154 solution_gradient /= p_tet_node->GetNumContainingElements();
155
156 switch (DIM)
157 {
158 case 1:
159 cell_iter->GetCellData()->SetItem(this->mDependentVariableName+"_grad_x", solution_gradient(0));
160 break;
161 case 2:
162 cell_iter->GetCellData()->SetItem(this->mDependentVariableName+"_grad_x", solution_gradient(0));
163 cell_iter->GetCellData()->SetItem(this->mDependentVariableName+"_grad_y", solution_gradient(1));
164 break;
165 case 3:
166 cell_iter->GetCellData()->SetItem(this->mDependentVariableName+"_grad_x", solution_gradient(0));
167 cell_iter->GetCellData()->SetItem(this->mDependentVariableName+"_grad_y", solution_gradient(1));
168 cell_iter->GetCellData()->SetItem(this->mDependentVariableName+"_grad_z", solution_gradient(2));
169 break;
170 default:
172 }
173 }
174 }
175}
176
177template<unsigned DIM>
179{
180 // No parameters to output, so just call method on direct parent class
182}
183
184// Explicit instantiation
#define NEVER_REACHED
unsigned GetLocationIndexUsingCell(CellPtr pCell)
virtual TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * GetTetrahedralMeshForPdeModifier()=0
virtual unsigned GetNumNodes()=0
void GenerateFeMesh(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
AbstractGrowingDomainPdeModifier(boost::shared_ptr< AbstractLinearPde< DIM, DIM > > pPde=boost::shared_ptr< AbstractLinearPde< DIM, DIM > >(), boost::shared_ptr< AbstractBoundaryCondition< DIM > > pBoundaryCondition=boost::shared_ptr< AbstractBoundaryCondition< DIM > >(), bool isNeumannBoundaryCondition=true, Vec solution=nullptr)
void UpdateCellData(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
static void ComputeTransformedBasisFunctionDerivatives(const ChastePoint< ELEMENT_DIM > &rPoint, const c_matrix< double, ELEMENT_DIM, ELEMENT_DIM > &rInverseJacobian, c_matrix< double, ELEMENT_DIM, ELEMENT_DIM+1 > &rReturnValue)
Definition Node.hpp:59
ContainingElementIterator ContainingElementsEnd() const
Definition Node.hpp:493
unsigned GetNumContainingElements() const
Definition Node.cpp:312
ContainingElementIterator ContainingElementsBegin() const
Definition Node.hpp:485