Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
EllipticBoxDomainPdeModifier.cpp
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34*/
35
36#include "EllipticBoxDomainPdeModifier.hpp"
37#include "SimpleLinearEllipticSolver.hpp"
38
39template<unsigned DIM>
41 boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition,
42 bool isNeumannBoundaryCondition,
43 boost::shared_ptr<ChasteCuboid<DIM> > pMeshCuboid,
44 double stepSize,
45 Vec solution)
47 pBoundaryCondition,
48 isNeumannBoundaryCondition,
49 pMeshCuboid,
50 stepSize,
51 solution)
52{
53}
54
55template<unsigned DIM>
59
60template<unsigned DIM>
62{
63 // Set up boundary conditions
64 std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > p_bcc = ConstructBoundaryConditionsContainer(rCellPopulation);
65
66 this->UpdateCellPdeElementMap(rCellPopulation);
67
68 // When using a PDE mesh which doesn't coincide with the cells, we must set up the source terms before solving the PDE.
69 // Pass in already updated CellPdeElementMap to speed up finding cells.
70 this->SetUpSourceTermsForAveragedSourcePde(this->mpFeMesh, &this->mCellPdeElementMap);
71
72 // Use SimpleLinearEllipticSolver as Averaged Source PDE
74 SimpleLinearEllipticSolver<DIM,DIM> solver(this->mpFeMesh,
75 boost::static_pointer_cast<AbstractLinearEllipticPde<DIM,DIM> >(this->GetPde()).get(),
76 p_bcc.get());
77
79 Vec old_solution_copy = this->mSolution;
80 this->mSolution = solver.Solve();
81 if (old_solution_copy != nullptr)
82 {
83 PetscTools::Destroy(old_solution_copy);
84 }
85
86 this->UpdateCellData(rCellPopulation);
87}
88
89template<unsigned DIM>
90void EllipticBoxDomainPdeModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory)
91{
92 AbstractBoxDomainPdeModifier<DIM>::SetupSolve(rCellPopulation,outputDirectory);
93
94 // Call these methods to solve the PDE on the initial step and output the results
95 UpdateAtEndOfTimeStep(rCellPopulation);
96 this->UpdateAtEndOfOutputTimeStep(rCellPopulation);
97}
98
99template<unsigned DIM>
100std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > EllipticBoxDomainPdeModifier<DIM>::ConstructBoundaryConditionsContainer(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
101{
102 std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > p_bcc(new BoundaryConditionsContainer<DIM,DIM,1>(false));
103
104 // To be well-defined, elliptic PDE problems on box domains require at least some Dirichlet boundary conditions
106 assert(!(this->IsNeumannBoundaryCondition()));
107
108 if (!this->mSetBcsOnBoxBoundary)
109 {
110 // Get the set of coarse element indices that contain cells
111 std::set<unsigned> coarse_element_indices_in_map;
112 for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
113 cell_iter != rCellPopulation.End();
114 ++cell_iter)
115 {
116 coarse_element_indices_in_map.insert(this->mCellPdeElementMap[*cell_iter]);
117 }
118
119 // Find the node indices associated with elements whose indices are NOT in the set coarse_element_indices_in_map
120 std::set<unsigned> coarse_mesh_boundary_node_indices;
121 for (unsigned i=0; i<this->mpFeMesh->GetNumElements(); i++)
122 {
123 if (coarse_element_indices_in_map.find(i) == coarse_element_indices_in_map.end())
124 {
125 Element<DIM,DIM>* p_element = this->mpFeMesh->GetElement(i);
126 for (unsigned j=0; j<DIM+1; j++)
127 {
128 unsigned node_index = p_element->GetNodeGlobalIndex(j);
129 coarse_mesh_boundary_node_indices.insert(node_index);
130 }
131 }
132 }
133
134 // Apply boundary condition to the nodes in the set coarse_mesh_boundary_node_indices
135 for (std::set<unsigned>::iterator iter = coarse_mesh_boundary_node_indices.begin();
136 iter != coarse_mesh_boundary_node_indices.end();
137 ++iter)
138 {
139 p_bcc->AddDirichletBoundaryCondition(this->mpFeMesh->GetNode(*iter), this->mpBoundaryCondition.get(), 0, false);
140 }
141 }
142 else // Apply BC at boundary nodes of box domain FE mesh
143 {
144 for (typename TetrahedralMesh<DIM,DIM>::BoundaryNodeIterator node_iter = this->mpFeMesh->GetBoundaryNodeIteratorBegin();
145 node_iter != this->mpFeMesh->GetBoundaryNodeIteratorEnd();
146 ++node_iter)
147 {
148 p_bcc->AddDirichletBoundaryCondition(*node_iter, this->mpBoundaryCondition.get());
149 }
150 }
151
152 return p_bcc;
153}
154
155template<unsigned DIM>
157{
158 // No parameters to output, so just call method on direct parent class
160}
161
162// Explicit instantiation
166
167// Serialization for Boost >= 1.36
170
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
unsigned GetNodeGlobalIndex(unsigned localIndex) const
std::vector< Node< SPACE_DIM > * >::const_iterator BoundaryNodeIterator
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual std::shared_ptr< BoundaryConditionsContainer< DIM, DIM, 1 > > ConstructBoundaryConditionsContainer(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
EllipticBoxDomainPdeModifier(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, boost::shared_ptr< ChasteCuboid< DIM > > pMeshCuboid=boost::shared_ptr< ChasteCuboid< DIM > >(), double stepSize=1.0, Vec solution=nullptr)
static void Destroy(Vec &rVec)