Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
ParabolicGrowingDomainPdeModifier.cpp
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35
36#include "ParabolicGrowingDomainPdeModifier.hpp"
37#include "CellBasedParabolicPdeSolver.hpp"
38#include "AveragedSourceParabolicPde.hpp"
39
40template<unsigned DIM>
42 boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition,
43 bool isNeumannBoundaryCondition,
44 Vec solution)
46 pBoundaryCondition,
47 isNeumannBoundaryCondition,
48 solution)
49{
50}
51
52template<unsigned DIM>
56
57template<unsigned DIM>
59{
60 this->GenerateFeMesh(rCellPopulation);
61
62 // Set up boundary conditions
63 std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > p_bcc = ConstructBoundaryConditionsContainer();
64
65 // Construct the solution vector from cell data (takes care of cells dividing);
66 UpdateSolutionVector(rCellPopulation);
67
68 // Use CellBasedParabolicPdeSolver as cell wise PDE
69 CellBasedParabolicPdeSolver<DIM> solver(this->mpFeMesh,
70 boost::static_pointer_cast<AbstractLinearParabolicPde<DIM,DIM> >(this->mpPde).get(),
71 p_bcc.get());
72
74 SimulationTime* p_simulation_time = SimulationTime::Instance();
75 double current_time = p_simulation_time->GetTime();
76 double dt = p_simulation_time->GetTimeStep();
77 solver.SetTimes(current_time,current_time + dt);
78 solver.SetTimeStep(dt);
79
80 // Use previous solution as the initial condition
81 Vec previous_solution = this->mSolution;
82 solver.SetInitialCondition(previous_solution);
83
84 // Note that the linear solver creates a vector, so we have to keep a handle on the old one
85 // in order to destroy it
86 this->mSolution = solver.Solve();
87 PetscTools::Destroy(previous_solution);
88 this->UpdateCellData(rCellPopulation);
89}
90
91template<unsigned DIM>
93{
94 AbstractGrowingDomainPdeModifier<DIM>::SetupSolve(rCellPopulation, outputDirectory);
95
96 if (boost::dynamic_pointer_cast<AveragedSourceParabolicPde<DIM> >(this->mpPde))
97 {
98 EXCEPTION("ParabolicGrowingDomainPdeModifier cannot be used with an AveragedSourceParabolicPde. Use a ParabolicBoxDomainPdeModifier instead.");
99 }
100
101 // Setup a finite element mesh on which to save the initial condition
102 this->GenerateFeMesh(rCellPopulation);
103
104 // Copy the cell data to mSolution (this is the initial condition)
105 UpdateSolutionVector(rCellPopulation);
106
107 // Output the initial conditions on FeMesh
108 this->UpdateAtEndOfOutputTimeStep(rCellPopulation);
109}
110
111template<unsigned DIM>
112std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > ParabolicGrowingDomainPdeModifier<DIM>::ConstructBoundaryConditionsContainer()
113{
114 std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > p_bcc(new BoundaryConditionsContainer<DIM,DIM,1>(false));
115
116 if (this->IsNeumannBoundaryCondition())
117 {
118 // Impose any Neumann boundary conditions
119 for (typename TetrahedralMesh<DIM,DIM>::BoundaryElementIterator elem_iter = this->mpFeMesh->GetBoundaryElementIteratorBegin();
120 elem_iter != this->mpFeMesh->GetBoundaryElementIteratorEnd();
121 ++elem_iter)
122 {
123 p_bcc->AddNeumannBoundaryCondition(*elem_iter, this->mpBoundaryCondition.get());
124 }
125 }
126 else
127 {
128 // Impose any Dirichlet boundary conditions
129 for (typename TetrahedralMesh<DIM,DIM>::BoundaryNodeIterator node_iter = this->mpFeMesh->GetBoundaryNodeIteratorBegin();
130 node_iter != this->mpFeMesh->GetBoundaryNodeIteratorEnd();
131 ++node_iter)
132 {
133 p_bcc->AddDirichletBoundaryCondition(*node_iter, this->mpBoundaryCondition.get());
134 }
135 }
136
137 return p_bcc;
138}
139
140template<unsigned DIM>
142{
143 // Clear (if it's not the first time) and resize the solution vector
144 if (this->mSolution)
145 {
146 PetscTools::Destroy(this->mSolution);
147 }
148 this->mSolution = PetscTools::CreateAndSetVec(this->mpFeMesh->GetNumNodes(), 0.0);
149
150 std::string& variable_name = this->mDependentVariableName;
151
152 for (typename TetrahedralMesh<DIM,DIM>::NodeIterator node_iter = this->mpFeMesh->GetNodeIteratorBegin();
153 node_iter != this->mpFeMesh->GetNodeIteratorEnd();
154 ++node_iter)
155 {
156 // Loop over nodes of the finite element mesh and get appropriate solution values from CellData
157 for (typename TetrahedralMesh<DIM,DIM>::NodeIterator node_iter = this->mpFeMesh->GetNodeIteratorBegin();
158 node_iter != this->mpFeMesh->GetNodeIteratorEnd();
159 ++node_iter)
160 {
161 unsigned node_index = node_iter->GetIndex();
162 bool dirichlet_bc_applies = (node_iter->IsBoundaryNode()) && (!(this->IsNeumannBoundaryCondition()));
163 double boundary_value = this->GetBoundaryCondition()->GetValue(node_iter->rGetLocation());
164
165 double solution_at_node = rCellPopulation.GetCellDataItemAtPdeNode(node_index, variable_name, dirichlet_bc_applies, boundary_value);
166
167 PetscVecTools::SetElement(this->mSolution, node_index, solution_at_node);
168 }
169 }
170}
171
172template<unsigned DIM>
174{
175 // No parameters to output, so just call method on direct parent class
177}
178
179// Explicit instantiation
183
184// Serialization for Boost >= 1.36
187
#define EXCEPTION(message)
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual double GetCellDataItemAtPdeNode(unsigned pdeNodeIndex, std::string &rVariableName, bool dirichletBoundaryConditionApplies=false, double dirichletBoundaryValue=0.0)=0
void SetTimes(double tStart, double tEnd)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
std::vector< Node< SPACE_DIM > * >::const_iterator BoundaryNodeIterator
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
std::vector< BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > * >::const_iterator BoundaryElementIterator
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
virtual std::shared_ptr< BoundaryConditionsContainer< DIM, DIM, 1 > > ConstructBoundaryConditionsContainer()
void OutputSimulationModifierParameters(out_stream &rParamsFile)
virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
ParabolicGrowingDomainPdeModifier(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 UpdateSolutionVector(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
static Vec CreateAndSetVec(int size, double value)
static void Destroy(Vec &rVec)
static void SetElement(Vec vector, PetscInt row, double value)
double GetTime() const
double GetTimeStep() const
static SimulationTime * Instance()