Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
ParabolicBoxDomainPdeModifier.cpp
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34*/
35
36#include "ParabolicBoxDomainPdeModifier.hpp"
37#include "SimpleLinearParabolicSolver.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 SimpleLinearParabolicSolver as averaged Source PDE
73 SimpleLinearParabolicSolver<DIM,DIM> solver(this->mpFeMesh,
74 boost::static_pointer_cast<AbstractLinearParabolicPde<DIM,DIM> >(this->GetPde()).get(),
75 p_bcc.get());
76
78 SimulationTime* p_simulation_time = SimulationTime::Instance();
79 double current_time = p_simulation_time->GetTime();
80 double dt = p_simulation_time->GetTimeStep();
81 solver.SetTimes(current_time,current_time + dt);
82 solver.SetTimeStep(dt);
83
84 // Use previous solution as the initial condition
85 Vec previous_solution = this->mSolution;
86 solver.SetInitialCondition(previous_solution);
87
88 // Note that the linear solver creates a vector, so we have to keep a handle on the old one
89 // in order to destroy it
90 this->mSolution = solver.Solve();
91 PetscTools::Destroy(previous_solution);
92 this->UpdateCellData(rCellPopulation);
93}
94
95template<unsigned DIM>
97{
98 AbstractBoxDomainPdeModifier<DIM>::SetupSolve(rCellPopulation,outputDirectory);
99
100 // Copy the cell data to mSolution (this is the initial condition)
101 SetupInitialSolutionVector(rCellPopulation);
102
103 // Output the initial conditions on FeMesh
104 this->UpdateAtEndOfOutputTimeStep(rCellPopulation);
105}
106
107template<unsigned DIM>
108std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > ParabolicBoxDomainPdeModifier<DIM>::ConstructBoundaryConditionsContainer(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
109{
110 std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > p_bcc(new BoundaryConditionsContainer<DIM,DIM,1>(false));
111
112 if (!this->mSetBcsOnBoxBoundary)
113 {
114 EXCEPTION("Boundary conditions cannot yet be set on the cell population boundary for a ParabolicBoxDomainPdeModifier");
115 }
116 else // Apply BC at boundary nodes of box domain FE mesh
117 {
118 if (this->IsNeumannBoundaryCondition())
119 {
120 // Impose any Neumann boundary conditions
121 for (typename TetrahedralMesh<DIM,DIM>::BoundaryElementIterator elem_iter = this->mpFeMesh->GetBoundaryElementIteratorBegin();
122 elem_iter != this->mpFeMesh->GetBoundaryElementIteratorEnd();
123 ++elem_iter)
124 {
125 p_bcc->AddNeumannBoundaryCondition(*elem_iter, this->mpBoundaryCondition.get());
126 }
127 }
128 else
129 {
130 // Impose any Dirichlet boundary conditions
131 for (typename TetrahedralMesh<DIM,DIM>::BoundaryNodeIterator node_iter = this->mpFeMesh->GetBoundaryNodeIteratorBegin();
132 node_iter != this->mpFeMesh->GetBoundaryNodeIteratorEnd();
133 ++node_iter)
134 {
135 p_bcc->AddDirichletBoundaryCondition(*node_iter, this->mpBoundaryCondition.get());
136 }
137 }
138 }
139
140 return p_bcc;
141}
142
143template<unsigned DIM>
145{
146 // Specify homogeneous initial conditions based upon the values stored in CellData.
147 // Note need all the CellDataValues to be the same.
148
149 double initial_condition = rCellPopulation.Begin()->GetCellData()->GetItem(this->mDependentVariableName);
150
151 for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
152 cell_iter != rCellPopulation.End();
153 ++cell_iter)
154 {
155 double initial_condition_at_cell = cell_iter->GetCellData()->GetItem(this->mDependentVariableName);
156 UNUSED_OPT(initial_condition_at_cell);
157 assert(fabs(initial_condition_at_cell - initial_condition)<1e-12);
158 }
159
160 // Initialise mSolution
161 this->mSolution = PetscTools::CreateAndSetVec(this->mpFeMesh->GetNumNodes(), initial_condition);
162}
163
164template<unsigned DIM>
166{
167 // No parameters to output, so just call method on direct parent class
169}
170
171// Explicit instantiation
175
176// Serialization for Boost >= 1.36
179
#define EXCEPTION(message)
#define UNUSED_OPT(var)
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
void SetTimes(double tStart, double tEnd)
std::vector< Node< SPACE_DIM > * >::const_iterator BoundaryNodeIterator
std::vector< BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > * >::const_iterator BoundaryElementIterator
void SetupInitialSolutionVector(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual std::shared_ptr< BoundaryConditionsContainer< DIM, DIM, 1 > > ConstructBoundaryConditionsContainer(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
ParabolicBoxDomainPdeModifier(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 Vec CreateAndSetVec(int size, double value)
static void Destroy(Vec &rVec)
double GetTime() const
double GetTimeStep() const
static SimulationTime * Instance()