AbstractPdeModifier.cpp

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#include "AbstractPdeModifier.hpp"
#include "VtkMeshWriter.hpp"
#include "ReplicatableVector.hpp"
#include "UniformSourceEllipticPde.hpp"
#include "AveragedSourceEllipticPde.hpp"
#include "AveragedSourceParabolicPde.hpp"
 
template<unsigned DIM>
AbstractPdeModifier<DIM>::AbstractPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM,DIM> > pPde,
                                              boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition,
                                              const bool isNeumannBoundaryCondition,
                                              Vec solution)
    : AbstractCellBasedSimulationModifier<DIM>(),
      mpPde(pPde),
      mpBoundaryCondition(pBoundaryCondition),
      mIsNeumannBoundaryCondition(isNeumannBoundaryCondition)
{
    if (solution)
    {
        mSolution = solution;
    }
}
AbstractPdeModifier<DIM>::AbstractPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM,DIM> > pPde, {…}
 
template<unsigned DIM>
AbstractPdeModifier<DIM>::~AbstractPdeModifier()
{
    if (mDeleteFeMesh and mpFeMesh!=nullptr)
    {
        delete mpFeMesh;
    }
    if (mSolution)
    {
        PetscTools::Destroy(mSolution);
    }
}
AbstractPdeModifier<DIM>::~AbstractPdeModifier() {…}
 
template<unsigned DIM>
boost::shared_ptr<AbstractLinearPde<DIM,DIM> > AbstractPdeModifier<DIM>::GetPde()
{
    return mpPde;
}
boost::shared_ptr<AbstractLinearPde<DIM,DIM> > AbstractPdeModifier<DIM>::GetPde() {…}
 
template<unsigned DIM>
boost::shared_ptr<AbstractBoundaryCondition<DIM> > AbstractPdeModifier<DIM>::GetBoundaryCondition()
{
    return mpBoundaryCondition;
}
boost::shared_ptr<AbstractBoundaryCondition<DIM> > AbstractPdeModifier<DIM>::GetBoundaryCondition() {…}
 
template<unsigned DIM>
bool AbstractPdeModifier<DIM>::IsNeumannBoundaryCondition() const
{
    return mIsNeumannBoundaryCondition;
}
bool AbstractPdeModifier<DIM>::IsNeumannBoundaryCondition() const {…}
 
template<unsigned DIM>
void AbstractPdeModifier<DIM>::SetDependentVariableName(const std::string& rName)
{
    mDependentVariableName = rName;
}
void AbstractPdeModifier<DIM>::SetDependentVariableName(const std::string& rName) {…}
 
template<unsigned DIM>
std::string& AbstractPdeModifier<DIM>::rGetDependentVariableName()
{
    return mDependentVariableName;
}
std::string& AbstractPdeModifier<DIM>::rGetDependentVariableName() {…}
 
template<unsigned DIM>
bool AbstractPdeModifier<DIM>::HasAveragedSourcePde()
{
    return ((boost::dynamic_pointer_cast<AveragedSourceEllipticPde<DIM> >(mpPde) != nullptr) ||
            (boost::dynamic_pointer_cast<AveragedSourceParabolicPde<DIM> >(mpPde) != nullptr)||
            (boost::dynamic_pointer_cast<UniformSourceEllipticPde<DIM> >(mpPde) != nullptr));
}
bool AbstractPdeModifier<DIM>::HasAveragedSourcePde() {…}
 
template<unsigned DIM>
void AbstractPdeModifier<DIM>::SetUpSourceTermsForAveragedSourcePde(TetrahedralMesh<DIM,DIM>* pMesh, std::map<CellPtr, unsigned>* pCellPdeElementMap)
{
    assert(HasAveragedSourcePde());
    if (boost::dynamic_pointer_cast<AveragedSourceEllipticPde<DIM> >(mpPde) != nullptr)
    {
        boost::static_pointer_cast<AveragedSourceEllipticPde<DIM> >(mpPde)->SetupSourceTerms(*pMesh, pCellPdeElementMap);
    }
    else if (boost::dynamic_pointer_cast<AveragedSourceParabolicPde<DIM> >(mpPde) != nullptr)
    {
        boost::static_pointer_cast<AveragedSourceParabolicPde<DIM> >(mpPde)->SetupSourceTerms(*pMesh, pCellPdeElementMap);
    }
    else if (boost::dynamic_pointer_cast<UniformSourceEllipticPde<DIM> >(mpPde) != nullptr)
    {
        //Don't do anything as don't need to set up source terms as just constant.
    }
}
void AbstractPdeModifier<DIM>::SetUpSourceTermsForAveragedSourcePde(TetrahedralMesh<DIM,DIM>* pMesh, std::map<CellPtr, unsigned>* pCellPdeElementMap) {…}
 
template<unsigned DIM>
Vec AbstractPdeModifier<DIM>::GetSolution()
{
    return mSolution;
}
Vec AbstractPdeModifier<DIM>::GetSolution() {…}
 
template<unsigned DIM>
Vec AbstractPdeModifier<DIM>::GetSolution() const
{
    return mSolution;
}
Vec AbstractPdeModifier<DIM>::GetSolution() const {…}
 
template<unsigned DIM>
TetrahedralMesh<DIM,DIM>* AbstractPdeModifier<DIM>::GetFeMesh() const
{
    return mpFeMesh;
}
TetrahedralMesh<DIM,DIM>* AbstractPdeModifier<DIM>::GetFeMesh() const {…}
 
template<unsigned DIM>
void AbstractPdeModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory)
{
    // Cache the output directory
    this->mOutputDirectory = outputDirectory;
 
    if (mOutputSolutionAtPdeNodes)
    {
        if (PetscTools::AmMaster())
        {
            OutputFileHandler output_file_handler(outputDirectory+"/", false);
            mpVizPdeSolutionResultsFile = output_file_handler.OpenOutputFile("results.vizpdesolution");
        }
    }
 
    // To make sure cell volume can be calculated
    rCellPopulation.Update();
}
void AbstractPdeModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory) {…}
 
template<unsigned DIM>
void AbstractPdeModifier<DIM>::UpdateAtEndOfOutputTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    if (mOutputSolutionAtPdeNodes)
    {
        if (PetscTools::AmMaster())
        {
            (*mpVizPdeSolutionResultsFile) << SimulationTime::Instance()->GetTime() << "\t";
 
            assert(mpFeMesh != nullptr);
            assert(!mDependentVariableName.empty());
 
            for (unsigned i=0; i<mpFeMesh->GetNumNodes(); i++)
            {
                (*mpVizPdeSolutionResultsFile) << i << " ";
                const c_vector<double,DIM>& r_location = mpFeMesh->GetNode(i)->rGetLocation();
                for (unsigned k=0; k<DIM; k++)
                {
                    (*mpVizPdeSolutionResultsFile) << r_location[k] << " ";
                }
 
                assert(mSolution != nullptr);
                ReplicatableVector solution_repl(mSolution);
                (*mpVizPdeSolutionResultsFile) << solution_repl[i] << " ";
            }
 
            (*mpVizPdeSolutionResultsFile) << "\n";
        }
    }
#ifdef CHASTE_VTK
    if (DIM > 1)
    {
        std::ostringstream time_string;
        time_string << SimulationTime::Instance()->GetTimeStepsElapsed();
        std::string results_file = "pde_results_" + mDependentVariableName + "_" + time_string.str();
        auto* p_vtk_mesh_writer = new VtkMeshWriter<DIM,DIM>(mOutputDirectory, results_file, false);
 
        ReplicatableVector solution_repl(mSolution);
        std::vector<double> pde_solution;
        for (unsigned i=0; i<mpFeMesh->GetNumNodes(); i++)
        {
           pde_solution.push_back(solution_repl[i]);
        }
 
        p_vtk_mesh_writer->AddPointData(mDependentVariableName, pde_solution);
        p_vtk_mesh_writer->AddPointData("IsDirichletBoundaryNode", mIsDirichletBoundaryNode);
 
        p_vtk_mesh_writer->WriteFilesUsingMesh(*mpFeMesh);
        delete p_vtk_mesh_writer;
    }
#endif //CHASTE_VTK
}
void AbstractPdeModifier<DIM>::UpdateAtEndOfOutputTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation) {…}
 
template<unsigned DIM>
void AbstractPdeModifier<DIM>::UpdateAtEndOfSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    if (mOutputSolutionAtPdeNodes)
    {
        if (PetscTools::AmMaster())
        {
            mpVizPdeSolutionResultsFile->close();
        }
    }
}
void AbstractPdeModifier<DIM>::UpdateAtEndOfSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation) {…}
 
template<unsigned DIM>
bool AbstractPdeModifier<DIM>::GetOutputGradient() const
{
    return mOutputGradient;
}
bool AbstractPdeModifier<DIM>::GetOutputGradient() const {…}
 
template<unsigned DIM>
void AbstractPdeModifier<DIM>::SetOutputGradient(bool outputGradient)
{
    mOutputGradient = outputGradient;
}
void AbstractPdeModifier<DIM>::SetOutputGradient(bool outputGradient) {…}
 
template<unsigned DIM>
void AbstractPdeModifier<DIM>::SetOutputSolutionAtPdeNodes(bool outputSolutionAtPdeNodes)
{
    mOutputSolutionAtPdeNodes = outputSolutionAtPdeNodes;
}
void AbstractPdeModifier<DIM>::SetOutputSolutionAtPdeNodes(bool outputSolutionAtPdeNodes) {…}
 
template<unsigned DIM>
void AbstractPdeModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile)
{
    // No parameters to output, so just call method on direct parent class
    AbstractCellBasedSimulationModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
}
void AbstractPdeModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile) {…}
 
// Explicit instantiation
template class AbstractPdeModifier<1>;
template class AbstractPdeModifier<2>;
template class AbstractPdeModifier<3>;