MicrovesselSolver.cpp

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#include <boost/lexical_cast.hpp>
#include "UblasIncludes.hpp"
#include "VesselSegment.hpp"
#include "VesselNode.hpp"
#include "MicrovesselSolver.hpp"
#include "VesselNetworkWriter.hpp"
#include "SolutionDependentDiscreteSource.hpp"

template<unsigned DIM>
MicrovesselSolver<DIM>::MicrovesselSolver() :
        mpNetwork(),
        mOutputFrequency(1),
        mpOutputFileHandler(),
        mDiscreteContinuumSolvers(),
        mpStructuralAdaptationSolver(),
        mpAngiogenesisSolver(),
        mpRegressionSolver(),
        mDiscreteContinuumSolversHaveCompatibleGridIndexing(false),
        mUpdatePdeEachSolve(true)
{

}

template<unsigned DIM>
MicrovesselSolver<DIM>::~MicrovesselSolver()
{

}

template<unsigned DIM>
boost::shared_ptr<MicrovesselSolver<DIM> > MicrovesselSolver<DIM>::Create()
{
    MAKE_PTR(MicrovesselSolver<DIM>, pSelf);
    return pSelf;
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::SetVesselNetwork(boost::shared_ptr<VesselNetwork<DIM> > pNetwork)
{
    mpNetwork = pNetwork;
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::SetUpdatePdeEachSolve(bool doUpdate)
{
    mUpdatePdeEachSolve = doUpdate;
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::AddDiscreteContinuumSolver(boost::shared_ptr<AbstractDiscreteContinuumSolver<DIM> > pDiscreteContinuumSolver)
{
    mDiscreteContinuumSolvers.push_back(pDiscreteContinuumSolver);
}

template<unsigned DIM>
std::vector<boost::shared_ptr<AbstractDiscreteContinuumSolver<DIM> > > MicrovesselSolver<DIM>::GetDiscreteContinuumSolvers()
{
    return mDiscreteContinuumSolvers;
}
template<unsigned DIM>
void MicrovesselSolver<DIM>::Increment()
{
    unsigned num_steps = SimulationTime::Instance()->GetTimeStepsElapsed();

    // If there is a structural adaptation or flow problem solve it
    std::cout << "ADAPT_IN****" << std::endl;
    if(mpStructuralAdaptationSolver)
    {
        mpStructuralAdaptationSolver->UpdateFlowSolver(true);
        mpStructuralAdaptationSolver->Solve();
    }
    std::cout << "ADAPT_OUT****" << std::endl;

    // If there are PDEs solve them
    if(mDiscreteContinuumSolvers.size()>0)
    {
        for(unsigned idx=0; idx<mDiscreteContinuumSolvers.size(); idx++)
        {
            if(num_steps>0 and !mUpdatePdeEachSolve)
            {
                break;
            }

            mDiscreteContinuumSolvers[idx]->Update();
            mDiscreteContinuumSolvers[idx]->SetFileName("/" + mDiscreteContinuumSolvers[idx]->GetLabel() +"_solution_" + boost::lexical_cast<std::string>(num_steps));

            // Transfer PDE solutions for coupled problems
            if(idx>0 and mDiscreteContinuumSolvers[idx]->GetPde())
            {
                for(unsigned jdx=0; jdx<mDiscreteContinuumSolvers[idx]->GetPde()->GetDiscreteSources().size(); jdx++)
                {
                    boost::shared_ptr<SolutionDependentDiscreteSource<DIM> > p_solution_dep_source =
                            boost::dynamic_pointer_cast<SolutionDependentDiscreteSource<DIM> >(mDiscreteContinuumSolvers[idx]->GetPde()->GetDiscreteSources()[jdx]);
                    if(p_solution_dep_source)
                    {
                        if(mDiscreteContinuumSolversHaveCompatibleGridIndexing)
                        {
                            p_solution_dep_source->SetSolution(mDiscreteContinuumSolvers[idx-1]->GetConcentrations());
                        }
                        else
                        {
                            EXCEPTION("Solution dependent PDEs only work with compatible grids at the moment.");
                        }
                    }
                }
            }

            if(mOutputFrequency > 0 && num_steps % mOutputFrequency == 0)
            {
                mDiscreteContinuumSolvers[idx]->SetWriteSolution(true);
            }
            else
            {
                mDiscreteContinuumSolvers[idx]->SetWriteSolution(false);
            }
            mDiscreteContinuumSolvers[idx]->Solve();
        }
    }

    // Do angiogenesis if the is a network and solver
    if(this->mpNetwork && mpAngiogenesisSolver)
    {
        mpAngiogenesisSolver->Increment();
    }

    // Do regression if the is a network and solver
    if(this->mpNetwork && mpRegressionSolver)
    {
        mpRegressionSolver->Increment();
    }

    // Manage vessel network output
    if (this->mpNetwork)
    {
        mpNetwork->UpdateAll();
        if (mOutputFrequency > 0 && num_steps % mOutputFrequency == 0)
        {
            boost::shared_ptr<VesselNetworkWriter<DIM> > p_network_writer = VesselNetworkWriter<DIM>::Create();
            p_network_writer->SetVesselNetwork(mpNetwork);
            p_network_writer->SetFileName(
                    mpOutputFileHandler->GetOutputDirectoryFullPath() + "/VesselNetwork_inc_"
                            + boost::lexical_cast<std::string>(num_steps + 1) + ".vtp");
            p_network_writer->Write();
        }
    }
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::Run()
{
    if (this->mpNetwork)
    {
        boost::shared_ptr<VesselNetworkWriter<DIM> > p_network_writer = VesselNetworkWriter<DIM>::Create();
        mpNetwork->UpdateAll(true);
        p_network_writer->SetVesselNetwork(mpNetwork);
        p_network_writer->SetFileName(mpOutputFileHandler->GetOutputDirectoryFullPath() + "/VesselNetwork_inc_0.vtp");
        p_network_writer->Write();
    }

    Setup();

    while (!SimulationTime::Instance()->IsFinished())
    {
        Increment();
        SimulationTime::Instance()->IncrementTimeOneStep();
    }
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::SetAngiogenesisSolver(boost::shared_ptr<AngiogenesisSolver<DIM> > pAngiogenesisSolver)
{
    mpAngiogenesisSolver = pAngiogenesisSolver;
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::SetOutputFileHandler(boost::shared_ptr<OutputFileHandler> pFileHandler)
{
    mpOutputFileHandler = pFileHandler;
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::SetOutputFrequency(unsigned frequency)
{
    mOutputFrequency = frequency;
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::SetupFromModifier(AbstractCellPopulation<DIM,DIM>& rCellPopulation,
                                               units::quantity<unit::length> cellReferenceLength,
                                               units::quantity<unit::concentration> cellReferenceConcentration,
                                               const std::string& rDirectory)
{
    // Set up an output file handler
    mpOutputFileHandler = boost::shared_ptr<OutputFileHandler>(new OutputFileHandler(rDirectory, false));

    // Set up all the DiscreteContinuum solvers
    for(unsigned idx=0; idx<mDiscreteContinuumSolvers.size(); idx++)
    {
        mDiscreteContinuumSolvers[idx]->SetCellPopulation(rCellPopulation, cellReferenceLength, cellReferenceConcentration);
        mDiscreteContinuumSolvers[idx]->SetFileHandler(mpOutputFileHandler);
        if(mpNetwork)
        {
            mDiscreteContinuumSolvers[idx]->SetVesselNetwork(mpNetwork);
        }
        mDiscreteContinuumSolvers[idx]->Setup();
    }

    Setup();
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::SetDiscreteContinuumSolversHaveCompatibleGridIndexing(bool compatibleIndexing)
{
    mDiscreteContinuumSolversHaveCompatibleGridIndexing = compatibleIndexing;
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::Setup()
{
    // Set up all the DiscreteContinuum solvers
    for(unsigned idx=0; idx<mDiscreteContinuumSolvers.size(); idx++)
    {
        mDiscreteContinuumSolvers[idx]->SetFileHandler(mpOutputFileHandler);
        if(mpNetwork)
        {
            mDiscreteContinuumSolvers[idx]->SetVesselNetwork(mpNetwork);
        }
        mDiscreteContinuumSolvers[idx]->Setup();
    }

    // Set up the flow and structural adaptation solvers
    if(mpStructuralAdaptationSolver)
    {
        mpStructuralAdaptationSolver->SetVesselNetwork(mpNetwork);
    }

    if(mpRegressionSolver)
    {
        mpRegressionSolver->SetVesselNetwork(mpNetwork);
    }
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::SetStructuralAdaptationSolver(boost::shared_ptr<StructuralAdaptationSolver<DIM> > pStructuralAdaptationSolver)
{
    mpStructuralAdaptationSolver = pStructuralAdaptationSolver;
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::UpdateCellData(std::vector<std::string> labels)
{
    if(labels.size()==0)
    {
        //update everything
        for(unsigned jdx=0; jdx<mDiscreteContinuumSolvers.size(); jdx++)
        {
            mDiscreteContinuumSolvers[jdx]->UpdateCellData();
        }
    }

    for(unsigned idx=0; idx<labels.size(); idx++)
    {
        for(unsigned jdx=0; jdx<mDiscreteContinuumSolvers.size(); jdx++)
        {
            if(labels[idx]==mDiscreteContinuumSolvers[idx]->GetLabel())
            {
                mDiscreteContinuumSolvers[jdx]->UpdateCellData();
            }
        }
    }
}

template<unsigned DIM>
void MicrovesselSolver<DIM>::SetRegressionSolver(boost::shared_ptr<RegressionSolver<DIM> > pRegressionSolver)
{
    mpRegressionSolver = pRegressionSolver;
}

// Explicit instantiation
template class MicrovesselSolver<2> ;
template class MicrovesselSolver<3> ;