AbstractCellBasedSimulation.cpp

/*

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*/

#include <cmath>
#include <ctime>
#include <iostream>
#include <fstream>
#include <set>

#include "AbstractCellBasedSimulation.hpp"
#include "CellBasedEventHandler.hpp"
#include "LogFile.hpp"
#include "Version.hpp"
#include "ExecutableSupport.hpp"
#include "Exception.hpp"
#include <typeinfo>

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::AbstractCellBasedSimulation(AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>& rCellPopulation,
                                              bool deleteCellPopulationInDestructor,
                                              bool initialiseCells)
    : mDt(DOUBLE_UNSET),
      mEndTime(DOUBLE_UNSET),  // hours - this is set later on
      mrCellPopulation(rCellPopulation),
      mDeleteCellPopulationInDestructor(deleteCellPopulationInDestructor),
      mInitialiseCells(initialiseCells),
      mNoBirth(false),
      mUpdateCellPopulation(true),
      mOutputDirectory(""),
      mSimulationOutputDirectory(mOutputDirectory),
      mNumBirths(0),
      mNumDeaths(0),
      mOutputDivisionLocations(false),
      mSamplingTimestepMultiple(1),
      mpCellBasedPdeHandler(NULL)
{
    // Set a random seed of 0 if it wasn't specified earlier
    RandomNumberGenerator::Instance();

    if (mInitialiseCells)
    {
        mrCellPopulation.InitialiseCells();
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::~AbstractCellBasedSimulation()
{
    if (mDeleteCellPopulationInDestructor)
    {
        delete &mrCellPopulation;
        delete mpCellBasedPdeHandler;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::SetCellBasedPdeHandler(CellBasedPdeHandler<SPACE_DIM>* pCellBasedPdeHandler)
{
    mpCellBasedPdeHandler = pCellBasedPdeHandler;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellBasedPdeHandler<SPACE_DIM>* AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::GetCellBasedPdeHandler()
{
    return mpCellBasedPdeHandler;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::DoCellBirth()
{
    if (mNoBirth)
    {
        return 0;
    }

    unsigned num_births_this_step = 0;

    // Iterate over all cells, seeing if each one can be divided
    for (typename AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>::Iterator cell_iter = mrCellPopulation.Begin();
         cell_iter != mrCellPopulation.End();
         ++cell_iter)
    {
        // Check if this cell is ready to divide - if so create a new cell etc.
        if (cell_iter->GetAge() > 0.0)
        {
            if (cell_iter->ReadyToDivide())
            {
                try
                {
                    // Store age before division
                    double cell_age =cell_iter->GetAge();

                    // Create a new cell
                    CellPtr p_new_cell = cell_iter->Divide();

                    // Call method that determines how cell division occurs and returns a vector
                    c_vector<double, SPACE_DIM> new_location = CalculateCellDivisionVector(*cell_iter);

                    // If required, output this location to file
                    if (mOutputDivisionLocations)
                    {
                        *mpDivisionLocationFile << SimulationTime::Instance()->GetTime() << "\t";
                        for (unsigned i=0; i<SPACE_DIM; i++)
                        {
                            *mpDivisionLocationFile << new_location[i] << "\t";
                        }
                        *mpDivisionLocationFile << "\t" << cell_age << "\n";
                    }

                    // Add new cell to the cell population
                    mrCellPopulation.AddCell(p_new_cell, new_location, *cell_iter);

                    // Update counter
                    num_births_this_step++;
                }
                catch (Exception& e)
                {
                    if (!(e.GetShortMessage()=="No free space to divide."))
                    {
                        NEVER_REACHED;
                        // If you do reach here, then uncomment the following line to see why.
                        //throw e;
                    }
                }
            }
        }
    }
    return num_births_this_step;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::DoCellRemoval()
{
    unsigned num_deaths_this_step = 0;

    /*
     * This labels cells as dead or apoptosing. It does not actually remove the cells,
     * mrCellPopulation.RemoveDeadCells() needs to be called for this.
     */
    for (typename std::vector<boost::shared_ptr<AbstractCellKiller<SPACE_DIM> > >::iterator killer_iter = mCellKillers.begin();
         killer_iter != mCellKillers.end();
         ++killer_iter)
    {
        (*killer_iter)->CheckAndLabelCellsForApoptosisOrDeath();
    }

    num_deaths_this_step += mrCellPopulation.RemoveDeadCells();

    return num_deaths_this_step;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::SetDt(double dt)
{
    assert(dt > 0);
    mDt = dt;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::GetDt()
{
    return mDt;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::GetNumBirths()
{
    return mNumBirths;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::GetNumDeaths()
{
    return mNumDeaths;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::SetEndTime(double endTime)
{
    assert(endTime > 0);
    mEndTime = endTime;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::SetOutputDirectory(std::string outputDirectory)
{
    mOutputDirectory = outputDirectory;
    mSimulationOutputDirectory = mOutputDirectory;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::string AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::GetOutputDirectory()
{
    return mOutputDirectory;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::SetSamplingTimestepMultiple(unsigned samplingTimestepMultiple)
{
    assert(samplingTimestepMultiple > 0);
    mSamplingTimestepMultiple = samplingTimestepMultiple;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>& AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::rGetCellPopulation()
{
    return mrCellPopulation;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
const AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>& AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::rGetCellPopulation() const
{
    return mrCellPopulation;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::SetUpdateCellPopulationRule(bool updateCellPopulation)
{
    mUpdateCellPopulation = updateCellPopulation;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::SetNoBirth(bool noBirth)
{
    mNoBirth = noBirth;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::AddCellKiller(boost::shared_ptr<AbstractCellKiller<SPACE_DIM> > pCellKiller)
{
    mCellKillers.push_back(pCellKiller);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::RemoveAllCellKillers()
{
    mCellKillers.clear();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<double> AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::GetNodeLocation(const unsigned& rNodeIndex)
{
    std::vector<double> location;
    for (unsigned i=0; i<SPACE_DIM; i++)
    {
        location.push_back(mrCellPopulation.GetNode(rNodeIndex)->rGetLocation()[i]);
    }
    return location;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::Solve()
{
    CellBasedEventHandler::BeginEvent(CellBasedEventHandler::EVERYTHING);
    CellBasedEventHandler::BeginEvent(CellBasedEventHandler::SETUP);

    // Set up the simulation time
    SimulationTime* p_simulation_time = SimulationTime::Instance();
    double current_time = p_simulation_time->GetTime();

    assert(mDt != DOUBLE_UNSET);  //Subclass constructors take care of this

    if (mEndTime == DOUBLE_UNSET)
    {
        EXCEPTION("SetEndTime has not yet been called.");
    }

    /*Note that mDt is used here for "ideal time step".  If this step doesn't divide the time remaining then
     * a *different* time step will be taken by the time-stepper.  The real time-step (used in the SimulationTime
     * singleton is currently not available to this class!
     * Should we over-write the value of mDt, or should we change this behaviour? \todo #2159
     */
    unsigned num_time_steps = (unsigned) ((mEndTime-current_time)/mDt+0.5);
    if (current_time > 0) // use the reset function if necessary
    {
        p_simulation_time->ResetEndTimeAndNumberOfTimeSteps(mEndTime, num_time_steps);
    }
    else
    {
        if (p_simulation_time->IsEndTimeAndNumberOfTimeStepsSetUp())
        {
            EXCEPTION("End time and number of timesteps already setup. You should not use SimulationTime::SetEndTimeAndNumberOfTimeSteps in cell-based tests.");
        }
        else
        {
            p_simulation_time->SetEndTimeAndNumberOfTimeSteps(mEndTime, num_time_steps);
        }
    }

    if (mOutputDirectory == "")
    {
        EXCEPTION("OutputDirectory not set");
    }

    double time_now = p_simulation_time->GetTime();
    std::ostringstream time_string;
    time_string << time_now;

    std::string results_directory = mOutputDirectory +"/results_from_time_" + time_string.str();
    mSimulationOutputDirectory = results_directory;

    // Set up simulation

    // Create output files for the visualizer
    OutputFileHandler output_file_handler(results_directory+"/", true);

    mrCellPopulation.CreateOutputFiles(results_directory+"/", false);

    if (mOutputDivisionLocations)
    {
        mpDivisionLocationFile = output_file_handler.OpenOutputFile("divisions.dat");
    }

    if (PetscTools::AmMaster())
    {
        mpVizSetupFile = output_file_handler.OpenOutputFile("results.vizsetup");
    }

    // If any PDEs have been defined, set up results files to store their solution
    if (mpCellBasedPdeHandler != NULL)
    {
        mpCellBasedPdeHandler->OpenResultsFiles(this->mSimulationOutputDirectory);
        if (PetscTools::AmMaster())
        {
            *this->mpVizSetupFile << "PDE \n";
        }
    }

    SetupSolve();

    // Age the cells to the correct time. Note that cells are created with
    // negative birth times so that some are initially almost ready to divide.
    LOG(1, "Setting up cells...");
    for (typename AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>::Iterator cell_iter = mrCellPopulation.Begin();
         cell_iter != mrCellPopulation.End();
         ++cell_iter)
    {
        // We don't use the result; this call is just to force the cells to age
        // to the current time running their cell-cycle models to get there
        cell_iter->ReadyToDivide();
    }
    LOG(1, "\tdone\n");

    // Write initial conditions to file for the visualizer
    WriteVisualizerSetupFile();

    if (PetscTools::AmMaster())
    {
        *mpVizSetupFile << std::flush;
    }

    mrCellPopulation.WriteResultsToFiles();

    OutputSimulationSetup();

    CellBasedEventHandler::EndEvent(CellBasedEventHandler::SETUP);


    // Enter main time loop
    while (!( p_simulation_time->IsFinished() || StoppingEventHasOccurred() ) )
    {
        LOG(1, "--TIME = " << p_simulation_time->GetTime() << "\n");

        // This function calls DoCellRemoval(), DoCellBirth() and CellPopulation::Update()
        UpdateCellPopulation();

        // Update cell locations and topology
        UpdateCellLocationsAndTopology();

        // If any PDEs have been defined, solve them and store their solution in results files
        if (mpCellBasedPdeHandler != NULL)
        {
            CellBasedEventHandler::BeginEvent(CellBasedEventHandler::PDE);
            mpCellBasedPdeHandler->SolvePdeAndWriteResultsToFile(this->mSamplingTimestepMultiple);
            CellBasedEventHandler::EndEvent(CellBasedEventHandler::PDE);
        }

        // Call UpdateAtEndOfTimeStep(), which may be implemented by child classes
        CellBasedEventHandler::BeginEvent(CellBasedEventHandler::UPDATESIMULATION);
        UpdateAtEndOfTimeStep();
        CellBasedEventHandler::EndEvent(CellBasedEventHandler::UPDATESIMULATION);

        // Increment simulation time here, so results files look sensible
        p_simulation_time->IncrementTimeOneStep();

        // Output current results to file
        CellBasedEventHandler::BeginEvent(CellBasedEventHandler::OUTPUT);
        if (p_simulation_time->GetTimeStepsElapsed()%mSamplingTimestepMultiple == 0)
        {
            mrCellPopulation.WriteResultsToFiles();
        }
        CellBasedEventHandler::EndEvent(CellBasedEventHandler::OUTPUT);
    }

    LOG(1, "--END TIME = " << p_simulation_time->GetTime() << "\n");

    // Carry out a final update so that cell population is coherent with new cell positions.
    // NB cell birth/death still need to be checked because they may be spatially-dependent.
    UpdateCellPopulation();

    // If any PDEs have been defined, close the results files storing their solution
    if (mpCellBasedPdeHandler != NULL)
    {
        mpCellBasedPdeHandler->CloseResultsFiles();
    }

    CellBasedEventHandler::BeginEvent(CellBasedEventHandler::UPDATESIMULATION);
    UpdateAtEndOfSolve();
    CellBasedEventHandler::EndEvent(CellBasedEventHandler::UPDATESIMULATION);

    CellBasedEventHandler::BeginEvent(CellBasedEventHandler::OUTPUT);

    mrCellPopulation.CloseOutputFiles();

    if (mOutputDivisionLocations)
    {
        mpDivisionLocationFile->close();
    }

    if (PetscTools::AmMaster())
    {
        *mpVizSetupFile << "Complete\n";
        mpVizSetupFile->close();
    }

    CellBasedEventHandler::EndEvent(CellBasedEventHandler::OUTPUT);
    CellBasedEventHandler::EndEvent(CellBasedEventHandler::EVERYTHING);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::StoppingEventHasOccurred()
{
    return false;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::UpdateCellPopulation()
{
    // Remove dead cells
    CellBasedEventHandler::BeginEvent(CellBasedEventHandler::DEATH);
    unsigned deaths_this_step = DoCellRemoval();
    mNumDeaths += deaths_this_step;
    LOG(1, "\tNum deaths = " << mNumDeaths << "\n");
    CellBasedEventHandler::EndEvent(CellBasedEventHandler::DEATH);

    // Divide cells
    CellBasedEventHandler::BeginEvent(CellBasedEventHandler::BIRTH);
    unsigned births_this_step = DoCellBirth();
    mNumBirths += births_this_step;
    LOG(1, "\tNum births = " << mNumBirths << "\n");
    CellBasedEventHandler::EndEvent(CellBasedEventHandler::BIRTH);

    // This allows NodeBasedCellPopulation::Update() to do the minimum amount of work
    bool births_or_death_occurred = ((births_this_step>0) || (deaths_this_step>0));

    // Update topology of cell population
    CellBasedEventHandler::BeginEvent(CellBasedEventHandler::UPDATECELLPOPULATION);
    if (mUpdateCellPopulation)
    {
        LOG(1, "\tUpdating cell population...");
        mrCellPopulation.Update(births_or_death_occurred);
        LOG(1, "\tdone.\n");
    }
    else if (births_or_death_occurred)
    {
        EXCEPTION("CellPopulation has had births or deaths but mUpdateCellPopulation is set to false, please set it to true.");
    }
    CellBasedEventHandler::EndEvent(CellBasedEventHandler::UPDATECELLPOPULATION);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::GetOutputDivisionLocations()
{
    return mOutputDivisionLocations;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::SetOutputDivisionLocations(bool outputDivisionLocations)
{
    mOutputDivisionLocations = outputDivisionLocations;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::OutputSimulationSetup()
{
    OutputFileHandler output_file_handler(this->mSimulationOutputDirectory + "/", false);

    // Output machine information
    ExecutableSupport::WriteMachineInfoFile(this->mSimulationOutputDirectory + "/system_info");

    // Output Chaste provenance information
    out_stream build_info_file = output_file_handler.OpenOutputFile("build.info");
    ExecutableSupport::WriteLibraryInfo(build_info_file);
    build_info_file->close();

    // Output simulation parameter and setup details
    out_stream parameter_file = output_file_handler.OpenOutputFile("results.parameters");

    // Output simulation details
    std::string simulation_type = GetIdentifier();

    *parameter_file << "<Chaste>\n";
    *parameter_file << "\n\t<" << simulation_type << ">\n";
    OutputSimulationParameters(parameter_file);
    *parameter_file << "\t</" << simulation_type << ">\n";
    *parameter_file << "\n";

    // Output cell population details (includes cell-cycle model details)
    mrCellPopulation.OutputCellPopulationInfo(parameter_file);

    // Loop over cell killers
    *parameter_file << "\n\t<CellKillers>\n";
    for (typename std::vector<boost::shared_ptr<AbstractCellKiller<SPACE_DIM> > >::iterator iter = mCellKillers.begin();
         iter != mCellKillers.end();
         ++iter)
    {
        // Output cell killer details
        (*iter)->OutputCellKillerInfo(parameter_file);
    }
    *parameter_file << "\t</CellKillers>\n";

    // This is used to output information about subclasses
    OutputAdditionalSimulationSetup(parameter_file);

    *parameter_file << "\n</Chaste>\n";
    parameter_file->close();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::OutputSimulationParameters(out_stream& rParamsFile)
{
    if (mpCellBasedPdeHandler != NULL)
    {
        mpCellBasedPdeHandler->OutputParameters(rParamsFile);
    }

    *rParamsFile << "\t\t<Dt>" << mDt << "</Dt>\n";
    *rParamsFile << "\t\t<EndTime>" << mEndTime << "</EndTime>\n";
    *rParamsFile << "\t\t<SamplingTimestepMultiple>" << mSamplingTimestepMultiple << "</SamplingTimestepMultiple>\n";
    *rParamsFile << "\t\t<OutputDivisionLocations>" << mOutputDivisionLocations << "</OutputDivisionLocations>\n";
}

// Explicit instantiation

template class AbstractCellBasedSimulation<1,1>;
template class AbstractCellBasedSimulation<1,2>;
template class AbstractCellBasedSimulation<2,2>;
template class AbstractCellBasedSimulation<1,3>;
template class AbstractCellBasedSimulation<2,3>;
template class AbstractCellBasedSimulation<3,3>;