OdeSolution.cpp

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*/
 
#include "OdeSolution.hpp"
 
#include <sstream>
 
#include "ColumnDataWriter.hpp"
#include "Exception.hpp"
#include "PetscTools.hpp"
#include "VectorHelperFunctions.hpp"
 
#if CHASTE_SUNDIALS_VERSION >= 60000
#include "CvodeContextManager.hpp"  // access to shared SUNContext object required by Sundials 6.0+
#endif
 
OdeSolution::OdeSolution()
    : mNumberOfTimeSteps(0u),
      mpOdeSystemInformation()
{
}
OdeSolution::OdeSolution() {…}
 
 
unsigned OdeSolution::GetNumberOfTimeSteps() const
{
    return mNumberOfTimeSteps;
}
unsigned OdeSolution::GetNumberOfTimeSteps() const {…}
 
 
void OdeSolution::SetNumberOfTimeSteps(unsigned numTimeSteps)
{
    mNumberOfTimeSteps = numTimeSteps;
    mTimes.reserve(numTimeSteps+1);
    mSolutions.reserve(numTimeSteps);
}
void OdeSolution::SetNumberOfTimeSteps(unsigned numTimeSteps) {…}
 
 
void OdeSolution::SetOdeSystemInformation(boost::shared_ptr<const AbstractOdeSystemInformation> pOdeSystemInfo)
{
    mpOdeSystemInformation = pOdeSystemInfo;
}
void OdeSolution::SetOdeSystemInformation(boost::shared_ptr<const AbstractOdeSystemInformation> pOdeSystemInfo) {…}
 
std::vector<double> OdeSolution::GetVariableAtIndex(unsigned index) const
{
    std::vector<double> answer;
    answer.reserve(mTimes.size());
    double temp_number;
    for (unsigned i=0; i< mTimes.size(); ++i)
    {
        if (index < mSolutions[0].size())
        {
            temp_number = mSolutions[i][index];
        }
        else
        {
            unsigned offset = mSolutions[0].size();
            if (index - offset < mParameters.size())
            {
                temp_number = mParameters[index - offset];
            }
            else
            {
                offset += mParameters.size();
                if (index - offset < mDerivedQuantities[0].size())
                {
                    temp_number = mDerivedQuantities[i][index - offset];
                }
                else
                {
                    EXCEPTION("Invalid index passed to ""GetVariableAtIndex()"".");
                }
            }
        }
        answer.push_back(temp_number);
    }
    return answer;
}
std::vector<double> OdeSolution::GetVariableAtIndex(unsigned index) const {…}
 
std::vector<double> OdeSolution::GetAnyVariable(const std::string& rName) const
{
    return GetVariableAtIndex(mpOdeSystemInformation->GetAnyVariableIndex(rName));
}
std::vector<double> OdeSolution::GetAnyVariable(const std::string& rName) const {…}
 
std::vector<double>& OdeSolution::rGetTimes()
{
    return mTimes;
}
std::vector<double>& OdeSolution::rGetTimes() {…}
 
const std::vector<double>& OdeSolution::rGetTimes() const
{
    return mTimes;
}
const std::vector<double>& OdeSolution::rGetTimes() const {…}
 
std::vector<std::vector<double> >& OdeSolution::rGetSolutions()
{
    return mSolutions;
}
std::vector<std::vector<double> >& OdeSolution::rGetSolutions() {…}
 
const std::vector<std::vector<double> >& OdeSolution::rGetSolutions() const
{
    return mSolutions;
}
const std::vector<std::vector<double> >& OdeSolution::rGetSolutions() const {…}
 
 
template<typename VECTOR>
void OdeSolution::CalculateDerivedQuantitiesAndParameters(AbstractParameterisedSystem<VECTOR>* pOdeSystem)
{
    assert(pOdeSystem->GetSystemInformation() == mpOdeSystemInformation); // Just in case...
    rGetParameters(pOdeSystem);
    rGetDerivedQuantities(pOdeSystem);
}
void OdeSolution::CalculateDerivedQuantitiesAndParameters(AbstractParameterisedSystem<VECTOR>* pOdeSystem) {…}
 
 
template<typename VECTOR>
std::vector<double>& OdeSolution::rGetParameters(AbstractParameterisedSystem<VECTOR>* pOdeSystem)
{
    mParameters.clear();
    const unsigned num_params = pOdeSystem->GetNumberOfParameters();
    if (num_params > 0)
    {
        mParameters.reserve(num_params);
        for (unsigned i=0; i<num_params; ++i)
        {
            mParameters.push_back(pOdeSystem->GetParameter(i));
        }
    }
    return mParameters;
}
std::vector<double>& OdeSolution::rGetParameters(AbstractParameterisedSystem<VECTOR>* pOdeSystem) {…}
 
 
std::vector<std::vector<double> >& OdeSolution::rGetDerivedQuantities(AbstractParameterisedSystem<std::vector<double> >* pOdeSystem)
{
    assert(pOdeSystem != nullptr);
    if (mDerivedQuantities.empty() && pOdeSystem->GetNumberOfDerivedQuantities() > 0)
    {
        assert(mTimes.size() == mSolutions.size()); // Paranoia
        mDerivedQuantities.reserve(mTimes.size());
        for (unsigned i=0; i<mTimes.size(); i++)
        {
            mDerivedQuantities.push_back(pOdeSystem->ComputeDerivedQuantities(mTimes[i], mSolutions[i]));
        }
    }
    return mDerivedQuantities;
}
std::vector<std::vector<double> >& OdeSolution::rGetDerivedQuantities(AbstractParameterisedSystem<std::vector<double> >* pOdeSystem) {…}
 
#ifdef CHASTE_CVODE
std::vector<std::vector<double> >& OdeSolution::rGetDerivedQuantities(AbstractParameterisedSystem<N_Vector>* pOdeSystem)
{
    assert(pOdeSystem != nullptr);
    if (mDerivedQuantities.empty() && pOdeSystem->GetNumberOfDerivedQuantities() > 0)
    {
        const unsigned num_solutions = mSolutions.size();
        assert(mTimes.size() == num_solutions); // Paranoia
        mDerivedQuantities.resize(mTimes.size());
#if CHASTE_SUNDIALS_VERSION >= 60000
        N_Vector state_vars = num_solutions > 0 ? N_VNew_Serial(mSolutions[0].size(), CvodeContextManager::Instance()->GetSundialsContext()) : nullptr;
#else
        N_Vector state_vars = num_solutions > 0 ? N_VNew_Serial(mSolutions[0].size()) : nullptr;
#endif
        for (unsigned i=0; i<num_solutions; i++)
        {
            CopyFromStdVector(mSolutions[i], state_vars);
            N_Vector dqs = pOdeSystem->ComputeDerivedQuantities(mTimes[i], state_vars);
            CopyToStdVector(dqs, mDerivedQuantities[i]);
            DeleteVector(dqs);
        }
        DeleteVector(state_vars);
    }
    assert(mDerivedQuantities.size()==mTimes.size());
    return mDerivedQuantities;
}
std::vector<std::vector<double> >& OdeSolution::rGetDerivedQuantities(AbstractParameterisedSystem<N_Vector>* pOdeSystem) {…}
#endif // CHASTE_CVODE
 
 
void OdeSolution::WriteToFile(std::string directoryName,
                              std::string baseResultsFilename,
                              std::string timeUnits,
                              unsigned stepsPerRow,
                              bool cleanDirectory,
                              unsigned precision,
                              bool includeDerivedQuantities)
{
    assert(stepsPerRow > 0);
    assert(mTimes.size() > 0);
    assert(mTimes.size() == mSolutions.size());
    assert(mpOdeSystemInformation.get() != nullptr);
    if (mpOdeSystemInformation->GetNumberOfParameters()==0 && mpOdeSystemInformation->GetNumberOfDerivedQuantities() == 0)
    {
        includeDerivedQuantities = false;
    }
 
    if (includeDerivedQuantities)
    {
        if ((mDerivedQuantities.empty() || mDerivedQuantities.size()!=mTimes.size()) && mParameters.empty())
        {
            EXCEPTION("You must first call ""CalculateDerivedQuantitiesAndParameters()"" in order to write derived quantities.");
        }
    }
 
    // Write data to a file using ColumnDataWriter
    ColumnDataWriter writer(directoryName, baseResultsFilename, cleanDirectory, precision);
 
    if (!PetscTools::AmMaster())
    {
        //Only the master actually writes to file
        return;
    }
 
    int time_var_id = writer.DefineUnlimitedDimension("Time", timeUnits);
 
    // Either: the ODE system should have no names&units defined, or it should
    // the same number as the number of solutions per timestep.
    assert(  mpOdeSystemInformation->rGetStateVariableNames().size()==0 ||
            (mpOdeSystemInformation->rGetStateVariableNames().size()==mSolutions[0].size()) );
 
    unsigned num_vars = mSolutions[0].size();
    unsigned num_params = mpOdeSystemInformation->GetNumberOfParameters();
    unsigned num_derived_quantities = mpOdeSystemInformation->GetNumberOfDerivedQuantities();
 
    std::vector<int> var_ids;
    var_ids.reserve(num_vars);
    if (mpOdeSystemInformation->rGetStateVariableNames().size() > 0)
    {
        for (unsigned i=0; i<num_vars; i++)
        {
            var_ids.push_back(writer.DefineVariable(mpOdeSystemInformation->rGetStateVariableNames()[i],
                                                    mpOdeSystemInformation->rGetStateVariableUnits()[i]));
        }
    }
    else
    {
        for (unsigned i=0; i<num_vars; i++)
        {
            std::stringstream string_stream;
            string_stream << "var_" << i;
            var_ids.push_back(writer.DefineVariable(string_stream.str(), ""));
        }
    }
 
    if (includeDerivedQuantities)
    {
        var_ids.reserve(num_vars + num_params + num_derived_quantities);
        for (unsigned i=0; i<num_params; ++i)
        {
            var_ids.push_back(writer.DefineVariable(mpOdeSystemInformation->rGetParameterNames()[i],
                                                    mpOdeSystemInformation->rGetParameterUnits()[i]));
        }
        for (unsigned i=0; i<num_derived_quantities; i++)
        {
            var_ids.push_back(writer.DefineVariable(mpOdeSystemInformation->rGetDerivedQuantityNames()[i],
                                                    mpOdeSystemInformation->rGetDerivedQuantityUnits()[i]));
        }
    }
 
    if (mSolverName != "")
    {
        writer.SetCommentForInfoFile("ODE SOLVER: " + mSolverName);
    }
 
    writer.EndDefineMode();
 
    for (unsigned i=0; i<mSolutions.size(); i+=stepsPerRow)
    {
        writer.PutVariable(time_var_id, mTimes[i]);
        for (unsigned j=0; j<num_vars; j++)
        {
            writer.PutVariable(var_ids[j], mSolutions[i][j]);
        }
        if (includeDerivedQuantities)
        {
            for (unsigned j=0; j<num_params; ++j)
            {
                writer.PutVariable(var_ids[j+num_vars], mParameters[j]);
            }
            for (unsigned j=0; j<num_derived_quantities; j++)
            {
                writer.PutVariable(var_ids[j+num_params+num_vars], mDerivedQuantities[i][j]);
            }
        }
        writer.AdvanceAlongUnlimitedDimension();
    }
    writer.Close();
}
void OdeSolution::WriteToFile(std::string directoryName, {…}
 
// Explicit instantiation
 
template std::vector<double>& OdeSolution::rGetParameters(AbstractParameterisedSystem<std::vector<double> >* pOdeSystem);
template void OdeSolution::CalculateDerivedQuantitiesAndParameters(AbstractParameterisedSystem<std::vector<double> >* pOdeSystem);
 
#ifdef CHASTE_CVODE
template std::vector<double>& OdeSolution::rGetParameters(AbstractParameterisedSystem<N_Vector>* pOdeSystem);
template void OdeSolution::CalculateDerivedQuantitiesAndParameters(AbstractParameterisedSystem<N_Vector>* pOdeSystem);
#endif // CHASTE_CVODE