OdeSolution.cpp

/*

Copyright (c) 2005-2012, University of Oxford.
All rights reserved.

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#include "OdeSolution.hpp"

#include <sstream>

#include "ColumnDataWriter.hpp"
#include "Exception.hpp"
#include "PetscTools.hpp"
#include "VectorHelperFunctions.hpp"

OdeSolution::OdeSolution()
    : mNumberOfTimeSteps(0u),
      mpOdeSystemInformation()
{
}


unsigned OdeSolution::GetNumberOfTimeSteps() const
{
    return mNumberOfTimeSteps;
}


void OdeSolution::SetNumberOfTimeSteps(unsigned numTimeSteps)
{
    mNumberOfTimeSteps = numTimeSteps;
    mTimes.reserve(numTimeSteps+1);
    mSolutions.reserve(numTimeSteps);
}


void OdeSolution::SetOdeSystemInformation(boost::shared_ptr<const AbstractOdeSystemInformation> pOdeSystemInfo)
{
    mpOdeSystemInformation = 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::GetAnyVariable(const std::string& rName) const
{
    return GetVariableAtIndex(mpOdeSystemInformation->GetAnyVariableIndex(rName));
}

std::vector<double>& OdeSolution::rGetTimes()
{
    return mTimes;
}

const std::vector<double>& OdeSolution::rGetTimes() const
{
    return mTimes;
}

std::vector<std::vector<double> >& OdeSolution::rGetSolutions()
{
    return mSolutions;
}

const std::vector<std::vector<double> >& OdeSolution::rGetSolutions() const
{
    return mSolutions;
}


template<typename VECTOR>
void OdeSolution::CalculateDerivedQuantitiesAndParameters(AbstractParameterisedSystem<VECTOR>* pOdeSystem)
{
    assert(pOdeSystem->GetSystemInformation() == mpOdeSystemInformation); // Just in case...
    rGetParameters(pOdeSystem);
    rGetDerivedQuantities(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<std::vector<double> >& OdeSolution::rGetDerivedQuantities(AbstractParameterisedSystem<std::vector<double> >* pOdeSystem)
{
    assert(pOdeSystem != NULL);
    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;
}

#ifdef CHASTE_CVODE
std::vector<std::vector<double> >& OdeSolution::rGetDerivedQuantities(AbstractParameterisedSystem<N_Vector>* pOdeSystem)
{
    assert(pOdeSystem != NULL);
    if (mDerivedQuantities.empty() && pOdeSystem->GetNumberOfDerivedQuantities() > 0)
    {
        const unsigned num_solutions = mSolutions.size();
        assert(mTimes.size() == num_solutions); // Paranoia
        mDerivedQuantities.resize(mTimes.size());
        N_Vector state_vars = num_solutions > 0 ? N_VNew_Serial(mSolutions[0].size()) : NULL;
        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;
}
#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() != NULL);
    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();
}

//
// 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