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// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
// vi: set et ts=4 sw=4 sts=4:
/*****************************************************************************
 *   See the file COPYING for full copying permissions.                      *
 *                                                                           *
 *   This program is free software: you can redistribute it and/or modify    *
 *   it under the terms of the GNU General Public License as published by    *
 *   the Free Software Foundation, either version 2 of the License, or       *
 *   (at your option) any later version.                                     *
 *                                                                           *
 *   This program is distributed in the hope that it will be useful,         *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of          *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the            *
 *   GNU General Public License for more details.                            *
 *                                                                           *
 *   You should have received a copy of the GNU General Public License       *
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.   *
 *****************************************************************************/
/*!
 * \file
 *
 * \brief Exercise for the two-phase n-component bio mineralization CC model.
 */
#include <config.h>

#include <ctime>
#include <iostream>

#include <dune/common/parallel/mpihelper.hh>
#include <dune/common/timer.hh>
#include <dune/grid/io/file/dgfparser/dgfexception.hh>
#include <dune/grid/io/file/vtk.hh>
#include <dune/istl/io.hh>

#include <dumux/common/properties.hh>
#include <dumux/common/parameters.hh>
#include <dumux/common/valgrind.hh>
#include <dumux/common/dumuxmessage.hh>
#include <dumux/common/defaultusagemessage.hh>

#include <dumux/linear/amgbackend.hh>
#include <dumux/nonlinear/privarswitchnewtonsolver.hh>

#include <dumux/assembly/fvassembler.hh>
#include <dumux/assembly/diffmethod.hh>

#include <dumux/discretization/methods.hh>

#include <dumux/io/vtkoutputmodule.hh>
#include <dumux/io/grid/gridmanager.hh>

#include "biominproblem.hh"

////////////////////////
// the main function
////////////////////////
int main(int argc, char** argv) try
{
    using namespace Dumux;

    // define the type tag for this problem
    using TypeTag = TTAG(ExerciseFourBioMinCCTpfaTypeTag);

    // initialize MPI, finalize is done automatically on exit
    const auto& mpiHelper = Dune::MPIHelper::instance(argc, argv);

    // print dumux start message
    if (mpiHelper.rank() == 0)
        DumuxMessage::print(/*firstCall=*/true);

    // parse command line arguments and input file
    Parameters::init(argc, argv);

    // try to create a grid (from the given grid file or the input file)
    GridManager<typename GET_PROP_TYPE(TypeTag, Grid)> gridManager;
    gridManager.init();

    ////////////////////////////////////////////////////////////
    // run instationary non-linear problem on this grid
    ////////////////////////////////////////////////////////////

    // we compute on the leaf grid view
    const auto& leafGridView = gridManager.grid().leafGridView();

    // create the finite volume grid geometry
    using FVGridGeometry = typename GET_PROP_TYPE(TypeTag, FVGridGeometry);
    auto fvGridGeometry = std::make_shared<FVGridGeometry>(leafGridView);
    fvGridGeometry->update();

    // the problem (initial and boundary conditions)
    using Problem = typename GET_PROP_TYPE(TypeTag, Problem);
    auto problem = std::make_shared<Problem>(fvGridGeometry);

    // the solution vector
    using SolutionVector = typename GET_PROP_TYPE(TypeTag, SolutionVector);
    SolutionVector x(fvGridGeometry->numDofs());
    problem->applyInitialSolution(x);
    auto xOld = x;

    // initialize the spatialParams separately to compute the referencePorosity and referencePermeability
    problem->spatialParams().computeReferencePorosity(*fvGridGeometry, x);
    problem->spatialParams().computeReferencePermeability(*fvGridGeometry, x);

    // the grid variables
    using GridVariables = typename GET_PROP_TYPE(TypeTag, GridVariables);
    auto gridVariables = std::make_shared<GridVariables>(problem, fvGridGeometry);
    gridVariables->init(x, xOld);

    // get some time loop parameters
    using Scalar = typename GET_PROP_TYPE(TypeTag, Scalar);
    const auto tEnd = getParam<Scalar>("TimeLoop.TEnd");
    const auto maxDt = getParam<Scalar>("TimeLoop.MaxTimeStepSize");
    auto dt = getParam<Scalar>("TimeLoop.DtInitial");

    // initialize the vtk output module
    using VtkOutputFields = typename GET_PROP_TYPE(TypeTag, VtkOutputFields);
    VtkOutputModule<TypeTag> vtkWriter(*problem, *fvGridGeometry, *gridVariables, x, problem->name());
    VtkOutputFields::init(vtkWriter); //!< Add model specific output fields
    //add specific output
    vtkWriter.addField(problem->getKxx(), "Kxx");
    vtkWriter.addField(problem->getKyy(), "Kyy");
    // update the output fields before write
    problem->updateVtkOutput(x);
    vtkWriter.write(0.0);

    // instantiate time loop
    auto timeLoop = std::make_shared<TimeLoop<Scalar>>(0.0, dt, tEnd);
    const auto injBioTime = getParam<Scalar>("Injection.InjBioTime")*86400;
    const auto maxDtCO2 = getParam<Scalar>("TimeLoop.MaxTimeStepSizeCO2");

    // the assembler with time loop for instationary problem
    using Assembler = FVAssembler<TypeTag, DiffMethod::numeric>;
    auto assembler = std::make_shared<Assembler>(problem, fvGridGeometry, gridVariables, timeLoop);

    // the linear solver
    using LinearSolver = AMGBackend<TypeTag>;
    auto linearSolver = std::make_shared<LinearSolver>(leafGridView, fvGridGeometry->dofMapper());

    // the non-linear solver
    using NewtonSolver = PriVarSwitchNewtonSolver<Assembler, LinearSolver,
                                                  typename GET_PROP_TYPE(TypeTag, PrimaryVariableSwitch)>;
    NewtonSolver nonLinearSolver(assembler, linearSolver);

    // time loop
    timeLoop->start(); do
    {
        // set previous solution for storage evaluations
        assembler->setPreviousSolution(xOld);

        // solve the non-linear system with time step control
        nonLinearSolver.solve(x, *timeLoop);

        //reset MaxTimeStepSize for CO2 Injection
        bool injCO2 = injBioTime < timeLoop->time() +  timeLoop->timeStepSize();
        timeLoop->setMaxTimeStepSize( injCO2 ? maxDtCO2 : maxDt);

        //set time in problem (is used in time-dependent Neumann boundary condition)
        problem->setTime(timeLoop->time()+timeLoop->timeStepSize());

        // make the new solution the old solution
        xOld = x;
        gridVariables->advanceTimeStep();

        // advance to the time loop to the next step
        timeLoop->advanceTimeStep();

        // update the output fields before write
        problem->updateVtkOutput(x);

        // write vtk output
        if (timeLoop->timeStepIndex()==0 || injCO2 == false || timeLoop->timeStepIndex() || timeLoop->willBeFinished())
            vtkWriter.write(timeLoop->time());

        // report statistics of this time step
        timeLoop->reportTimeStep();

        // set new dt as suggested by newton controller
        timeLoop->setTimeStepSize(nonLinearSolver.suggestTimeStepSize(timeLoop->timeStepSize()));

    } while (!timeLoop->finished());

    timeLoop->finalize(leafGridView.comm());

    ////////////////////////////////////////////////////////////
    // finalize, print dumux message to say goodbye
    ////////////////////////////////////////////////////////////

    // print dumux end message
    if (mpiHelper.rank() == 0)
    {
        Parameters::print();
        DumuxMessage::print(/*firstCall=*/false);
    }

    return 0;
} // end main
catch (Dumux::ParameterException &e)
{
    std::cerr << std::endl << e << " ---> Abort!" << std::endl;
    return 1;
}
catch (Dune::DGFException & e)
{
    std::cerr << "DGF exception thrown (" << e <<
                 "). Most likely, the DGF file name is wrong "
                 "or the DGF file is corrupted, "
                 "e.g. missing hash at end of file or wrong number (dimensions) of entries."
                 << " ---> Abort!" << std::endl;
    return 2;
}
catch (Dune::Exception &e)
{
    std::cerr << "Dune reported error: " << e << " ---> Abort!" << std::endl;
    return 3;
}
catch (...)
{
    std::cerr << "Unknown exception thrown! ---> Abort!" << std::endl;
    return 4;
}