/*

Copyright (c) 2005-2014, University of Oxford.
All rights reserved.

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This file is part of Chaste.

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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
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HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#ifndef TESTSTANDINGWAVE_HPP_
#define TESTSTANDINGWAVE_HPP_

#include <cxxtest/TestSuite.h>

#include "BidomainProblem.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "PetscSetupAndFinalize.hpp"

#include "AbstractCardiacCellFactory.hpp"
#include "RegularStimulus.hpp"
#include "li_mouse_2010Cvode.hpp"

#ifdef CHASTE_CVODE

class MouseCellFactory : public AbstractCardiacCellFactory<2>
{
private:
    boost::shared_ptr<RegularStimulus> mpStimulus;

public:
    MouseCellFactory(const double& rPeriod)
    : AbstractCardiacCellFactory<2>(),
      mpStimulus(new RegularStimulus(-40000.0, 2, rPeriod, 10))
    {
    }

    AbstractCardiacCellInterface* CreateCardiacCellForTissueNode(Node<2u>* pNode)
    {
        AbstractCardiacCellInterface* p_cell;
        boost::shared_ptr<AbstractIvpOdeSolver> p_empty_solver;

        const double x = pNode->rGetLocation()[0];
        //const double y = pNode->rGetLocation()[1];

        if ( (x<0.05+1e-6)  ) // Left hand edge
        {
            p_cell = new Cellli_mouse_2010FromCellMLCvode(p_empty_solver, mpStimulus);
        }
        else
        {
            p_cell = new Cellli_mouse_2010FromCellMLCvode(p_empty_solver, this->mpZeroStimulus);
        }

        return p_cell;
    }
};

#endif // CHASTE_CVODE

class TestStandingWave: public CxxTest::TestSuite
{

public:
    void TestBasic2dPropagation() throw (Exception)
    {
#ifdef CHASTE_CVODE
        /**
         * SET OPTIONS FOR THIS RUN
         */

        double pacing_cycle_length = 45;
        double end_time = 260;

        /**
         * SET UP MESH
         */
        DistributedTetrahedralMesh<2,2> mesh;
        double h=0.01;
        double region_width = 0.5;
        mesh.ConstructRegularSlabMesh(h, 2.0*region_width, 0.5*region_width);

        /**
         * SET STANDARD OPTIONS
         */
        HeartConfig::Instance()->SetSimulationDuration(end_time); //ms
        HeartConfig::Instance()->SetOutputDirectory("StandingWave");
        HeartConfig::Instance()->SetOutputFilenamePrefix("results");
        HeartConfig::Instance()->SetVisualizeWithVtk(true);
        HeartConfig::Instance()->SetVisualizeWithMeshalyzer(false);

        /**
         * NUMERICAL METHOD PARAMETERS
         */
        HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.1, 0.1, 0.1);

        /*
         * SET UP HETEROGENEOUS CONDUCTIVITY
         */
        const double intra_conductivity = 1.75; // Chaste Defaults
        const double extra_conductivity = 7.0; // Chaste Defaults

        // Elsewhere we use the defaults.
        HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(intra_conductivity, intra_conductivity));
        HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(extra_conductivity, extra_conductivity));

        {
            // Interrogate a model to get all the state variables
            boost::shared_ptr<AbstractStimulusFunction> p_stimulus;
            boost::shared_ptr<AbstractIvpOdeSolver> p_solver;
            Cellli_mouse_2010FromCellMLCvode cell(p_solver, p_stimulus);
            // Copy all the state variable names from the temporary cell into
            // HeartConfig so that they are all printed out to HDF5
            HeartConfig::Instance()->SetOutputVariables( cell.rGetStateVariableNames() );
        }

        /**
         * COMPLETE THE SET UP OF PROBLEM
         */

        // Make a cell factory
        MouseCellFactory cell_factory(pacing_cycle_length);

        BidomainProblem<2> problem( &cell_factory );
        problem.SetMesh( &mesh );

        problem.SetWriteInfo(); // Writes max and min voltages through time to std::cout.
        problem.Initialise();

        problem.Solve();

#else
        std::cout << "CVODE is not installed, or CHASTE is not configured to use it, check your hostconfig settings." << std::endl;
        TS_ASSERT(false);
#endif // CHASTE_CVODE
    }
};

#endif // TESTSTANDINGWAVE_HPP_