lifev/electrophysiology/testsuite/test_0DMinimalModel/main.cpp

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/*
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    Copyright (C) 2004, 2005, 2007 EPFL, Politecnico di Milano, INRIA
    Copyright (C) 2010 EPFL, Politecnico di Milano, Emory University

    This file is part of LifeV.

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/*!
    @file
    @brief 0D test with the minimal model

    Run  the test using one of the xml files:
    ./Electrophysiology_test_0DMinimalModel -i xml_file_name

    @date 01 - 2013
    @author Simone Rossi <simone.rossi@epfl.ch>

    @contributor
    @mantainer Simone Rossi <simone.rossi@epfl.ch>
 */

// Tell the compiler to ignore specific kind of warnings:
#pragma GCC diagnostic ignored "-Wunused-variable"
#pragma GCC diagnostic ignored "-Wunused-parameter"

#include <Epetra_ConfigDefs.h>
#ifdef EPETRA_MPI
#include <mpi.h>
#include <Epetra_MpiComm.h>
#else
#include <Epetra_SerialComm.h>
#endif

//Tell the compiler to restore the warning previously silented
#pragma GCC diagnostic warning "-Wunused-variable"
#pragma GCC diagnostic warning "-Wunused-parameter"


#include <fstream>

#include <lifev/core/filter/GetPot.hpp>

#include <lifev/electrophysiology/solver/IonicModels/IonicMinimalModel.hpp>
#include <lifev/core/LifeV.hpp>

#include <lifev/electrophysiology/stimulus/StimulusPacingProtocol.hpp>
#include <Teuchos_RCP.hpp>
#include <Teuchos_ParameterList.hpp>
#include "Teuchos_XMLParameterListHelpers.hpp"


using namespace LifeV;

#define SolutionTestNorm  14412.225993765172461

Int main ( Int argc, char** argv )
{
    //! Initializing Epetra communicator
    MPI_Init (&argc, &argv);
    Epetra_MpiComm Comm (MPI_COMM_WORLD);
    if ( Comm.MyPID() == 0 )
    {
        std::cout << "% using MPI" << std::endl;
    }


    //********************************************//
    // Import parameters from an xml list. Use    //
    // Teuchos to create a list from a given file //
    // in the execution directory.                //
    //********************************************//

    GetPot commandLine ( argc, argv );
    std::string xmlParameterFilename = commandLine.follow ("ParametersTNNP.xml", 2, "-i", "--file"); ;

    std::cout << "Importing parameters list...";
    //    Teuchos::ParameterList ParameterList = * ( Teuchos::getParametersFromXmlFile ( "Parameters.xml" ) );
    Teuchos::ParameterList ParameterList = * ( Teuchos::getParametersFromXmlFile ( xmlParameterFilename ) );
    std::cout << " Done!" << std::endl;


    //********************************************//
    // Creates a new model object representing the//
    // model from Bueno Orovio 2008. The          //
    // model input are the parameters. Pass  the  //
    // parameter list in the constructor          //
    //********************************************//
    std::cout << "Building Constructor for Minimal  Model with parameters ... ";
    IonicMinimalModel  ionicModel (ParameterList);
    std::cout << " Done!" << std::endl;


    //********************************************//
    // Show the parameters of the model as well as//
    // other informations  about the object.      //
    //********************************************//
    ionicModel.showMe();


    //********************************************//
    // Initialize the solution with the default   //
    // values                                     //
    //********************************************//
    std::cout << "Initializing solution vector...";
    std::vector<Real> states (ionicModel.Size(), 0);
    ionicModel.initialize (states);
    std::cout << " Done!" << std::endl;


    //********************************************//
    // Initialize the rhs to 0. The rhs is the    //
    // vector containing the numerical values of  //
    // the time derivatives of the state          //
    // variables, that is, the right hand side of //
    // the differential equation.                 //
    //********************************************//
    std::cout << "Initializing rhs..." ;
    std::vector<Real> rhs (ionicModel.Size(), 0);
    std::cout << " Done! "  << std::endl;




    //********************************************//
    // The model needs as external informations   //
    // the contraction velocity and the Calcium   //
    // concentration.                             //
    //********************************************//
    Real Iapp (0.0);


    //********************************************//
    // Simulation starts on t=0 and ends on t=TF. //
    // The timestep is given by dt                //
    //********************************************//
    Real TF (400);
    Real dt (0.02);

    //********************************************//
    // We record the norm of the solution to      //
    // check the failure of the test              //
    //********************************************//
    Real SolutionNorm = states[0];

    //********************************************//
    // Open the file "output.txt" to save the     //
    // solution.                                  //
    //********************************************//
    std::string filename = "output.txt";
    std::ofstream output ("output.txt");

    std::cout << "Potential: " << states[0] << std::endl;
    //********************************************//
    // Time loop starts.                          //
    //********************************************//
    std::cout << "Time loop starts...\n";
    for ( Real t = 0; t < TF; )
    {

        //********************************************//
        // Compute the applied current. This is a     //
        // simple switch.                             //
        //********************************************//
        if ( t >= 10 && t <= 12 )
        {
            Iapp = 0.4;
        }
        else
        {
            Iapp = 0.0;
        }
        std::cout << "\r " << t << " ms.       " << std::flush;

        //********************************************//
        // Compute the rhs using the model equations  //
        //********************************************//
        ionicModel.setAppliedCurrent (Iapp);
        ionicModel.computeRhs ( states, rhs);
        rhs[0] += Iapp;

        //********************************************//
        // Use forward Euler method to advance the    //
        // solution in time.                          //
        //********************************************//

        for ( int j (0); j < ionicModel.Size(); j++)
        {
            states[j] = states[j]  + dt * rhs[j];
        }

        //********************************************//
        // Writes solution on file.                   //
        //********************************************//
        output << t << ", ";
        for ( int j (0); j < ionicModel.Size() - 1; j++)
        {
            output << states[j] << ", ";
        }
        output << states[ ionicModel.Size() - 1] << "\n";

        //********************************************//
        // Update the time.                           //
        //********************************************//
        t = t + dt;

        //********************************************//
        // Update the norm of the solution to check   //
        // test failure                               //
        //********************************************//
        SolutionNorm = SolutionNorm + states[0];

    }
    std::cout << "\n...Time loop ends.\n";
    std::cout << "Solution written on file: " << filename << "\n";
    //********************************************//
    // Close exported file.                       //
    //********************************************//
    output.close();

    //! Finalizing Epetra communicator
    MPI_Finalize();
    Real returnValue;

    Real err = std::abs (SolutionTestNorm - SolutionNorm) / std::abs (SolutionTestNorm);
    std::cout << std::setprecision (20) << "\nError: " << err << "\nSolution norm: " << SolutionNorm << "\n";
    if ( err > 1e-12 )
    {
        std::cout << "\nTest Failed!\n";
        returnValue = EXIT_FAILURE; // Norm of solution did not match
    }
    else
    {
        returnValue = EXIT_SUCCESS;
    }
    return ( returnValue );
}

#undef SolutionTestNorm