lifev/structure/examples/example_computingJacobian/main.cpp

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//@HEADER
/*
*******************************************************************************

    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.

    LifeV is free software; you can redistribute it and/or modify
    it under the terms of the GNU Lesser General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    LifeV 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
    Lesser General Public License for more details.

    You should have received a copy of the GNU Lesser General Public License
    along with LifeV.  If not, see <http://www.gnu.org/licenses/>.

*******************************************************************************
*/
//@HEADER
/**
   \file main.cpp
   \author Paolo Tricerri <paolo.tricerri@epfl.ch>
   \date 2012-05-01
 */
#undef HAVE_HDF5
#ifdef TWODIM
#error test_structure cannot be compiled in 2D
#endif

// 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 <lifev/core/LifeV.hpp>

#include <lifev/core/array/MapEpetra.hpp>

#include <lifev/core/mesh/MeshData.hpp>
#include <lifev/core/mesh/MeshPartitioner.hpp>

#include <lifev/structure/solver/StructuralConstitutiveLawData.hpp>
#include <lifev/structure/solver/StructuralConstitutiveLaw.hpp>
#include <lifev/structure/solver/StructuralOperator.hpp>

//Not Used
#include <lifev/structure/solver/VenantKirchhoffMaterialLinear.hpp>
#include <lifev/structure/solver/VenantKirchhoffMaterialNonLinear.hpp>
#include <lifev/structure/solver/NeoHookeanMaterialNonLinear.hpp>
#include <lifev/structure/solver/ExponentialMaterialNonLinear.hpp>

#include <lifev/core/filter/ExporterEnsight.hpp>
#ifdef HAVE_HDF5
#include <lifev/core/filter/ExporterHDF5.hpp>
#endif
#include <lifev/core/filter/ExporterEmpty.hpp>

#include <iostream>


using namespace LifeV;

int returnValue = EXIT_FAILURE;

std::set<UInt> parseList ( const std::string& list )
{
    std::string stringList = list;
    std::set<UInt> setList;
    if ( list == "" )
    {
        return setList;
    }
    size_t commaPos = 0;
    while ( commaPos != std::string::npos )
    {
        commaPos = stringList.find ( "," );
        setList.insert ( atoi ( stringList.substr ( 0, commaPos ).c_str() ) );
        stringList = stringList.substr ( commaPos + 1 );
    }
    setList.insert ( atoi ( stringList.c_str() ) );
    return setList;
}


class Structure
{
public:

    typedef LifeV::RegionMesh<LinearTetra>                              mesh_Type;

    // Filters
    typedef LifeV::Exporter<mesh_Type  >                       filter_Type;
    typedef std::shared_ptr< LifeV::Exporter<mesh_Type  > >           filterPtr_Type;

    typedef LifeV::ExporterEmpty<mesh_Type >                            emptyFilter_Type;
    typedef std::shared_ptr<emptyFilter_Type>                         emptyFilterPtr_Type;
    typedef LifeV::ExporterEnsight<mesh_Type >                          ensightFilter_Type;
    typedef std::shared_ptr<ensightFilter_Type>                       ensightFilterPtr_Type;

#ifdef HAVE_HDF5
    typedef LifeV::ExporterHDF5<mesh_Type >                             hdf5Filter_Type;
    typedef std::shared_ptr<hdf5Filter_Type>                          hdf5FilterPtr_Type;
#endif



    /** @name Constructors, destructor
     */
    //@{
    Structure ( int                                   argc,
                char**                                argv,
                std::shared_ptr<Epetra_Comm>        structComm );

    ~Structure()
    {}
    //@}

    //@{
    void run()
    {
        run3d();
    }
    //@}

protected:

private:

    /**
     * run the 2D driven cylinder simulation
     */
    void run2d();

    /**
     * run the 3D driven cylinder simulation
     */
    void run3d();

private:
    struct Private;
    std::shared_ptr<Private> parameters;
    filterPtr_Type M_importer;
    filterPtr_Type M_exporter;
};



struct Structure::Private
{
    Private() :
        rho (1),
        poisson (1),
        young (1),
        bulk (1),
        alpha (1),
        gamma (1)
    {}
    typedef std::function<Real ( Real const&, Real const&, Real const&, Real const&, ID const& ) > fct_type;
    double rho, poisson, young, bulk, alpha, gamma;

    std::string data_file_name;

    std::shared_ptr<Epetra_Comm>     comm;

};



Structure::Structure ( int                                   argc,
                       char**                                argv,
                       std::shared_ptr<Epetra_Comm>        structComm) :
    parameters ( new Private() )
{
    GetPot command_line (argc, argv);
    std::string data_file_name = command_line.follow ("data", 2, "-f", "--file");
    GetPot dataFile ( data_file_name );
    parameters->data_file_name = data_file_name;

    parameters->rho     = dataFile ( "solid/physics/density", 1. );
    parameters->young   = dataFile ( "solid/physics/young",   1. );
    parameters->poisson = dataFile ( "solid/physics/poisson", 1. );
    parameters->bulk    = dataFile ( "solid/physics/bulk",    1. );
    parameters->alpha   = dataFile ( "solid/physics/alpha",   1. );
    parameters->gamma   = dataFile ( "solid/physics/gamma",   1. );

    std::cout << "density = " << parameters->rho     << std::endl
              << "young   = " << parameters->young   << std::endl
              << "poisson = " << parameters->poisson << std::endl
              << "bulk    = " << parameters->bulk    << std::endl
              << "alpha   = " << parameters->alpha   << std::endl
              << "gamma   = " << parameters->gamma   << std::endl;

    parameters->comm = structComm;
    int ntasks = parameters->comm->NumProc();

    if (!parameters->comm->MyPID() )
    {
        std::cout << "My PID = " << parameters->comm->MyPID() << " out of " << ntasks << " running." << std::endl;
    }
}



void
Structure::run2d()
{
    std::cout << "2D cylinder test case is not available yet\n";
}



void
Structure::run3d()
{
    // General typedefs
    typedef StructuralOperator<mesh_Type >::vector_Type vector_Type;
    typedef std::shared_ptr<vector_Type>                        vectorPtr_Type;
    typedef FESpace< mesh_Type, MapEpetra >                       solidFESpace_Type;
    typedef std::shared_ptr<solidFESpace_Type>                  solidFESpacePtr_Type;

    typedef ETFESpace< RegionMesh<LinearTetra>, MapEpetra, 3, 3 >       solidETFESpace_Type;
    typedef std::shared_ptr<solidETFESpace_Type>                      solidETFESpacePtr_Type;

    bool verbose = (parameters->comm->MyPID() == 0);

    //! dataElasticStructure for parameters
    GetPot dataFile ( parameters->data_file_name.c_str() );
    std::shared_ptr<StructuralConstitutiveLawData> dataStructure (new StructuralConstitutiveLawData( ) );
    dataStructure->setup (dataFile);

    //! Read and partition mesh
    MeshData             meshData;
    meshData.setup (dataFile, "solid/space_discretization");

    std::shared_ptr<mesh_Type > fullMeshPtr (new RegionMesh<LinearTetra> ( ( parameters->comm ) ) );
    readMesh (*fullMeshPtr, meshData);

    MeshPartitioner< mesh_Type > meshPart ( fullMeshPtr, parameters->comm );

    //! Functional spaces - needed for the computations of the gradients
    std::string dOrder =  dataFile ( "solid/space_discretization/order", "P1");
    solidFESpacePtr_Type dFESpace ( new solidFESpace_Type (meshPart, dOrder, 3, parameters->comm) );
    solidETFESpacePtr_Type dETFESpace ( new solidETFESpace_Type (meshPart, & (dFESpace->refFE() ), & (dFESpace->fe().geoMap() ), parameters->comm) );


    if (verbose)
    {
        std::cout << std::endl;
    }

    //! 1. Constructor of the class to compute the tensions
    StructuralOperator<RegionMesh<LinearTetra> >  solid;

    //! face BChandler object
    std::shared_ptr<BCHandler> BCh ( new BCHandler() );

    //! 2. Its setup
    solid.setup (dataStructure,
                 dFESpace,
                 dETFESpace,
                 BCh,
                 parameters->comm);

    //! 3. Creation of the importers to read the displacement field
    std::string const filename    = dataFile ( "importer/filename", "structure");
    std::string const importerType = dataFile ( "importer/type", "hdf5");

    std::string iterationString; //useful to iterate over the strings

    if (verbose)
    {
        std::cout << "The filename is    : " << filename << std::endl;
        std::cout << "The importerType is: " << importerType << std::endl;
    }

#ifdef HAVE_HDF5
    if (importerType.compare ("hdf5") == 0)
    {
        M_importer.reset ( new hdf5Filter_Type (dataFile, filename) );
    }
    else
#endif
    {
        if (importerType.compare ("none") == 0)
        {
            M_importer.reset ( new emptyFilter_Type ( dataFile, dFESpace->mesh(), "solid", dFESpace->map().comm().MyPID() ) );
        }
        else
        {
            M_importer.reset ( new ensightFilter_Type ( dataFile, filename ) );
        }
    }
    M_importer->setMeshProcId (dFESpace->mesh(), dFESpace->map().comm().MyPID() );

    // The vector where the solution will be stored
    vectorPtr_Type solidDisp (new vector_Type (dFESpace->map(), LifeV::Unique ) );

    //! 6. Post-processing setting
    std::shared_ptr< Exporter<RegionMesh<LinearTetra> > > exporter;

    std::string const exporterType =  dataFile ( "exporter/type", "hdf5");
    std::string const nameExporter =  dataFile ( "exporter/name", "jacobian");

#ifdef HAVE_HDF5
    if (exporterType.compare ("hdf5") == 0)
    {
        M_exporter.reset ( new hdf5Filter_Type ( dataFile, nameExporter ) );
    }
    else
#endif
    {
        if (exporterType.compare ("none") == 0)
        {
            M_exporter.reset ( new emptyFilter_Type ( dataFile, meshPart.meshPartition(), nameExporter, parameters->comm->MyPID() ) ) ;
        }

        else
        {
            M_exporter.reset ( new ensightFilter_Type ( dataFile, meshPart.meshPartition(), nameExporter, parameters->comm->MyPID() ) ) ;
        }
    }

    M_exporter->setMeshProcId (dFESpace->mesh(), dFESpace->map().comm().MyPID() );

    vectorPtr_Type jacobianVector ( new vector_Type (solid.displacement(),  LifeV::Unique ) );
    vectorPtr_Type meshColors ( new vector_Type (solid.displacement(),  LifeV::Unique ) );

    M_exporter->addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField, "determinantF", dFESpace, jacobianVector, UInt (0) );
    M_exporter->addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField, "colors", dFESpace, meshColors, UInt (0) );
    M_exporter->addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField, "displacementField", dFESpace, solidDisp, UInt (0) );

    M_exporter->postProcess ( 0.0 );

    //! =================================================================================
    //! Analysis - Istant or Interval
    //! =================================================================================

    MPI_Barrier (MPI_COMM_WORLD);

    //! 5. For each interval, the analysis is performed
    LifeV::Real dt =  dataFile ( "solid/time_discretization/timestep", 0.0);
    std::string const nameField =  dataFile ( "importer/nameField", "displacement");

    //Get the iteration number
    iterationString = dataFile ("importer/iteration", "00000");
    LifeV::Real time = dataFile ("importer/time", 1.0);

    /*!Definition of the ExporterData, used to load the solution inside the previously defined vectors*/
    LifeV::ExporterData<mesh_Type> solutionDispl  (LifeV::ExporterData<mesh_Type>::VectorField, nameField + "." + iterationString, dFESpace, solidDisp, UInt (0), LifeV::ExporterData<mesh_Type>::UnsteadyRegime );

    //Read the variable
    M_importer->readVariable (solutionDispl);
    M_importer->closeFile();

    //Set the current solution as the displacement vector to use
    solid.jacobianDistribution ( solidDisp, *jacobianVector);

    //color the mesh according to the marker of the volume
    solid.colorMesh ( *meshColors );

    //Extracting the tensions
    std::cout << std::endl;
    std::cout << "Norm of the J = det(F) : " << jacobianVector->norm2() << std::endl;

    M_exporter->postProcess ( time );

    if (verbose )
    {
        std::cout << "Analysis Completed!" << std::endl;
    }

    //Closing files
    M_exporter->closeFile();

    if (verbose )
    {
        std::cout << "finished" << std::endl;
    }

    MPI_Barrier (MPI_COMM_WORLD);
    //!---------------------------------------------.-----------------------------------------------------
}

int
main ( int argc, char** argv )
{

#ifdef HAVE_MPI
    MPI_Init (&argc, &argv);
    std::shared_ptr<Epetra_MpiComm> Comm (new Epetra_MpiComm ( MPI_COMM_WORLD ) );
    if ( Comm->MyPID() == 0 )
    {
        std::cout << "% using MPI" << std::endl;
    }
#else
    std::shared_ptr<Epetra_SerialComm> Comm ( new Epetra_SerialComm() );
    std::cout << "% using serial Version" << std::endl;
#endif

    Structure structure ( argc, argv, Comm );
    structure.run();

#ifdef HAVE_MPI
    MPI_Finalize();
#endif
    return returnValue ;
}