mainAnisotropic.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


   The general procedure to use this example is the following:
    - read the set of solutions from the hdf5 file
    - compute the sigma tensor using the reconstruction procedure
      shown in testsuite/evaluateNodalETA/
    - use the method StructuralOperator::computeEigenvalue to,
      given a certain dof to compute the set of eigenvalues.
    - post process the vector of eigenvalues
 */
#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>

#include <lifev/structure/fem/ExpressionDefinitions.hpp>

#include <lifev/structure/solver/isotropic/ExponentialMaterialNonLinear.hpp>
#include <lifev/structure/solver/isotropic/NeoHookeanMaterialNonLinear.hpp>
#include <lifev/structure/solver/anisotropic/HolzapfelMaterialNonLinear.hpp>

// Evaluation operations
#include <lifev/core/array/MatrixSmall.hpp>
#include <lifev/eta/expression/Evaluate.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>
#include "ud_functions.hpp"

#include <functional>

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();
    void checkResultHolzapfelModel (const Real tensNorm);
    void resultCorrect ( void );
private:
    struct Private;
    std::shared_ptr<Private> parameters;
};



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;

    static Real displacementHolzapfelModel (const Real& /*t*/, const Real& x, const Real& y, const Real& z, const ID& i)
    {

        switch (i)
        {
            case 0:
                return -0.025697538387539 * ( x - 0.5 );
                break;
            case 1:
                return  0.083508698014296 / 2.0  * ( y );
                break;
            case 2:
                return -0.013480042559669  * ( z + 0.5  );
                break;
            default:
                ERROR_MSG ("This entry is not allowed: ud_functions.hpp");
                return 0.;
                break;
        }

    }


};



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->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()
{
    typedef std::shared_ptr<VectorEpetra>                              vectorPtr_Type;

    // typedefs for fibers
    // std function for fiber direction
    typedef std::function<Real ( Real const&, Real const&, Real const&, Real const&, ID const& ) > fiberFunction_Type;
    typedef std::shared_ptr<fiberFunction_Type> fiberFunctionPtr_Type;

    typedef std::vector<fiberFunctionPtr_Type>                          vectorFiberFunction_Type;
    typedef std::shared_ptr<vectorFiberFunction_Type>                 vectorFiberFunctionPtr_Type;

    // 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;

    typedef ETFESpace< RegionMesh<LinearTetra>, MapEpetra, 3, 1 >       scalarETFESpace_Type;
    typedef std::shared_ptr<scalarETFESpace_Type>                     scalarETFESpacePtr_Type;

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

    //! BChandler use to create the StructuralOperator object
    std::shared_ptr<BCHandler> BCh ( new BCHandler() );

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

    dataStructure->setup (dataFile);

    dataStructure->showMe();

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

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

    MeshPartitioner< mesh_Type > meshPart ( fullMeshPtr, parameters->comm );
    localMeshPtr = meshPart.meshPartition();

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

    //! Scalar ETFEspace to evaluate scalar quantities
    solidFESpacePtr_Type dScalarFESpace ( new solidFESpace_Type (localMeshPtr, dOrder, 1, parameters->comm) );
    scalarETFESpacePtr_Type dScalarETFESpace ( new scalarETFESpace_Type (meshPart, & (dFESpace->refFE() ), & (dFESpace->fe().geoMap() ), parameters->comm) );

    // Setting the fibers
    vectorFiberFunctionPtr_Type pointerToVectorOfFamilies( new vectorFiberFunction_Type( ) );
    (*pointerToVectorOfFamilies).resize( dataStructure->numberFibersFamilies( ) );

    if( verbose )
        std::cout << "Number of families: " << (*pointerToVectorOfFamilies).size() << std::endl;

    fibersDirectionList setOfFiberFunctions;
    setOfFiberFunctions.setupFiberDefinitions( dataStructure->numberFibersFamilies( ) );

    // Setting the vector of fibers functions
    for( UInt k(1); k <= pointerToVectorOfFamilies->size( ); k++ )
    {
        // Setting up the name of the function to define the family
        std::string family="Family";
        // adding the number of the family
        std::string familyNumber;
        std::ostringstream number;
        number << ( k );
        familyNumber = number.str();

        // Name of the function to create
        std::string creationString = family + familyNumber;
        (*pointerToVectorOfFamilies)[ k-1 ].reset( new fiberFunction_Type() );
        (*pointerToVectorOfFamilies)[ k-1 ] = setOfFiberFunctions.fiberDefinition( creationString );
    }

    // Interpolate fibers
    std::vector<vectorPtr_Type> vectorInterpolated(0);

    // Interpolating fiber fields
    vectorInterpolated.resize( (*pointerToVectorOfFamilies).size() );

    for( UInt k(0); k < (*pointerToVectorOfFamilies).size(); k++ )
    {
        vectorInterpolated[ k ].reset( new vector_Type( dFESpace->map() ) );
        dFESpace->interpolate ( *( ( *(pointerToVectorOfFamilies) )[ k ] ) ,
                                * ( ( vectorInterpolated )[ k ] ),
                                0.0 );
    }

    // Creating the StructuralOperator object
    //! 1. Constructor of the structuralSolver
    StructuralOperator< RegionMesh<LinearTetra> > solid;

    //! 2. Setup of the structuralSolver
    solid.setup (dataStructure,
                 dFESpace,
                 dETFESpace,
                 BCh,
                 parameters->comm);

    if( !dataStructure->constitutiveLaw().compare("anisotropic") )
      {
          //! 3.b Setting the fibers in the abstract class of Anisotropic materials
          solid.material()->anisotropicLaw()->setupFiberDirections( pointerToVectorOfFamilies );
      }


    // How many solution do we have to read?
    UInt numberOfSol(0);
    numberOfSol = dataFile.vector_variable_size ( "importer/iteration"  );

    ASSERT( numberOfSol, "You did not set any solution to read!! ");

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

        else
        {
            exporter.reset ( new ensightFilter_Type ( dataFile, meshPart.meshPartition(), nameExporter, parameters->comm->MyPID() ) ) ;
        }
    }
    exporter->setMeshProcId (dFESpace->mesh(), dFESpace->map().comm().MyPID() );

    vectorPtr_Type patchAreaVector;

    /*
       Vector to pass to the StructuralOperator and to export
       what is read.
    */
    vectorPtr_Type disp;
    vectorPtr_Type dispRead;

    // Vectors to export Cauchy stress tensors
    vectorPtr_Type sigma_1;
    vectorPtr_Type sigma_2;
    vectorPtr_Type sigma_3;

    // Vector for the eigenvalues
    vectorPtr_Type vectorEigenvalues;

    patchAreaVector.reset ( new vector_Type ( dETFESpace->map() ) );

    disp.reset( new vector_Type( dFESpace->map() ) );
    dispRead.reset( new vector_Type( dFESpace->map() ) );

    sigma_1.reset( new vector_Type( dFESpace->map() ) );
    sigma_2.reset( new vector_Type( dFESpace->map() ) );
    sigma_3.reset( new vector_Type( dFESpace->map() ) );

    vectorEigenvalues.reset( new vector_Type( dFESpace->map() ) );

    exporter->addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField, "displacement",
                              dFESpace, dispRead, UInt (0) );

    exporter->addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField, "sigma_1",
                              dFESpace, sigma_1, UInt (0) );

    exporter->addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField, "sigma_2",
                              dFESpace, sigma_2, UInt (0) );

    exporter->addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField, "sigma_3",
                              dFESpace, sigma_3, UInt (0) );

    exporter->addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField, "vectorEigenvalues",
                              dFESpace, vectorEigenvalues, UInt (0) );

    exporter->postProcess ( 0.0 );

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

    MPI_Barrier (MPI_COMM_WORLD);

    QuadratureRule fakeQuadratureRule;

    Real refElemArea (0); //area of reference element
    //compute the area of reference element
    for (UInt iq = 0; iq < dFESpace->qr().nbQuadPt(); iq++)
    {
        refElemArea += dFESpace->qr().weight (iq);
    }

    Real wQuad (refElemArea / dFESpace->refFE().nbDof() );

    //Setting the quadrature Points = DOFs of the element and weight = 1
    std::vector<GeoVector> coords = dFESpace->refFE().refCoor();
    std::vector<Real> weights (dFESpace->fe().nbFEDof(), wQuad);
    fakeQuadratureRule.setDimensionShape ( shapeDimension (dFESpace->refFE().shape() ), dFESpace->refFE().shape() );
    fakeQuadratureRule.setPoints (coords, weights);


    //fakeQuadratureRule.showMe();
    using namespace ExpressionAssembly;

    // Trying to compute the Jacobian using ET
    MatrixSmall<3,3> identity;
    identity (0, 0) = 1.0;
    identity (0, 1) = 0.0;
    identity (0, 2) = 0.0;
    identity (1, 0) = 0.0;
    identity (1, 1) = 1.0;
    identity (1, 2) = 0.0;
    identity (2, 0) = 0.0;
    identity (2, 1) = 0.0;
    identity (2, 2) = 1.0;

    ExpressionVectorFromNonConstantScalar<ExpressionMeas, 3  > vMeas( meas_K );
    evaluateNode( elements ( dETFESpace->mesh() ),
      fakeQuadratureRule,
      dETFESpace,
      dot( vMeas , phi_i )
      ) >> patchAreaVector;
    patchAreaVector->globalAssemble();

    std::string const nameField =  dataFile ( "importer/nameField", "displacement");

    *sigma_1 *=0.0;
    *sigma_2 *=0.0;
    *sigma_3 *=0.0;
    *vectorEigenvalues *=0.0;

    // Reading the solution
    // resetting the element of the vector
    *disp *= 0.0;
    *dispRead *= 0.0;

    // Interpolating the displacement
    dFESpace->interpolate( static_cast<solidFESpace_Type::function_Type> ( Private::displacementHolzapfelModel ),
                           *disp, 0.0 );

    *dispRead = *disp;

    solid.computeCauchyStressTensor( disp, fakeQuadratureRule, sigma_1, sigma_2, sigma_3 );

    // Concluding reconstruction
    *sigma_1 = *sigma_1 / *patchAreaVector;
    *sigma_2 = *sigma_2 / *patchAreaVector;
    *sigma_3 = *sigma_3 / *patchAreaVector;

    // Computing eigenvalues
    solid.computePrincipalTensions( sigma_1, sigma_2, sigma_3, vectorEigenvalues );

    exporter->postProcess( 1.0 );

    // Check the result
    checkResultHolzapfelModel ( vectorEigenvalues->norm2()  );
    // End of check

    std::cout.precision(16);
    std::cout << "Norm 2 of the vector: " << vectorEigenvalues->norm2() << std::endl;

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

    //Closing files
    exporter->closeFile( );

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

void Structure::checkResultHolzapfelModel (const Real testETA)
{
    if ( ( ( std::fabs (testETA - 7802999.6608) / 7802999.6608) <= 1e-5 ) )
    {
        this->resultCorrect( );
    }
}

void Structure::resultCorrect ( void )
{
    std::cout << "Correct Result after the Analysis" << std::endl;
    returnValue = EXIT_SUCCESS;
}

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 ;
}