Nektar::Utilities::ProcessJac Class Reference

This processing module calculates the Jacobian of elements using SpatialDomains::GeomFactors and the Element::GetGeom method. For now it simply prints a list of elements which have negative Jacobian. More...

#include <ProcessJac.h>

Inheritance diagram for Nektar::Utilities::ProcessJac:

Public Member Functions
	ProcessJac (NekMeshUtils::MeshSharedPtr m)
virtual	~ProcessJac ()
virtual void	Process ()
	Write mesh to output file. More...
Public Member Functions inherited from Nektar::NekMeshUtils::ProcessModule
NEKMESHUTILS_EXPORT	ProcessModule (MeshSharedPtr p_m)
Public Member Functions inherited from Nektar::NekMeshUtils::Module
NEKMESHUTILS_EXPORT	Module (MeshSharedPtr p_m)
NEKMESHUTILS_EXPORT void	RegisterConfig (std::string key, std::string value=std::string())
	Register a configuration option with a module. More...
NEKMESHUTILS_EXPORT void	PrintConfig ()
	Print out all configuration options for a module. More...
NEKMESHUTILS_EXPORT void	SetDefaults ()
	Sets default configuration options for those which have not been set. More...
NEKMESHUTILS_EXPORT MeshSharedPtr	GetMesh ()
virtual NEKMESHUTILS_EXPORT void	ProcessVertices ()
	Extract element vertices. More...
virtual NEKMESHUTILS_EXPORT void	ProcessEdges (bool ReprocessEdges=true)
	Extract element edges. More...
virtual NEKMESHUTILS_EXPORT void	ProcessFaces (bool ReprocessFaces=true)
	Extract element faces. More...
virtual NEKMESHUTILS_EXPORT void	ProcessElements ()
	Generate element IDs. More...
virtual NEKMESHUTILS_EXPORT void	ProcessComposites ()
	Generate composites. More...
virtual NEKMESHUTILS_EXPORT void	ClearElementLinks ()

Static Public Member Functions
static std::shared_ptr< Module >	create (NekMeshUtils::MeshSharedPtr m)
	Creates an instance of this class. More...

Static Public Attributes
static NekMeshUtils::ModuleKey	className

Additional Inherited Members
Protected Member Functions inherited from Nektar::NekMeshUtils::Module
NEKMESHUTILS_EXPORT void	ReorderPrisms (PerMap &perFaces)
	Reorder node IDs so that prisms and tetrahedra are aligned correctly. More...
NEKMESHUTILS_EXPORT void	PrismLines (int prism, PerMap &perFaces, std::set< int > &prismsDone, std::vector< ElementSharedPtr > &line)
Protected Attributes inherited from Nektar::NekMeshUtils::Module
MeshSharedPtr	m_mesh
	Mesh object. More...
std::map< std::string, ConfigOption >	m_config
	List of configuration values. More...

Detailed Description

This processing module calculates the Jacobian of elements using SpatialDomains::GeomFactors and the Element::GetGeom method. For now it simply prints a list of elements which have negative Jacobian.

Definition at line 51 of file ProcessJac.h.

Constructor & Destructor Documentation

ProcessJac()

Nektar::Utilities::ProcessJac::ProcessJac

(

NekMeshUtils::MeshSharedPtr

m

)

Definition at line 51 of file ProcessJac.cpp.

References Nektar::NekMeshUtils::Module::m_config.

                                      : ProcessModule(m)
{
    m_config["extract"] =
        ConfigOption(false, "0.0", "Extract non-valid elements from mesh.");
    m_config["list"] = ConfigOption(
        true, "0", "Print list of elements having negative Jacobian.");
}

~ProcessJac()

Nektar::Utilities::ProcessJac::~ProcessJac ( )

virtual

Definition at line 59 of file ProcessJac.cpp.

{
}

Member Function Documentation

create()

static std::shared_ptr<Module> Nektar::Utilities::ProcessJac::create ( NekMeshUtils::MeshSharedPtr  m )

inlinestatic

Creates an instance of this class.

Definition at line 55 of file ProcessJac.h.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr().

    {
        return MemoryManager<ProcessJac>::AllocateSharedPtr(m);
    }

Process()

void Nektar::Utilities::ProcessJac::Process ( )

virtual

Write mesh to output file.

Implements Nektar::NekMeshUtils::Module.

Definition at line 63 of file ProcessJac.cpp.

References Nektar::eFULL, CellMLToNektar.pycml::extract(), Nektar::NekMeshUtils::Module::m_config, Nektar::NekMeshUtils::Module::m_mesh, CellMLToNektar.cellml_metadata::p, Nektar::NekMeshUtils::Module::ProcessComposites(), Nektar::NekMeshUtils::Module::ProcessEdges(), Nektar::NekMeshUtils::Module::ProcessElements(), Nektar::NekMeshUtils::Module::ProcessFaces(), Nektar::NekMeshUtils::Module::ProcessVertices(), Nektar::LibUtilities::ShapeTypeMap, Vmath::Vmax(), and Vmath::Vmin().

{
    if (m_mesh->m_verbose)
    {
        cout << "ProcessJac: Calculating Jacobians... " << endl;
    }

    bool extract   = m_config["extract"].beenSet;
    bool printList = m_config["list"].as<bool>();
    NekDouble thres = m_config["extract"].as<NekDouble>();

    vector<ElementSharedPtr> el = m_mesh->m_element[m_mesh->m_expDim];

    if (extract)
    {
        m_mesh->m_element[m_mesh->m_expDim].clear();
    }

    if (printList)
    {
        cout << "Elements with negative Jacobian:" << endl;
    }

    int nNeg = 0;

    Array<OneD, int> bin(20, 0);

    // Iterate over list of elements of expansion dimension.
    for (int i = 0; i < el.size(); ++i)
    {
        // Create elemental geometry.
        SpatialDomains::GeometrySharedPtr geom =
            el[i]->GetGeom(m_mesh->m_spaceDim);

        // Generate geometric factors.
        SpatialDomains::GeomFactorsSharedPtr gfac = geom->GetGeomFactors();

        LibUtilities::PointsKeyVector p = geom->GetXmap()->GetPointsKeys();
        SpatialDomains::DerivStorage deriv = gfac->GetDeriv(p);
        const int pts = deriv[0][0].num_elements();
        Array<OneD,NekDouble> jc(pts);
        for (int k = 0; k < pts; ++k)
        {
            DNekMat jac(m_mesh->m_expDim, m_mesh->m_expDim, 0.0, eFULL);

            for (int l = 0; l < m_mesh->m_expDim; ++l)
            {
                for (int j = 0; j < m_mesh->m_expDim; ++j)
                {
                    jac(j,l) = deriv[l][j][k];
                }
            }

            if(m_mesh->m_expDim == 2)
            {
                jc[k] = jac(0,0) * jac(1,1) - jac(0,1)*jac(1,0);
            }
            else if(m_mesh->m_expDim == 3)
            {
                jc[k] =  jac(0,0) * (jac(1,1)*jac(2,2) - jac(2,1)*jac(1,2)) -
                         jac(0,1) * (jac(1,0)*jac(2,2) - jac(2,0)*jac(1,2)) +
                         jac(0,2) * (jac(1,0)*jac(2,1) - jac(2,0)*jac(1,1));
            }
        }

        NekDouble scaledJac = Vmath::Vmin(jc.num_elements(),jc,1) /
                              Vmath::Vmax(jc.num_elements(),jc,1);

        bool valid = gfac->IsValid();

        if (extract && (scaledJac < thres || !valid))
        {
            m_mesh->m_element[m_mesh->m_expDim].push_back(el[i]);
        }

        // Get the Jacobian and, if it is negative, print a warning
        // message.
        if (!valid)
        {
            nNeg++;

            if (printList)
            {
                cout << "  - " << el[i]->GetId() << " ("
                     << LibUtilities::ShapeTypeMap[el[i]->GetConf().m_e] << ")"
                     << "  " << scaledJac
                     << endl;
            }
        }
    }

    if (extract)
    {
        m_mesh->m_element[m_mesh->m_expDim - 1].clear();
        ProcessVertices();
        ProcessEdges();
        ProcessFaces();
        ProcessElements();
        ProcessComposites();
    }

    if (printList || m_mesh->m_verbose)
    {
        cout << "Total negative Jacobians: " << nNeg << endl;
    }
    else if (nNeg > 0)
    {
        cout << "WARNING: Detected " << nNeg << " element"
             << (nNeg == 1 ? "" : "s") << " with negative Jacobian." << endl;
    }
}

Member Data Documentation

className

ModuleKey Nektar::Utilities::ProcessJac::className

static

Initial value:

= GetModuleFactory().RegisterCreatorFunction(
    ModuleKey(eProcessModule, "jac"),
    ProcessJac::create,
    "Process elements based on values of Jacobian.")

Definition at line 59 of file ProcessJac.h.