Nektar::Utilities::ProcessPerAlign Class Reference

#include <ProcessPerAlign.h>

Inheritance diagram for Nektar::Utilities::ProcessPerAlign:

Collaboration diagram for Nektar::Utilities::ProcessPerAlign:

Public Member Functions
	ProcessPerAlign (MeshSharedPtr m)
	Default constructor. More...
virtual	~ProcessPerAlign ()
	Destructor. More...
virtual void	Process ()
	Write mesh to output file. More...
Public Member Functions inherited from Nektar::Utilities::ProcessModule
	ProcessModule ()
	ProcessModule (FieldSharedPtr p_f)
	ProcessModule (MeshSharedPtr p_m)
Public Member Functions inherited from Nektar::Utilities::Module
	Module (FieldSharedPtr p_f)
virtual void	Process (po::variables_map &vm)=0
virtual std::string	GetModuleName ()=0
void	RegisterConfig (string key, string value)
	Register a configuration option with a module. More...
void	PrintConfig ()
	Print out all configuration options for a module. More...
void	SetDefaults ()
	Sets default configuration options for those which have not been set. More...
bool	GetRequireEquiSpaced (void)
void	SetRequireEquiSpaced (bool pVal)
void	EvaluateTriFieldAtEquiSpacedPts (LocalRegions::ExpansionSharedPtr &exp, const Array< OneD, const NekDouble > &infield, Array< OneD, NekDouble > &outfield)
	Module (MeshSharedPtr p_m)
void	RegisterConfig (std::string key, std::string value)
void	PrintConfig ()
void	SetDefaults ()
MeshSharedPtr	GetMesh ()
virtual void	ProcessVertices ()
	Extract element vertices. More...
virtual void	ProcessEdges (bool ReprocessEdges=true)
	Extract element edges. More...
virtual void	ProcessFaces (bool ReprocessFaces=true)
	Extract element faces. More...
virtual void	ProcessElements ()
	Generate element IDs. More...
virtual void	ProcessComposites ()
	Generate composites. More...
virtual void	ClearElementLinks ()

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

Static Public Attributes
static ModuleKey	className

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

Detailed Description

Definition at line 46 of file ProcessPerAlign.h.

Constructor & Destructor Documentation

Nektar::Utilities::ProcessPerAlign::ProcessPerAlign

(

MeshSharedPtr

m

)

Default constructor.

Definition at line 66 of file ProcessPerAlign.cpp.

References Nektar::Utilities::Module::m_config.

                                                : ProcessModule(m)
{
    m_config["surf1"] =
        ConfigOption(false, "-1", "Tag identifying first surface.");
    m_config["surf2"] =
        ConfigOption(false, "-1", "Tag identifying first surface.");
    m_config["dir"] = ConfigOption(
        false, "", "Direction in which to align (either x, y, or z)");
    m_config["orient"] =
        ConfigOption(true, "0", "Attempt to reorient tets and prisms");
}

Nektar::Utilities::ProcessPerAlign::~ProcessPerAlign ( )

virtual

Destructor.

Definition at line 81 of file ProcessPerAlign.cpp.

{
}

Member Function Documentation

static boost::shared_ptr<Module> Nektar::Utilities::ProcessPerAlign::create ( MeshSharedPtr  m )

inlinestatic

Creates an instance of this class.

Definition at line 50 of file ProcessPerAlign.h.

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

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

void Nektar::Utilities::ProcessPerAlign::Process ( )

virtual

Write mesh to output file.

Implements Nektar::Utilities::Module.

Definition at line 85 of file ProcessPerAlign.cpp.

References Nektar::NekMeshUtils::Node::abs2(), ASSERTL0, ASSERTL1, Nektar::LibUtilities::eSegment, Nektar::iterator, Nektar::Utilities::Module::m_config, Nektar::NekMeshUtils::Node::m_id, Nektar::Utilities::Module::m_mesh, Nektar::NekMeshUtils::Node::m_x, Nektar::NekMeshUtils::Node::m_y, Nektar::NekMeshUtils::Node::m_z, and Nektar::Utilities::Module::ReorderPrisms().

{
    int surf1   = m_config["surf1"].as<int>();
    int surf2   = m_config["surf2"].as<int>();
    string dir  = m_config["dir"].as<string>();
    bool orient = m_config["orient"].as<bool>();

    if (surf1 == -1)
    {
        cerr << "WARNING: surf1 must be set to a positive integer. "
             << "Skipping periodic alignment." << endl;
        return;
    }

    if (surf2 == -1)
    {
        cerr << "WARNING: surf2 must be set to a positive integer. "
             << "Skipping periodic alignment." << endl;
        return;
    }

    if (dir != "x" && dir != "y" && dir != "z")
    {
        cerr << "WARNING: dir must be set to either x, y or z. "
             << "Skipping periodic alignment." << endl;
        return;
    }

    NekDouble vec[3];
    vec[0] = dir == "x" ? 1.0 : 0.0;
    vec[1] = dir == "y" ? 1.0 : 0.0;
    vec[2] = dir == "z" ? 1.0 : 0.0;

    CompositeMap::iterator it1 = m_mesh->m_composite.find(surf1);
    CompositeMap::iterator it2 = m_mesh->m_composite.find(surf2);

    if (it1 == m_mesh->m_composite.end())
    {
        cerr << "WARNING: Couldn't find surface " << surf1
             << ". Skipping periodic alignment." << endl;
        return;
    }

    if (it2 == m_mesh->m_composite.end())
    {
        cerr << "WARNING: Couldn't find surface " << surf2 << ", "
             << "skipping periodic alignment." << endl;
        return;
    }

    CompositeSharedPtr c1 = it1->second;
    CompositeSharedPtr c2 = it2->second;

    if (c1->m_items.size() != c2->m_items.size())
    {
        cerr << "WARNING: Surfaces " << surf1 << " and " << surf2
             << " have different numbers of elements. Skipping periodic"
             << " alignment." << endl;
        return;
    }

    c1->m_reorder = false;
    c2->m_reorder = false;

    map<int, pair<FaceSharedPtr, vector<int> > > perFaces;

    // Loop over elements, calculate centroids of elements in c2.
    map<int, Node> centroidMap;
    map<int, Node>::iterator it;
    for (int i = 0; i < c2->m_items.size(); ++i)
    {
        Node centroid;
        for (int j = 0; j < c2->m_items[i]->GetVertexCount(); ++j)
        {
            centroid += *(c2->m_items[i]->GetVertex(j));
        }
        centroid /= (NekDouble)c2->m_items[i]->GetVertexCount();
        centroidMap[i] = centroid;
    }

    boost::unordered_set<int> elmtDone;
    map<int, int> elmtPairs;
    map<int, int> vertCheck;

    for (int i = 0; i < c1->m_items.size(); ++i)
    {
        Node centroid;
        for (int j = 0; j < c1->m_items[i]->GetVertexCount(); ++j)
        {
            centroid += *(c1->m_items[i]->GetVertex(j));
        }
        centroid /= (NekDouble)c1->m_items[i]->GetVertexCount();

        for (it = centroidMap.begin(); it != centroidMap.end(); ++it)
        {
            if (elmtDone.count(it->first) > 0)
            {
                continue;
            }

            Node dx = it->second - centroid;
            if (fabs(fabs(dx.m_x * vec[0] + dx.m_y * vec[1] + dx.m_z * vec[2]) /
                         sqrt(dx.abs2()) -
                     1.0) < 1e-8)
            {
                // Found match
                int id1, id2;

                if (c1->m_items[i]->GetConf().m_e == LibUtilities::eSegment)
                {
                    id1 = c1->m_items[i]->GetEdgeLink()->m_id;
                    id2 = c2->m_items[it->first]->GetEdgeLink()->m_id;
                }
                else
                {
                    id1 = c1->m_items[i]->GetFaceLink()->m_id;
                    id2 = c2->m_items[it->first]->GetFaceLink()->m_id;
                }

                elmtDone.insert(it->first);
                elmtPairs[i] = it->first;

                // Identify periodic vertices
                int nVerts = c1->m_items[i]->GetVertexCount();
                vector<int> perVerts(nVerts, 0), perVertsInv(nVerts, 0);

                if (orient)
                {
                    for (int k = 0; k < nVerts; ++k)
                    {
                        NodeSharedPtr n1 =
                            c1->m_items[i]->GetFaceLink()->m_vertexList[k];
                        int l;

                        for (l = 0; l < nVerts; ++l)
                        {
                            NodeSharedPtr n2 = c2->m_items[it->first]
                                                   ->GetFaceLink()
                                                   ->m_vertexList[l];

                            Node dn = *n2 - *n1;
                            if (fabs(fabs(dn.m_x * vec[0] + dn.m_y * vec[1] +
                                          dn.m_z * vec[2]) /
                                         sqrt(dn.abs2()) -
                                     1.0) < 1e-8)
                            {
                                perVerts[k]    = l;
                                perVertsInv[l] = k;

                                int id1 = n1->m_id;
                                int id2 = n2->m_id;
                                if (vertCheck.count(id1) == 0)
                                {
                                    vertCheck[id1] = id2;
                                }
                                else
                                {
                                    ASSERTL0(vertCheck[id1] == id2,
                                             "Periodic vertex already "
                                             "identified!");
                                }
                                break;
                            }
                        }
                        ASSERTL1(l < nVerts,
                                 "Could not identify periodic vertices.");
                    }

                    int tot1 = 0, tot2 = 0;
                    for (int k = 0; k < nVerts; ++k)
                    {
                        tot1 += perVerts[k];
                        tot2 += perVertsInv[k];
                    }
                    ASSERTL0(tot1 == nVerts * (nVerts - 1) / 2 &&
                                 tot2 == nVerts * (nVerts - 1) / 2,
                             "Error identifying periodic vertices");
                }

                if (c2->m_items[i]->GetConf().m_e != LibUtilities::eSegment)
                {
                    perFaces[id1] = make_pair(
                        c2->m_items[it->first]->GetFaceLink(), perVerts);
                    perFaces[id2] =
                        make_pair(c1->m_items[i]->GetFaceLink(), perVertsInv);
                }
                break;
            }
        }

        if (it == centroidMap.end())
        {
            cerr << "WARNING: Could not find matching edge for surface "
                 << "element " << c1->m_items[i]->GetId() << ". "
                 << "Skipping periodic alignment." << endl;
            return;
        }
    }

    // Reorder vectors.
    vector<ElementSharedPtr> tmp = c2->m_items;

    map<int, int>::iterator mIt;

    for (int i = 0; i < tmp.size(); ++i)
    {
        c2->m_items[i] = tmp[elmtPairs[i]];
    }

    if (orient)
    {
        ReorderPrisms(perFaces);
    }
}

Member Data Documentation

ModuleKey Nektar::Utilities::ProcessPerAlign::className

static

Initial value:

=
    GetModuleFactory().RegisterCreatorFunction(
        ModuleKey(eProcessModule, "peralign"), ProcessPerAlign::create)

Definition at line 54 of file ProcessPerAlign.h.