MeshConvert/Module.cpp

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////////////////////////////////////////////////////////////////////////////////
//
//  File: Module.cpp
//
//  For more information, please see: http://www.nektar.info/
//
//  The MIT License
//
//  Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
//  Department of Aeronautics, Imperial College London (UK), and Scientific
//  Computing and Imaging Institute, University of Utah (USA).
//
//  License for the specific language governing rights and limitations under
//  Permission is hereby granted, free of charge, to any person obtaining a
//  copy of this software and associated documentation files (the "Software"),
//  to deal in the Software without restriction, including without limitation
//  the rights to use, copy, modify, merge, publish, distribute, sublicense,
//  and/or sell copies of the Software, and to permit persons to whom the
//  Software is furnished to do so, subject to the following conditions:
//
//  The above copyright notice and this permission notice shall be included
//  in all copies or substantial portions of the Software.
//
//  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
//  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
//  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
//  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
//  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
//  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
//  DEALINGS IN THE SOFTWARE.
//
//  Description: Abstract input/output modules.
//
////////////////////////////////////////////////////////////////////////////////

#include <string>
#include "Module.h"

using namespace std;

namespace Nektar
{
    namespace Utilities
    {
        /**
         * Returns an instance of the module factory, held as a singleton.
         */
        ModuleFactory& GetModuleFactory()
        {
            typedef Loki::SingletonHolder<ModuleFactory,
                Loki::CreateUsingNew,
                Loki::NoDestroy,
                Loki::SingleThreaded> Type;
            return Type::Instance();
        }

        /**
         * Prints a given module key to a stream.
         */
        std::ostream& operator<<(std::ostream& os, const ModuleKey& rhs)
        {
            return os << ModuleTypeMap[rhs.first] << ": " << rhs.second;
        }

        InputModule::InputModule(MeshSharedPtr m) : Module(m)
        {
            m_config["infile"] = ConfigOption(false, "", "Input filename.");
        }

        OutputModule::OutputModule(MeshSharedPtr m) : Module(m)
        {
            m_config["outfile"] = ConfigOption(false, "", "Output filename.");
        }

        /**
         * @brief Open a file for input.
         */
        void InputModule::OpenStream()
        {
            string fname = m_config["infile"].as<string>();
            m_mshFile.open(fname.c_str());
            if (!m_mshFile.good())
            {
                cerr << "Error opening file: " << fname << endl;
                abort();
            }
        }

        /**
         * @brief Open a file for output.
         */
        void OutputModule::OpenStream()
        {
            string fname = m_config["outfile"].as<string>();
            m_mshFile.open(fname.c_str());
            if (!m_mshFile.good())
            {
                cerr << "Error opening file: " << fname << endl;
                abort();
            }
        }

        /**
         * @brief Create a unique set of mesh vertices from elements stored in
         * Mesh::element.
         *
         * Each element is processed in turn and the vertices extracted and
         * inserted into #m_vertexSet, which at the end of the routine
         * contains all unique vertices in the mesh.
         */
        void Module::ProcessVertices()
        {
            vector<ElementSharedPtr> &elmt = m_mesh->m_element[m_mesh->m_expDim];

            m_mesh->m_vertexSet.clear();

            for (int i = 0, vid = 0; i < elmt.size(); ++i)
            {
                for (int j = 0; j < elmt[i]->GetVertexCount(); ++j)
                {
                    pair<NodeSet::iterator,bool> testIns =
                        m_mesh->m_vertexSet.insert(elmt[i]->GetVertex(j));

                    if (testIns.second)
                    {
                        (*(testIns.first))->m_id = vid++;
                    }
                    else
                    {
                        elmt[i]->SetVertex(j,*testIns.first);
                    }
                }
            }
        }

        /**
         * @brief Create a unique set of mesh edges from elements stored in
         * Mesh::element.
         *
         * All elements are first scanned and a list of unique, enumerated
         * edges produced in #m_edgeSet. Since each element generated its
         * edges independently, we must now ensure that each element only uses
         * edge objects from the #m_edgeSet set This ensures there are no
         * duplicate edge objects. Finally, we scan the list of elements for
         * 1-D boundary elements which correspond to an edge in
         * #m_edgeSet. For such elements, we set its edgeLink to reference the
         * corresponding edge in #m_edgeSet.
         *
         * This routine only proceeds if the expansion dimension is 2 or 3.
         */
        void Module::ProcessEdges(bool ReprocessEdges)
        {
            if (m_mesh->m_expDim < 2) return;

            if(ReprocessEdges)
            {
                vector<ElementSharedPtr> &elmt = m_mesh->m_element[m_mesh->m_expDim];

                m_mesh->m_edgeSet.clear();

                // Scan all elements and generate list of unique edges
                for (int i = 0, eid = 0; i < elmt.size(); ++i)
                {
                    for (int j = 0; j < elmt[i]->GetEdgeCount(); ++j)
                    {
                        pair<EdgeSet::iterator,bool> testIns;
                        EdgeSharedPtr ed = elmt[i]->GetEdge(j);
                        testIns = m_mesh->m_edgeSet.insert(ed);

                        if (testIns.second)
                        {
                            (*(testIns.first))->m_id = eid++;
                        }
                        else
                        {
                            EdgeSharedPtr e2 = *(testIns.first);
                            elmt[i]->SetEdge(j, e2);
                            if (e2->m_edgeNodes.size() == 0 &&
                                ed->m_edgeNodes.size() > 0)
                            {
                                e2->m_curveType = ed->m_curveType;
                                e2->m_edgeNodes = ed->m_edgeNodes;

                                // Reverse nodes if appropriate.
                                if (e2->m_n1->m_id != ed->m_n1->m_id)
                                {
                                    reverse(e2->m_edgeNodes.begin(),
                                            e2->m_edgeNodes.end());
                                }
                            }

                            // Update edge to element map.
                            (*(testIns.first))->m_elLink.push_back(
                                pair<ElementSharedPtr,int>(elmt[i],j));
                        }
                    }
                }
            }

            // Create links for 1D elements
            for (int i = 0; i < m_mesh->m_element[1].size(); ++i)
            {
                NodeSharedPtr v0 = m_mesh->m_element[1][i]->GetVertex(0);
                NodeSharedPtr v1 = m_mesh->m_element[1][i]->GetVertex(1);
                vector<NodeSharedPtr> edgeNodes;
                EdgeSharedPtr E = boost::shared_ptr<Edge>(
                                       new Edge(v0, v1, edgeNodes,
                             m_mesh->m_element[1][i]->GetConf().m_edgeCurveType));
                EdgeSet::iterator it = m_mesh->m_edgeSet.find(E);
                if (it == m_mesh->m_edgeSet.end())
                {
                    cerr << "Cannot find corresponding element edge for "
                         << "1D element " << i << endl;
                    abort();
                }
                m_mesh->m_element[1][i]->SetEdgeLink(*it);

                // Update 2D element boundary map.
                ASSERTL0((*it)->m_elLink.size() != 0,
                         "Empty boundary map!");
                ASSERTL0((*it)->m_elLink.size() == 1,
                         "Too many elements in boundary map!");
                pair<ElementSharedPtr, int> eMap = (*it)->m_elLink.at(0);
                eMap.first->SetBoundaryLink(eMap.second, i);

                // Copy curvature to edge.
                if ((*it)->m_edgeNodes.size() > 0)
                {
                    ElementSharedPtr edge = m_mesh->m_element[1][i];
                    if (edge->GetVertex(0) == (*it)->m_n1)
                    {
                        edge->SetVolumeNodes((*it)->m_edgeNodes);
                    }
                }
            }
        }


        /**
         * @brief Create a unique set of mesh faces from elements stored in
         * Mesh::element.
         *
         * All elements are scanned and a unique list of enumerated faces is
         * produced in #m_faceSet. Since elements created their own faces
         * independently, we examine each element only uses face objects from
         * #m_faceSet. Duplicate faces of those in #m_face are replaced with
         * the corresponding entry in #m_faceSet. Finally, we scan the list of
         * elements for 2-D boundary faces which correspond to faces in
         * #m_faceSet. For such elements, we set its faceLink to reference the
         * corresponding face in #m_faceSet.
         *
         * This routine only proceeds if the expansion dimension is 3.
         */
        void Module::ProcessFaces(bool ReprocessFaces)
        {
            if (m_mesh->m_expDim < 3) return;

            if(ReprocessFaces)
            {
                vector<ElementSharedPtr> &elmt = m_mesh->m_element[m_mesh->m_expDim];

                m_mesh->m_faceSet.clear();

                // Scan all elements and generate list of unique faces
                for (int i = 0, fid = 0; i < elmt.size(); ++i)
                {
                    for (int j = 0; j < elmt[i]->GetFaceCount(); ++j)
                    {
                        pair<FaceSet::iterator,bool> testIns;
                        testIns = m_mesh->m_faceSet.insert(elmt[i]->GetFace(j));

                        if (testIns.second)
                        {
                            (*(testIns.first))->m_id = fid++;
                        }
                        else
                        {
                            elmt[i]->SetFace(j,*testIns.first);
                            // Update face to element map.
                            (*(testIns.first))->m_elLink.push_back(
                            pair<ElementSharedPtr,int>(elmt[i],j));
                        }
                    }
                }
            }

            // Create links for 2D elements
            for (int i = 0; i < m_mesh->m_element[2].size(); ++i)
            {
                vector<NodeSharedPtr> vertices = m_mesh->m_element[2][i]->GetVertexList();
                vector<NodeSharedPtr> faceNodes;
                vector<EdgeSharedPtr> edgeList = m_mesh->m_element[2][i]->GetEdgeList();
                FaceSharedPtr F = boost::shared_ptr<Face>(
                    new Face(vertices, faceNodes, edgeList,
                             m_mesh->m_element[2][i]->GetConf().m_faceCurveType));
                FaceSet::iterator it = m_mesh->m_faceSet.find(F);
                if (it == m_mesh->m_faceSet.end())
                {
                    cout << "Cannot find corresponding element face for 2D "
                         << "element " << i << endl;
                    abort();
                }
                m_mesh->m_element[2][i]->SetFaceLink(*it);

                // Update 3D element boundary map.
                ASSERTL0((*it)->m_elLink.size() != 0,
                         "Empty element link map!");
                ASSERTL0((*it)->m_elLink.size() == 1,
                         "Too many elements in element link map!");
                pair<ElementSharedPtr, int> eMap = (*it)->m_elLink.at(0);
                eMap.first->SetBoundaryLink(eMap.second, i);
            }
        }

        /**
         * @brief Enumerate elements stored in Mesh::element.
         *
         * For all elements of equal dimension to the mesh dimension, we
         * enumerate sequentially. All other elements in the list should be of
         * lower dimension and have ID set by a corresponding edgeLink or
         * faceLink (as set in #ProcessEdges or #ProcessFaces).
         */
        void Module::ProcessElements()
        {
            int cnt = 0;
            for (int i = 0; i < m_mesh->m_element[m_mesh->m_expDim].size(); ++i)
            {
                m_mesh->m_element[m_mesh->m_expDim][i]->SetId(cnt++);
            }
        }

        /**
         * @brief Generate a list of composites (groups of elements) from tag
         * IDs stored in mesh vertices/edges/faces/elements.
         *
         * Each element is assigned to a composite ID by an input module. First
         * we scan the element list and generate a list of composite IDs. We
         * then generate the composite objects and populate them with a second
         * scan through the element list.
         */
        void Module::ProcessComposites()
        {
            m_mesh->m_composite.clear();

            // For each element, check to see if a composite has been
            // created. If not, create a new composite. Otherwise, add the
            // element to the composite.
            for (int d = 0; d <= m_mesh->m_expDim; ++d)
            {
                vector<ElementSharedPtr> &elmt = m_mesh->m_element[d];

                for (int i = 0; i < elmt.size(); ++i)
                {
                    CompositeMap::iterator it;
                    unsigned int tagid = elmt[i]->GetTagList()[0];

                    it = m_mesh->m_composite.find(tagid);

                    if (it == m_mesh->m_composite.end())
                    {
                        CompositeSharedPtr tmp = boost::shared_ptr<Composite>(
                                                            new Composite());
                        pair<CompositeMap::iterator, bool> testIns;
                        tmp->m_id  = tagid;
                        tmp->m_tag = elmt[i]->GetTag();
                        if(m_mesh->m_faceLabels.count(tmp->m_id) != 0)
                        {
                            tmp->m_label =  m_mesh->m_faceLabels[tmp->m_id];
                        }

                        testIns  = m_mesh->m_composite.insert(
                            pair<unsigned int, CompositeSharedPtr>(tagid,tmp));
                        it       = testIns.first;
                    }

                    if (elmt[i]->GetTag() != it->second->m_tag)
                    {
                        cout << "Different types of elements in same composite!" << endl;
                        cout << " -> Composite uses " << it->second->m_tag << endl;
                        cout << " -> Element uses   " << elmt[i]->GetTag() << endl;
                        cout << "Have you specified physical volumes and surfaces?" << endl;
                    }
                    it->second->m_items.push_back(elmt[i]);
                }
            }
        }

        /**
         * @brief Reorder node IDs so that prisms and tetrahedra are aligned
         * correctly.
         *
         * Orientation of prism lines (i.e. a large prism which has been split
         * into subprisms) cannot be guaranteed when elements are created
         * one-by-one, or when periodic boundary conditions are used. This
         * routine uses the following strategy:
         *
         *   - Destroy the existing node numbering.
         *   - Detect a line of prisms using the PrismLines routine.
         *   - For each line, renumber node IDs consistently so that highest ID
         *     per-element corresponds to the line of collapsed coordinate
         *     points.
         *   - Recreate each prism in the line using the new ordering, and apply
         *     the existing OrientPrism routine to orient nodes accordingly.
         *   - When all prism lines are processed, recreate all tetrahedra using
         *     the existing orientation code.
         *   - Finally renumber any other nodes (i.e. those belonging to
         *     hexahedra).
         *
         * The last step is to eliminate duplicate edges/faces and reenumerate.
         *
         * NOTE: This routine does not copy face-interior high-order information
         * yet!
         */
        void Module::ReorderPrisms(PerMap &perFaces)
        {
            // Loop over elements and extract any that are prisms.
            int i, j, k;

            if (m_mesh->m_expDim < 3)
            {
                return;
            }

            map<int, int>    lines;
            set<int>         prismsDone, tetsDone;
            PerMap::iterator pIt;

            // Compile list of prisms and tets.
            for (i = 0; i < m_mesh->m_element[3].size(); ++i)
            {
                ElementSharedPtr el = m_mesh->m_element[3][i];

                if (el->GetConf().m_e == LibUtilities::ePrism)
                {
                    prismsDone.insert(i);
                }
                else if (el->GetConf().m_e == LibUtilities::eTetrahedron)
                {
                    tetsDone.insert(i);
                }
            }

            // Destroy existing node numbering.
            NodeSet::iterator it;
            for (it = m_mesh->m_vertexSet.begin(); it != m_mesh->m_vertexSet.end(); ++it)
            {
                (*it)->m_id = -1;
            }

            // Counter for new node IDs.
            int nodeId = 0;
            int prismTris[2][3] = {{0,1,4}, {3,2,5}};

            // Warning flag for high-order curvature information.
            bool warnCurvature = false;

            // facesDone tracks face IDs inside prisms which have already been
            // aligned.
            boost::unordered_set<int> facesDone;
            boost::unordered_set<int>::iterator fIt[2], fIt2;

            // Loop over prisms until we've found all lines of prisms.
            while (prismsDone.size() > 0)
            {
                vector<ElementSharedPtr> line;

                // Call PrismLines to identify all prisms connected to
                // prismDone.begin() and place them in line[].
                PrismLines(*prismsDone.begin(), perFaces, prismsDone, line);

                // Loop over each prism, figure out which line of vertices
                // contains the vertex with highest ID.
                for (i = 0; i < line.size(); ++i)
                {
                    // Copy tags and nodes from existing element.
                    vector<int>           tags  = line[i]->GetTagList();
                    vector<NodeSharedPtr> nodes = line[i]->GetVertexList();

                    // See if either face of this prism has been renumbered
                    // already.
                    FaceSharedPtr f[2] = {
                        line[i]->GetFace(1), line[i]->GetFace(3)
                    };

                    fIt[0] = facesDone.find(f[0]->m_id);
                    fIt[1] = facesDone.find(f[1]->m_id);

                    // See if either of these faces is periodic. If it is, then
                    // assign ids accordingly.
                    for (j = 0; j < 2; ++j)
                    {
                        pIt = perFaces.find(f[j]->m_id);

                        if (pIt == perFaces.end())
                        {
                            continue;
                        }

                        fIt2 = facesDone.find(pIt->second.first->m_id);

                        if (fIt[j] == facesDone.end() &&
                            fIt2   != facesDone.end())
                        {
                            fIt[j] = fIt2;
                        }
                    }

                    if (fIt[0] != facesDone.end() &&
                        fIt[1] != facesDone.end())
                    {
                        // Should not be the case that both faces have already
                        // been renumbered.
                        ASSERTL0(false, "Renumbering error!");
                    }
                    else if (fIt[0] == facesDone.end() &&
                             fIt[1] == facesDone.end())
                    {
                        // Renumber both faces.
                        for (j = 0; j < 2; ++j)
                        {
                            for (k = 0; k < 3; ++k)
                            {
                                NodeSharedPtr n = nodes[prismTris[j][k]];
                                if (n->m_id == -1)
                                {
                                    n->m_id = nodeId++;
                                }
                            }
                        }

                        facesDone.insert(f[0]->m_id);
                        facesDone.insert(f[1]->m_id);
                    }
                    else
                    {
                        // Renumber face. t identifies the face not yet
                        // numbered, o identifies the other face.
                        int t = fIt[0] == facesDone.end() ? 0 : 1;
                        int o = (t+1) % 2;
                        ASSERTL1(fIt[o] != facesDone.end(),"Renumbering error");

                        // Determine which of the three vertices on the 'other'
                        // face corresponds to the highest ID - this signifies
                        // the singular point of the line of prisms.
                        int tmp1[3] = {
                            nodes[prismTris[o][0]]->m_id,
                            nodes[prismTris[o][1]]->m_id,
                            nodes[prismTris[o][2]]->m_id
                        };
                        int tmp2[3] = {0,1,2};

                        if (tmp1[0] > tmp1[1])
                        {
                            swap(tmp1[0], tmp1[1]);
                            swap(tmp2[0], tmp2[1]);
                        }

                        if (tmp1[1] > tmp1[2])
                        {
                            swap(tmp1[1], tmp1[2]);
                            swap(tmp2[1], tmp2[2]);
                        }

                        if (tmp1[0] > tmp1[2])
                        {
                            swap(tmp1[0], tmp1[2]);
                            swap(tmp2[0], tmp2[2]);
                        }

                        // Renumber this face so that highest ID matches.
                        for (j = 0; j < 3; ++j)
                        {
                            NodeSharedPtr n = nodes[prismTris[t][tmp2[j]]];
                            if (n->m_id == -1)
                            {
                                n->m_id = nodeId++;
                            }
                        }

                        facesDone.insert(f[t]->m_id);
                    }

                    for (j = 0; j < 6; ++j)
                    {
                        ASSERTL1(nodes[j]->m_id != -1, "Renumbering error");
                    }

                    // Recreate prism with the new ordering.
                    ElmtConfig conf(LibUtilities::ePrism, 1, false, false, true);
                    ElementSharedPtr el = GetElementFactory().CreateInstance(
                        LibUtilities::ePrism, conf, nodes, tags);

                    // Now transfer high-order information back into
                    // place. TODO: Face curvature.
                    for (j = 0; j < 9; ++j)
                    {
                        EdgeSharedPtr e1 = line[i]->GetEdge(j);
                        for (k = 0; k < 9; ++k)
                        {
                            EdgeSharedPtr e2 = el->GetEdge(k);
                            if (e1->m_n1 == e2->m_n1 && e1->m_n2 == e2->m_n2)
                            {
                                e2->m_edgeNodes = e1->m_edgeNodes;
                            }
                            else if (e1->m_n1 == e2->m_n1 && e1->m_n2 == e2->m_n2)
                            {
                                e2->m_edgeNodes = e1->m_edgeNodes;
                                std::reverse(e2->m_edgeNodes.begin(),
                                             e2->m_edgeNodes.end());
                            }
                        }
                    }

                    // Warn users that we're throwing away face curvature
                    if (!warnCurvature)
                    {
                        for (j = 0; j < 5; ++j)
                        {
                            if (line[i]->GetFace(j)->m_faceNodes.size() > 0)
                            {
                                warnCurvature = true;
                                break;
                            }
                        }
                    }

                    // Replace old prism.
                    m_mesh->m_element[3][line[i]->GetId()] = el;
                }
            }

            if (warnCurvature)
            {
                cerr << "[ReorderPrisms] WARNING: Face curvature detected in "
                     << "some prisms; this will be ignored in further module "
                     << "evaluations."
                     << endl;
            }

            // Loop over periodic faces, enumerate vertices.
            for (pIt = perFaces.begin(); pIt != perFaces.end(); ++pIt)
            {
                FaceSharedPtr f2       = pIt->second.first;
                FaceSharedPtr f1       = perFaces[f2->m_id].first;
                vector<int>   perVerts = pIt->second.second;
                int           nVerts   = perVerts.size();

                // Number periodic vertices first.
                for (j = 0; j < nVerts; ++j)
                {
                    NodeSharedPtr n1 = f1->m_vertexList[j];
                    NodeSharedPtr n2 = f2->m_vertexList[perVerts[j]];

                    if (n1->m_id == -1 && n2->m_id == -1)
                    {
                        n1->m_id = nodeId++;
                        n2->m_id = nodeId++;
                    }
                    else if (n1->m_id != -1 && n2->m_id != -1)
                    {
                        continue;
                    }
                    else
                    {
                        ASSERTL0(false, "Periodic face renumbering error");
                    }
                }
            }

            // Recreate tets.
            set<int>::iterator it2;
            for (it2 = tetsDone.begin(); it2 != tetsDone.end(); ++it2)
            {
                ElementSharedPtr el = m_mesh->m_element[3][*it2];
                vector<NodeSharedPtr> nodes = el->GetVertexList();
                vector<int> tags = el->GetTagList();

                for (i = 0; i < 4; ++i)
                {
                    if (nodes[i]->m_id == -1)
                    {
                        nodes[i]->m_id = nodeId++;
                    }
                }

                // Recreate tet.
                ElmtConfig conf(LibUtilities::eTetrahedron, 1, false, false, true);
                m_mesh->m_element[3][*it2] = GetElementFactory().CreateInstance(
                    LibUtilities::eTetrahedron, conf, nodes, tags);
            }

            // Enumerate rest of vertices.
            for (it = m_mesh->m_vertexSet.begin(); it != m_mesh->m_vertexSet.end(); ++it)
            {
                if ((*it)->m_id == -1)
                {
                    (*it)->m_id = nodeId++;
                }
            }

            ProcessEdges   ();
            ProcessFaces   ();
            ProcessElements();
        }

        void Module::PrismLines(int                       prism,
                                PerMap                   &perFaces,
                                set<int>                 &prismsDone,
                                vector<ElementSharedPtr> &line)
        {
            int                i;
            set<int>::iterator it = prismsDone.find(prism);
            PerMap::iterator   it2;

            if (it == prismsDone.end())
            {
                return;
            }

            // Remove this prism from the list.
            prismsDone.erase(it);
            line.push_back(m_mesh->m_element[3][prism]);

            // Now find prisms connected to this one through a triangular face.
            for (i = 1; i <= 3; i += 2)
            {
                FaceSharedPtr f = m_mesh->m_element[3][prism]->GetFace(i);
                int nextId;

                // See if this face is periodic.
                it2 = perFaces.find(f->m_id);

                if (it2 != perFaces.end())
                {
                    int id2 = it2->second.first->m_id;
                    nextId  = it2->second.first->m_elLink[0].first->GetId();
                    perFaces.erase(it2);
                    perFaces.erase(id2);
                    PrismLines(nextId, perFaces, prismsDone, line);
                }

                // Nothing else connected to this face.
                if (f->m_elLink.size() == 1)
                {
                    continue;
                }

                nextId = f->m_elLink[0].first->GetId();
                if (nextId == m_mesh->m_element[3][prism]->GetId())
                {
                    nextId = f->m_elLink[1].first->GetId();
                }

                PrismLines(nextId, perFaces, prismsDone, line);
            }
        }

        /**
         * @brief Register a configuration option with a module.
         */
        void Module::RegisterConfig(string key, string val)
        {
            map<string, ConfigOption>::iterator it = m_config.find(key);
            if (it == m_config.end())
            {
                cerr << "WARNING: Unrecognised config option " << key
                     << ", proceeding anyway." << endl;
            }

            it->second.beenSet = true;

            if (it->second.isBool)
            {
                it->second.value = "1";
            }
            else
            {
                it->second.value = val;
            }
        }

        /**
         * @brief Print out all configuration options for a module.
         */
        void Module::PrintConfig()
        {
            map<string, ConfigOption>::iterator it;

            if (m_config.size() == 0)
            {
                cerr << "No configuration options for this module." << endl;
                return;
            }

            for (it = m_config.begin(); it != m_config.end(); ++it)
            {
                cerr << setw(10) << it->first << ": " << it->second.desc
                     << endl;
            }
        }

        /**
         * @brief Sets default configuration options for those which have not
         * been set.
         */
        void Module::SetDefaults()
        {
            map<string, ConfigOption>::iterator it;

            for (it = m_config.begin(); it != m_config.end(); ++it)
            {
                if (!it->second.beenSet)
                {
                    it->second.value = it->second.defValue;
                }
            }
        }

        /**
         * @brief Print a brief summary of information.
         */
        void InputModule::PrintSummary()
        {
            // Compute the number of full-dimensional elements and boundary
            // elements.
            cerr << "Expansion dimension is " << m_mesh->m_expDim << endl;
            cerr << "Space dimension is " << m_mesh->m_spaceDim << endl;
            cerr << "Read " << m_mesh->m_node.size() << " nodes" << endl;
            cerr << "Read " << m_mesh->GetNumElements() << " "
                 << m_mesh->m_expDim << "-D elements" << endl;
            cerr << "Read " << m_mesh->GetNumBndryElements()
                 << " boundary elements" << endl;
        }
    }
}