InputSem.cpp

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////////////////////////////////////////////////////////////////////////////////
//
//  File: InputSem.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).
//
//  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: Semtex session converter.
//
////////////////////////////////////////////////////////////////////////////////

#include <NekMeshUtils/MeshElements/Element.h>

#include "InputSem.h"

using namespace std;
using namespace Nektar::NekMeshUtils;

namespace Nektar
{
namespace Utilities
{

ModuleKey InputSem::className =
    GetModuleFactory().RegisterCreatorFunction(ModuleKey(eInputModule, "sem"),
                                               InputSem::create,
                                               "Reads Semtex session files.");

/**
 * @brief Initialises the InputSem class.
 */
InputSem::InputSem(MeshSharedPtr m) : InputModule(m)
{
}

InputSem::~InputSem()
{
}

/**
 * @brief Process a Semtex session file.
 *
 * Semtex files are defined by a tokenized markup format. We first
 * populate #sectionMap which stores the location of the various tags in
 * the session file so that they can be jumped to, since no ordering is
 * defined. The converter only requires the NODES and ELEMENTS sections
 * to exist, but can also read CURVES and SURFACES. High-order curves
 * rely on the meshfile session.msh to be created with the Semtex
 * utility meshpr first.
 *
 * @param pFilename Filename of Semtex session to read.
 */
void InputSem::Process()
{
    // Open the file stream.
    OpenStream();

    if (m_mesh->m_verbose)
    {
        cout << "InputSem: Start reading file..." << endl;
    }

    // Read through input file and populate the section map.
    string fileContents, line, word;
    stringstream ss, ssFile;
    streampos linePos;

    sectionMap["NODES"]    = -1;
    sectionMap["ELEMENTS"] = -1;
    sectionMap["CURVES"]   = -1;
    sectionMap["SURFACES"] = -1;
    sectionMap["GROUPS"]   = -1;
    sectionMap["BCS"]      = -1;
    sectionMap["FIELDS"]   = -1;

    // We need to read entire file into a string and wrap around a stringstream,
    // since boost::io::filtered_stream does not support seeking with zlib.
    m_fileStream << m_mshFile.rdbuf();

    while (!m_fileStream.eof())
    {
        linePos = m_fileStream.tellg();
        getline(m_fileStream, line);
        ss.clear();
        ss.str(line);
        ss >> word;

        // Iterate over all tokens and see if section exists on this
        // line.
        for (auto &it : sectionMap)
        {
            if (word == "<" + it.first || word == "<" + it.first + ">")
            {
                sectionMap[it.first] = linePos;
            }
        }
    }

    // Clear eofbit and go back to the beginning of the file.
    m_fileStream.clear();
    m_fileStream.seekg(0);

    // Check that required sections exist in the file.
    if (sectionMap["NODES"] == std::streampos(-1))
    {
        cerr << "Unable to locate NODES section in session file." << endl;
        abort();
    }

    if (sectionMap["ELEMENTS"] == std::streampos(-1))
    {
        cerr << "Unable to locate ELEMENTS section in session file." << endl;
        abort();
    }

    if (sectionMap["SURFACES"] != std::streampos(-1))
    {
        if (sectionMap["BCS"] == std::streampos(-1))
        {
            cerr << "SURFACES section defined but BCS section not "
                 << "found." << endl;
            abort();
        }

        if (sectionMap["GROUPS"] == std::streampos(-1))
        {
            cerr << "SURFACES section defined but GROUPS section not "
                 << "found." << endl;
            abort();
        }

        if (sectionMap["FIELDS"] == std::streampos(-1))
        {
            cerr << "SURFACES section defined but FIELDS section not "
                 << "found." << endl;
            abort();
        }
    }

    m_mesh->m_expDim = 0;
    string tag;
    int start, end, nVertices, nEntities, nCurves, nSurf, nGroups, nBCs;
    int id, i, j, k;
    vector<double> hoXData, hoYData;
    LibUtilities::ShapeType elType = LibUtilities::eQuadrilateral;
    ifstream homeshFile;

    // Begin by reading in list of nodes which define the linear
    // elements.
    m_fileStream.seekg(sectionMap["NODES"]);
    getline(m_fileStream, line);
    ss.clear();
    ss.str(line);
    ss >> word;

    tag       = ss.str();
    start     = tag.find_first_of('=');
    end       = tag.find_first_of('>');
    nVertices = atoi(tag.substr(start + 1, end).c_str());

    i = id = 0;
    while (i < nVertices)
    {
        getline(m_fileStream, line);
        if (line.length() < 7)
            continue;
        ss.clear();
        ss.str(line);
        double x = 0, y = 0, z = 0;
        ss >> id >> x >> y >> z;

        if ((y * y) > 0.000001 && m_mesh->m_spaceDim != 3)
        {
            m_mesh->m_spaceDim = 2;
        }
        if ((z * z) > 0.000001)
        {
            m_mesh->m_spaceDim = 3;
        }
        id -= 1; // counter starts at 0
        m_mesh->m_node.push_back(
            std::shared_ptr<Node>(new Node(id, x, y, z)));
        ++i;
    }

    // Now read in elements
    m_fileStream.seekg(sectionMap["ELEMENTS"]);
    getline(m_fileStream, line);
    ss.clear();
    ss.str(line);
    ss >> word;

    tag       = ss.str();
    start     = tag.find_first_of('=');
    end       = tag.find_first_of('>');
    nEntities = atoi(tag.substr(start + 1, end).c_str());

    i = id = 0;
    while (i < nEntities)
    {
        getline(m_fileStream, line);
        if (line.length() < 18)
        {
            continue;
        }

        // Create element tags
        vector<int> tags;
        tags.push_back(0); // composite

        // Read element node list
        ss.clear();
        ss.str(line);
        ss >> id >> word;
        vector<NodeSharedPtr> nodeList;
        for (j = 0; j < 4; ++j)
        {
            int node = 0;
            ss >> node;
            nodeList.push_back(m_mesh->m_node[node - 1]);
        }

        // Create element
        ElmtConfig conf(elType, 1, false, false);
        ElementSharedPtr E =
            GetElementFactory().CreateInstance(elType, conf, nodeList, tags);

        // Determine mesh expansion dimension
        if (E->GetDim() > m_mesh->m_expDim)
        {
            m_mesh->m_expDim = E->GetDim();
        }
        m_mesh->m_element[E->GetDim()].push_back(E);
        ++i;
    }

    // Finally, process curves.
    if (sectionMap["CURVES"] != std::streampos(-1))
    {
        int np, nel, nodeId = m_mesh->m_node.size();

        m_fileStream.seekg(sectionMap["CURVES"]);
        getline(m_fileStream, line);
        ss.clear();
        ss.str(line);
        ss >> word;

        tag     = ss.str();
        start   = tag.find_first_of('=');
        end     = tag.find_first_of('>');
        nCurves = atoi(tag.substr(start + 1, end).c_str());

        // Some session files have empty curves sections; if nCurves
        // is 0, no nead to load high order mesh file.
        if (nCurves > 0)
        {
            string fname    = m_config["infile"].as<string>();
            int ext         = fname.find_last_of('.');
            string meshfile = fname.substr(0, ext) + ".msh";

            homeshFile.open(meshfile.c_str());
            if (!homeshFile.is_open())
            {
                cerr << "Cannot open or find mesh file: " << meshfile << endl
                     << "Make sure to run meshpr on your session "
                     << "file first." << endl;
                abort();
            }

            // Make sure we have matching header.
            getline(homeshFile, line);
            ss.clear();
            ss.str(line);
            ss >> np >> nel >> nel >> nel;

            if (nel != m_mesh->m_element[m_mesh->m_expDim].size())
            {
                cerr << "Number of elements mismatch in mesh file." << endl;
                abort();
            }

            // Now read in all mesh data. This is horribly inefficient
            // since not all elements are curved, but it is the
            // easiest way of finding element data.
            hoXData.resize(nel * np * np);
            hoYData.resize(nel * np * np);

            for (j = 0; j < nel * np * np; ++j)
            {
                getline(homeshFile, line);
                ss.clear();
                ss.str(line);
                ss >> hoXData[j] >> hoYData[j];
            }

            homeshFile.close();
        }

        i = id = 0;
        while (i < nCurves)
        {
            getline(m_fileStream, line);
            if (line.length() < 18)
            {
                continue;
            }
            int elmt = 0, side = 0;
            ss.clear();
            ss.str(line);
            ss >> id >> elmt >> side >> word;
            id--;
            elmt--;

            vector<NodeSharedPtr> edgeNodes;

            if (word != "<SPLINE>" && word != "<ARC>")
            {
                cerr << "Unknown curve tag: " << word << endl;
                abort();
            }

            // See if we have already retrieved high-order data
            // for this elements; prevents unnecessary computation
            // for elements with multiple curves.
            if (m_mesh->m_element[2][elmt]->GetConf().m_order > 1)
            {
                ++i;
                continue;
            }

            // Now set high order data for requested element.
            for (int side = 0; side < 4; ++side)
            {
                int offset = elmt * np * np;
                int stride = 0;

                switch (side)
                {
                    case 0: // Bottom edge
                        offset += 0;
                        stride = 1;
                        break;
                    case 1: // Right edge
                        offset += np - 1;
                        stride = np;
                        break;
                    case 2: // Top edge
                        offset += np * np - 1;
                        stride = -1;
                        break;
                    case 3: // Left edge
                        offset += np * (np - 1);
                        stride = -np;
                        break;
                    default:
                        cerr << "Unknown side for curve id " << id << endl;
                        abort();
                }

                for (j = 1; j < np - 1; ++j, ++nodeId)
                {
                    double x = hoXData[offset + j * stride];
                    double y = hoYData[offset + j * stride];
                    NodeSharedPtr n =
                        std::shared_ptr<Node>(new Node(nodeId, x, y, 0.0));
                    edgeNodes.push_back(n);
                }
            }

            // Add internal points.
            for (j = 1; j < np - 1; ++j)
            {
                int offset = j * np + 1;
                for (k = 1; k < np - 1; ++k, ++nodeId)
                {
                    double x = hoXData[offset + k];
                    double y = hoYData[offset + k];
                    NodeSharedPtr n =
                        std::shared_ptr<Node>(new Node(nodeId, x, y, 0.0));
                    edgeNodes.push_back(n);
                }
            }

            // Grab existing element from list and retrieve tags and
            // vertices; insert these into existing edge nodes.
            ElementSharedPtr e           = m_mesh->m_element[2][elmt];
            vector<NodeSharedPtr> elvert = e->GetVertexList();
            vector<int> tags = e->GetTagList();
            edgeNodes.insert(edgeNodes.begin(), elvert.begin(), elvert.end());

            // Create new element and replace with an incomplete
            // quadrilateral of the correct order.
            ElmtConfig conf(elType,
                            np - 1,
                            true,
                            false,
                            true,
                            LibUtilities::eGaussLobattoLegendre);
            m_mesh->m_element[2][elmt] = GetElementFactory().CreateInstance(
                elType, conf, edgeNodes, tags);

            ++i;
        }
    }

    // Process field names
    if (sectionMap["FIELDS"] != std::streampos(-1))
    {
        m_fileStream.seekg(sectionMap["FIELDS"]);
        getline(m_fileStream, line);
        getline(m_fileStream, line);
        ss.clear();
        ss.str(line);

        while (ss >> tag)
        {
            m_mesh->m_fields.push_back(tag);
        }
    }

    // Process surfaces if they exist. This is deliberately done after
    // curves to ensure high-order points are preserved.
    if (sectionMap["SURFACES"] != std::streampos(-1))
    {
        map<string, int> conditionMap;
        int maxTag = -1;

        // First read in list of groups, which defines each condition tag.
        m_fileStream.seekg(sectionMap["GROUPS"]);
        getline(m_fileStream, line);
        ss.clear();
        ss.str(line);
        ss >> word;

        tag     = ss.str();
        start   = tag.find_first_of('=');
        end     = tag.find_first_of('>');
        nGroups = atoi(tag.substr(start + 1, end).c_str());

        i = id = 0;
        while (i < nGroups)
        {
            getline(m_fileStream, line);
            ss.clear();
            ss.str(line);
            ss >> id >> tag;
            conditionMap[tag] = i++;
        }

        maxTag = i;

        // Now read in actual values for boundary conditions from BCS
        // section.
        m_fileStream.seekg(sectionMap["BCS"]);
        getline(m_fileStream, line);
        ss.clear();
        ss.str(line);
        ss >> word;

        tag   = ss.str();
        start = tag.find_first_of('=');
        end   = tag.find_first_of('>');
        nBCs  = atoi(tag.substr(start + 1, end).c_str());

        i = id = 0;
        while (i < nBCs)
        {
            int nF;
            string tmp;
            ConditionSharedPtr p;
            getline(m_fileStream, line);
            ss.clear();
            ss.str(line);
            ss >> id >> tag >> nF;

            p                                      = ConditionSharedPtr(new Condition());
            m_mesh->m_condition[conditionMap[tag]] = p;

            // Read boundary condition.
            j = 0;
            while (j < nF)
            {
                getline(m_fileStream, line);
                ss.clear();
                ss.str(line);
                ss >> tmp;

                // First string should be condition type.
                if (tmp == "<D>")
                {
                    p->type.push_back(eDirichlet);
                }
                else if (tmp == "<N>")
                {
                    p->type.push_back(eNeumann);
                }
                else if (tmp == "<H>")
                {
                    p->type.push_back(eHOPCondition);
                    p->value.push_back("0");
                    p->field.push_back("p");
                    ++j;
                    continue;
                }
                else
                {
                    cerr << "Unsupported boundary condition type " << tmp
                         << endl;
                    abort();
                }

                // Second string should be field.
                ss >> tmp;
                p->field.push_back(tmp);

                // Third string should be equals sign.
                ss >> tmp;
                if (tmp != "=")
                {
                    cerr << "Couldn't read boundary condition type " << tag
                         << endl;
                    abort();
                }

                // Fourth string should be value. CAUTION: Assumes
                // expression is defined without any spaces in it!
                ss >> tmp;
                p->value.push_back(tmp);

                ++j;
            }

            // Finally set composite for condition. In this case, all
            // composites will be lines so there is one set per
            // composite.
            p->m_composite.push_back(conditionMap[tag] + 1);

            ++i;
        }

        // Finally read surface information.
        m_fileStream.seekg(sectionMap["SURFACES"]);
        getline(m_fileStream, line);
        ss.clear();
        ss.str(line);
        ss >> word;

        tag   = ss.str();
        start = tag.find_first_of('=');
        end   = tag.find_first_of('>');
        nSurf = atoi(tag.substr(start + 1, end).c_str());

        i = id = 0;
        int elmt, side;
        int periodicTagId = -1;

        set<pair<int, int> > visitedPeriodic;

        while (i < nSurf)
        {
            getline(m_fileStream, line);
            ss.clear();
            ss.str(line);
            ss >> id >> elmt >> side >> word;
            elmt--;
            side--;

            if (word == "<P>")
            {
                // If this is the first periodic boundary condition
                // encountered, then set up m_mesh->m_condition with two
                // periodic conditions.
                if (periodicTagId == -1)
                {
                    periodicTagId         = maxTag;
                    ConditionSharedPtr in = ConditionSharedPtr(new Condition());
                    ConditionSharedPtr out =
                        ConditionSharedPtr(new Condition());
                    for (j = 0; j < m_mesh->m_fields.size(); ++j)
                    {
                        in->type.push_back(ePeriodic);
                        out->type.push_back(ePeriodic);
                        in->field.push_back(m_mesh->m_fields[j]);
                        out->field.push_back(m_mesh->m_fields[j]);
                        in->value.push_back("[" + boost::lexical_cast<string>(
                                                      periodicTagId + 1) +
                                            "]");
                        out->value.push_back(
                            "[" + boost::lexical_cast<string>(periodicTagId) +
                            "]");
                    }
                    in->m_composite.push_back(periodicTagId + 1);
                    out->m_composite.push_back(periodicTagId + 2);
                    m_mesh->m_condition[periodicTagId]     = in;
                    m_mesh->m_condition[periodicTagId + 1] = out;
                }

                int elmtB, sideB;

                ss >> elmtB >> sideB;
                elmtB--;
                sideB--;

                pair<int, int> c1(elmt, side);
                pair<int, int> c2(elmtB, sideB);

                if (visitedPeriodic.count(c1) == 0 &&
                    visitedPeriodic.count(c2) == 0)
                {
                    visitedPeriodic.insert(make_pair(elmtB, sideB));
                    visitedPeriodic.insert(make_pair(elmt, side));
                    insertEdge(elmt, side, periodicTagId + 1);
                    insertEdge(elmtB, sideB, periodicTagId + 2);
                }
            }
            else if (word == "<B>")
            {
                ss >> tag;
                insertEdge(elmt, side, conditionMap[tag] + 1);
            }
            else
            {
                cerr << "Unrecognised or unsupported tag " << word << endl;
                abort();
            }
            ++i;
        }
    }

    PrintSummary();

    // Process rest of mesh.
    ProcessVertices();
    ProcessEdges();
    ProcessFaces();
    ProcessElements();
    ProcessComposites();
}

void InputSem::insertEdge(int elmt, int side, int tagId)
{
    EdgeSharedPtr edge              = m_mesh->m_element[2][elmt]->GetEdge(side);
    vector<NodeSharedPtr> edgeNodes = edge->m_edgeNodes;
    edgeNodes.insert(edgeNodes.begin(), edge->m_n2);
    edgeNodes.insert(edgeNodes.begin(), edge->m_n1);
    int order = edgeNodes.size() - 1;

    vector<int> tags;
    tags.push_back(tagId);

    ElmtConfig conf(LibUtilities::eSegment,
                    order,
                    order > 1,
                    false,
                    true,
                    LibUtilities::eGaussLobattoLegendre);
    ElementSharedPtr E = GetElementFactory().CreateInstance(
        LibUtilities::eSegment, conf, edgeNodes, tags);
    m_mesh->m_element[1].push_back(E);
}
}
}