PtsIO.cpp

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////////////////////////////////////////////////////////////////////////////////
//
// File: PtsIO.cpp
//
// For more information, please see: http://www.nektar.info/
//
// The MIT License
//
// Copyright (c) 2014 Kilian Lackhove
// 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: I/O routines relating to Pts data
//
////////////////////////////////////////////////////////////////////////////////
 
#include <LibUtilities/BasicUtils/PtsIO.h>
#include <boost/algorithm/string.hpp>
 
#include <fstream>
 
#include <boost/format.hpp>
 
#ifdef NEKTAR_USE_MPI
#include <mpi.h>
#endif
 
#include <LibUtilities/BasicUtils/FileSystem.h>
#include <LibUtilities/BasicUtils/ParseUtils.h>
 
using namespace std;
 
namespace Nektar
{
namespace LibUtilities
{
 
PtsIO::PtsIO(CommSharedPtr pComm, bool sharedFilesystem)
    : FieldIOXml(pComm, sharedFilesystem)
{
}
 
/**
 * @brief Import a pts field from file
 *
 * @param inFile    filename of the file to read
 * @param ptsField  the resulting pts field.
 */
void PtsIO::Import(const string &inFile, PtsFieldSharedPtr &ptsField,
                   FieldMetaDataMap &fieldmetadatamap, DomainRangeShPtr &Range)
{
    std::string infile = inFile;
 
    fs::path pinfilename(infile);
 
    // check to see that infile is a directory
    if (fs::is_directory(pinfilename))
    {
        fs::path infofile("Info.xml");
        fs::path fullpath = pinfilename / infofile;
        infile            = PortablePath(fullpath);
 
        std::vector<std::string> filenames;
        std::vector<std::vector<unsigned int>> elementIDs_OnPartitions;
 
        ImportMultiFldFileIDs(infile, filenames, elementIDs_OnPartitions,
                              fieldmetadatamap);
 
        // Load metadata
        ImportFieldMetaData(infile, fieldmetadatamap);
 
        if (filenames.size() == m_comm->GetSpaceComm()->GetSize())
        {
            // only load the file that matches this rank
            filenames.clear();
            boost::format pad("P%1$07d.%2$s");
            pad % m_comm->GetSpaceComm()->GetRank() % GetFileEnding();
            filenames.push_back(pad.str());
        }
 
        for (int i = 0; i < filenames.size(); ++i)
        {
            fs::path pfilename(filenames[i]);
            fullpath     = pinfilename / pfilename;
            string fname = PortablePath(fullpath);
 
            if (i == 0)
            {
                ImportFieldData(fname, ptsField, Range);
            }
            else
            {
                LibUtilities::PtsFieldSharedPtr newPtsField;
                ImportFieldData(fname, newPtsField, Range);
                Array<OneD, Array<OneD, NekDouble>> pts;
                newPtsField->GetPts(pts);
                ptsField->AddPoints(pts);
            }
        }
    }
    else
    {
        ImportFieldData(infile, ptsField, Range);
    }
}
 
/**
 * @brief Save a pts field to a file
 *
 * @param outFile    filename of the file
 * @param ptsField  the pts field
 */
void PtsIO::Write(const string &outFile,
                  const Nektar::LibUtilities::PtsFieldSharedPtr &ptsField,
                  const bool backup)
{
    size_t nTotvars = ptsField->GetNFields() + ptsField->GetDim();
    size_t np       = ptsField->GetNpoints();
 
    std::string filename = SetUpOutput(outFile, true, backup);
    SetUpFieldMetaData(outFile);
 
    // until tinyxml gains support for line break, write the xml manually
    std::ofstream ptsFile;
    ptsFile.open(filename.c_str());
 
    ptsFile << "<?xml version=\"1.0\" encoding=\"utf-8\" ?>" << endl;
    ptsFile << "<NEKTAR>" << endl;
    ptsFile << "  <POINTS ";
    ptsFile << "DIM=\"" << ptsField->GetDim() << "\" ";
    string fn = boost::algorithm::join(ptsField->GetFieldNames(), ",");
    ptsFile << "FIELDS=\"" << fn << "\" ";
    ptsFile << ">" << endl;
 
    Array<OneD, Array<OneD, NekDouble>> pts;
    ptsField->GetPts(pts);
    for (size_t i = 0; i < np; ++i)
    {
        ptsFile << "    ";
        ptsFile << pts[0][i];
        for (size_t j = 1; j < nTotvars; ++j)
        {
            ptsFile << " " << pts[j][i];
        }
        ptsFile << endl;
    }
    ptsFile << "  </POINTS>" << endl;
    ptsFile << "</NEKTAR>" << endl;
 
    ptsFile.close();
 
    // this is what the above cpart would read if tinyxml
    // supported line breaks
    /*
    // Create the file (partition)
    TiXmlDocument doc;
    TiXmlDeclaration *decl = new TiXmlDeclaration("1.0", "utf-8", "");
    doc.LinkEndChild(decl);
 
    TiXmlElement *root = new TiXmlElement("NEKTAR");
    doc.LinkEndChild(root);
 
    TiXmlElement *pointsTag = new TiXmlElement("POINTS");
    root->LinkEndChild(pointsTag);
 
    pointsTag->SetAttribute("DIM", ptsField->GetDim());
 
    string fn = boost::algorithm::join(ptsField->GetFieldNames(), ",");
    pointsTag->SetAttribute("FIELDS", fn);
 
    Array <OneD, Array <OneD, NekDouble > > pts;
    ptsField->GetPts(pts);
    ostringstream os;
    for (int i = 0; i < np; ++i)
    {
        os << pts[0][i];
        for (int j = 1; j < nTotvars; ++j)
        {
            os << " " << pts[j][i];
        }
        os << " ";
    }
 
    pointsTag->LinkEndChild(new TiXmlText(os.str()));
 
    doc.SaveFile(filename);
    */
}
void PtsIO::ImportFieldData(const string inFile, PtsFieldSharedPtr &ptsField,
                            DomainRangeShPtr &Range)
{
    v_ImportFieldData(inFile, ptsField, Range);
}
 
void PtsIO::v_ImportFieldData(const string inFile, PtsFieldSharedPtr &ptsField,
                              DomainRangeShPtr &Range)
{
    boost::ignore_unused(Range);
    TiXmlDocument docInput(inFile);
    bool loadOkay1 = docInput.LoadFile();
 
    std::stringstream errstr;
    errstr << "Unable to load file: " << inFile << std::endl;
    errstr << "Reason: " << docInput.ErrorDesc() << std::endl;
    errstr << "Position: Line " << docInput.ErrorRow() << ", Column "
           << docInput.ErrorCol() << std::endl;
    ASSERTL0(loadOkay1, errstr.str());
 
    TiXmlElement *nektar = docInput.FirstChildElement("NEKTAR");
    TiXmlElement *points = nektar->FirstChildElement("POINTS");
    int dim;
    int err = points->QueryIntAttribute("DIM", &dim);
 
    ASSERTL0(err == TIXML_SUCCESS, "Unable to read attribute DIM.");
 
    std::string fields = points->Attribute("FIELDS");
 
    vector<string> fieldNames;
    if (!fields.empty())
    {
        bool valid = ParseUtils::GenerateVector(fields, fieldNames);
        ASSERTL0(
            valid,
            "Unable to process list of field variable in  FIELDS attribute:  " +
                fields);
    }
 
    map<PtsInfo, int> ptsInfo = NullPtsInfoMap;
 
    const char *ptinfo = points->Attribute("PTSINFO");
    if (ptinfo && boost::iequals(ptinfo, "EquiSpaced"))
    {
        ptsInfo[eIsEquiSpacedData] = 1;
    }
 
    int np;
    err = points->QueryIntAttribute("PTSPERELMTEDGE", &np);
    if (err == TIXML_SUCCESS)
    {
        ptsInfo[ePtsPerElmtEdge] = np;
    }
 
    size_t nfields = fieldNames.size();
    size_t totvars = dim + nfields;
 
    TiXmlNode *pointsBody = points->FirstChild();
 
    std::istringstream pointsDataStrm(pointsBody->ToText()->Value());
 
    vector<NekDouble> ptsSerial;
    Array<OneD, Array<OneD, NekDouble>> pts(totvars);
 
    try
    {
        NekDouble ptsStream;
        while (!pointsDataStrm.fail())
        {
            pointsDataStrm >> ptsStream;
 
            ptsSerial.push_back(ptsStream);
        }
    }
    catch (...)
    {
        NEKERROR(ErrorUtil::efatal, "Unable to read Points data.");
    }
 
    size_t npts = ptsSerial.size() / totvars;
 
    for (size_t i = 0; i < totvars; ++i)
    {
        pts[i] = Array<OneD, NekDouble>(npts);
    }
 
    for (size_t i = 0; i < npts; ++i)
    {
        for (size_t j = 0; j < totvars; ++j)
        {
            pts[j][i] = ptsSerial[i * totvars + j];
        }
    }
 
    ptsField = MemoryManager<PtsField>::AllocateSharedPtr(dim, fieldNames, pts,
                                                          ptsInfo);
}
 
void PtsIO::SetUpFieldMetaData(const string outname)
{
    ASSERTL0(!outname.empty(), "Empty path given to SetUpFieldMetaData()");
 
    int nprocs = m_comm->GetSpaceComm()->GetSize();
    int rank   = m_comm->GetSpaceComm()->GetRank();
 
    fs::path specPath(outname);
 
    // Collate per-process element lists on root process to generate
    // the info file.
    if (rank == 0)
    {
        // Set up output names
        std::vector<std::string> filenames;
        std::vector<std::vector<unsigned int>> ElementIDs;
        for (int i = 0; i < nprocs; ++i)
        {
            boost::format pad("P%1$07d.%2$s");
            pad % i % GetFileEnding();
            filenames.push_back(pad.str());
 
            std::vector<unsigned int> tmp;
            tmp.push_back(0);
            ElementIDs.push_back(tmp);
        }
 
        // Write the Info.xml file
        string infofile =
            LibUtilities::PortablePath(specPath / fs::path("Info.xml"));
 
        cout << "Writing: " << specPath << endl;
 
        const FieldMetaDataMap fieldmetadatamap;
        WriteMultiFldFileIDs(infofile, filenames, ElementIDs, fieldmetadatamap);
    }
}
} // namespace LibUtilities
} // namespace Nektar