Nektar::FieldUtils::InputXml Class Reference

#include <InputXml.h>

Inheritance diagram for Nektar::FieldUtils::InputXml:

Collaboration diagram for Nektar::FieldUtils::InputXml:

Public Member Functions
	InputXml (FieldSharedPtr f)
	Set up InputXml object. More...
virtual	~InputXml ()
virtual void	Process (po::variables_map &vm)
virtual std::string	GetModuleName ()
Public Member Functions inherited from Nektar::FieldUtils::InputModule
	InputModule (FieldSharedPtr p_m)
FIELD_UTILS_EXPORT void	AddFile (string fileType, string fileName)
Public Member Functions inherited from Nektar::FieldUtils::Module
FIELD_UTILS_EXPORT	Module (FieldSharedPtr p_f)
FIELD_UTILS_EXPORT void	RegisterConfig (string key, string value)
	Register a configuration option with a module. More...
FIELD_UTILS_EXPORT void	PrintConfig ()
	Print out all configuration options for a module. More...
FIELD_UTILS_EXPORT void	SetDefaults ()
	Sets default configuration options for those which have not been set. More...
FIELD_UTILS_EXPORT bool	GetRequireEquiSpaced (void)
FIELD_UTILS_EXPORT void	SetRequireEquiSpaced (bool pVal)
FIELD_UTILS_EXPORT void	EvaluateTriFieldAtEquiSpacedPts (LocalRegions::ExpansionSharedPtr &exp, const Array< OneD, const NekDouble > &infield, Array< OneD, NekDouble > &outfield)

Static Public Member Functions
static ModuleSharedPtr	create (FieldSharedPtr f)
	Creates an instance of this class. More...

Static Public Attributes
static ModuleKey	m_className []
	ModuleKey for class. More...

Additional Inherited Members
Protected Member Functions inherited from Nektar::FieldUtils::InputModule
void	PrintSummary ()
	Print summary of elements. More...
Protected Member Functions inherited from Nektar::FieldUtils::Module
	Module ()
Protected Attributes inherited from Nektar::FieldUtils::InputModule
set< string >	m_allowedFiles
Protected Attributes inherited from Nektar::FieldUtils::Module
FieldSharedPtr	m_f
	Field object. More...
map< string, ConfigOption >	m_config
	List of configuration values. More...
bool	m_requireEquiSpaced

Detailed Description

Input module for Xml files.

Definition at line 49 of file InputXml.h.

Constructor & Destructor Documentation

Nektar::FieldUtils::InputXml::InputXml

(

FieldSharedPtr

f

)

Set up InputXml object.

Definition at line 65 of file InputXml.cpp.

References Nektar::FieldUtils::InputModule::m_allowedFiles.

                                   : InputModule(f)
{
    m_allowedFiles.insert("xml");
    m_allowedFiles.insert("xml.gz");
    m_allowedFiles.insert("fld"); // these files could be allowed with xml files
    m_allowedFiles.insert("chk");
    m_allowedFiles.insert("rst");
}

Nektar::FieldUtils::InputXml::~InputXml ( )

virtual

Definition at line 77 of file InputXml.cpp.

{
}

Member Function Documentation

static ModuleSharedPtr Nektar::FieldUtils::InputXml::create ( FieldSharedPtr  f )

inlinestatic

Creates an instance of this class.

Definition at line 57 of file InputXml.h.

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

    {
        return MemoryManager<InputXml>::AllocateSharedPtr(f);
    }

virtual std::string Nektar::FieldUtils::InputXml::GetModuleName ( )

inlinevirtual

Implements Nektar::FieldUtils::Module.

Definition at line 64 of file InputXml.h.

    {
        return "InputXml";
    }

void Nektar::FieldUtils::InputXml::Process ( po::variables_map &  vm )

virtual

Implements Nektar::FieldUtils::Module.

Definition at line 84 of file InputXml.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, Nektar::LibUtilities::SessionReader::CreateInstance(), Nektar::ParseUtils::GenerateUnOrderedVector(), Nektar::FieldUtils::Module::m_f, Nektar::FieldUtils::Module::m_requireEquiSpaced, Nektar::SpatialDomains::NullDomainRangeShPtr, Nektar::SpatialDomains::MeshGraph::Read(), Nektar::LibUtilities::ReduceMax, Nektar::LibUtilities::ShapeTypeMap, Nektar::LibUtilities::SIZE_ShapeType, Nektar::Timer::Start(), Nektar::Timer::Stop(), and Nektar::Timer::TimePerTest().

{
    Timer timerpart;

    // check for multiple calls to inputXml due to split xml
    // files. If so just return
    int expsize = m_f->m_exp.size();
    m_f->m_comm->AllReduce(expsize, LibUtilities::ReduceMax);

    if (expsize != 0)
    {
        return;
    }

    if (m_f->m_verbose)
    {
        if (m_f->m_comm->TreatAsRankZero())
        {
            cout << "Processing input xml file" << endl;
            timerpart.Start();
        }
    }

    // check to see if fld file defined so can use in
    // expansion defintion if required
    string fldending;
    bool fldfilegiven = true;

    // Determine appropriate field input
    if (m_f->m_inputfiles.count("fld") != 0)
    {
        fldending = "fld";
    }
    else if (m_f->m_inputfiles.count("chk") != 0)
    {
        fldending = "chk";
    }
    else if (m_f->m_inputfiles.count("rst") != 0)
    {
        fldending = "rst";
    }
    else
    {
        fldfilegiven = false;
    }

    string xml_ending    = "xml";
    string xml_gz_ending = "xml.gz";

    std::vector<std::string> files;
    // load .xml ending
    for (int i = 0; i < m_f->m_inputfiles[xml_ending].size(); ++i)
    {
        files.push_back(m_f->m_inputfiles[xml_ending][i]);
    }

    // load any .xml.gz endings
    for (int j = 0; j < m_f->m_inputfiles[xml_gz_ending].size(); ++j)
    {
        files.push_back(m_f->m_inputfiles[xml_gz_ending][j]);
    }

    SpatialDomains::DomainRangeShPtr rng = SpatialDomains::NullDomainRangeShPtr;

    // define range to process output
    if (vm.count("range"))
    {
        vector<NekDouble> values;
        ASSERTL0(ParseUtils::GenerateUnOrderedVector(
                     vm["range"].as<string>().c_str(), values),
                 "Failed to interpret range string");

        ASSERTL0(values.size() > 1, "Do not have minimum values of xmin,xmax");
        ASSERTL0(values.size() % 2 == 0,
                 "Do not have an even number of range values");

        int nvalues = values.size() / 2;
        rng = MemoryManager<SpatialDomains::DomainRange>::AllocateSharedPtr();

        rng->m_doZrange   = false;
        rng->m_doYrange   = false;
        rng->m_checkShape = false;

        switch (nvalues)
        {
            case 3:
                rng->m_doZrange = true;
                rng->m_zmin     = values[4];
                rng->m_zmax     = values[5];
            case 2:
                rng->m_doYrange = true;
                rng->m_ymin     = values[2];
                rng->m_ymax     = values[3];
            case 1:
                rng->m_doXrange = true;
                rng->m_xmin     = values[0];
                rng->m_xmax     = values[1];
                break;
            default:
                ASSERTL0(false, "too many values specfied in range");
        }
    }

    // define range to only take a single shape.
    if (vm.count("onlyshape"))
    {
        if (rng == SpatialDomains::NullDomainRangeShPtr)
        {
            rng =
                MemoryManager<SpatialDomains::DomainRange>::AllocateSharedPtr();
            rng->m_doXrange = false;
            rng->m_doYrange = false;
            rng->m_doZrange = false;
        }

        rng->m_checkShape = true;

        string shapematch = boost::to_upper_copy(vm["onlyshape"].as<string>());
        int i;
        for (i = 0; i < LibUtilities::SIZE_ShapeType; ++i)
        {
            string shapeval = LibUtilities::ShapeTypeMap[i];
            boost::to_upper(shapeval);
            if (shapematch.compare(shapeval) == 0)
            {
                rng->m_shapeType = (LibUtilities::ShapeType)i;
                break;
            }
        }
        ASSERTL0(i != LibUtilities::SIZE_ShapeType,
                 "Failed to find shape type in -onlyshape command line "
                 "argument");
    }

    // Set up command lines options that will be passed through to SessionReader
    vector<string> cmdArgs;
    cmdArgs.push_back("FieldConvert");

    if (m_f->m_verbose)
    {
        cmdArgs.push_back("--verbose");
    }

    if (vm.count("part-only"))
    {
        cmdArgs.push_back("--part-only");
        cmdArgs.push_back(
            boost::lexical_cast<string>(vm["part-only"].as<int>()));
    }

    if (vm.count("part-only-overlapping"))
    {
        cmdArgs.push_back("--part-only-overlapping");
        cmdArgs.push_back(
            boost::lexical_cast<string>(vm["part-only-overlapping"].as<int>()));
    }

    if (vm.count("npz"))
    {
        cmdArgs.push_back("--npz");
        cmdArgs.push_back(boost::lexical_cast<string>(vm["npz"].as<int>()));
    }

    int argc          = cmdArgs.size();
    const char **argv = new const char *[argc];
    for (int i = 0; i < argc; ++i)
    {
        argv[i] = cmdArgs[i].c_str();
    }

    m_f->m_session = LibUtilities::SessionReader::CreateInstance(
        argc, (char **)argv, files, m_f->m_comm);

    // Free up memory.
    delete[] argv;

    if (m_f->m_verbose)
    {
        if (m_f->m_comm->TreatAsRankZero())
        {
            timerpart.Stop();
            NekDouble cpuTime = timerpart.TimePerTest(1);

            stringstream ss;
            ss << cpuTime << "s";
            cout << "\t InputXml session reader CPU Time: " << setw(8) << left
                 << ss.str() << endl;
            timerpart.Start();
        }
    }

    m_f->m_graph = SpatialDomains::MeshGraph::Read(m_f->m_session, rng);

    if (m_f->m_verbose)
    {
        if (m_f->m_comm->TreatAsRankZero())
        {
            timerpart.Stop();
            NekDouble cpuTime = timerpart.TimePerTest(1);

            stringstream ss;
            ss << cpuTime << "s";
            cout << "\t InputXml mesh graph setup  CPU Time: " << setw(8)
                 << left << ss.str() << endl;
            timerpart.Start();
        }
    }

    // currently load all field (possibly could read data from
    // expansion list but it is re-arranged in expansion)
    const SpatialDomains::ExpansionMap &expansions =
        m_f->m_graph->GetExpansions();

    // if Range has been speficied it is possible to have a
    // partition which is empty so ccheck this and return if
    // no elements present.
    if (!expansions.size())
    {
        return;
    }

    m_f->m_exp.resize(1);

    // load fielddef header if fld file is defined. This gives
    // precedence to Homogeneous definition in fld file
    int NumHomogeneousDir = 0;
    if (fldfilegiven)
    {
        // use original expansion to identify which elements are in
        // this partition/subrange

        Array<OneD, int> ElementGIDs(expansions.size());
        SpatialDomains::ExpansionMap::const_iterator expIt;

        int i = 0;
        for (expIt = expansions.begin(); expIt != expansions.end(); ++expIt)
        {
            ElementGIDs[i++] = expIt->second->m_geomShPtr->GetGlobalID();
        }

        m_f->m_fielddef.clear();
        m_f->m_data.clear();

        m_f->FieldIOForFile(m_f->m_inputfiles[fldending][0])->Import(
            m_f->m_inputfiles[fldending][0], m_f->m_fielddef, m_f->m_data,
            m_f->m_fieldMetaDataMap, ElementGIDs);
        NumHomogeneousDir = m_f->m_fielddef[0]->m_numHomogeneousDir;

        //----------------------------------------------
        // Set up Expansion information to use mode order from field
        m_f->m_graph->SetExpansions(m_f->m_fielddef);
    }
    else
    {
        if (m_f->m_session->DefinesSolverInfo("HOMOGENEOUS"))
        {
            std::string HomoStr = m_f->m_session->GetSolverInfo("HOMOGENEOUS");

            if ((HomoStr == "HOMOGENEOUS1D") || (HomoStr == "Homogeneous1D") ||
                (HomoStr == "1D") || (HomoStr == "Homo1D"))
            {
                NumHomogeneousDir = 1;
            }
            if ((HomoStr == "HOMOGENEOUS2D") || (HomoStr == "Homogeneous2D") ||
                (HomoStr == "2D") || (HomoStr == "Homo2D"))
            {
                NumHomogeneousDir = 2;
            }
        }
    }

    // reset expansion defintion to use equispaced points if required.
    if (m_requireEquiSpaced || vm.count("output-points"))
    {
        int nPointsNew = 0;

        if (vm.count("output-points"))
        {
            nPointsNew = vm["output-points"].as<int>();
        }

        m_f->m_graph->SetExpansionsToEvenlySpacedPoints(nPointsNew);
    }
    else
    {
        if (vm.count("output-points"))
        {
            int nPointsNew = vm["output-points"].as<int>();
            m_f->m_graph->SetExpansionsToPointOrder(nPointsNew);
        }
    }

    if (m_f->m_verbose)
    {
        if (m_f->m_comm->TreatAsRankZero())
        {
            timerpart.Stop();
            NekDouble cpuTime = timerpart.TimePerTest(1);

            stringstream ss;
            ss << cpuTime << "s";
            cout << "\t InputXml setexpansion CPU Time: " << setw(8) << left
                 << ss.str() << endl;
            timerpart.Start();
        }
    }

    // Override number of planes with value from cmd line
    if (NumHomogeneousDir == 1 && vm.count("output-points-hom-z"))
    {
        int expdim = m_f->m_graph->GetMeshDimension();
        m_f->m_fielddef[0]->m_numModes[expdim] =
            vm["output-points-hom-z"].as<int>();
    }

    m_f->m_exp[0] = m_f->SetUpFirstExpList(NumHomogeneousDir, fldfilegiven);

    if (m_f->m_verbose)
    {
        if (m_f->m_comm->TreatAsRankZero())
        {
            timerpart.Stop();
            NekDouble cpuTime = timerpart.TimePerTest(1);

            stringstream ss1;

            ss1 << cpuTime << "s";
            cout << "\t InputXml set first exp CPU Time: " << setw(8) << left
                 << ss1.str() << endl;
        }
    }
}

Member Data Documentation

ModuleKey Nektar::FieldUtils::InputXml::m_className

static

Initial value:

= {
    GetModuleFactory().RegisterCreatorFunction(
        ModuleKey(eInputModule, "xml"), InputXml::create, "Reads Xml file."),
    GetModuleFactory().RegisterCreatorFunction(
        ModuleKey(eInputModule, "xml.gz"), InputXml::create, "Reads Xml file."),
}

ModuleKey for class.

Definition at line 62 of file InputXml.h.