Nektar::Utilities::InputXml Class Reference

#include <InputXml.h>

Inheritance diagram for Nektar::Utilities::InputXml:

Collaboration diagram for Nektar::Utilities::InputXml:

Public Member Functions
	InputXml (FieldSharedPtr f)
	Set up InputXml object. More...
virtual	~InputXml ()
virtual void	Process (po::variables_map &vm)
Public Member Functions inherited from Nektar::Utilities::InputModule
	InputModule (FieldSharedPtr p_m)
void	AddFile (string fileType, string fileName)
	InputModule (MeshSharedPtr p_m)
void	OpenStream ()
	Open a file for input. More...
Public Member Functions inherited from Nektar::Utilities::Module
	Module (FieldSharedPtr p_f)
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)
virtual void	Process ()=0
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 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::Utilities::InputModule
void	PrintSummary ()
	Print summary of elements. More...
void	PrintSummary ()
	Print summary of elements. More...
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::InputModule
set< string >	m_allowedFiles
std::ifstream	m_mshFile
	Input stream. More...
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

Input module for Xml files.

Definition at line 49 of file InputXml.h.

Constructor & Destructor Documentation

Nektar::Utilities::InputXml::InputXml

(

FieldSharedPtr

f

)

Set up InputXml object.

Definition at line 68 of file InputXml.cpp.

References Nektar::Utilities::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::Utilities::InputXml::~InputXml ( )

virtual

Definition at line 81 of file InputXml.cpp.

{
}

Member Function Documentation

static ModuleSharedPtr Nektar::Utilities::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);
        }

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

virtual

Implements Nektar::Utilities::Module.

Definition at line 89 of file InputXml.cpp.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, Nektar::LibUtilities::SessionReader::CreateInstance(), Nektar::ParseUtils::GenerateUnOrderedVector(), Nektar::Utilities::Module::m_f, Nektar::Utilities::Module::m_requireEquiSpaced, Nektar::SpatialDomains::NullDomainRangeShPtr, Nektar::LibUtilities::NullFieldMetaDataMap, Nektar::LibUtilities::NullVectorNekDoubleVector, 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 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->GetRank() == 0)
        {
            cout << "Processing input xml file" << endl;
            timer.Start();
            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("shared-filesystem"))
    {
        cmdArgs.push_back("--shared-filesystem");
    }

    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>()));
    }

    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->GetRank() == 0)
        {
            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);
    m_f->m_fld = MemoryManager<LibUtilities::FieldIO>
                    ::AllocateSharedPtr(m_f->m_session->GetComm());

    if(m_f->m_verbose)
    {
        if(m_f->m_comm->GetRank() == 0)
        {
            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_fld->Import(m_f->m_inputfiles[fldending][0],m_f->m_fielddef,
                           LibUtilities::NullVectorNekDoubleVector,
                           LibUtilities::NullFieldMetaDataMap,
                           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->GetRank() == 0)
        {
            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();
        }
    }

    if(m_f->m_verbose)
    {
        if(m_f->m_comm->GetRank() == 0)
        {
            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->GetRank() == 0)
        {
            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;

            
            timer.Stop();
            cpuTime = timer.TimePerTest(1);
            
            stringstream ss;
            ss << cpuTime << "s";
            cout << "InputXml  CPU Time: " << setw(8) << left
                 << ss.str() << endl;

        }
    }
}

Member Data Documentation

ModuleKey Nektar::Utilities::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.