Nektar::FieldUtils::InputXml Class Reference

#include <InputXml.h>

Inheritance diagram for Nektar::FieldUtils::InputXml:

Public Member Functions
	InputXml (FieldSharedPtr f)
	Set up InputXml object.
	~InputXml () override
Public Member Functions inherited from Nektar::FieldUtils::InputModule
	InputModule (FieldSharedPtr p_m)
void	PrintSummary ()
	Print a brief summary of information.
Public Member Functions inherited from Nektar::FieldUtils::Module
FIELD_UTILS_EXPORT	Module (FieldSharedPtr p_f)
virtual	~Module ()=default
void	Process (po::variables_map &vm)
std::string	GetModuleName ()
std::string	GetModuleDescription ()
const ConfigOption &	GetConfigOption (const std::string &key) const
ModulePriority	GetModulePriority ()
std::vector< ModuleKey >	GetModulePrerequisites ()
FIELD_UTILS_EXPORT void	RegisterConfig (std::string key, std::string value="")
	Register a configuration option with a module.
FIELD_UTILS_EXPORT void	PrintConfig ()
	Print out all configuration options for a module.
FIELD_UTILS_EXPORT void	SetDefaults ()
	Sets default configuration options for those which have not been set.
FIELD_UTILS_EXPORT void	AddFile (std::string fileType, std::string fileName)
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.
Static Public Member Functions inherited from Nektar::FieldUtils::InputModule
static FIELD_UTILS_EXPORT std::string	GuessFormat (std::string fileName)
	Tries to guess the format of the input file.

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

Protected Member Functions
void	v_Process (po::variables_map &vm) override
std::string	v_GetModuleName () override
std::string	v_GetModuleDescription () override
ModulePriority	v_GetModulePriority () override
Protected Member Functions inherited from Nektar::FieldUtils::Module
	Module ()
virtual std::vector< ModuleKey >	v_GetModulePrerequisites ()

Additional Inherited Members
Public Attributes inherited from Nektar::FieldUtils::Module
FieldSharedPtr	m_f
	Field object.
Protected Attributes inherited from Nektar::FieldUtils::Module
std::map< std::string, ConfigOption >	m_config
	List of configuration values.
std::set< std::string >	m_allowedFiles
	List of allowed file formats.

Detailed Description

Input module for Xml files.

Definition at line 46 of file InputXml.h.

Constructor & Destructor Documentation

InputXml()

Nektar::FieldUtils::InputXml::InputXml

(

FieldSharedPtr

f

)

Set up InputXml object.

Definition at line 61 of file InputXml.cpp.

                                   : InputModule(f)
{
    m_allowedFiles.insert("xml");
    m_allowedFiles.insert("xml.gz");
    m_config["range"]     = ConfigOption(false, "", "range values");
    m_config["comprange"] = ConfigOption(false, "", "composite range values");
}

References Nektar::FieldUtils::Module::m_allowedFiles, and Nektar::FieldUtils::Module::m_config.

~InputXml()

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

override

Definition at line 72 of file InputXml.cpp.

{
}

Member Function Documentation

create()

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

inlinestatic

Creates an instance of this class.

Definition at line 52 of file InputXml.h.

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

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

v_GetModuleDescription()

std::string Nektar::FieldUtils::InputXml::v_GetModuleDescription ( )

inlineoverrideprotectedvirtual

Reimplemented from Nektar::FieldUtils::Module.

Definition at line 67 of file InputXml.h.

    {
        return "Processing input xml file";
    }

v_GetModuleName()

std::string Nektar::FieldUtils::InputXml::v_GetModuleName ( )

inlineoverrideprotectedvirtual

Reimplemented from Nektar::FieldUtils::Module.

Definition at line 62 of file InputXml.h.

    {
        return "InputXml";
    }

v_GetModulePriority()

ModulePriority Nektar::FieldUtils::InputXml::v_GetModulePriority ( )

inlineoverrideprotectedvirtual

Reimplemented from Nektar::FieldUtils::Module.

Definition at line 72 of file InputXml.h.

    {
        return eCreateGraph;
    }

References Nektar::FieldUtils::eCreateGraph.

v_Process()

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

overrideprotectedvirtual

Reimplemented from Nektar::FieldUtils::Module.

Definition at line 79 of file InputXml.cpp.

{
    string range     = m_config["range"].as<string>();
    string comprange = m_config["comprange"].as<string>();
 
    LibUtilities::Timer timerpart;
    if (m_f->m_verbose)
    {
        if (m_f->m_comm->TreatAsRankZero())
        {
            timerpart.Start();
        }
    }
 
    // check for multiple calls to inputXml due to split xml
    // files. If so just return
    if (m_f->m_graph)
    {
        return;
    }
 
    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]);
    }
 
    LibUtilities::DomainRangeShPtr rng = LibUtilities::NullDomainRangeShPtr;
 
    // define range to process output
    if (vm.count("range"))
    {
        NEKERROR(ErrorUtil::ewarning,
                 "The command line option \"range\" (FieldConvert -r xmin,xmax,"
                 "ymin,ymax) is deprecated. Please use the InputXml "
                 "option instead, i.e. \n \t"
                 "FieldConvert myfile.xml:xml:range=\"xmin,xmax,ymin,ymax\" "
                 "out.vtu");
    }
 
    if (vm.count("range") || range.size())
    {
        vector<NekDouble> values;
 
        if (range.size())
        {
            ASSERTL0(ParseUtils::GenerateVector(range, values),
                     "Failed to interpret range string");
        }
        else
        {
            ASSERTL0(
                ParseUtils::GenerateVector(vm["range"].as<string>(), values),
                "Failed to interpret range string");
        }
 
        if (values.size())
        {
            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<LibUtilities::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];
                    /* Falls through. */
                case 2:
                    rng->m_doYrange = true;
                    rng->m_ymin     = values[2];
                    rng->m_ymax     = values[3];
                    /* Falls through. */
                case 1:
                    rng->m_doXrange = true;
                    rng->m_xmin     = values[0];
                    rng->m_xmax     = values[1];
                    break;
                default:
                    NEKERROR(ErrorUtil::efatal,
                             "too many values specfied in range");
            }
        }
    }
 
    if (comprange.size())
    {
        if ((m_f->m_comm->GetSize() > 1) && (m_f->m_comm->GetRank() == 0))
        {
            NEKERROR(ErrorUtil::ewarning,
                     "Using the comprange option in parallel may  cause "
                     "problems with partitioning (particuarly with Scotch) "
                     "since the elements are not contiguous");
        }
 
        vector<unsigned> compvalues;
 
        ASSERTL0(ParseUtils::GenerateVector(comprange, compvalues),
                 "Failed to interpret comprange string");
 
        if (compvalues.size())
        {
            if (rng == LibUtilities::NullDomainRangeShPtr)
            {
                rng = MemoryManager<
                    LibUtilities::DomainRange>::AllocateSharedPtr();
            }
            // initialise with 3D and check when graph setup
            rng->m_compElmts = 3;
 
            for (auto it : compvalues)
            {
                rng->m_comps.insert(it);
            }
        }
    }
 
    // define range to only take a single shape.
    if (vm.count("onlyshape"))
    {
        if (rng == LibUtilities::NullDomainRangeShPtr)
        {
            rng = MemoryManager<LibUtilities::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(std::to_string(vm["part-only"].as<int>()));
    }
 
    if (vm.count("part-only-overlapping"))
    {
        cmdArgs.push_back("--part-only-overlapping");
        cmdArgs.push_back(
            std::to_string(vm["part-only-overlapping"].as<int>()));
    }
 
    if (vm.count("npz"))
    {
        cmdArgs.push_back("--npz");
        cmdArgs.push_back(std::to_string(vm["npz"].as<int>()));
    }
 
    // Parallel-in-time
    if (vm.count("npt"))
    {
        cmdArgs.push_back("--npt");
        cmdArgs.push_back(std::to_string(vm["npt"].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);
 
    if (vm.count("nparts"))
    {
        // make sure have pre-partitioned mesh for nparts option
        ASSERTL0(boost::icontains(files[0], "_xml"),
                 "Expect the mesh to have been pre-partitioned when "
                 " using the \"--nparts\" option. Please use \"--part-only\" "
                 "option to prepartition xml file.");
    }
 
    // 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::MeshGraphIO::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();
        }
    }
}

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, Nektar::LibUtilities::SessionReader::CreateInstance(), Nektar::ErrorUtil::efatal, Nektar::ErrorUtil::ewarning, Nektar::ParseUtils::GenerateVector(), Nektar::FieldUtils::Module::m_config, Nektar::FieldUtils::Module::m_f, NEKERROR, Nektar::LibUtilities::NullDomainRangeShPtr, Nektar::SpatialDomains::MeshGraphIO::Read(), Nektar::LibUtilities::ShapeTypeMap, Nektar::LibUtilities::SIZE_ShapeType, and Nektar::LibUtilities::Timer::Start().

Member Data Documentation

m_className

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 57 of file InputXml.h.