Nektar::Utilities::ProcessInterpPoints Class Reference

This processing module interpolates one field to another. More...

#include <ProcessInterpPoints.h>

Inheritance diagram for Nektar::Utilities::ProcessInterpPoints:

Collaboration diagram for Nektar::Utilities::ProcessInterpPoints:

Public Member Functions
	ProcessInterpPoints (FieldSharedPtr f)
virtual	~ProcessInterpPoints ()
virtual void	Process (po::variables_map &vm)
	Write mesh to output file.
Public Member Functions inherited from Nektar::Utilities::ProcessModule
	ProcessModule ()
	ProcessModule (FieldSharedPtr p_f)
	ProcessModule (MeshSharedPtr p_m)
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.
void	PrintConfig ()
	Print out all configuration options for a module.
void	SetDefaults ()
	Sets default configuration options for those which have not been set.
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 (string key, string value)
void	PrintConfig ()
void	SetDefaults ()
MeshSharedPtr	GetMesh ()
virtual void	ProcessVertices ()
	Extract element vertices.

Static Public Member Functions
static boost::shared_ptr< Module >	create (FieldSharedPtr f)
	Creates an instance of this class.

Static Public Attributes
static ModuleKey	className

Private Member Functions
void	InterpolateFieldToPts (vector< MultiRegions::ExpListSharedPtr > &field0, Array< OneD, Array< OneD, NekDouble > > &pts, NekDouble clamp_low, NekDouble clamp_up, NekDouble def_value)

Private Attributes
FieldSharedPtr	m_fromField

Additional Inherited Members
Protected Member Functions inherited from Nektar::Utilities::Module
	Module ()
virtual void	ProcessEdges (bool ReprocessEdges=true)
	Extract element edges.
virtual void	ProcessFaces (bool ReprocessFaces=true)
	Extract element faces.
virtual void	ProcessElements ()
	Generate element IDs.
virtual void	ProcessComposites ()
	Generate composites.
void	ReorderPrisms (PerMap &perFaces)
	Reorder node IDs so that prisms and tetrahedra are aligned correctly.
void	PrismLines (int prism, PerMap &perFaces, set< int > &prismsDone, vector< ElementSharedPtr > &line)
Protected Attributes inherited from Nektar::Utilities::Module
FieldSharedPtr	m_f
	Field object.
map< string, ConfigOption >	m_config
	List of configuration values.
bool	m_requireEquiSpaced
MeshSharedPtr	m_mesh
	Mesh object.

Detailed Description

This processing module interpolates one field to another.

Definition at line 48 of file ProcessInterpPoints.h.

Constructor & Destructor Documentation

Nektar::Utilities::ProcessInterpPoints::ProcessInterpPoints

(

FieldSharedPtr

f

)

Definition at line 57 of file ProcessInterpPoints.cpp.

References ASSERTL0, and Nektar::Utilities::Module::m_config.

                                                         : ProcessModule(f)
{

    m_config["fromxml"] =
            ConfigOption(false, "NotSet",
                         "Xml file from which to interpolate field");

    ASSERTL0(m_config["fromxml"].as<string>().compare("NotSet") != 0,
             "Need to specify fromxml=file.xml");

    m_config["fromfld"] =
            ConfigOption(false,"NotSet",
                         "Fld file from which to interpolate field");

    ASSERTL0(m_config["fromfld"].as<string>().compare("NotSet") != 0,
             "Need to specify fromfld=file.fld ");

    m_config["clamptolowervalue"] =
            ConfigOption(false, "-10000000",
                         "Lower bound for interpolation value");
    m_config["clamptouppervalue"] =
            ConfigOption(false, "10000000",
                         "Upper bound for interpolation value");
    m_config["defaultvalue"] =
            ConfigOption(false, "0",
                         "Default value if point is outside domain");
    m_config["line"] =
            ConfigOption(false, "NotSet",
                         "Specify a line of N points using "
                         "line=N,x0,y0,z0,z1,y1,z1");

    m_config["plane"] =
            ConfigOption(false, "NotSet",
                         "Specify a plane of N1 x N1 points using "
                         "plane=N1,N2,x0,y0,z0,z1,y1,z1,x2,y2,z2,x3,"
                         "y3,z3");
}

Nektar::Utilities::ProcessInterpPoints::~ProcessInterpPoints ( )

virtual

Definition at line 95 of file ProcessInterpPoints.cpp.

{
}

Member Function Documentation

static boost::shared_ptr<Module> Nektar::Utilities::ProcessInterpPoints::create ( FieldSharedPtr  f )

inlinestatic

Creates an instance of this class.

Definition at line 52 of file ProcessInterpPoints.h.

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

void Nektar::Utilities::ProcessInterpPoints::InterpolateFieldToPts ( vector< MultiRegions::ExpListSharedPtr > &  field0, Array< OneD, Array< OneD, NekDouble > > &  pts, NekDouble  clamp_low, NekDouble  clamp_up, NekDouble  def_value  )

private

Definition at line 326 of file ProcessInterpPoints.cpp.

References ASSERTL0, and Nektar::Utilities::Module::m_f.

Referenced by Process().

{
    int expdim = field0[0]->GetCoordim(0);

    Array<OneD, NekDouble> coords(expdim), Lcoords(expdim);
    int nq1 = pts[0].num_elements();
    int elmtid, offset;
    int r, f;
    static int intpts = 0;

    // resize data field
    m_f->m_data.resize(field0.size());

    for (f = 0; f < field0.size(); ++f)
    {
        m_f->m_data[f].resize(nq1);
    }

    for (r = 0; r < nq1; r++)
    {
        coords[0] = pts[0][r];
        coords[1] = pts[1][r];
        if (expdim == 3)
        {
            coords[2] = pts[2][r];
        }

        // Obtain Element and LocalCoordinate to interpolate
        elmtid = field0[0]->GetExpIndex(coords, Lcoords, 1e-3);

        if(elmtid >= 0)
        {
            offset = field0[0]->GetPhys_Offset(field0[0]->
                                               GetOffset_Elmt_Id(elmtid));

            for (f = 0; f < field0.size(); ++f)
            {
                NekDouble value;
                value = field0[f]->GetExp(elmtid)->
                    StdPhysEvaluate(Lcoords, field0[f]->GetPhys() +offset);

                if ((boost::math::isnan)(value))
                {
                    ASSERTL0(false, "new value is not a number");
                }
                else
                {
                    value = (value > clamp_up)? clamp_up :
                        ((value < clamp_low)? clamp_low :
                         value);

                    m_f->m_data[f][r] = value;
                }
            }
        }
        else
        {
            for (f = 0; f < field0.size(); ++f)
            {
                m_f->m_data[f][r] = def_value;
            }
        }

        if (intpts%1000 == 0)
        {
            cout <<"." << flush;
        }
        intpts ++;
    }
}

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

virtual

Write mesh to output file.

Implements Nektar::Utilities::Module.

Definition at line 99 of file ProcessInterpPoints.cpp.

References ASSERTL0, Nektar::LibUtilities::SessionReader::CreateInstance(), Nektar::Utilities::ePtsLine, Nektar::Utilities::ePtsPlane, Nektar::ParseUtils::GenerateUnOrderedVector(), InterpolateFieldToPts(), Nektar::Utilities::Module::m_config, Nektar::Utilities::Module::m_f, m_fromField, npts, Nektar::LibUtilities::NullFieldMetaDataMap, Nektar::Utilities::NullFieldPts, Nektar::SpatialDomains::MeshGraph::Read(), Vmath::Vmax(), and Vmath::Vmin().

{

    if(m_f->m_verbose)
    {
        cout << "Processing point interpolation" << endl;
    }


    // Check for command line point specification if no .pts file specified
    if(m_f->m_fieldPts == NullFieldPts)
    {
        int dim = 0;
        if(m_config["line"].as<string>().compare("NotSet") != 0)
        {
            string help = m_config["line"].as<string>();
            vector<NekDouble> values;
            ASSERTL0(ParseUtils::GenerateUnOrderedVector(
                        m_config["line"].as<string>().c_str(),values),
                     "Failed to interpret line string");

            ASSERTL0(values.size() > 3,
                     "line string should contain 2Dim+1 values "
                     "N,x0,y0,z0,x1,y1,z1");

            m_f->m_fieldPts = MemoryManager<FieldPts>::AllocateSharedPtr();

            dim = m_f->m_fieldPts->m_ptsDim = (values.size()-1)/2;

            int npts = values[0];
            m_f->m_fieldPts->m_npts.push_back(values[0]);
            m_f->m_fieldPts->m_ptype = Utilities::ePtsLine;

            m_f->m_fieldPts->m_pts = Array<OneD, Array<OneD, NekDouble> > (m_f->m_fieldPts->m_ptsDim);

            for(int i = 0; i < dim; ++i)
            {
                m_f->m_fieldPts->m_pts[i] = Array<OneD,NekDouble>(npts);
            }

            for(int i = 0; i < npts; ++i)
            {
                m_f->m_fieldPts->m_pts[0][i] = values[1]
                        + i/((NekDouble)(npts-1))*(values[dim+1] - values[1]);
                if(dim > 1)
                {
                    m_f->m_fieldPts->m_pts[1][i] = values[2]
                        + i/((NekDouble)(npts-1))*(values[dim+2] - values[2]);

                    if(dim > 2)
                    {
                        m_f->m_fieldPts->m_pts[2][i] = values[3]
                        + i/((NekDouble)(npts-1))*(values[dim+3] - values[3]);
                    }
                }
            }
        }
        else if(m_config["plane"].as<string>().compare("NotSet") != 0)
        {
            string help = m_config["plane"].as<string>();
            vector<NekDouble> values;
            ASSERTL0(ParseUtils::GenerateUnOrderedVector(
                             m_config["plane"].as<string>().c_str(),values),
                     "Failed to interpret plane string");

            ASSERTL0(values.size() > 3,
                     "line string should contain 2Dim+1 values "
                     "N,x0,y0,z0,x1,y1,z1");

            m_f->m_fieldPts = MemoryManager<FieldPts>::AllocateSharedPtr();

            dim = m_f->m_fieldPts->m_ptsDim = (values.size()-1)/4;

            int npts1 = values[0];
            int npts2 = values[1];
            m_f->m_fieldPts->m_npts.push_back(npts1);
            m_f->m_fieldPts->m_npts.push_back(npts2);
            m_f->m_fieldPts->m_ptype = Utilities::ePtsPlane;

            m_f->m_fieldPts->m_pts = Array<OneD, Array<OneD, NekDouble> > (m_f->m_fieldPts->m_ptsDim);

            for(int i = 0; i < dim; ++i)
            {
                m_f->m_fieldPts->m_pts[i] = Array<OneD,NekDouble>(npts1*npts2);
            }

            for(int j = 0; j < npts2; ++j)
            {
                for(int i = 0; i < npts1; ++i)
                {
                    m_f->m_fieldPts->m_pts[0][i+j*npts1] =
                        (values[2] + i/((NekDouble)(npts1-1))*(values[dim+2] - values[2]))*(1.0-j/((NekDouble)(npts2-1))) +
                        (values[3*dim+2] + i/((NekDouble)(npts1-1))*(values[2*dim+2] - values[3*dim+2]))*(j/((NekDouble)(npts2-1)));
                    if(dim > 1)
                    {
                        m_f->m_fieldPts->m_pts[1][i+j*npts1] =
                            (values[3] + i/((NekDouble)(npts1-1))*(values[dim+3] - values[3]))*(1.0-j/((NekDouble)(npts2-1))) +
                            (values[3*dim+3] + i/((NekDouble)(npts1-1))*(values[2*dim+3] - values[3*dim+3]))*(j/((NekDouble)(npts2-1)));

                        if(dim > 2)
                        {
                            m_f->m_fieldPts->m_pts[2][i+j*npts1] =
                                (values[4] + i/((NekDouble)(npts1-1))*(values[dim+4] - values[4]))*(1.0-j/((NekDouble)(npts2-1))) +
                                (values[3*dim+4] + i/((NekDouble)(npts1-1))*(values[2*dim+4] - values[3*dim+4]))*(j/((NekDouble)(npts2-1)));
                        }
                    }
                }
            }
        }
    }


    m_fromField =  boost::shared_ptr<Field>(new Field());

    std::vector<std::string> files;
    // set up session file for from field
    files.push_back(m_config["fromxml"].as<string>());
    m_fromField->m_session = LibUtilities::SessionReader::
        CreateInstance(0, 0, files);

    // Set up range based on min and max of local parallel partition
    SpatialDomains::DomainRangeShPtr rng = MemoryManager<SpatialDomains::DomainRange>::AllocateSharedPtr();

    int coordim = m_f->m_fieldPts->m_ptsDim;
    int npts    = m_f->m_fieldPts->m_pts[0].num_elements();
    Array<OneD, Array<OneD, NekDouble> > coords = m_f->m_fieldPts->m_pts;

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

    // setup rng parameters.
    m_fromField->m_graph = SpatialDomains::MeshGraph::Read(m_fromField->m_session,rng);

    // Read in local from field partitions
    const SpatialDomains::ExpansionMap &expansions = m_fromField->m_graph->GetExpansions();

    m_fromField->m_fld = MemoryManager<LibUtilities::FieldIO>
        ::AllocateSharedPtr(m_fromField->m_session->GetComm());

    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();
    }

    string fromfld = m_config["fromfld"].as<string>();
    m_fromField->m_fld->Import(fromfld,m_fromField->m_fielddef,
                  m_fromField->m_data,
                  LibUtilities::NullFieldMetaDataMap,
                               ElementGIDs);

    int NumHomogeneousDir = m_fromField->m_fielddef[0]->m_numHomogeneousDir;

    //----------------------------------------------
    // Set up Expansion information to use mode order from field
    m_fromField->m_graph->SetExpansions(m_fromField->m_fielddef);

    int nfields = m_fromField->m_fielddef[0]->m_fields.size();

    m_fromField->m_exp.resize(nfields);
    m_fromField->m_exp[0] = m_fromField->SetUpFirstExpList(NumHomogeneousDir,true);

    m_f->m_exp.resize(nfields);

    // declare auxiliary fields.
    for(i = 1; i < nfields; ++i)
    {
        m_fromField->m_exp[i] = m_fromField->AppendExpList(NumHomogeneousDir);
    }

    // load field into expansion in fromfield.
    for(int j = 0; j < nfields; ++j)
    {
        for (i = 0; i < m_fromField->m_fielddef.size(); i++)
        {
            m_fromField->m_exp[j]->ExtractDataToCoeffs(
                                        m_fromField->m_fielddef[i],
                                        m_fromField->m_data[i],
                                        m_fromField->m_fielddef[0]->m_fields[j],
                                        m_fromField->m_exp[j]->UpdateCoeffs());
        }
        m_fromField->m_exp[j]->BwdTrans(m_fromField->m_exp[j]->GetCoeffs(),
                                        m_fromField->m_exp[j]->UpdatePhys());
        m_f->m_fieldPts->m_fields.push_back(m_fromField->m_fielddef[0]->m_fields[j]);

    }

    if(m_fromField->m_session->GetComm()->GetRank() == 0)
    {
        cout << "Interpolating [" << flush;
    }

    NekDouble clamp_low = m_config["clamptolowervalue"].as<NekDouble>();
    NekDouble clamp_up  = m_config["clamptouppervalue"].as<NekDouble>();
    NekDouble def_value = m_config["defaultvalue"].as<NekDouble>();

    InterpolateFieldToPts(m_fromField->m_exp, m_f->m_fieldPts->m_pts,
                          clamp_low, clamp_up, def_value);

    if(m_fromField->m_session->GetComm()->GetRank() == 0)
    {
        cout << "]" << endl;
    }

}

Member Data Documentation

ModuleKey Nektar::Utilities::ProcessInterpPoints::className

static

Initial value:

    GetModuleFactory().RegisterCreatorFunction(
       ModuleKey(eProcessModule, "interppoints"),
       ProcessInterpPoints::create,
       "Interpolates a set of points to another, requires fromfld and "
       "fromxml to be defined, a line or plane of points can be "
       "defined")

Definition at line 55 of file ProcessInterpPoints.h.

FieldSharedPtr Nektar::Utilities::ProcessInterpPoints::m_fromField

private

Definition at line 64 of file ProcessInterpPoints.h.

Referenced by Process().