ProcessInterpPoints.cpp

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////////////////////////////////////////////////////////////////////////////////
//
//  File: ProcessInterpPoints.cpp
//
//  For more information, please see: http://www.nektar.info/
//
//  The MIT License
//
//  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: Interpolate  field to a series of specified points.
//
////////////////////////////////////////////////////////////////////////////////
 
#include <iostream>
#include <string>
using namespace std;
 
#include <boost/core/ignore_unused.hpp>
#include <boost/geometry.hpp>
#include <boost/lexical_cast.hpp>
#include <boost/math/special_functions/fpclassify.hpp>
 
#include <FieldUtils/Interpolator.h>
#include <LibUtilities/BasicUtils/ParseUtils.h>
#include <LibUtilities/BasicUtils/Progressbar.hpp>
#include <LibUtilities/BasicUtils/SharedArray.hpp>
#include <LibUtilities/BasicUtils/PtsIO.h>
#include <LibUtilities/BasicUtils/CsvIO.h>
 
#include "ProcessInterpPoints.h"
 
namespace bg  = boost::geometry;
namespace bgi = boost::geometry::index;
 
namespace Nektar
{
namespace FieldUtils
{
 
ModuleKey ProcessInterpPoints::className =
    GetModuleFactory().RegisterCreatorFunction(
        ModuleKey(eProcessModule, "interppoints"),
        ProcessInterpPoints::create,
        "Interpolates a field to a set of points. Requires fromfld, fromxml "
        "to be defined, and a topts, line, plane or block of target points  ");
 
ProcessInterpPoints::ProcessInterpPoints(FieldSharedPtr f) : ProcessModule(f)
{
    m_config["fromxml"] = ConfigOption(
        false, "NotSet", "Xml file from which to interpolate field");
 
    m_config["fromfld"] = ConfigOption(
        false, "NotSet", "Fld file from which to interpolate field");
 
    m_config["topts"] = ConfigOption(
        false, "NotSet", "Pts file to which interpolate field");
    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 N2 points using "
                         "plane=N1,N2,x0,y0,z0,z1,y1,z1,x2,y2,z2,x3,y3,z3");
    m_config["box"] = ConfigOption(
        false, "NotSet", "Specify a rectangular box of N1 x N2 x N3 points "
                         "using a box of points limited by box="
                         "N1,N2,N3,xmin,xmax,ymin,ymax,zmin,zmax");
 
    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["cp"] =
        ConfigOption(false, "NotSet",
                     "Parameters p0 and q to determine pressure coefficients");
    m_config["realmodetoimag"] = ConfigOption(
        false, "NotSet", "Take fields as sin mode");
}
 
ProcessInterpPoints::~ProcessInterpPoints()
{
}
 
void ProcessInterpPoints::Process(po::variables_map &vm)
{
    m_f->SetUpExp(vm);
 
    CreateFieldPts(vm);
 
    FieldSharedPtr fromField = std::shared_ptr<Field>(new Field());
    std::vector<std::string> files;
    ParseUtils::GenerateVector(m_config["fromxml"].as<string>(), files);
 
    // set up session file for from field
    char *argv[] = { const_cast<char *>("FieldConvert"), nullptr };
    fromField->m_session =
        LibUtilities::SessionReader::CreateInstance(
            1, argv, files,
            LibUtilities::GetCommFactory().CreateInstance("Serial", 0, 0));
 
    // Set up range based on min and max of local parallel partition
    LibUtilities::DomainRangeShPtr rng =
        MemoryManager<LibUtilities::DomainRange>::AllocateSharedPtr();
    
    int coordim = m_f->m_fieldPts->GetDim();
    int npts    = m_f->m_fieldPts->GetNpoints();
    std::vector<std::string> fieldNames = m_f->m_fieldPts->GetFieldNames();
    for (auto &it : fieldNames)
    {
        m_f->m_fieldPts->RemoveField(it);
    }
 
    Array<OneD, Array<OneD, NekDouble> > pts;
    m_f->m_fieldPts->GetPts(pts);
 
    rng->m_checkShape = false;
    rng->m_zmin       = -1;
    rng->m_zmax       =  1;
    rng->m_ymin       = -1;
    rng->m_ymax       =  1;
    switch (coordim)
    {
        case 3:
            rng->m_doZrange = true;
            rng->m_zmin     = Vmath::Vmin(npts, pts[2], 1);
            rng->m_zmax     = Vmath::Vmax(npts, pts[2], 1);
            if (rng->m_zmax == rng->m_zmin)
            {
                rng->m_zmin -= 1;
                rng->m_zmax += 1;
            }
            /* Falls through. */
        case 2:
            rng->m_doYrange = true;
            rng->m_ymin     = Vmath::Vmin(npts, pts[1], 1);
            rng->m_ymax     = Vmath::Vmax(npts, pts[1], 1);
            /* Falls through. */
        case 1:
            rng->m_doXrange = true;
            rng->m_xmin     = Vmath::Vmin(npts, pts[0], 1);
            rng->m_xmax     = Vmath::Vmax(npts, pts[0], 1);
            break;
        default:
            NEKERROR(ErrorUtil::efatal, "Too many values specified in range");
    }
 
    // setup rng parameters.
    fromField->m_graph =
        SpatialDomains::MeshGraph::Read(fromField->m_session, rng);
 
    // Read in local from field partitions
    const SpatialDomains::ExpansionInfoMap &expansions =
        fromField->m_graph->GetExpansionInfo();
    Array<OneD, int> ElementGIDs(expansions.size());
 
    int i = 0;
    for (auto &expIt : expansions)
    {
        ElementGIDs[i++] = expIt.second->m_geomShPtr->GetGlobalID();
    }
    // check to see that we do have some element in the domain since
    // possibly all points could be outside of the domain
    ASSERTL0(i > 0, "No elements are set. Are the interpolated points "
                    "within the domain given by the xml files?");
    string fromfld = m_config["fromfld"].as<string>();
    m_f->FieldIOForFile(fromfld)->Import(
        fromfld, fromField->m_fielddef, fromField->m_data,
        LibUtilities::NullFieldMetaDataMap, ElementGIDs);
    int NumHomogeneousDir = fromField->m_fielddef[0]->m_numHomogeneousDir;
    for (i=0; i<fromField->m_fielddef.size(); ++i)
    {
        int d1 = fromField->m_fielddef[i]->m_basis.size();
        d1 -= 1;
        if (d1 >= 0 &&
            (fromField->m_fielddef[i]->m_basis[d1] ==
                LibUtilities::eFourierHalfModeRe ||
             fromField->m_fielddef[i]->m_basis[d1] ==
                LibUtilities::eFourierHalfModeIm) )
        {
            fromField->m_fielddef[i]->m_homogeneousZIDs[0] += 2;
            fromField->m_fielddef[i]->m_numModes[d1] = 4;
            fromField->m_fielddef[i]->m_basis[d1] = LibUtilities::eFourier;
        }
    }
 
    //----------------------------------------------
    // Set up Expansion information to use mode order from field
    fromField->m_graph->SetExpansionInfo(fromField->m_fielddef);
    int nfields = fromField->m_fielddef[0]->m_fields.size();
    fromField->m_exp.resize(nfields);
    fromField->m_exp[0] = fromField->SetUpFirstExpList(NumHomogeneousDir, true);
    m_f->m_exp.resize(nfields);
 
    // declare auxiliary fields.
    for (i = 1; i < nfields; ++i)
    {
        fromField->m_exp[i] = fromField->AppendExpList(NumHomogeneousDir);
    }
    // load field into expansion in fromfield.
    set<int> sinmode;
    if (m_config["realmodetoimag"].as<string>().compare("NotSet"))
    {
        vector<int> value;
        ASSERTL0(ParseUtils::GenerateVector(
            m_config["realmodetoimag"].as<string>(), value),
            "Failed to interpret realmodetoimag string");
        for (int j: value)
        {
            sinmode.insert(j);
        }
    }
    for (int j = 0; j < nfields; ++j)
    {
        for (i = 0; i < fromField->m_fielddef.size(); i++)
        {
            fromField->m_exp[j]->ExtractDataToCoeffs(
                fromField->m_fielddef[i], fromField->m_data[i],
                fromField->m_fielddef[0]->m_fields[j],
                fromField->m_exp[j]->UpdateCoeffs());
        }
        if (NumHomogeneousDir == 1)
        {
            fromField->m_exp[j]->SetWaveSpace(true);
            if (sinmode.count(j))
            {
                int Ncoeff = fromField->m_exp[j]->GetPlane(2)->GetNcoeffs();
                Vmath::Smul(Ncoeff, -1.,
                    fromField->m_exp[j]->GetPlane(2)->GetCoeffs()   , 1,
                    fromField->m_exp[j]->GetPlane(3)->UpdateCoeffs(), 1);
                Vmath::Zero(Ncoeff,
                    fromField->m_exp[j]->GetPlane(2)->UpdateCoeffs(), 1);
            }
        }
        fromField->m_exp[j]->BwdTrans(fromField->m_exp[j]->GetCoeffs(),
                                      fromField->m_exp[j]->UpdatePhys());
        Array<OneD, NekDouble> newPts(m_f->m_fieldPts->GetNpoints());
        m_f->m_fieldPts->AddField(newPts,
                                  fromField->m_fielddef[0]->m_fields[j]);
        m_f->m_variables.push_back(fromField->m_fielddef[0]->m_fields[j]);
    }
 
    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(fromField->m_exp, m_f->m_fieldPts, clamp_low,
                          clamp_up, def_value);
 
    if (!boost::iequals(m_config["cp"].as<string>(), "NotSet"))
    {
        calcCp0();
    }
}
 
void ProcessInterpPoints::CreateFieldPts(po::variables_map &vm)
{
    boost::ignore_unused(vm);
 
    int rank   = m_f->m_comm->GetRank();
    int nprocs = m_f->m_comm->GetSize();
    // Check for command line point specification
 
    if (m_config["topts"].as<string>().compare("NotSet") != 0)
    {
        string inFile = m_config["topts"].as<string>();
 
        if (boost::filesystem::path(inFile).extension() == ".pts")
        {
            LibUtilities::PtsIOSharedPtr ptsIO =
                MemoryManager<LibUtilities::PtsIO>::AllocateSharedPtr(
                    m_f->m_comm);
 
            ptsIO->Import(inFile, m_f->m_fieldPts);
        }
        else if (boost::filesystem::path(inFile).extension() == ".csv")
        {
            LibUtilities::CsvIOSharedPtr csvIO =
                MemoryManager<LibUtilities::CsvIO>::AllocateSharedPtr(
                    m_f->m_comm);
 
            csvIO->Import(inFile, m_f->m_fieldPts);
        }
        else
        {
            ASSERTL0(false, "unknown topts file type");
        }
 
    }
    else if (m_config["line"].as<string>().compare("NotSet") != 0)
    {
        vector<NekDouble> values;
        ASSERTL0(ParseUtils::GenerateVector(
                     m_config["line"].as<string>(), values),
                 "Failed to interpret line string");
 
        ASSERTL0(values.size() > 2,
                 "line string should contain 2*Dim+1 values "
                 "N,x0,y0,z0,x1,y1,z1");
 
        double tmp;
        ASSERTL0(std::modf(values[0], &tmp) == 0.0, "N is not an integer");
        ASSERTL0(values[0] > 1, "N is not a valid number");
 
        int dim  = (values.size() - 1) / 2;
        int npts = values[0];
 
        // Information for partitioning
        int ptsPerProc = npts / nprocs;
        int extraPts   = (rank < nprocs - 1) ? 0: npts % nprocs;
        int locPts     = ptsPerProc + extraPts;
        int start      = rank * ptsPerProc;
        int end        = start + locPts;
 
        Array<OneD, Array<OneD, NekDouble> > pts(dim);
        Array<OneD, NekDouble>               delta(dim);
        for (int i = 0; i < dim; ++i)
        {
            pts[i]   = Array<OneD, NekDouble>(locPts);
            delta[i] = (values[dim + i + 1] - values[ i + 1]) / (npts - 1);
        }
 
 
 
        for (int i = 0, cntLoc = 0; i < npts; ++i)
        {
            if (i >= start && i < end)
            {
                for (int n = 0; n < dim; ++n)
                {
                    pts[n][cntLoc] = values[n+1] + i * delta[n];
                }
                ++cntLoc;
            }
        }
 
        vector<size_t> ppe;
        ppe.push_back(npts);
        m_f->m_fieldPts =
            MemoryManager<LibUtilities::PtsField>::AllocateSharedPtr(dim,
                                                                     pts);
        m_f->m_fieldPts->SetPtsType(LibUtilities::ePtsLine);
        m_f->m_fieldPts->SetPointsPerEdge(ppe);
    }
    else if (m_config["plane"].as<string>().compare("NotSet") != 0)
    {
        vector<NekDouble> values;
        ASSERTL0(ParseUtils::GenerateVector(
                     m_config["plane"].as<string>(), values),
                 "Failed to interpret plane string");
 
        ASSERTL0(values.size() > 9,
                 "plane string should contain 4 Dim+2 values "
                 "N1,N2,x0,y0,z0,x1,y1,z1,x2,y2,z2,x3,y3,z3");
 
        double tmp;
        ASSERTL0(std::modf(values[0], &tmp) == 0.0, "N1 is not an integer");
        ASSERTL0(std::modf(values[1], &tmp) == 0.0, "N2 is not an integer");
 
        ASSERTL0(values[0] > 1, "N1 is not a valid number");
        ASSERTL0(values[1] > 1, "N2 is not a valid number");
 
        int dim = (values.size() - 2) / 4;
 
        Array<OneD, int> npts(2);
        npts[0] = values[0];
        npts[1] = values[1];
 
        int totpts  = npts[0] * npts[1];
 
        // Information for partitioning
        int ptsPerProc = totpts / nprocs;
        int extraPts   = (rank < nprocs - 1) ? 0: totpts % nprocs;
        int locPts     = ptsPerProc + extraPts;
        int start      = rank * ptsPerProc;
        int end        = start + locPts;
 
        Array<OneD, Array<OneD, NekDouble> > pts(dim);
        Array<OneD, NekDouble>               delta1(dim);
        Array<OneD, NekDouble>               delta2(dim);
        for (int i = 0; i < dim; ++i)
        {
            pts[i]    = Array<OneD, NekDouble>(locPts);
            delta1[i] = (values[2+1*dim + i] - values[2+0*dim + i])/(npts[0]-1);
            delta2[i] = (values[2+2*dim + i] - values[2+3*dim + i])/(npts[0]-1);
        }
 
        for (int j = 0, cnt = 0, cntLoc = 0; j < npts[1]; ++j)
        {
            for (int i = 0; i < npts[0]; ++i, ++cnt)
            {
                if (cnt >= start && cnt < end)
                {
                    for (int n = 0; n < dim; ++n)
                    {
                        pts[n][cntLoc] =
                            (values[2+n] + i * delta1[n]) *
                                (1.0 - j / ((NekDouble)(npts[1]-1))) +
                            (values[2 + 3*dim + n] + i * delta2[n]) *
                                (      j / ((NekDouble)(npts[1]-1)));
                    }
                    ++cntLoc;
                }
            }
        }
 
        vector<size_t> ppe;
        ppe.push_back(npts[0]);
        ppe.push_back(npts[1]);
        m_f->m_fieldPts =
            MemoryManager<LibUtilities::PtsField>::AllocateSharedPtr(dim,
                                                                     pts);
        m_f->m_fieldPts->SetPtsType(LibUtilities::ePtsPlane);
        m_f->m_fieldPts->SetPointsPerEdge(ppe);
    }
    else if (m_config["box"].as<string>().compare("NotSet") != 0)
    {
        vector<NekDouble> values;
        ASSERTL0(ParseUtils::GenerateVector(
                     m_config["box"].as<string>(), values),
                 "Failed to interpret box string");
 
        ASSERTL0(values.size() == 9,
                 "box string should contain 9 values "
                 "N1,N2,N3,xmin,xmax,ymin,ymax,zmin,zmax");
 
        int dim = 3;
        Array<OneD, int> npts(3);
        npts[0] = values[0];
        npts[1] = values[1];
        npts[2] = values[2];
 
        int totpts  = npts[0]*npts[1]*npts[2];
 
        Array<OneD, Array<OneD, NekDouble> > pts(dim);
        Array<OneD, NekDouble>               delta(dim);
 
        // Information for partitioning
        int ptsPerProc = totpts / nprocs;
        int extraPts   = (rank < nprocs - 1) ? 0: totpts % nprocs;
        int locPts     = ptsPerProc + extraPts;
        int start      = rank * ptsPerProc;
        int end        = start + locPts;
 
        for (int i = 0; i < dim; ++i)
        {
            pts[i]   = Array<OneD, NekDouble>(locPts);
            delta[i] = (values[4 + 2*i] - values[3 + 2*i]) / (npts[i] - 1);
        }
 
 
 
        for (int k = 0, cnt = 0, cntLoc = 0; k < npts[2]; ++k)
        {
            for (int j = 0; j < npts[1]; ++j)
            {
                for (int i = 0; i < npts[0]; ++i, ++cnt)
                {
                    if (cnt >= start && cnt < end)
                    {
                        pts[0][cntLoc] = values[3] + i * delta[0];
                        pts[1][cntLoc] = values[5] + j * delta[1];
                        pts[2][cntLoc] = values[7] + k * delta[2];
                        ++cntLoc;
                    }
                }
            }
        }
 
        vector<size_t> ppe;
        ppe.push_back(npts[0]);
        ppe.push_back(npts[1]);
        ppe.push_back(npts[2]);
        m_f->m_fieldPts =
            MemoryManager<LibUtilities::PtsField>::AllocateSharedPtr(dim,
                                                                     pts);
        m_f->m_fieldPts->SetPtsType(LibUtilities::ePtsBox);
        m_f->m_fieldPts->SetPointsPerEdge(ppe);
        vector<NekDouble> boxdim;
        boxdim.assign(&values[3], &values[3] + 6);
        m_f->m_fieldPts->SetBoxSize(boxdim);
    }
    else
    {
        ASSERTL0(false,
            "Missing target points for ProcessInterpPoints.");
    }
}
 
void ProcessInterpPoints::InterpolateFieldToPts(
    vector<MultiRegions::ExpListSharedPtr> &field0,
    LibUtilities::PtsFieldSharedPtr &pts,
    NekDouble clamp_low,
    NekDouble clamp_up,
    NekDouble def_value)
{
    boost::ignore_unused(def_value);
 
    ASSERTL0(pts->GetNFields() == field0.size(), "ptField has too few fields");
 
    int nfields = field0.size();
 
    Interpolator interp;
    if (m_f->m_comm->GetRank() == 0)
    {
        interp.SetProgressCallback(&ProcessInterpPoints::PrintProgressbar,
                                   this);
    }
    interp.Interpolate(field0, pts);
    if (m_f->m_comm->GetRank() == 0)
    {
        cout << endl;
    }
 
    for (int f = 0; f < nfields; ++f)
    {
        for (int i = 0; i < pts->GetNpoints(); ++i)
        {
            if (pts->GetPointVal(f, i) > clamp_up)
            {
                pts->SetPointVal(f, i, clamp_up);
            }
            else if (pts->GetPointVal(f, i) < clamp_low)
            {
                pts->SetPointVal(f, i, clamp_low);
            }
        }
    }
}
 
void ProcessInterpPoints::calcCp0()
{
    LibUtilities::PtsFieldSharedPtr pts = m_f->m_fieldPts;
    int dim = pts->GetDim();
    int nq1 = pts->GetNpoints();
    int r, f;
    int pfield = -1;
    NekDouble p0,qinv;
    vector<int> velid;
 
    vector<NekDouble> values;
    ASSERTL0(ParseUtils::GenerateVector(m_config["cp"].as<string>(), values),
             "Failed to interpret cp string");
 
    ASSERTL0(values.size() == 2,
                "cp string should contain 2 values "
                "p0 and q (=1/2 rho u^2)");
 
    p0  =  values[0];
    qinv = 1.0/values[1];
 
    for(int i = 0; i < pts->GetNFields(); ++i)
    {
        if(boost::iequals(pts->GetFieldName(i),"p"))
        {
            pfield = i;
        }
 
        if(boost::iequals(pts->GetFieldName(i),"u")||
            boost::iequals(pts->GetFieldName(i),"v")||
            boost::iequals(pts->GetFieldName(i),"w"))
        {
            velid.push_back(i);
        }
    }
 
    if(pfield != -1)
    {
        if(!velid.size())
        {
            WARNINGL0(false,"Did not find velocity components for Cp0");
        }
    }
    else
    {
        WARNINGL0(false,"Failed to find 'p' field to determine cp0");
    }
 
    // Allocate data storage
    Array<OneD, Array< OneD, NekDouble> > data(2);
 
    for (f = 0; f < 2; ++f)
    {
        data[f] = Array< OneD, NekDouble>(nq1, 0.0);
    }
 
    for (r = 0; r < nq1; r++)
    {
        if(pfield != -1) // calculate cp
        {
            data[0][r] = qinv*(pts->GetPointVal(dim + pfield, r) - p0);
 
            if(velid.size()) // calculate cp0
            {
                NekDouble q = 0;
                for(int i = 0; i < velid.size(); ++i)
                {
                    q += 0.5*pts->GetPointVal(dim + velid[i], r)*
                             pts->GetPointVal(dim + velid[i], r);
                }
                data[1][r] = qinv*(pts->GetPointVal(dim + pfield, r)+q - p0);
            }
        }
    }
 
    if(pfield != -1)
    {
        pts->AddField(data[0], "Cp");
        m_f->m_variables.push_back("Cp");
        if(velid.size())
        {
            pts->AddField(data[1], "Cp0");
            m_f->m_variables.push_back("Cp0");
        }
    }
}
 
void ProcessInterpPoints::PrintProgressbar(const int position,
                                           const int goal) const
{
    LibUtilities::PrintProgressbar(position, goal, "Interpolating");
}
}
}