OutputFld.cpp

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////////////////////////////////////////////////////////////////////////////////
//
//  File: OutputFld.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).
//
//  License for the specific language governing rights and limitations under
//  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: FLD file format output.
//
////////////////////////////////////////////////////////////////////////////////

#include <set>
#include <string>
using namespace std;

#include "OutputFld.h"
#include <LibUtilities/BasicUtils/FileSystem.h>

namespace Nektar
{
namespace Utilities
{

ModuleKey OutputFld::m_className[2] = {
    GetModuleFactory().RegisterCreatorFunction(
        ModuleKey(eOutputModule, "fld"), OutputFld::create,
        "Writes a Fld file."),
    GetModuleFactory().RegisterCreatorFunction(
        ModuleKey(eOutputModule, "chk"), OutputFld::create,
        "Writes a Fld file."),
};

OutputFld::OutputFld(FieldSharedPtr f) : OutputModule(f)
{
}

OutputFld::~OutputFld()
{
}

void OutputFld::Process(po::variables_map &vm)
{
    // Extract the output filename and extension
    string filename = m_config["outfile"].as<string>();

    if (m_f->m_writeBndFld)
    {
        ModuleKey      module;

        // Extract data to boundaryconditions
        if (m_f->m_fldToBnd)        {
            for (int i = 0; i < m_f->m_exp.size(); ++i)
            {
                m_f->m_exp[i]->FillBndCondFromField();
            }
        }

        if (m_f->m_verbose)
        {
            cout << "OutputFld: Writing boundary file(s): ";
            for(int i = 0; i < m_f->m_bndRegionsToWrite.size(); ++i)
            {
                if(i < m_f->m_bndRegionsToWrite.size()-1)
                {
                    cout << ",";
                }
            }
            cout << endl;
        }

        int nfields = m_f->m_exp.size();
        Array<OneD, Array<OneD, const MultiRegions::ExpListSharedPtr> >
            BndExp(nfields);
        for (int i = 0; i < nfields; ++i)
        {
            BndExp[i] = m_f->m_exp[i]->GetBndCondExpansions();
        }

        // get hold of partition boundary regions so we can match it to desired
        // region extraction
        SpatialDomains::BoundaryConditions bcs(m_f->m_session,
                                               m_f->m_exp[0]->GetGraph());
        const SpatialDomains::BoundaryRegionCollection bregions  =
                                                    bcs.GetBoundaryRegions();
        SpatialDomains::BoundaryRegionCollection::const_iterator breg_it;
        map<int,int> BndRegionMap;
        int cnt =0;
        for(breg_it = bregions.begin(); breg_it != bregions.end();
                ++breg_it, ++cnt)
        {
            BndRegionMap[breg_it->first] = cnt;
        }

        // find ending of output file and insert _b1, _b2
        int    dot  = filename.find_last_of('.') + 1;
        string ext  = filename.substr(dot, filename.length() - dot);
        string name = filename.substr(0, dot-1);

        LibUtilities::BndRegionOrdering BndOrder =
                                    m_f->m_session->GetBndRegionOrdering();

        for(int i = 0; i < m_f->m_bndRegionsToWrite.size(); ++i)
        {
            string outname = name  + "_b"
                    + boost::lexical_cast<string>(m_f->m_bndRegionsToWrite[i])
                    + "." + ext;

            std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
            std::vector<std::vector<NekDouble> > FieldData;

            if(BndRegionMap.count(m_f->m_bndRegionsToWrite[i]) == 1)
            {
                int Border = BndRegionMap[m_f->m_bndRegionsToWrite[i]];

                FieldDef = BndExp[0][Border]->GetFieldDefinitions();
                FieldData.resize(FieldDef.size());

                for (int j = 0; j < nfields; ++j)
                {
                    for (int k = 0; k < FieldDef.size(); ++k)
                    {
                        BndExp[j][Border]->AppendFieldData(FieldDef[k],
                                                           FieldData[k]);

                        if (m_f->m_fielddef.size() > 0)
                        {
                            FieldDef[k]->m_fields.push_back(
                                m_f->m_fielddef[0]->m_fields[j]);
                        }
                        else
                        {
                            FieldDef[k]->m_fields.push_back(
                                m_f->m_session->GetVariable(j));
                        }
                    }
                }

                if(m_f->m_addNormals)
                {
                    ASSERTL0(m_f->m_exp[0]->GetCoordim(0) == 3,
                             "Add normals to extracted boundaries only set up in 3 dimensions");
                    int normdim = 3; // currently assuming 3D normals;
                    string normstr[3] = {"Norm_x","Norm_y","Norm_z"};

                    // Add normal information
                    StdRegions::StdExpansionSharedPtr elmt;
                    StdRegions::StdExpansion2DSharedPtr bc;
                    Array<OneD, int> BoundarytoElmtID, BoundarytoTraceID;

                    m_f->m_exp[0]->GetBoundaryToElmtMap(BoundarytoElmtID,
                                                        BoundarytoTraceID);

                    // determine offset of this Bnd Expansion Border
                    int cnt = 0;
                    for(int n = 0; n < Border; ++n)
                    {
                        cnt += BndExp[0][n]->GetExpSize();
                    }

                    Array<OneD, NekDouble> tmp_array;
                    Array<OneD, Array<OneD, NekDouble> > NormCoeff(normdim);

                    for(int j = 0; j < normdim; ++j)
                    {
                        NormCoeff[j] = Array<OneD, NekDouble>(BndExp[0][Border]->GetNcoeffs(),0.0);
                    }

                    // setup coeff arrays of normals.
                    for(int j = 0; j < BndExp[0][Border]->GetExpSize();
                        ++j, cnt++)
                    {
                        // find element and face of this expansion.
                        int elmtid = BoundarytoElmtID[cnt];
                        elmt = m_f->m_exp[0]->GetExp(elmtid);

                        // Get face 2D expansion from element expansion
                        bc  =  boost::dynamic_pointer_cast<StdRegions::StdExpansion2D> (BndExp[0][Border]->GetExp(j));

                        //identify boundary of element looking at.
                        int boundary = BoundarytoTraceID[cnt];

                        //Get face normals
                        const Array<OneD, const Array<OneD, NekDouble> > normals = elmt->GetFaceNormal(boundary);

                        for(int k = 0; k < normdim; ++k)
                        {
                            bc->FwdTrans(normals[k],tmp_array = NormCoeff[k]+BndExp[0][Border]->GetCoeff_Offset(j));
                        }
                    }

                    // add normal coefficients to list to be dumped
                    for (int j = 0; j < normdim; ++j)
                    {
                        Vmath::Vcopy(BndExp[0][Border]->GetNcoeffs(),
                                     NormCoeff[j],1,
                                     BndExp[0][Border]->UpdateCoeffs(),1);

                        for (int k = 0; k < FieldDef.size(); ++k)
                        {
                            BndExp[0][Border]->AppendFieldData(FieldDef[k],
                                                               FieldData[k]);
                            FieldDef[k]->m_fields.push_back(normstr[j]);
                        }
                    }
                }

                // output error for regression checking.
                if (vm.count("error"))
                {
                    int rank = m_f->m_session->GetComm()->GetRank();

                    for (int j = 0; j < nfields; ++j)
                    {
                        BndExp[j][Border]->BwdTrans(BndExp[j][Border]->GetCoeffs(),
                                                BndExp[j][Border]->UpdatePhys());

                        //Note currently these calls will
                        //hange since not all partitions will
                        //call error.
                        NekDouble l2err   = BndExp[j][Border]
                                           ->L2(BndExp[j][Border]->GetPhys());

                        NekDouble linferr = BndExp[j][Border]
                                           ->Linf(BndExp[j][Border]->GetPhys());

                        if (rank == 0)
                        {
                            cout << "L 2 error (variable "
                                 << FieldDef[0]->m_fields[j]
                                 << ") : " << l2err  << endl;

                            cout << "L inf error (variable "
                                 << FieldDef[0]->m_fields[j]
                                 << ") : " << linferr << endl;
                        }
                    }
                }
            }

            m_f->m_fld->Write(outname, FieldDef, FieldData,
                                                 m_f->m_fieldMetaDataMap);

        }
    }
    else
    {
        if (m_f->m_verbose)
        {
            cout << "OutputFld: Writing file..." << endl;
        }

        fs::path writefile(filename);
        int writefld = 1;
        if(fs::exists(writefile)&&(vm.count("forceoutput") == 0))
        {
            LibUtilities::CommSharedPtr comm = m_f->m_session->GetComm();
            int rank = comm->GetRank();
            writefld = 0; // set to zero for reduce all to be correct. 

            if(rank == 0)
            {
                string answer;
                cout << "Did you wish to overwrite " << filename << " (y/n)? ";
                getline(cin,answer);
                if(answer.compare("y") == 0)
                {
                    writefld = 1;
                }
                else
                {
                    cout << "Not writing file " << filename << " because it already exists" << endl;
                }
            }
            
            comm->AllReduce(writefld,LibUtilities::ReduceSum);
            
        }

        if(writefld)
        {
            m_f->m_fld->Write(filename, m_f->m_fielddef, m_f->m_data);
        }

        // output error for regression checking.
        if (vm.count("error"))
        {
            int rank = m_f->m_session->GetComm()->GetRank();

            for (int j = 0; j < m_f->m_exp.size(); ++j)
            {
                if (m_f->m_exp[j]->GetPhysState() == false)
                {
                    m_f->m_exp[j]->BwdTrans(
                                        m_f->m_exp[j]->GetCoeffs(),
                                        m_f->m_exp[j]->UpdatePhys());
                }

                NekDouble l2err = m_f->m_exp[j]->L2(
                                        m_f->m_exp[j]->GetPhys());

                NekDouble linferr = m_f->m_exp[j]->Linf(
                                        m_f->m_exp[j]->GetPhys());
                if (rank == 0)
                {
                    cout << "L 2 error (variable "
                         << m_f->m_fielddef[0]->m_fields[j]
                         << ") : " << l2err  << endl;

                    cout << "L inf error (variable "
                         << m_f->m_fielddef[0]->m_fields[j]
                         << ") : " << linferr << endl;
                }
            }
        }
    }
}

}
}