ProcessCombineAvg.cpp

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////////////////////////////////////////////////////////////////////////////////
//
//  File: ProcessCombineAvg.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: Combines two fld files containing average fields.
//
////////////////////////////////////////////////////////////////////////////////

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

#include "ProcessCombineAvg.h"

#include <LibUtilities/BasicUtils/SharedArray.hpp>
#include <LibUtilities/BasicUtils/ParseUtils.hpp>

namespace Nektar
{
namespace Utilities
{

ModuleKey ProcessCombineAvg::className =
    GetModuleFactory().RegisterCreatorFunction(
        ModuleKey(eProcessModule, "combineAvg"),
        ProcessCombineAvg::create, "combine two fields containing averages (and possibly Reynolds stresses). Must specify fromfld.");

ProcessCombineAvg::ProcessCombineAvg(FieldSharedPtr f) : ProcessModule(f)
{
    m_config["fromfld"] = ConfigOption(false, "NotSet",
                                "Fld file form which to add field");

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

}

ProcessCombineAvg::~ProcessCombineAvg()
{
}

void ProcessCombineAvg::Process(po::variables_map &vm)
{
    if (m_f->m_verbose)
    {
        if(m_f->m_comm->TreatAsRankZero())
        {
            cout << "ProcessCombineAvg: Combining new fld into input avg fld..."
                 << endl;
        }
    }

    ASSERTL0(m_f->m_exp.size()  != 0,"No input expansion defined");

    int nfields   = m_f->m_fielddef[0]->m_fields.size();
    int nq        = m_f->m_exp[0]->GetTotPoints();
    int expdim    = m_f->m_graph->GetMeshDimension();
    int spacedim  = expdim;
    if ((m_f->m_fielddef[0]->m_numHomogeneousDir) == 1 ||
        (m_f->m_fielddef[0]->m_numHomogeneousDir) == 2)
    {
        spacedim += m_f->m_fielddef[0]->m_numHomogeneousDir;
    }

    // Allocate storage for new field and correction (for Reynolds stress)
    Array<OneD, Array<OneD, NekDouble> >  fromPhys(nfields);
    Array<OneD, Array<OneD, NekDouble> >  correction(nfields);
    for (int j = 0; j < nfields; ++j)
    {
        fromPhys[j]   = Array<OneD, NekDouble> (nq, 0.0);
        correction[j] = Array<OneD, NekDouble> (nq, 0.0);
    }

    string         fromfld           = m_config["fromfld"].as<string>();
    FieldSharedPtr fromField         = boost::shared_ptr<Field>(new Field());
    LibUtilities::FieldMetaDataMap     fromFieldMetaDataMap;

    // Set up ElementGIDs in case of parallel processing
    Array<OneD,int> ElementGIDs(m_f->m_exp[0]->GetExpSize());
    for (int i = 0; i < m_f->m_exp[0]->GetExpSize(); ++i)
    {
        ElementGIDs[i] = m_f->m_exp[0]->GetExp(i)->GetGeom()->GetGlobalID();
    }
    // Import fromfld file
    m_f->m_fld->Import(fromfld,
                       fromField->m_fielddef,
                       fromField->m_data,
                       fromFieldMetaDataMap,
                       ElementGIDs);
    ASSERTL0(fromField->m_fielddef[0]->m_fields.size() == nfields,
             "Mismatch in number of fields");
    // Extract data to fromPhys
    for (int j = 0; j < nfields; ++j)
    {
        ASSERTL0(fromField->m_fielddef[0]->m_fields[j] == 
                 m_f->m_fielddef[0]->m_fields[j], "Field names do not match.");

        // load new field (overwrite m_f->m_exp coeffs for now)
        for (int i = 0; i < fromField->m_data.size(); ++i)
        {
            m_f->m_exp[j]->ExtractDataToCoeffs(
                                   fromField->m_fielddef[i],
                                   fromField->m_data[i],
                                   fromField->m_fielddef[i]->m_fields[j],
                                   m_f->m_exp[j]->UpdateCoeffs());
        }
        m_f->m_exp[j]->BwdTrans(m_f->m_exp[j]->GetCoeffs(), fromPhys[j]);
    }

    // Load number of samples in each file
    ASSERTL0(m_f->m_fieldMetaDataMap.count("NumberOfFieldDumps") != 0,
             "Missing NumberOfFieldDumps metadata.");
    ASSERTL0(fromFieldMetaDataMap.count("NumberOfFieldDumps") != 0,
             "Missing NumberOfFieldDumps metadata.");
    string s_num;
    s_num  = m_f->m_fieldMetaDataMap["NumberOfFieldDumps"];
    int na = atoi(s_num.c_str());
    s_num  = fromFieldMetaDataMap["NumberOfFieldDumps"];
    int nb = atoi(s_num.c_str());

    // Look for Reynolds stresses
    int stress = -1;
    for (int j = 0; j < nfields; ++j)
    {
        if (m_f->m_fielddef[0]->m_fields[j] == "uu")
        {
            stress = j;
            break;
        }
    }

    // Calculate correction for Reynolds stresses
    if (stress != -1)
    {
        Array<OneD, NekDouble> tmp  (nq, 0.0);
        int n = stress;
        // Follow same numbering as FilterReynoldsStresses
        for (int i = 0; i < spacedim; ++i)
        {
            for (int j = i; j < spacedim; ++j, ++n)
            {
                // correction is zero for averages and
                //      = (\bar{x_a}-\bar{x_b})*(\bar{y_a}-\bar{y_b})*na*nb/N
                //      for Reynolds stresses   
                NekDouble fac = ((NekDouble) (na*nb)) / ((NekDouble) (na+nb));
                Vmath::Vsub(nq, m_f->m_exp[i]->GetPhys(), 1,
                                fromPhys[i], 1, correction[n], 1);
                Vmath::Vsub(nq, m_f->m_exp[j]->GetPhys(), 1,
                                fromPhys[j], 1, tmp, 1);
                Vmath::Vmul(nq, correction[n], 1, tmp,  1, correction[n], 1);
                Vmath::Smul(nq, fac, correction[n], 1, correction[n], 1);
            }
        }
    }
    // Combine fields
    for (int j = 0; j < nfields; ++j)
    {
        // The new value is: (x_a*na + x_b*nb + correction)/N
        Vmath::Smul(nq, 1.0*na, m_f->m_exp[j]->GetPhys(), 1,
                            m_f->m_exp[j]->UpdatePhys(), 1);
        Vmath::Svtvp(nq, 1.0*nb, fromPhys[j], 1,
                            m_f->m_exp[j]->GetPhys(), 1,
                            m_f->m_exp[j]->UpdatePhys(), 1);
        Vmath::Vadd(nq, m_f->m_exp[j]->GetPhys(), 1,
                            correction[j], 1,
                            m_f->m_exp[j]->UpdatePhys(), 1);
        Vmath::Smul(nq, 1.0/(na+nb),
                            m_f->m_exp[j]->GetPhys(), 1,
                            m_f->m_exp[j]->UpdatePhys(), 1);

        m_f->m_exp[j]->FwdTrans_IterPerExp(m_f->m_exp[j]->GetPhys(),
                            m_f->m_exp[j]->UpdateCoeffs());
    }

    // Update metadata
    m_f->m_fieldMetaDataMap["NumberOfFieldDumps"] = 
            boost::lexical_cast<std::string>(na+nb);
    NekDouble t0      = -1;
    NekDouble finTime = -1;
    if(m_f->m_fieldMetaDataMap.count("InitialTime"))
    {
        string s_t  = m_f->m_fieldMetaDataMap["InitialTime"];
        NekDouble t = atof(s_t.c_str());

        t0          = t;
    }
    if(fromFieldMetaDataMap.count("InitialTime"))
    {
        string s_t  = fromFieldMetaDataMap["InitialTime"];
        NekDouble t = atof(s_t.c_str());

        if (t0 == -1)
        {
            t0      = t;
        }
        else
        {
            t0          = std::min(t0, t);
        }
    }
    if(m_f->m_fieldMetaDataMap.count("FinalTime"))
    {
        string s_t  = m_f->m_fieldMetaDataMap["FinalTime"];
        NekDouble t = atof(s_t.c_str());

        finTime     = std::max(t0, t);
    }
    if(fromFieldMetaDataMap.count("FinalTime"))
    {
        string s_t  = fromFieldMetaDataMap["FinalTime"];
        NekDouble t = atof(s_t.c_str());

        finTime     = std::max(t0, t);
    }
    if (t0 != -1)
    {
        m_f->m_fieldMetaDataMap["InitialTime"] = 
            boost::lexical_cast<std::string>(t0);
    }
    if (finTime != -1)
    {
        m_f->m_fieldMetaDataMap["FinalTime"] = 
            boost::lexical_cast<std::string>(finTime);
    }

    // Update field def and data
    std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef
        = m_f->m_exp[0]->GetFieldDefinitions();
    std::vector<std::vector<NekDouble> > FieldData(FieldDef.size());
    for(int i = 0; i < nfields; ++i)
    {
        for (int j = 0; j < FieldDef.size(); ++j)
        {
            FieldDef[j]->m_fields.push_back(m_f->m_fielddef[0]->m_fields[i]);
            m_f->m_exp[i]->AppendFieldData(FieldDef[j], FieldData[j]);
        }
    }

    m_f->m_fielddef = FieldDef;
    m_f->m_data     = FieldData;
}

}
}