///////////////////////////////////////////////////////////////////////////////
//
// File: ForcingAbsorption.cpp
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
// Copyright (c) 2016 Kilian Lackhove
// 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: Absorption layer forcing
//
///////////////////////////////////////////////////////////////////////////////

#include <SolverUtils/Forcing/ForcingAbsorption.h>

#include <LibUtilities/BasicUtils/ParseUtils.h>

namespace Nektar::SolverUtils
{

std::string ForcingAbsorption::className =
    GetForcingFactory().RegisterCreatorFunction(
        "Absorption", ForcingAbsorption::create, "Forcing Absorption");

ForcingAbsorption::ForcingAbsorption(
    const LibUtilities::SessionReaderSharedPtr &pSession,
    const std::weak_ptr<EquationSystem> &pEquation)
    : Forcing(pSession, pEquation), m_hasRefFlow(false), m_hasRefFlowTime(false)
{
}

void ForcingAbsorption::v_InitObject(
    const Array<OneD, MultiRegions::ExpListSharedPtr> &pFields,
    const unsigned int &pNumForcingFields, const TiXmlElement *pForce)
{
    m_NumVariable = pNumForcingFields;
    int npts      = pFields[0]->GetTotPoints();

    // Check for homogeneous expansion
    // for later transformation of evaluated Absorption (SessionFunction)
    m_homogeneous = pFields[0]->GetExpType() == MultiRegions::e3DH1D ||
                    pFields[0]->GetExpType() == MultiRegions::e3DH2D;

    CalcAbsorption(pFields, pForce);

    m_Forcing = Array<OneD, Array<OneD, NekDouble>>(m_NumVariable);
    for (int i = 0; i < m_NumVariable; ++i)
    {
        m_Forcing[i] = Array<OneD, NekDouble>(npts, 0.0);
    }

    const TiXmlElement *funcNameElmt = pForce->FirstChildElement("REFFLOW");
    if (funcNameElmt)
    {
        std::string funcName = funcNameElmt->GetText();
        ASSERTL0(m_session->DefinesFunction(funcName),
                 "Function '" + funcName + "' not defined.");
        m_Refflow = Array<OneD, Array<OneD, NekDouble>>(m_NumVariable);
        for (int i = 0; i < m_NumVariable; ++i)
        {
            std::string s_FieldStr = m_session->GetVariable(i);
            ASSERTL0(m_session->DefinesFunction(funcName, s_FieldStr),
                     "Variable '" + s_FieldStr + "' not defined.");
            m_Refflow[i] = Array<OneD, NekDouble>(npts, 0.0);
            GetFunction(pFields, m_session, funcName)
                ->Evaluate(s_FieldStr, m_Refflow[i]);
        }
        m_hasRefFlow = true;
    }

    funcNameElmt = pForce->FirstChildElement("REFFLOWTIME");
    if (funcNameElmt)
    {
        m_funcNameTime   = funcNameElmt->GetText();
        m_hasRefFlowTime = true;
        m_hasRefFlow     = true;
        m_Refflow        = Array<OneD, Array<OneD, NekDouble>>(m_NumVariable);
        for (int i = 0; i < m_NumVariable; ++i)
        {
            std::string s_FieldStr = m_session->GetVariable(i);
            ASSERTL0(m_session->DefinesFunction(m_funcNameTime, s_FieldStr),
                     "Variable '" + s_FieldStr + "' not defined.");
            m_Refflow[i] = Array<OneD, NekDouble>(npts, 0.0);
        }
    }
}

void ForcingAbsorption::CalcAbsorption(
    const Nektar::Array<Nektar::OneD, Nektar::MultiRegions::ExpListSharedPtr>
        &pFields,
    const TiXmlElement *pForce)
{
    const TiXmlElement *funcNameElmt = pForce->FirstChildElement("COEFF");
    ASSERTL0(funcNameElmt,
             "Requires COEFF tag, specifying function "
             "name which prescribes absorption layer coefficient.");
    std::string funcName = funcNameElmt->GetText();
    ASSERTL0(m_session->DefinesFunction(funcName),
             "Function '" + funcName + "' not defined.");

    int npts = pFields[0]->GetTotPoints();

    m_Absorption = Array<OneD, Array<OneD, NekDouble>>(m_NumVariable);
    for (int i = 0; i < m_NumVariable; ++i)
    {
        m_Absorption[i] = Array<OneD, NekDouble>(npts, 0.0);
    }

    funcNameElmt = pForce->FirstChildElement("BOUNDARYREGIONS");
    if (funcNameElmt)
    {
        ASSERTL0(
            ParseUtils::GenerateVector(funcNameElmt->GetText(), m_bRegions),
            "Unable to process list of BOUNDARYREGIONS in Absorption "
            "Forcing: " +
                std::string(funcNameElmt->GetText()));

        // alter m_bRegions so that it contains the boundaryRegions of this rank
        std::vector<unsigned int> localBRegions;
        SpatialDomains::BoundaryConditions bcs(m_session,
                                               pFields[0]->GetGraph());
        SpatialDomains::BoundaryRegionCollection regions =
            bcs.GetBoundaryRegions();
        SpatialDomains::BoundaryRegionCollection::iterator it1;
        int n = 0;
        for (it1 = regions.begin(); it1 != regions.end(); ++it1)
        {
            if (std::find(m_bRegions.begin(), m_bRegions.end(), it1->first) !=
                m_bRegions.end())
            {
                localBRegions.push_back(n);
            }
            n++;
        }
        m_bRegions = localBRegions;

        if (m_bRegions.size() == 0)
        {
            return;
        }

        std::vector<Array<OneD, const NekDouble>> points;

        Array<OneD, Array<OneD, NekDouble>> x(3);
        for (int i = 0; i < 3; i++)
        {
            x[i] = Array<OneD, NekDouble>(npts, 0.0);
        }
        pFields[0]->GetCoords(x[0], x[1], x[2]);
        for (int i = 0; i < 3; i++)
        {
            points.push_back(x[i]);
        }

        Array<OneD, NekDouble> t(npts, 0.0);
        points.push_back(t);

        Array<OneD, NekDouble> r(npts, 0.0);
        std::vector<unsigned int>::iterator it;
        std::vector<BPointPair> inPoints;
        Array<OneD, Array<OneD, NekDouble>> b(3);
        for (it = m_bRegions.begin(); it != m_bRegions.end(); ++it)
        {
            int bpts = pFields[0]->GetBndCondExpansions()[*it]->GetNpoints();
            for (int i = 0; i < 3; i++)
            {
                b[i] = Array<OneD, NekDouble>(bpts, 0.0);
            }
            pFields[0]->GetBndCondExpansions()[*it]->GetCoords(b[0], b[1],
                                                               b[2]);
            for (int i = 0;
                 i < pFields[0]->GetBndCondExpansions()[*it]->GetNpoints(); ++i)
            {
                inPoints.push_back(
                    BPointPair(BPoint(b[0][i], b[1][i], b[2][i]), i));
            }
        }
        m_rtree = MemoryManager<BRTree>::AllocateSharedPtr();
        m_rtree->insert(inPoints.begin(), inPoints.end());

        for (int i = 0; i < npts; ++i)
        {
            std::vector<BPointPair> result;
            BPoint sPoint(x[0][i], x[1][i], x[2][i]);
            m_rtree->query(bgi::nearest(sPoint, 1), std::back_inserter(result));
            r[i] = bg::distance(sPoint, result[0].first);
        }
        points.push_back(r);

        std::string s_FieldStr;
        for (int i = 0; i < m_NumVariable; ++i)
        {
            s_FieldStr = m_session->GetVariable(i);
            ASSERTL0(m_session->DefinesFunction(funcName, s_FieldStr),
                     "Variable '" + s_FieldStr + "' not defined.");

            LibUtilities::EquationSharedPtr ffunc =
                m_session->GetFunction(funcName, s_FieldStr);
            ASSERTL0(ffunc->GetVlist() == "x y z t r",
                     "EVARS of " + funcName + " must be 'r'");

            ffunc->Evaluate(points, m_Absorption[i]);
        }
    }
    else
    {
        for (int i = 0; i < m_NumVariable; ++i)
        {
            std::string s_FieldStr = m_session->GetVariable(i);
            GetFunction(pFields, m_session, funcName)
                ->Evaluate(s_FieldStr, m_Absorption[i]);
        }
    }

    // If homogeneous expansion is used, transform the forcing term to
    // be in the Fourier space
    if (m_homogeneous)
    {
        for (int i = 0; i < m_NumVariable; ++i)
        {
            pFields[i]->HomogeneousFwdTrans(pFields[i]->GetTotPoints(),
                                            m_Absorption[i], m_Absorption[i]);
        }
    }
}

void ForcingAbsorption::v_Apply(
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &outarray, const NekDouble &time)
{
    int nq = m_Forcing[0].size();
    CalculateForcing(fields, inarray, time);
    for (int i = 0; i < m_NumVariable; ++i)
    {
        Vmath::Vadd(nq, m_Forcing[i], 1, outarray[i], 1, outarray[i], 1);
    }
}

void ForcingAbsorption::v_ApplyCoeff(
    const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &outarray, const NekDouble &time)
{
    int ncoeff = outarray[m_NumVariable - 1].size();
    Array<OneD, NekDouble> tmp(ncoeff, 0.0);
    CalculateForcing(fields, inarray, time);

    for (int i = 0; i < m_NumVariable; ++i)
    {
        fields[i]->FwdTrans(m_Forcing[i], tmp);
        Vmath::Vadd(ncoeff, tmp, 1, outarray[i], 1, outarray[i], 1);
    }
}

void ForcingAbsorption::CalculateForcing(
    [[maybe_unused]] const Array<OneD, MultiRegions::ExpListSharedPtr> &fields,
    const Array<OneD, Array<OneD, NekDouble>> &inarray, const NekDouble &time)
{
    int nq = m_Forcing[0].size();

    std::string s_FieldStr;
    Array<OneD, NekDouble> TimeScale(1);
    Array<OneD, Array<OneD, NekDouble>> RefflowScaled(m_NumVariable);

    if (m_hasRefFlow)
    {
        for (int i = 0; i < m_NumVariable; i++)
        {
            RefflowScaled[i] = Array<OneD, NekDouble>(nq);
            if (m_hasRefFlowTime)
            {
                s_FieldStr = m_session->GetVariable(i);

                std::string s_FieldStr = m_session->GetVariable(i);
                GetFunction(fields, m_session, m_funcNameTime)
                    ->Evaluate(s_FieldStr, m_Refflow[i], time);
                Vmath::Vcopy(nq, m_Refflow[i], 1, RefflowScaled[i], 1);
            }
            else
            {
                Vmath::Vcopy(nq, m_Refflow[i], 1, RefflowScaled[i], 1);
            }

            Vmath::Vsub(nq, inarray[i], 1, RefflowScaled[i], 1, m_Forcing[i],
                        1);
            Vmath::Vmul(nq, m_Absorption[i], 1, m_Forcing[i], 1, m_Forcing[i],
                        1);
        }
    }
    else
    {
        for (int i = 0; i < m_NumVariable; i++)
        {
            Vmath::Vmul(nq, m_Absorption[i], 1, inarray[i], 1, m_Forcing[i], 1);
        }
    }
}

} // namespace Nektar::SolverUtils
