IterativeElasticSystem.cpp

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///////////////////////////////////////////////////////////////////////////////
//
// File: IterativeElasticSystem.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
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// DEALINGS IN THE SOFTWARE.
//
// Description: IterativeElasticSystem solve routines
//
///////////////////////////////////////////////////////////////////////////////
 
#include <boost/format.hpp>
 
#include <GlobalMapping/Deform.h>
#include <LibUtilities/BasicUtils/Filesystem.hpp>
#include <LibUtilities/Foundations/Interp.h>
#include <LocalRegions/MatrixKey.h>
#include <MultiRegions/ContField.h>
#include <MultiRegions/GlobalLinSysDirectStaticCond.h>
#include <SpatialDomains/MeshGraphIO.h>
#include <StdRegions/StdQuadExp.h>
#include <StdRegions/StdTriExp.h>
 
#include <LinearElasticSolver/EquationSystems/IterativeElasticSystem.h>
 
namespace Nektar
{
 
std::string IterativeElasticSystem::className =
    GetEquationSystemFactory().RegisterCreatorFunction(
        "IterativeElasticSystem", IterativeElasticSystem::create);
 
IterativeElasticSystem::IterativeElasticSystem(
    const LibUtilities::SessionReaderSharedPtr &pSession,
    const SpatialDomains::MeshGraphSharedPtr &pGraph)
    : LinearElasticSystem(pSession, pGraph)
{
}
 
void IterativeElasticSystem::v_InitObject(bool DeclareFields)
{
    LinearElasticSystem::v_InitObject(DeclareFields);
 
    const int nVel = m_fields[0]->GetCoordim(0);
 
    // Read in number of steps to take.
    m_session->LoadParameter("NumSteps", m_numSteps, 0);
    ASSERTL0(m_numSteps > 0, "You must specify at least one step");
 
    // Read in whether to repeatedly apply boundary conditions (for e.g.
    // rotation purposes).
    std::string bcType;
    m_session->LoadSolverInfo("BCType", bcType, "Normal");
    m_repeatBCs = bcType != "Normal";
 
    if (!m_repeatBCs)
    {
        // Loop over BCs, identify which ones we need to deform.
        const Array<OneD, const SpatialDomains::BoundaryConditionShPtr>
            &bndCond = m_fields[0]->GetBndConditions();
 
        for (int i = 0; i < bndCond.size(); ++i)
        {
            if (boost::iequals(bndCond[i]->GetUserDefined(), "Wall"))
            {
                m_toDeform.push_back(i);
            }
        }
 
        int numDeform = m_toDeform.size();
        m_comm->AllReduce(numDeform, LibUtilities::ReduceMax);
        ASSERTL0(numDeform > 0, "You must specify at least one WALL tag on"
                                "a boundary condition");
 
        m_savedBCs =
            Array<OneD, Array<OneD, Array<OneD, NekDouble>>>(m_toDeform.size());
 
        for (int i = 0; i < m_toDeform.size(); ++i)
        {
            m_savedBCs[i] = Array<OneD, Array<OneD, NekDouble>>(nVel);
            for (int j = 0; j < nVel; ++j)
            {
                const int id = m_toDeform[i];
                MultiRegions::ExpListSharedPtr bndCondExp =
                    m_fields[j]->GetBndCondExpansions()[id];
                int nCoeffs = bndCondExp->GetNcoeffs();
 
                m_savedBCs[i][j] = Array<OneD, NekDouble>(nCoeffs);
                Vmath::Smul(nCoeffs, 1.0 / m_numSteps, bndCondExp->GetCoeffs(),
                            1, bndCondExp->UpdateCoeffs(), 1);
                Vmath::Vcopy(nCoeffs, bndCondExp->GetCoeffs(), 1,
                             m_savedBCs[i][j], 1);
            }
        }
    }
}
 
void IterativeElasticSystem::v_GenerateSummary(SolverUtils::SummaryList &s)
{
    LinearElasticSystem::v_GenerateSummary(s);
}
 
void IterativeElasticSystem::v_DoSolve()
{
    int i, j, k;
 
    // Write initial geometry for consistency/script purposes
    WriteGeometry(0);
 
    Array<OneD, Array<OneD, NekDouble>> physvals(m_fields.size());
 
    for (int i = 0; i < m_fields.size(); ++i)
    {
        physvals[i] = m_fields[i]->UpdatePhys();
    }
 
    // Now loop over desired number of steps
    for (i = 1; i <= m_numSteps; ++i)
    {
        int invalidElmtId = -1;
 
        // Perform solve for this iteration and update geometry accordingly.
        LinearElasticSystem::v_DoSolve();
        GlobalMapping::UpdateGeometry(m_graph, m_fields, physvals);
        WriteGeometry(i);
 
        // Check for invalid elements.
        for (j = 0; j < m_fields[0]->GetExpSize(); ++j)
        {
            SpatialDomains::GeomFactorsSharedPtr geomFac =
                m_fields[0]->GetExp(j)->GetGeom()->GetGeomFactors();
 
            if (!geomFac->IsValid())
            {
                invalidElmtId =
                    m_fields[0]->GetExp(j)->GetGeom()->GetGlobalID();
                break;
            }
        }
 
        m_session->GetComm()->AllReduce(invalidElmtId, LibUtilities::ReduceMax);
 
        // If we found an invalid element, exit loop without writing output.
        if (invalidElmtId >= 0)
        {
            if (m_session->GetComm()->GetRank() == 0)
            {
                std::cout << "- Detected negative Jacobian in element "
                          << invalidElmtId
                          << "; terminating at"
                             " step: "
                          << i << std::endl;
            }
 
            break;
        }
 
        if (m_session->GetComm()->GetRank() == 0)
        {
            std::cout << "Step: " << i << std::endl;
        }
 
        // Update boundary conditions
        if (m_repeatBCs)
        {
            for (j = 0; j < m_fields.size(); ++j)
            {
                std::string varName = m_session->GetVariable(j);
                m_fields[j]->EvaluateBoundaryConditions(m_time, varName);
            }
        }
        else
        {
            for (j = 0; j < m_fields.size(); ++j)
            {
                const Array<OneD, const MultiRegions::ExpListSharedPtr>
                    &bndCondExp = m_fields[j]->GetBndCondExpansions();
 
                for (k = 0; k < m_toDeform.size(); ++k)
                {
                    const int id      = m_toDeform[k];
                    const int nCoeffs = bndCondExp[id]->GetNcoeffs();
                    Vmath::Vcopy(nCoeffs, m_savedBCs[k][j], 1,
                                 bndCondExp[id]->UpdateCoeffs(), 1);
                }
            }
        }
    }
}
 
/**
 * @brief Write out a file in serial or directory in parallel containing new
 * mesh geometry.
 */
void IterativeElasticSystem::WriteGeometry(const int i)
{
    fs::path filename;
    std::stringstream s;
    s << m_session->GetSessionName() << "-" << i;
 
    if (m_session->GetComm()->GetSize() > 1)
    {
        s << "_xml";
 
        std::string ss = s.str();
        if (!fs::is_directory(ss))
        {
            fs::create_directory(ss);
        }
 
        boost::format pad("P%1$07d.xml");
        pad % m_session->GetComm()->GetRank();
        filename = fs::path(ss) / fs::path(pad.str());
    }
    else
    {
        s << ".xml";
        filename = fs::path(s.str());
    }
 
    std::string fname    = LibUtilities::PortablePath(filename);
    std::string geomType = m_session->GetGeometryType();
    auto graphIO =
        SpatialDomains::GetMeshGraphIOFactory().CreateInstance(geomType);
    graphIO->SetMeshGraph(m_graph);
    graphIO->WriteGeometry(fname);
}
 
} // namespace Nektar