Merge branch 'feature/transformMRF' into 'master'

Transform coordinates and vectors for the MRF method

See merge request nektar/nektar!1830

CHANGELOG.md

@@ -22,8 +22,10 @@ v5.7.0
 
 **NekMesh**
 - Added revolve module (!1825)
+
 **FieldConvert**
 - Add vortexinducedvelocity module to compute the vortex-induced velocity (!1824)
+- Add a module to transform coordinates and vectors for the moving reference frame method (!1830)
 
 **Miscellaneous**
 - Use std::stod instead of boost::lexical_cast<NekDouble> (!1819)

library/FieldUtils/CMakeLists.txt

@@ -44,6 +44,7 @@ SET(FieldUtilsHeaders
     ProcessModules/ProcessJacobianEnergy.h
     ProcessModules/ProcessL2Criterion.h
     ProcessModules/ProcessMapping.h
+    ProcessModules/ProcessMRF.h
     ProcessModules/ProcessNumModes.h
     ProcessModules/ProcessMean.h
     ProcessModules/ProcessMeanMode.h
@@ -113,6 +114,7 @@ SET(FieldUtilsSources
     ProcessModules/ProcessJacobianEnergy.cpp
     ProcessModules/ProcessL2Criterion.cpp
     ProcessModules/ProcessMapping.cpp
+    ProcessModules/ProcessMRF.cpp
     ProcessModules/ProcessNumModes.cpp
     ProcessModules/ProcessMean.cpp
     ProcessModules/ProcessMeanMode.cpp

library/FieldUtils/ProcessModules/ProcessMRF.cpp

+////////////////////////////////////////////////////////////////////////////////
+//
+//  File: ProcessMRF.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: Add transformed coordinates to field
+//
+////////////////////////////////////////////////////////////////////////////////
+
+#include <iostream>
+#include <string>
+using namespace std;
+
+#include "ProcessMRF.h"
+#include <LibUtilities/BasicUtils/ParseUtils.h>
+#include <LibUtilities/BasicUtils/SharedArray.hpp>
+
+namespace Nektar::FieldUtils
+{
+ModuleKey ProcessMRF::className = GetModuleFactory().RegisterCreatorFunction(
+    ModuleKey(eProcessModule, "MRF"), ProcessMRF::create,
+    "Add transformed coordinates to output file.");
+
+ProcessMRF::ProcessMRF(FieldSharedPtr f) : ProcessModule(f)
+{
+    m_config["vectors"] = ConfigOption(false, "NotSet", "Select variables");
+}
+
+ProcessMRF::~ProcessMRF()
+{
+}
+
+void ProcessMRF::v_Process(po::variables_map &vm)
+{
+    m_f->SetUpExp(vm);
+    ReadMRFData();
+
+    // Skip in case of empty partition
+    if (m_f->m_exp[0]->GetNumElmts() == 0)
+    {
+        return;
+    }
+
+    // Determine dimensions
+    m_spacedim = m_f->m_graph->GetMeshDimension() + m_f->m_numHomogeneousDir;
+
+    // transform coordinates
+    int nfields          = m_f->m_variables.size();
+    int addfields        = m_spacedim;
+    int npoints          = m_f->m_exp[0]->GetNpoints();
+    string fieldNames[3] = {"xCoord", "yCoord", "zCoord"};
+    for (int i = 0; i < addfields; ++i)
+    {
+        m_f->m_variables.push_back(fieldNames[i]);
+    }
+    m_f->m_exp.resize(nfields + addfields);
+    vector<Array<OneD, NekDouble>> coords(m_spacedim);
+    for (int i = 0; i < m_spacedim; ++i)
+    {
+        coords[i] = Array<OneD, NekDouble>(npoints);
+    }
+    if (m_spacedim == 1)
+    {
+        m_f->m_exp[0]->GetCoords(coords[0]);
+    }
+    else if (m_spacedim == 2)
+    {
+        m_f->m_exp[0]->GetCoords(coords[0], coords[1]);
+    }
+    else
+    {
+        m_f->m_exp[0]->GetCoords(coords[0], coords[1], coords[2]);
+    }
+    for (int i = 0; i < m_spacedim; ++i)
+    {
+        Vmath::Sadd(npoints, -m_pivot[i], coords[i], 1, coords[i], 1);
+    }
+    TransformVector(coords);
+    for (int i = 0; i < m_spacedim; ++i)
+    {
+        Vmath::Sadd(npoints, m_pivot[i] + m_origin[i], coords[i], 1, coords[i],
+                    1);
+    }
+    // Add new information to m_f
+    for (int i = 0; i < addfields; ++i)
+    {
+        m_f->m_exp[nfields + i] = m_f->AppendExpList(m_f->m_numHomogeneousDir);
+        Vmath::Vcopy(npoints, coords[i], 1,
+                     m_f->m_exp[nfields + i]->UpdatePhys(), 1);
+        m_f->m_exp[nfields + i]->FwdTransLocalElmt(
+            coords[i], m_f->m_exp[nfields + i]->UpdateCoeffs());
+    }
+
+    // tranform vectors
+    vector<Array<OneD, NekDouble>> data(m_spacedim);
+    vector<int> vars;
+    if (m_config["vectors"].as<string>().compare("NotSet"))
+    {
+        ParseUtils::GenerateVariableVector(m_config["vectors"].as<string>(),
+                                           m_f->m_variables, vars);
+    }
+    ASSERTL0(vars.size() % m_spacedim == 0,
+             "The number of vector variables is not divisible by the space "
+             "dimension.");
+    for (int i = 0; i < vars.size() / m_spacedim; ++i)
+    {
+        for (int d = 0; d < m_spacedim; ++d)
+        {
+            data[d] = m_f->m_exp[vars[m_spacedim * i + d]]->UpdatePhys();
+        }
+        TransformVector(data);
+        for (int d = 0; d < m_spacedim; ++d)
+        {
+            int nv = vars[m_spacedim * i + d];
+            m_f->m_exp[nv]->FwdTransLocalElmt(data[d],
+                                              m_f->m_exp[nv]->UpdateCoeffs());
+        }
+    }
+}
+
+void ProcessMRF::ReadMRFData()
+{
+    vector<string> strOrigin = {"X", "Y", "Z"};
+    vector<string> strTheta  = {"Theta_x", "Theta_y", "Theta_z"};
+    vector<string> strPivot  = {"X0", "Y0", "Z0"};
+    m_origin.resize(3, 0.);
+    m_pivot.resize(3, 0.);
+    for (size_t i = 0; i < strOrigin.size(); ++i)
+    {
+        if (m_f->m_fieldMetaDataMap.count(strOrigin[i]))
+        {
+            m_origin[i] = stod(m_f->m_fieldMetaDataMap[strOrigin[i]]);
+        }
+    }
+    for (size_t i = 0; i < strTheta.size(); ++i)
+    {
+        if (m_f->m_fieldMetaDataMap.count(strTheta[i]))
+        {
+            if (m_theta.size() < 3)
+            {
+                m_theta.resize(3, 0.);
+            }
+            m_theta[i] = stod(m_f->m_fieldMetaDataMap[strTheta[i]]);
+        }
+    }
+    for (size_t i = 0; i < strPivot.size(); ++i)
+    {
+        if (m_f->m_fieldMetaDataMap.count(strPivot[i]))
+        {
+            m_pivot[i] = stod(m_f->m_fieldMetaDataMap[strPivot[i]]);
+        }
+    }
+}
+
+void ProcessMRF::TransformVector(vector<Array<OneD, NekDouble>> &data)
+{
+    if (m_theta.size() < 3)
+    {
+        return;
+    }
+    if (data.size() < m_spacedim)
+    {
+        NEKERROR(ErrorUtil::efatal,
+                 "data size is small than the space dimension.");
+    }
+
+    int npoint   = data[0].size();
+    int dim      = 2;
+    NekDouble sz = sin(m_theta[2]), cz = cos(m_theta[2]);
+    Array<OneD, Array<OneD, NekDouble>> tmp(dim);
+    for (int i = 0; i < dim; ++i)
+    {
+        tmp[i] = Array<OneD, NekDouble>(npoint);
+        Vmath::Vcopy(npoint, data[i], 1, tmp[i], 1);
+    }
+    Vmath::Svtsvtp(npoint, cz, tmp[0], 1, -sz, tmp[1], 1, data[0], 1);
+    Vmath::Svtsvtp(npoint, sz, tmp[0], 1, cz, tmp[1], 1, data[1], 1);
+}
+} // namespace Nektar::FieldUtils

library/FieldUtils/ProcessModules/ProcessMRF.h

+////////////////////////////////////////////////////////////////////////////////
+//
+//  File: ProcessMRF.h
+//
+//  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: Add transformed coordinates to field
+//
+////////////////////////////////////////////////////////////////////////////////
+
+#ifndef FIELDUTILS_ProcessMRF
+#define FIELDUTILS_ProcessMRF
+
+#include "../Module.h"
+#include <GlobalMapping/Mapping.h>
+
+namespace Nektar::FieldUtils
+{
+
+/**
+ * @brief This processing module scales the input fld file
+ *
+ */
+class ProcessMRF : public ProcessModule
+{
+public:
+    /// Creates an instance of this class
+    static std::shared_ptr<Module> create(FieldSharedPtr f)
+    {
+        return MemoryManager<ProcessMRF>::AllocateSharedPtr(f);
+    }
+    static ModuleKey className;
+
+    ProcessMRF(FieldSharedPtr f);
+    ~ProcessMRF() override;
+
+protected:
+    /// Write mesh to output file.
+    void v_Process(po::variables_map &vm) override;
+
+    std::string v_GetModuleName() override
+    {
+        return "ProcessMRF";
+    }
+
+    std::string v_GetModuleDescription() override
+    {
+        return "Applying mapping to field";
+    }
+
+    ModulePriority v_GetModulePriority() override
+    {
+        return eModifyExp;
+    }
+    void ReadMRFData();
+    void TransformVector(std::vector<Array<OneD, NekDouble>> &data);
+
+private:
+    NekInt m_spacedim;
+    std::vector<NekDouble> m_origin;
+    std::vector<NekDouble> m_theta;
+    std::vector<NekDouble> m_pivot;
+};
+} // namespace Nektar::FieldUtils
+
+#endif

library/LibUtilities/BasicUtils/ParseUtils.cpp

@@ -168,6 +168,23 @@ LIB_UTILITIES_EXPORT bool ParseUtils::GenerateVector(
 bool ParseUtils::GenerateVariableSet(const std::string &str,
                                      const std::vector<std::string> &variables,
                                      std::set<int> &out)
+{
+    std::vector<int> tempvect;
+    GenerateVariableVector(str, variables, tempvect);
+    out.clear();
+    for (auto i : tempvect)
+    {
+        out.insert(i);
+    }
+    return true;
+}
+
+/**
+ *
+ */
+bool ParseUtils::GenerateVariableVector(
+    const std::string &str, const std::vector<std::string> &variables,
+    std::vector<int> &out)
 {
     out.clear();
     std::vector<std::string> vars;
@@ -191,7 +208,7 @@ bool ParseUtils::GenerateVariableSet(const std::string &str,
         }
         else
         {
-            out.insert(v);
+            out.push_back(v);
         }
     }
     return true;

library/LibUtilities/BasicUtils/ParseUtils.h

@@ -125,6 +125,10 @@ public:
     LIB_UTILITIES_EXPORT static bool GenerateVariableSet(
         const std::string &str, const std::vector<std::string> &variables,
         std::set<int> &out);
+
+    LIB_UTILITIES_EXPORT static bool GenerateVariableVector(
+        const std::string &str, const std::vector<std::string> &variables,
+        std::vector<int> &out);
 };
 
 } // namespace Nektar

utilities/FieldConvert/CMakeLists.txt

@@ -63,6 +63,7 @@ ADD_NEKTAR_TEST(halfmodetofourier)
 ADD_NEKTAR_TEST(averagefld)
 ADD_NEKTAR_TEST(powerspectrum)
 ADD_NEKTAR_TEST(chanflow_m8_addfld)
+ADD_NEKTAR_TEST(MRF)
 ADD_NEKTAR_TEST(vortexinducedvelocity)
 
 IF (NEKTAR_USE_METIS OR NEKTAR_USE_SCOTCH)

utilities/FieldConvert/FieldConvert.cpp

@@ -94,8 +94,7 @@ int main(int argc, char *argv[])
          "Specify modules which are to be used.")
         ("use-session-variables", "Use variables defined in session for output")
         ("use-session-expansion", "Use expansion defined in session.")
-        ("verbose,v", "Enable verbose mode.")
-        ("MRF", "Transform coordinates for moving reference frame.");
+        ("verbose,v", "Enable verbose mode.");
     // clang-format on
 
     po::options_description hidden("Hidden options");

utilities/FieldConvert/Tests/MRF.tst

+<?xml version="1.0" encoding="utf-8"?>
+<test>
+    <description> Process Moving Reference Frame field </description>
+    <executable>FieldConvert</executable>
+    <parameters> -f -e -m MRF:vectors=u,v MRF.xml MRF.fld MRF.plt</parameters>
+    <files>
+        <file description="Session File">MRF.xml</file>
+        <file description="Session File">MRF.fld</file>
+    </files>
+     <metrics>
+        <metric type="L2" id="1">
+            <value variable="x"   tolerance="1e-4">61.2382</value>
+            <value variable="y"   tolerance="1e-4">35.3556</value>
+            <value variable="u"   tolerance="1e-4">10.6066</value>
+            <value variable="v" tolerance="1e-4">6.12375</value>
+            <value variable="p" tolerance="1e-4">0</value>
+            <value variable="xCoord" tolerance="1e-4">55.9028</value>
+            <value variable="yCoord" tolerance="1e-4">43.3013</value>
+        </metric>
+        <metric type="Linf" id="2">
+            <value variable="x"   tolerance="1e-4">10.001</value>
+            <value variable="y"   tolerance="1e-4">5</value>
+            <value variable="u"   tolerance="1e-4">0.866033</value>
+            <value variable="v" tolerance="1e-4">0.500005</value>
+            <value variable="p" tolerance="1e-4">0</value>
+            <value variable="xCoord" tolerance="1e-4">11.1603</value>
+            <value variable="yCoord" tolerance="1e-4">9.33013</value>
+        </metric>
+    </metrics>
+</test>
+

utilities/FieldConvert/Tests/MRF.xml

+<?xml version="1.0" encoding="utf-8" ?>
+<NEKTAR>
+    <EXPANSIONS>
+        <E COMPOSITE="C[5]" NUMMODES="6" TYPE="MODIFIED" FIELDS="u,v,p" />
+    </EXPANSIONS>
+    <CONDITIONS>
+        <SOLVERINFO>
+            <I PROPERTY="EQTYPE" VALUE="UnsteadyNavierStokes" />
+            <I PROPERTY="SolverType" VALUE="VelocityCorrectionScheme" />
+            <I PROPERTY="EvolutionOperator" VALUE="Nonlinear"/>
+            <I PROPERTY="AdvectionForm" VALUE="Convective"/>
+            <I PROPERTY="Projection" VALUE="Galerkin" />
+            <I PROPERTY="TimeIntegrationMethod" VALUE="IMEXOrder2" />
+            <I PROPERTY="DEALIASING" VALUE="True" />
+            <I PROPERTY="SPECTRALDEALIASING" VALUE="True" />
+            <I PROPERTY="SPECTRALHPDEALIASING" VALUE="True" />
+            <I PROPERTY="SpectralVanishingViscosity" VALUE="DGKernel" />
+        </SOLVERINFO>
+        <PARAMETERS>
+            <P> TimeStep      = 1e-4                      </P>
+            <P> NumSteps      = 1250               	   </P>
+            <P> IO_CheckSteps = 1250               	   </P>
+            <P> IO_InfoSteps  = 1               	   </P>
+            <P> IO_CFLSteps  =  1                         </P>
+            <P> C             = 1.0               	   </P>
+            <P> D0            = 1.0               	   </P>
+            <P> Uinf          = 1.              	   </P>
+            <P> AoA           = 30*PI/180              	   </P>
+            <P> Uinfx         = Uinf*cos(AoA)         	   </P>
+            <P> Uinfy         = Uinf*sin(AoA)          	   </P>
+            <P> Re            = 200.                        </P>
+            <P> Kinvis        = Uinf*C/Re          	   </P>
+            <P> t0            = 0.0                        </P>
+            <P> freq          = 2.                         </P>
+            <P> amp           = 30.*PI/180.              </P>
+            <P> omega         = 2.*PI*freq                 </P>
+        </PARAMETERS>
+
+        <VARIABLES>
+            <V ID="0"> u </V>
+            <V ID="1"> v </V>
+            <V ID="2"> p </V>
+        </VARIABLES>
+        <BOUNDARYREGIONS>
+            <B ID="0"> C[1] </B>      <!-- inflow -->
+            <B ID="1"> C[2] </B>      <!-- outflow -->
+            <B ID="2"> C[3] </B>      <!-- Far Field -->
+            <B ID="3"> C[4] </B>      <!-- Far Field -->
+        </BOUNDARYREGIONS>
+        <BOUNDARYCONDITIONS>
+            <REGION REF="0">
+                <D VAR="u" USERDEFINEDTYPE="MovingFrameFar" VALUE="Uinfx" />
+                <D VAR="v" USERDEFINEDTYPE="MovingFrameFar" VALUE="Uinfy" />
+                <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" />
+            </REGION>
+            <REGION REF="1">
+                <D VAR="u" USERDEFINEDTYPE="MovingFrameFar" VALUE="Uinfx" />
+                <D VAR="v" USERDEFINEDTYPE="MovingFrameFar" VALUE="Uinfy" />
+                <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" />
+            </REGION>
+            <REGION REF="2">
+                <D VAR="u" USERDEFINEDTYPE="MovingFrameFar" VALUE="Uinfx" />
+                <D VAR="v" USERDEFINEDTYPE="MovingFrameFar" VALUE="Uinfy" />
+                <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" />
+            </REGION>
+            <REGION REF="3">
+                <D VAR="u" USERDEFINEDTYPE="MovingFrameFar" VALUE="Uinfx" />
+                <D VAR="v" USERDEFINEDTYPE="MovingFrameFar" VALUE="Uinfy" />
+                <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" />
+            </REGION>
+
+        </BOUNDARYCONDITIONS>
+        <FUNCTION NAME="InitialConditions">
+            <E VAR="u" VALUE="Uinfx" />
+            <E VAR="v" VALUE="Uinfy" />
+            <E VAR="p" VALUE="0" />
+        </FUNCTION>
+
+        <FUNCTION NAME="VelMRF">
+            <E VAR="u" VALUE="0.0" />
+            <E VAR="v" VALUE="0" />
+            <E VAR="Omega_z" VALUE="amp*omega*cos(omega*(t-t0))"/>
+        </FUNCTION>
+
+        <FUNCTION NAME="ExactSolution">
+            <E VAR="u" VALUE=" Uinfx*cos(amp*sin(omega*(t-t0))) + Uinfy*sin(amp*sin(omega*(t-t0)))" />
+            <E VAR="v" VALUE="-Uinfx*sin(amp*sin(omega*(t-t0))) + Uinfy*cos(amp*sin(omega*(t-t0)))" />
+            <E VAR="p" VALUE="0"/>
+        </FUNCTION>
+
+    </CONDITIONS>
+    <FORCING>
+        <FORCE TYPE="MovingReferenceFrame">
+            <FRAMEVELOCITY> VelMRF </FRAMEVELOCITY>
+        </FORCE>
+    </FORCING>
+
+    <FILTERS>
+        <FILTER TYPE="AeroForces">
+            <PARAM NAME="OutputFile">dragLift</PARAM>
+            <PARAM NAME="OutputFrequency">10</PARAM>
+            <PARAM NAME="Boundary"> B[0] </PARAM>
+            <PARAM NAME="MomentPoint">0.25 0.0 0. </PARAM>
+        </FILTER>
+    </FILTERS>
+
+
+    <GEOMETRY DIM="2" SPACE="2">
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+        <COMPOSITE>
+            <C ID="1"> E[3,45,74,103,132,161,190,219,248] </C>
+            <C ID="2"> E[273,244,215,186,157,128,99,70,41] </C>
+            <C ID="3"> E[247,250,252,254,256,258,260,262,264,266,268,270,272,274] </C>
+            <C ID="4"> E[40,37,34,31,28,25,22,19,16,13,10,7,4,0] </C>
+            <C ID="5"> Q[0-125] </C>
+        </COMPOSITE>
+        <DOMAIN>
+            <D ID="0"> C[5] </D>
+        </DOMAIN>
+    </GEOMETRY>
+    <Metadata>
+        <Provenance>
+            <GitBranch>refs/heads/fix/IncBCs</GitBranch>
+            <GitSHA1>acd951460c86c4f1805ce3fa05dd6d9390e293d3</GitSHA1>
+            <Hostname>debian-34</Hostname>
+            <NektarVersion>5.6.0</NektarVersion>
+            <Timestamp>02-Jul-2024 10:56:33</Timestamp>
+        </Provenance>
+        <NekMeshCommandLine>test.xml MRF.xml </NekMeshCommandLine>
+    </Metadata>
+</NEKTAR>