Zero an input homo-plane in wavespace

CHANGELOG.md

@@ -26,6 +26,7 @@ v5.5.0
 **FieldConvert**
 - Fix typo in user-guide and fix but for parallel-in-time FieldConvert (!1645)
 - Fixed FieldConvert -m addfld (!1500)
+- Add a new FieldConvert module to zero a plane in wavespace (!1632)
 - Fix tecplot output for line and plane points (!1497)
 
 **CI**

docs/user-guide/utilities/fieldconvert.tex

@@ -433,7 +433,8 @@ possibly also Reynolds stresses) into single file;
   project the velocity components from Cartesian coordinate system into the new 
   coordinate system;
 \item \inltt{averagefld}: Compute the averaging of several field files;
-\item \inltt{powerspectrum}: Compute power spectrum at given regions from a 3DH1D expansion.
+\item \inltt{powerspectrum}: Compute power spectrum at given regions from a 3DH1D expansion;
+\item \inltt{zero-homo-plane}: Zero a specfied homogeneous plane in wavespace.
 \end{enumerate}
 The module list above can be seen by running the command
 %
@@ -1507,6 +1508,23 @@ filter to process data. See \ref{filters:BodyFittedVelocity}.
 %
 %
 
+\subsection{Zero a homogeneous plane in wavespace: \textit{zero-homo-plane} module}
+\label{s:utilities:fieldconvert:sub:zero-homo-plane}
+In cases the users would like to visualize the fluctuations in a 3DH1D flow
+field, the mean mode is expected to be removed (in the Fourier space). This can 
+be achieved by running the current module:
+\begin{lstlisting}[style=BashInputStyle]
+FieldConvert -m zero-homo-plane:planeid=0 mesh.xml session.xml field.fld \
+    field-zeroMean.fld
+\end{lstlisting}
+
+In general, \inltt{planeid} can be any meaningful plane id, which is 0 by 
+default. 
+
+%
+%
+%
+
 \subsection{Manipulating meshes with FieldConvert}
 FieldConvert has support for two modules that can be used in conjunction with
 the linear elastic solver, as shown in chapter~\ref{s:elasticity}. To do this,

library/FieldUtils/CMakeLists.txt

@@ -64,6 +64,7 @@ SET(FieldUtilsHeaders
     ProcessModules/ProcessC0Projection.h
     ProcessModules/ProcessQCriterion.h
     ProcessModules/ProcessQualityMetric.h
+    ProcessModules/ProcessZeroHomogeneousPlane.h
 )
 
 SET(FieldUtilsSources
@@ -131,6 +132,7 @@ SET(FieldUtilsSources
     ProcessModules/ProcessC0Projection.cpp
     ProcessModules/ProcessQCriterion.cpp
     ProcessModules/ProcessQualityMetric.cpp
+    ProcessModules/ProcessZeroHomogeneousPlane.cpp
 )
 
 IF (NEKTAR_USE_VTK)

library/FieldUtils/ProcessModules/ProcessZeroHomogeneousPlane.cpp

+////////////////////////////////////////////////////////////////////////////////
+//
+//  File: ProcessZeroHomogeneousPlane.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: Zero the homogeneous plane in wavespace of a 3DH1D field to
+//  visualise the fluctuation.
+//
+////////////////////////////////////////////////////////////////////////////////
+
+#include <iostream>
+#include <string>
+using namespace std;
+
+#include <boost/core/ignore_unused.hpp>
+
+#include <LibUtilities/BasicUtils/SharedArray.hpp>
+
+#include "ProcessZeroHomogeneousPlane.h"
+
+namespace Nektar
+{
+namespace FieldUtils
+{
+
+ModuleKey ProcessZeroHomogeneousPlane::className =
+    GetModuleFactory().RegisterCreatorFunction(
+        ModuleKey(eProcessModule, "zero-homo-plane"),
+        ProcessZeroHomogeneousPlane::create,
+        "Extracts a plane from a 3DH1D expansion, requires planeid to be "
+        "defined.");
+
+ProcessZeroHomogeneousPlane::ProcessZeroHomogeneousPlane(FieldSharedPtr f)
+    : ProcessModule(f)
+{
+    m_config["planeid"] = ConfigOption(
+        false, "0",
+        "plane id in wavespace to be set zero. Default planeid is zero");
+}
+
+ProcessZeroHomogeneousPlane::~ProcessZeroHomogeneousPlane()
+{
+}
+
+void ProcessZeroHomogeneousPlane::v_Process(po::variables_map &vm)
+{
+    m_f->SetUpExp(vm);
+
+    if (m_f->m_numHomogeneousDir != 1)
+    {
+        NEKERROR(ErrorUtil::efatal,
+                 "ProcessZeroHomogeneousPlane only works for Homogeneous1D.");
+    }
+
+    // Skip in case of empty partition
+    if (m_f->m_exp[0]->GetNumElmts() == 0)
+    {
+        return;
+    }
+
+    int planeid = m_config["planeid"].as<int>();
+    int nfields = m_f->m_variables.size();
+
+    int nstrips;
+    m_f->m_session->LoadParameter("Strip_Z", nstrips, 1);
+
+    // Look for correct plane (because of parallel case)
+    int plane = -1;
+    for (int i = 0; i < m_f->m_exp[0]->GetZIDs().size(); ++i)
+    {
+        if (m_f->m_exp[0]->GetZIDs()[i] == planeid)
+        {
+            plane = i;
+        }
+    }
+
+    if (plane != -1)
+    {
+        for (int s = 0; s < nstrips; ++s)
+        {
+            for (int i = 0; i < nfields; ++i)
+            {
+                int n = s * nfields + i;
+
+                // Find the memory location, set zeros
+                int Ncoeff = m_f->m_exp[n]->GetPlane(plane)->GetNcoeffs();
+                Vmath::Zero(Ncoeff,
+                            m_f->m_exp[n]->GetPlane(plane)->UpdateCoeffs(), 1);
+
+                m_f->m_exp[n]->BwdTrans(m_f->m_exp[n]->GetCoeffs(),
+                                        m_f->m_exp[n]->UpdatePhys());
+            }
+        }
+    }
+    else
+    {
+        NEKERROR(ErrorUtil::efatal, "Plane not found.");
+    }
+}
+} // namespace FieldUtils
+} // namespace Nektar

library/FieldUtils/ProcessModules/ProcessZeroHomogeneousPlane.h

+////////////////////////////////////////////////////////////////////////////////
+//
+//  File: ProcessZeroHomogeneousPlane.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: Zero the homogeneous plane in wavespace of a 3DH1D field to
+//  visualise the fluctuation.
+//
+////////////////////////////////////////////////////////////////////////////////
+
+#ifndef FIELDUTILS_PROCESSZEROHOMOGENEOUSPLANE
+#define FIELDUTILS_PROCESSZEROHOMOGENEOUSPLANE
+
+#include "../Module.h"
+
+namespace Nektar
+{
+namespace FieldUtils
+{
+
+/**
+ * @brief This processing module replaces all expansions by a single plane from
+ * 3DH1D fields, defined by the parameter planeid
+ */
+class ProcessZeroHomogeneousPlane : public ProcessModule
+{
+public:
+    /// Creates an instance of this class
+    static std::shared_ptr<Module> create(FieldSharedPtr f)
+    {
+        return MemoryManager<ProcessZeroHomogeneousPlane>::AllocateSharedPtr(f);
+    }
+    static ModuleKey className;
+
+    ProcessZeroHomogeneousPlane(FieldSharedPtr f);
+    virtual ~ProcessZeroHomogeneousPlane();
+
+protected:
+    /// Write mesh to output file.
+    virtual void v_Process(po::variables_map &vm) override;
+
+    virtual std::string v_GetModuleName() override
+    {
+        return "ProcessZeroHomogeneousPlane";
+    }
+
+    virtual std::string v_GetModuleDescription() override
+    {
+        return "Zero the homogeneous plane to visualise the oscillations";
+    }
+
+    virtual ModulePriority v_GetModulePriority() override
+    {
+        return eModifyExp;
+    }
+};
+} // namespace FieldUtils
+} // namespace Nektar
+
+#endif

utilities/FieldConvert/Tests/session_zero-homo-plane.xml

+<?xml version="1.0" encoding="utf-8"?>
+<NEKTAR>
+    <EXPANSIONS>
+        <E COMPOSITE="C[100,101]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED"            />
+    </EXPANSIONS>
+    <CONDITIONS>
+        <SOLVERINFO>
+            <I PROPERTY="SolverType"                           VALUE="VelocityCorrectionScheme" />
+            <I PROPERTY="EQTYPE"                               VALUE="UnsteadyNavierStokes"     />
+            <I PROPERTY="AdvectionForm"                        VALUE="Convective"               />
+            <I PROPERTY="Projection"                           VALUE="Galerkin"                 />
+            <I PROPERTY="TimeIntegrationMethod"                VALUE="IMEXOrder2"               />
+            <I PROPERTY="SpectralhpDealiasing"                 VALUE="True"                     />
+            <I PROPERTY="SpectralVanishingViscositySpectralHP" VALUE="True"                     />
+            <I PROPERTY="SpectralVanishingViscosityHomo1D"     VALUE="True"                     />
+            <I PROPERTY="HOMOGENEOUS"                          VALUE="1D"                       />
+            <!--<I PROPERTY="UseFFT"                               VALUE="FFTW"                     />-->
+            <I PROPERTY="GlobalSysSoln"                        VALUE="XxtMultiLevelStaticCond"  />
+        </SOLVERINFO>
+        <PARAMETERS>
+            <P> TimeStep        = 1.0e-3                 </P>
+            <P> NumSteps        = 5e3                    </P>
+            <P> IO_CheckSteps   = 1e4                    </P>
+            <P> IO_InfoSteps    = 1e3                    </P>
+            <P> IO_CFLSteps     = 1e3                    </P>
+            <P> Re              = 100.0                  </P>
+            <P> uInf            = 1.0                    </P>
+            <P> vInf            = 0.0                    </P>
+            <P> wInf            = 0.0                    </P>
+            <P> Kinvis          = 1.0/Re                 </P>
+            <P> LZ              = 1.0                    </P>
+            <P> HomModesZ       = 4                      </P>
+            <P> SVVDiffCoeff    = 0.1                    </P>
+            <P> SVVCutoffRatio  = 0.7                    </P>
+        </PARAMETERS>
+
+        <VARIABLES>
+            <V ID="0"> u </V>
+            <V ID="1"> v </V>
+            <V ID="2"> w </V>
+            <V ID="3"> p </V>
+        </VARIABLES>
+
+        <BOUNDARYREGIONS>
+            <B ID="0"> C[3] </B>  	<!-- bottom -->
+            <B ID="1"> C[1] </B>  	<!-- inflow -->
+            <B ID="2"> C[2] </B>  	<!-- outflow -->
+            <B ID="3"> C[4] </B>  	<!-- top -->
+        </BOUNDARYREGIONS>
+
+        <BOUNDARYCONDITIONS>
+            <!-- bottom -->
+            <REGION REF="0">
+                <P VAR="u"  VALUE="[3]" />
+                <P VAR="v"  VALUE="[3]" />
+                <P VAR="w"  VALUE="[3]" />
+                <P VAR="p"  VALUE="[3]" />
+            </REGION>
+            <!-- top -->
+            <REGION REF="3">
+                <P VAR="u"  VALUE="[0]" />
+                <P VAR="v"  VALUE="[0]" />
+                <P VAR="w"  VALUE="[0]" />
+                <P VAR="p"  VALUE="[0]" />
+            </REGION>
+            <!-- outflow -->
+            <REGION REF="1">
+                <N VAR="u" USERDEFINEDTYPE="HOutflow" VALUE="0" />
+                <N VAR="v" USERDEFINEDTYPE="HOutflow" VALUE="0" />
+                <N VAR="w" USERDEFINEDTYPE="HOutflow" VALUE="0" />
+                <D VAR="p" USERDEFINEDTYPE="HOutflow" VALUE="0" />
+            </REGION>
+            <!-- inflow -->
+            <REGION REF="2">
+                <D VAR="u" VALUE="uInf" />
+                <D VAR="v" VALUE="vInf" />
+                <D VAR="w" VALUE="wInf" />
+                <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" />
+            </REGION>
+        </BOUNDARYCONDITIONS>
+
+        <FUNCTION NAME="InitialConditions">
+            <E VAR="u" VALUE="uInf" />
+            <E VAR="v" VALUE="vInf" />
+            <E VAR="w" VALUE="wInf" />
+            <E VAR="p" VALUE="0"    />
+        </FUNCTION>
+    </CONDITIONS>
+
+</NEKTAR>

utilities/FieldConvert/Tests/square_mix.xml

+<?xml version="1.0" encoding="utf-8" ?>
+<NEKTAR>
+    <GEOMETRY DIM="2" SPACE="2">
+        <VERTEX COMPRESSED="B64Z-LittleEndian" BITSIZE="64">eJxjYMAPGKH098X/geC9Pbo8E1b5D3B1zFhNRcizoEo4oKtkxSqP0M8Gpcs8UMTh5rBjtR8hz4FdHC4PAGLNFKcA</VERTEX>
+        <EDGE COMPRESSED="B64Z-LittleEndian" BITSIZE="64">eJx1j7kNADAIA/P/2X/dVFfEkt1YJ8BACL+i8WQ8G0dFcuBquAmzpwvTN4Tpm2ZuCTO/Td6Re6hfyefvB2HQAMoA</EDGE>
+        <ELEMENT>
+            <T COMPRESSED="B64Z-LittleEndian" BITSIZE="64">eJxjYoAAdijNAaU5oTQzlOaC0txo6lmgNBuU5kFTz4pmHi+UZoLSAB5gAHcA</T>
+            <Q COMPRESSED="B64Z-LittleEndian" BITSIZE="64">eJxjYEAFjFCaCUozo4mzQGlWKM2GJg8AAxgAGAAA</Q>
+        </ELEMENT>
+        <COMPOSITE>
+            <C ID="1"> E[13,3] </C>
+            <C ID="2"> E[5,12] </C>
+            <C ID="3"> E[0,4] </C>
+            <C ID="4"> E[8,11] </C>
+            <C ID="100"> Q[0-1] </C>
+            <C ID="101"> T[2-5] </C>
+        </COMPOSITE>
+        <DOMAIN> C[100-101] </DOMAIN>
+    </GEOMETRY>
+    <Metadata>
+        <Provenance>
+            <GitBranch>refs/heads/master</GitBranch>
+            <GitSHA1>e29c5b6f2f5e7ce6e75f364d485472399668baf7</GitSHA1>
+            <Hostname>LAPTOP-FIIC1OQ2</Hostname>
+            <NektarVersion>5.0.0</NektarVersion>
+            <Timestamp>26-Oct-2023 17:29:22</Timestamp>
+        </Provenance>
+        <NekMeshCommandLine>-m peralign:surf1=3:surf2=4:dir=y square_mix.xml square_mix_aligned.xml </NekMeshCommandLine>
+    </Metadata>
+    <EXPANSIONS>
+        <E COMPOSITE="C[100]" NUMMODES="4" TYPE="MODIFIED" FIELDS="u" />
+        <E COMPOSITE="C[101]" NUMMODES="4" TYPE="MODIFIED" FIELDS="u" />
+    </EXPANSIONS>
+</NEKTAR>

utilities/FieldConvert/Tests/zero-homo-plane.tst

+<?xml version="1.0" encoding="utf-8" ?>
+<test>
+    <description>Test the zero-homo-plane FieldConvert module</description>
+    <executable>FieldConvert</executable>
+    <parameters>-m zero-homo-plane:planeid=0 square_mix.xml session_zero-homo-plane.xml zero-homo-plane_pre.fld zero-homo-plane_post.fld -f -e</parameters>
+    <files>
+        <file description="Session File">square_mix.xml</file>
+        <file description="Session File">session_zero-homo-plane.xml</file>
+        <file description="Session File">zero-homo-plane_pre.fld</file>
+    </files>
+    <metrics>
+        
+        <metric type="L2" id="1">
+            <value variable="x" tolerance="1e-6">1.63299</value>
+            <value variable="y" tolerance="1e-6">1.63299</value>
+            <value variable="z" tolerance="1e-6">0.661438</value>
+            <value variable="u" tolerance="1e-6">0.0</value>
+            <value variable="v" tolerance="1e-6">0.0</value>
+            <value variable="w" tolerance="1e-6">0.0</value>
+            <value variable="p" tolerance="1e-6">0.0</value> 
+        </metric>
+
+        <metric type="Linf" id="2">
+            <value variable="x" tolerance="1e-6">2.0</value>
+            <value variable="y" tolerance="1e-6">2.0</value>
+            <value variable="z" tolerance="1e-6">0.75</value>
+            <value variable="u" tolerance="1e-6">0.0</value>
+            <value variable="v" tolerance="1e-6">0.0</value>
+            <value variable="w" tolerance="1e-6">0.0</value>
+            <value variable="p" tolerance="1e-6">0.0</value>
+        </metric>
+        
+    </metrics>
+</test>

utilities/FieldConvert/Tests/zero-homo-plane_pre.fld

+<?xml version="1.0" encoding="utf-8" ?>
+<NEKTAR>
+    <Metadata>
+        <Provenance>
+            <GitBranch>refs/heads/feature/zero_mean_mode</GitBranch>
+            <GitSHA1>95f7c96a08b3fe457b152280295ffd80ea38900a</GitSHA1>
+            <Hostname>ae-gl19</Hostname>
+            <NektarVersion>5.3.0</NektarVersion>
+            <Timestamp>30-Oct-2023 00:22:16</Timestamp>
+        </Provenance>
+        <ChkFileNum>1</ChkFileNum>
+        <Kinvis>0.01</Kinvis>
+        <SessionName0>square_mix.opt</SessionName0>
+        <SessionName1>square_mix.xml</SessionName1>
+        <SessionName2>session_zero-homo-plane.xml</SessionName2>
+        <Time>5.0000000000000044</Time>
+        <TimeStep>0.001</TimeStep>
+    </Metadata>
+    <ELEMENTS FIELDS="u,v,w,p" SHAPE="Triangle-HomogenousExp1D" BASIS="Modified_A,Modified_B,Fourier" HOMOGENEOUSLENGTHS="1" HOMOGENEOUSZIDS="0,1,2,3" NUMMODESPERDIR="UNIORDER:3,3,4" ID="2-5" COMPRESSED="B64Z-LittleEndian" BITSIZE="64">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</ELEMENTS>
+    <ELEMENTS FIELDS="u,v,w,p" SHAPE="Quadrilateral-HomogenousExp1D" BASIS="Modified_A,Modified_A,Fourier" HOMOGENEOUSLENGTHS="1" HOMOGENEOUSZIDS="0,1,2,3" NUMMODESPERDIR="UNIORDER:3,3,4" ID="0-1" COMPRESSED="B64Z-LittleEndian" BITSIZE="64">eJzT52QAgg/2TXIQ+s+x+1UXnhntvXT5PxC8t3+gDhEHkQ256/eCaIbn/WC6K2HDXhfjufWGEy7aMgxTAAsXCO+DvZbKg5NHI3v2IocLjC5I6oSHC0z/ulWvOCcxrRm24bO9SJDp8pEHtrl3Gi9mT27cy/j+wvFm5Sd7q64uNbS79MA2Ks1py4FJ9bZvUhoWsC59ujfgUvyKqTrL955heHS3z6nBNiF16Qe3h6f3ErZpaAJYuMD4/1IuetoEXN0LCxeYeObfCT4eQTfh4QITP9x9qeeY3JRhGz6jYBRQAt4IgsgH+z/MA9VX9/e7KP6bEZxatJdjPYRffwBCV5qzqaXMmA7JV1aTbNnFpyeprpu/9+rhpRPiD+8ftvkLFi47TUC8B/vPhB03rZdYvhcWLq9X/APTK6c7sJ1P3bkXFi4m3TPcNe4s2zt356vte/kfD9v6CwCFWMUV</ELEMENTS>
+</NEKTAR>