Commit ed5efec2 authored by Dave Moxey's avatar Dave Moxey
Browse files

Merge branch 'feature/FCcombineAvg' into 'master'

FieldConvert module for combining average fields

This MR introduces a new FieldConvert module that combines fields obtained through `FilterAverageFields` or `FilterReynoldsStresses` (the Reynolds stresses are added correctly, what is not possible using only `addfld`).

The number of samples in each field is automatically considered and the total number of samples is stored in the output file, allowing for multiple files from simulations with different numsteps to be combined easily. 

See merge request !620
parents cd44abd2 b2048df8
......@@ -17,6 +17,7 @@ v4.3.2
**FieldConvert**:
- Fix appearence of duplicate messages when running in parallel (!626)
- Fix issue with efficiency when using large number of 3DH1D planes (!627)
- Add module for combining average fields (!620)
**Packaging**:
- Fixes for DEB package dependencies (!630)
......
......@@ -96,6 +96,8 @@ Specifically, FieldConvert has these additional functionalities
\item \inltt{C0Projection}: Computes the C0 projection of a given output file;
\item \inltt{QCriterion}: Computes the Q-Criterion for a given output file;
\item \inltt{addFld}: Sum two .fld files;
\item \inltt{combineAvg}: Combine two \nekpp binary output (.chk or .fld) field file containing averages of fields (and
possibly also Reynolds stresses) into single file;
\item \inltt{concatenate}: Concatenate a \nekpp binary output (.chk or .fld) field file into single file;
\item \inltt{equispacedoutput}: Write data as equi-spaced output using simplices to represent the data for connecting points;
\item \inltt{extract}: Extract a boundary field;
......@@ -202,6 +204,21 @@ the result either in Tecplot, Paraview or VisIt.
%
%
%
\subsection{Combine two .fld files containing time averages: \textit{combineAvg} module}
To combine two .fld files obtained through the AverageFields or ReynoldsStresses filters,
use the \inltt{combineAvg} module of FieldConvert
%
\begin{lstlisting}[style=BashInputStyle]
FieldConvert -m combineAvg:fromfld=file1.fld file1.xml file2.fld \
file3.fld
\end{lstlisting}
%
\inltt{file3.fld} can be processed in a similar way as described
in section \ref{s:utilities:fieldconvert:sub:convert} to visualise
the result either in Tecplot, Paraview or VisIt.
%
%
%
\subsection{Concatenate two files: \textit{concatenate} module}
To concatenate \inltt{file1.fld} and \inltt{file2.fld} into \inltt{file-conc.fld}
one can run the following command
......
......@@ -14,6 +14,7 @@ SET(FieldConvertHeaders
OutputModules/OutputXml.h
ProcessModules/ProcessAddFld.h
ProcessModules/ProcessBoundaryExtract.h
ProcessModules/ProcessCombineAvg.h
ProcessModules/ProcessConcatenateFld.h
ProcessModules/ProcessDeform.h
ProcessModules/ProcessDisplacement.h
......@@ -58,6 +59,7 @@ SET(FieldConvertSources
OutputModules/OutputXml.cpp
ProcessModules/ProcessAddFld.cpp
ProcessModules/ProcessBoundaryExtract.cpp
ProcessModules/ProcessCombineAvg.cpp
ProcessModules/ProcessConcatenateFld.cpp
ProcessModules/ProcessDeform.cpp
ProcessModules/ProcessDisplacement.cpp
......
////////////////////////////////////////////////////////////////////////////////
//
// 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->GetRank() == 0)
{
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;
}
}
}
////////////////////////////////////////////////////////////////////////////////
//
// File: ProcessCombineAvg.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).
//
// 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.
//
////////////////////////////////////////////////////////////////////////////////
#ifndef UTILITIES_PREPROCESSING_FIELDCONVERT_PROCESSCOMBINEAVG
#define UTILITIES_PREPROCESSING_FIELDCONVERT_PROCESSCOMBINEAVG
#include "../Module.h"
namespace Nektar
{
namespace Utilities
{
/**
* @brief This processing module combines two fld files containing average fields
*
*/
class ProcessCombineAvg : public ProcessModule
{
public:
/// Creates an instance of this class
static boost::shared_ptr<Module> create(FieldSharedPtr f)
{
return MemoryManager<ProcessCombineAvg>::AllocateSharedPtr(f);
}
static ModuleKey className;
ProcessCombineAvg(FieldSharedPtr f);
virtual ~ProcessCombineAvg();
/// Write mesh to output file.
virtual void Process(po::variables_map &vm);
virtual std::string GetModuleName()
{
return "ProcessCombineAvg";
}
private:
};
}
}
#endif
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