Problem in Implementing a non-linear SGS model

wyldckat · February 4, 2015, 14:37

Quote:

Originally Posted by zoptirik

but it gave me compalition error (error 1)

Quick answer:

Use the package from post #13
Provide more details on the exact steps you've used.
Please indicate which OpenFOAM version you're using.

zoptirik · February 8, 2015, 07:12

Quote:

Originally Posted by wyldckat

Quick answer:

Use the package from post #13
Provide more details on the exact steps you've used.
Please indicate which OpenFOAM version you're using.

Hi wyldckat

I used the package from post 13, i followed the way that u said post 13. first unpack than build cd nonlinearLESkit ./Allwmake... after compilation

Code:

generic@generic-M4700:~/OpenFOAM/generic-2.3.0/src/turbulenceModels/incompressible/nonlinearLESkit$ ./Allwmake
wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file LESNonlinearModel.C
Making dependency list for source file GennonlinearSGS.C
SOURCE=LESNonlinearModel.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/opt/openfoam230/src/turbulenceModels -I/opt/openfoam230/src/turbulenceModels/LES/LESdeltas/lnInclude -I/opt/openfoam230/src/turbulenceModels/LES/LESfilters/lnInclude -I/opt/openfoam230/src/transportModels -I/opt/openfoam230/src/finiteVolume/lnInclude -I/opt/openfoam230/src/meshTools/lnInclude -IlnInclude -I. -I/opt/openfoam230/src/OpenFOAM/lnInclude -I/opt/openfoam230/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/LESNonlinearModel.o
SOURCE=GennonlinearSGS.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/opt/openfoam230/src/turbulenceModels -I/opt/openfoam230/src/turbulenceModels/LES/LESdeltas/lnInclude -I/opt/openfoam230/src/turbulenceModels/LES/LESfilters/lnInclude -I/opt/openfoam230/src/transportModels -I/opt/openfoam230/src/finiteVolume/lnInclude -I/opt/openfoam230/src/meshTools/lnInclude -IlnInclude -I. -I/opt/openfoam230/src/OpenFOAM/lnInclude -I/opt/openfoam230/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/GennonlinearSGS.o
'/home/generic/OpenFOAM/generic-2.3.0/platforms/linux64GccDPOpt/lib/libLESNonlinearModels.so' is up to date.
wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file Smagorinsky.C
SOURCE=Smagorinsky.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/opt/openfoam230/src/turbulenceModels -I/opt/openfoam230/src/turbulenceModels/LES/LESdeltas/lnInclude -I/opt/openfoam230/src/turbulenceModels/LES/LESfilters/lnInclude -I/opt/openfoam230/src/transportModels -I/opt/openfoam230/src/finiteVolume/lnInclude -I/opt/openfoam230/src/meshTools/lnInclude -I../LESNonlinear/lnInclude -IlnInclude -I. -I/opt/openfoam230/src/OpenFOAM/lnInclude -I/opt/openfoam230/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/Smagorinsky.o
In file included from ../LESNonlinear/lnInclude/GennonlinearSGS.H:42:0,
                 from Smagorinsky.H:53,
                 from Smagorinsky.C:26:
../LESNonlinear/lnInclude/LESNonlinearModel.H: In static member function ‘static Foam::autoPtr<Foam::incompressible::LESNonlinearModel> Foam::incompressible::LESNonlinearModel::adddictionaryConstructorToTable<LESNonlinearModelType>::New(const volVectorField&, const surfaceScalarField&, Foam::transportModel&, const Foam::word&) [with LESNonlinearModelType = Foam::incompressible::LESNonlinearModels::Smagorinsky, Foam::volVectorField = Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh>, Foam::surfaceScalarField = Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh>]’:
../LESNonlinear/lnInclude/LESNonlinearModel.H:115:9:   instantiated from ‘Foam::incompressible::LESNonlinearModel::adddictionaryConstructorToTable<LESNonlinearModelType>::adddictionaryConstructorToTable(const Foam::word&) [with LESNonlinearModelType = Foam::incompressible::LESNonlinearModels::Smagorinsky]’
Smagorinsky.C:41:1:   instantiated from here
../LESNonlinear/lnInclude/LESNonlinearModel.H:115:9: error: cannot allocate an object of abstract type ‘Foam::incompressible::LESNonlinearModels::Smagorinsky’
Smagorinsky.H:68:7: note:   because the following virtual functions are pure within ‘Foam::incompressible::LESNonlinearModels::Smagorinsky’:
/opt/openfoam230/src/turbulenceModels/incompressible/turbulenceModel/turbulenceModel.H:217:37: note:     virtual Foam::tmp<Foam::fvMatrix<Foam::Vector<double> > > Foam::incompressible::turbulenceModel::divDevRhoReff(const volScalarField&, Foam::volVectorField&) const
../LESNonlinear/lnInclude/LESNonlinearModel.H:115:9: warning: control reaches end of non-void function [-Wreturn-type]
make: *** [Make/linux64GccDPOpt/Smagorinsky.o] Error 1

Openfoam version is 2.3.0

zoptirik · February 10, 2015, 06:35

I tried to compile the files separately. LESNonlinear file was compiled successfuly. But when i tried to compile SM-non, it gave me following error

Code:

wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file Smagorinsky.C
SOURCE=Smagorinsky.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/opt/openfoam230/src/turbulenceModels -I/opt/openfoam230/src/turbulenceModels/LES/LESdeltas/lnInclude -I/opt/openfoam230/src/turbulenceModels/LES/LESfilters/lnInclude -I/opt/openfoam230/src/transportModels -I/opt/openfoam230/src/finiteVolume/lnInclude -I/opt/openfoam230/src/meshTools/lnInclude -I../LESNonlinear/lnInclude -IlnInclude -I. -I/opt/openfoam230/src/OpenFOAM/lnInclude -I/opt/openfoam230/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/Smagorinsky.o
In file included from ../LESNonlinear/lnInclude/GennonlinearSGS.H:42:0,
                 from Smagorinsky.H:53,
                 from Smagorinsky.C:26:
../LESNonlinear/lnInclude/LESNonlinearModel.H: In static member function ‘static Foam::autoPtr<Foam::incompressible::LESNonlinearModel> Foam::incompressible::LESNonlinearModel::adddictionaryConstructorToTable<LESNonlinearModelType>::New(const volVectorField&, const surfaceScalarField&, Foam::transportModel&, const Foam::word&) [with LESNonlinearModelType = Foam::incompressible::LESNonlinearModels::Smagorinsky, Foam::volVectorField = Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh>, Foam::surfaceScalarField = Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh>]’:
../LESNonlinear/lnInclude/LESNonlinearModel.H:115:9:   instantiated from ‘Foam::incompressible::LESNonlinearModel::adddictionaryConstructorToTable<LESNonlinearModelType>::adddictionaryConstructorToTable(const Foam::word&) [with LESNonlinearModelType = Foam::incompressible::LESNonlinearModels::Smagorinsky]’
Smagorinsky.C:41:1:   instantiated from here
../LESNonlinear/lnInclude/LESNonlinearModel.H:115:9: error: cannot allocate an object of abstract type ‘Foam::incompressible::LESNonlinearModels::Smagorinsky’
Smagorinsky.H:68:7: note:   because the following virtual functions are pure within ‘Foam::incompressible::LESNonlinearModels::Smagorinsky’:
/opt/openfoam230/src/turbulenceModels/incompressible/turbulenceModel/turbulenceModel.H:217:37: note: 	virtual Foam::tmp<Foam::fvMatrix<Foam::Vector<double> > > Foam::incompressible::turbulenceModel::divDevRhoReff(const volScalarField&, Foam::volVectorField&) const
../LESNonlinear/lnInclude/LESNonlinearModel.H:115:9: warning: control reaches end of non-void function [-Wreturn-type]
make: *** [Make/linux64GccDPOpt/Smagorinsky.o] Error 1

zoptirik · March 2, 2015, 07:38

Hi All

As i said before I am dealing with the SGS stress instead of the eddy viscosity. i tried to compiled nonlinearLEskit, but it gave me compalition error. I couldnt solve the error. Therefore I have used to DeardorffDiffStress based on GenSGSStress. but this model also use nu_sgs in the calculation of divDevReff(U). for making same things with nonlinearLEskit in the computation of divdevreff, i product 0 to nu_sgs term as follows

Code:

 nuSgs_ = 0*rho()*sqrt(K)*delta()

Could I have done something wrong?

Best

huangxianbei · March 19, 2015, 03:34

Quote:

Originally Posted by zoptirik

I tried to compile the files separately. LESNonlinear file was compiled successfuly. But when i tried to compile SM-non, it gave me following error

Code:

wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file Smagorinsky.C
SOURCE=Smagorinsky.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/opt/openfoam230/src/turbulenceModels -I/opt/openfoam230/src/turbulenceModels/LES/LESdeltas/lnInclude -I/opt/openfoam230/src/turbulenceModels/LES/LESfilters/lnInclude -I/opt/openfoam230/src/transportModels -I/opt/openfoam230/src/finiteVolume/lnInclude -I/opt/openfoam230/src/meshTools/lnInclude -I../LESNonlinear/lnInclude -IlnInclude -I. -I/opt/openfoam230/src/OpenFOAM/lnInclude -I/opt/openfoam230/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/Smagorinsky.o
In file included from ../LESNonlinear/lnInclude/GennonlinearSGS.H:42:0,
                 from Smagorinsky.H:53,
                 from Smagorinsky.C:26:
../LESNonlinear/lnInclude/LESNonlinearModel.H: In static member function ‘static Foam::autoPtr<Foam::incompressible::LESNonlinearModel> Foam::incompressible::LESNonlinearModel::adddictionaryConstructorToTable<LESNonlinearModelType>::New(const volVectorField&, const surfaceScalarField&, Foam::transportModel&, const Foam::word&) [with LESNonlinearModelType = Foam::incompressible::LESNonlinearModels::Smagorinsky, Foam::volVectorField = Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh>, Foam::surfaceScalarField = Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh>]’:
../LESNonlinear/lnInclude/LESNonlinearModel.H:115:9:   instantiated from ‘Foam::incompressible::LESNonlinearModel::adddictionaryConstructorToTable<LESNonlinearModelType>::adddictionaryConstructorToTable(const Foam::word&) [with LESNonlinearModelType = Foam::incompressible::LESNonlinearModels::Smagorinsky]’
Smagorinsky.C:41:1:   instantiated from here
../LESNonlinear/lnInclude/LESNonlinearModel.H:115:9: error: cannot allocate an object of abstract type ‘Foam::incompressible::LESNonlinearModels::Smagorinsky’
Smagorinsky.H:68:7: note:   because the following virtual functions are pure within ‘Foam::incompressible::LESNonlinearModels::Smagorinsky’:
/opt/openfoam230/src/turbulenceModels/incompressible/turbulenceModel/turbulenceModel.H:217:37: note: 	virtual Foam::tmp<Foam::fvMatrix<Foam::Vector<double> > > Foam::incompressible::turbulenceModel::divDevRhoReff(const volScalarField&, Foam::volVectorField&) const
../LESNonlinear/lnInclude/LESNonlinearModel.H:115:9: warning: control reaches end of non-void function [-Wreturn-type]
make: *** [Make/linux64GccDPOpt/Smagorinsky.o] Error 1

Hi,
sorry for the late reply. This may be solved when you turn on the debug mode. I can compile this when debug mode is turned on, although I didn't find any error in opti mode on another computer. This is strange, but this may overcome this problem. Anthoer solution may be changing the OF version, to 2.1.1 as I used.

I'm not sure if you have solved your problem, but I have a question that you may also face: how to implement a wall function for nonlinear models?

As in OF, the nuSgs wall function is implemented to correct the turbulent viscosity, however, if as I have done, the SGS stress is treated instead of the turbulent viscosity, so this method can't be used in the nonlinear models.

Do you have any suggestions?

Xianbei

Astrodan · May 19, 2015, 13:30

Quote:

Originally Posted by wyldckat

Oh, the missing important detail is that this line:

Code:

    constructdictionaryConstructorTables();

It was missing from the "LESNonlinearModel::New" method... although I haven't figured out why "LESModel" doesn't need this hack... I'll dig deeper and edit this post to report back if I can figure it out.

------------------

edit: OK, I've figured it out. When optimized, there are some-things that aren't called because it's non-optimal to call something that isn't going to be used in the first place. This might not be the exact situation in this case, but it's probably very close to the truth.
So, if the example simulation case has this entry in the "controlDict" file:

Code:

libs
(
  "libSmagorinsky.so"
);

it will enforce that the table is constructed in order to add the very first new model. If no models were added, then the table would not be constructed in the first place. This pretty much happens in the file "Smagorinsky.C", in this line:

Code:

addToRunTimeSelectionTable(LESNonlinearModel, Smagorinsky, dictionary);

which will construct said table for the first time.

-----------------

Best regards,
Bruno

Hey Bruno & Xianbei,

I just had the same problem with an empty constructorTablePtr_, and it took me 2h to debug and finally find this thread here. It really did annoy me, because I was sure there was nothing wrong, and checked my code five times anyway.. and the stack message is not really helpful.

Do you have any idea if there is any OF-internal possibility to catch this error? I can work with the runTimeSelection interface, but I'm not really familiar, so I don't know where this check could be placed..

wyldckat · May 21, 2015, 16:29

Quote:

Originally Posted by Astrodan

Do you have any idea if there is any OF-internal possibility to catch this error? I can work with the runTimeSelection interface, but I'm not really familiar, so I don't know where this check could be placed..

Quick answer: If you can give us a clear example of what you're trying to fix/solve/catch, it would make it a lot easier to diagnose/search for the solution.
I ask this because I wrote that post 4 months ago and I barely remember what it was all about

Astrodan · May 24, 2015, 11:55

Quote:

Originally Posted by wyldckat

Quick answer: If you can give us a clear example of what you're trying to fix/solve/catch, it would make it a lot easier to diagnose/search for the solution.
I ask this because I wrote that post 4 months ago and I barely remember what it was all about

Sorry, I just read it, so this seemed obvious. My Problem is that this line

Code:

dictionaryConstructorTable::iterator cstrIter = dictionaryConstructorTablePtr_->find(exampleType);

produces a segmentation fault when there is no model in the list, as you described:

Quote:

Originally Posted by wyldckat

...
If no models were added, then the table would not be constructed in the first place. This pretty much happens in the file "Smagorinsky.C", in this line:

Code:

addToRunTimeSelectionTable(LESNonlinearModel, Smagorinsky, dictionary);

which will construct said table for the first time.
...

Whoever wants to reproduce, I attached an example objet library and a solver that creates such an object.

Just compile (./Allwmake) and run exampleFoam.

The error occurs in lib/exampleBaseClassNew.C:18:

Code:

Selecting exampleType randomClass
Veni...
Vidi...
Segmentation fault (core dumped)

(Where Veni vidi vici would be my oldschool debug output)

wyldckat · May 24, 2015, 16:28

Quote:

Originally Posted by Astrodan

Whoever wants to reproduce, I attached an example objet library and a solver that creates such an object.

Just compile (./Allwmake) and run exampleFoam.

Quick answer: There is no attachment in your post

Astrodan · May 26, 2015, 03:33

Reasonable argument. Apparently this thread has some negative influence on my concentration

.

I uploaded the file and added some additional notes at the end of the last post.

wyldckat · September 20, 2015, 13:26

Greetings to all!

OK, this was on my to-do list since... March of this year? And I've finally managed to look into this.

I've used the code from my post #13 and started a new repository for handling all of the modifications of this proof of concept: https://github.com/wyldckat/nonlinearLESkit

The repository now provides the source code adapted to work on:

OpenFOAM 2.1.1, which is the source code from post #13.
OpenFOAM 2.1.x
OpenFOAM 2.3.x - which should work with OpenFOAM versions 2.3.0 to 2.3.x and possibly with OpenFOAM 2.2.

Instructions on how to download and build are provided on the front-page of the project.

Best regards,
Bruno

March 2, 2015, 07:38		#24
zoptirik New Member karar Join Date: Feb 2013 Posts: 13 Rep Power: 13	Hi All As i said before I am dealing with the SGS stress instead of the eddy viscosity. i tried to compiled nonlinearLEskit, but it gave me compalition error. I couldnt solve the error. Therefore I have used to DeardorffDiffStress based on GenSGSStress. but this model also use nu_sgs in the calculation of divDevReff(U). for making same things with nonlinearLEskit in the computation of divdevreff, i product 0 to nu_sgs term as follows Code: nuSgs_ = 0rho()sqrt(K)*delta() Could I have done something wrong? Best

May 26, 2015, 03:33		#30
Astrodan Member Timm Severin Join Date: Mar 2014 Location: Munich Posts: 63 Rep Power: 12	Reasonable argument. Apparently this thread has some negative influence on my concentration . I uploaded the file and added some additional notes at the end of the last post. __________________ PhD Student at the Institute of Biochemical Engineering at TU München Modelling of fluid dynamics in open photobioreactors. System: OpenFOAM 2.3.x, 64bit, 8 Core Xeon Workstation

September 20, 2015, 13:26		#31
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,975 Blog Entries: 45 Rep Power: 128	Greetings to all! OK, this was on my to-do list since... March of this year? And I've finally managed to look into this. I've used the code from my post #13 and started a new repository for handling all of the modifications of this proof of concept: https://github.com/wyldckat/nonlinearLESkit The repository now provides the source code adapted to work on: OpenFOAM 2.1.1, which is the source code from post #13. OpenFOAM 2.1.x OpenFOAM 2.3.x - which should work with OpenFOAM versions 2.3.0 to 2.3.x and possibly with OpenFOAM 2.2. Instructions on how to download and build are provided on the front-page of the project. Best regards, Bruno cfdonline2mohsen likes this. __________________ OpenFOAM: FAQ \| Getting started Forum: How to get help, to post code/output and forum guide Read this before sending me PM

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