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Problem running perturbUCyl

The question might seem trivial to some, but I am only a beginner with OpenFoam, just 2 weeks into it.

I am trying to simulate pipe flow using LES. I generated the mesh using ICEM CFD and then imported it as Fluent Mesh (.msh file) and then converted it using fluentMeshtoFoam.

I then try to generate turbulence quickly, and hence I try using PerturbCylinder. When I try to run PerturbUcyl on the terminal, the following error message is generated. Any idea, as to how it can be fixed. I am modifying the ChannelFoam inbuilt solver to set up my code.

Quote:

| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.1.0 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.1.0-0bc225064152
Exec : perturbUCyl
Date : Mar 08 2012
Time : 12:44:01
Host : "fwss116"
PID : 13356
Case : /home/sen04/OpenFOAM/sen04-2.1.0/testMesh
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Time = 0
Reading U

--> FOAM FATAL IO ERROR:
size 60000 is not equal to the given value of 180297

file: /home/sen04/OpenFOAM/sen04-2.1.0/testMesh/0/U from line 18 to line 60068.

From function Field<Type>::Field(const word& keyword, const dictionary&, const label)
in file /opt/openfoam210/src/OpenFOAM/lnInclude/Field.C at line 236.

FOAM exiting

Many thanks.

Hi sen,

I am also a newie in OpenFOAM, and I am also simulating the channel flow in OF using LES. I am also trying to use this utility PeturbU, to generate turbulence in the initial field, but did not get a correct version of it, that can run on my machine. Can you tell me the link?

Quote:

Originally Posted by sen.1986 (Post 348384)

Quote:

Originally Posted by dhruv (Post 348889)

You can download it from here,

http://http://www.cfd-online.com/Forums/openfoam-solving/58905-les-turbulent-pipe-flow.html

It seems ok to me.

Though I have solved the problem that I had stated previously, which was caused due to wrong initialisations in the 0 directory, I am still trying to find my way. As it stands now, I have extremely high Courant numbers. The time step that I deduced from the experimental data is 2d-5. Does someone have a suggestion as to how one might go about it, or maybe, what one might try?

Hi,

Thanks for the reply. Regarding the Courant no, did you fix the maxCo in controlDict? It happened in my case too, when I ran the calculation, but then I had fixed it, and it was stable.

Regards,
dhruv.

Quote:

Originally Posted by sen.1986 (Post 348906)

Hi,

Can you tell me how did you compile it. I am using wmake perturbU, and it gives in the following error.

Quote:

Making dependency list for source file perturbU.C
could not open file fvCFD.H for source file perturbU.C
g++ perturbU.C -o perturbU
perturbU.C:43:19: error: fvCFD.H: No such file or directory
perturbU.C:44:20: error: Random.H: No such file or directory
perturbU.C:50:28: error: setRootCase.H: No such file or directory
perturbU.C:52:27: error: createTime.H: No such file or directory
perturbU.C:53:27: error: createMesh.H: No such file or directory
perturbU.C: In function ‘int main(int, char**)’:
perturbU.C:62: error: ‘IOdictionary’ was not declared in this scope
perturbU.C:62: error: expected ‘;’ before ‘perturbDict’
perturbU.C:73: error: ‘scalar’ does not name a type
perturbU.C:74: error: ‘scalar’ does not name a type
perturbU.C:75: error: ‘perturbDict’ was not declared in this scope
perturbU.C:75: error: ‘readBool’ was not declared in this scope
perturbU.C:77: error: ‘direction’ does not name a type
perturbU.C:78: error: ‘direction’ does not name a type
perturbU.C:80: error: ‘Info’ was not declared in this scope
perturbU.C:80: error: ‘h’ was not declared in this scope
perturbU.C:80: error: ‘nl’ was not declared in this scope
perturbU.C:81: error: ‘Retau’ was not declared in this scope
perturbU.C:82: error: ‘Switch’ was not declared in this scope
perturbU.C:84: error: ‘streamDir’ was not declared in this scope
perturbU.C:85: error: ‘spanDir’ was not declared in this scope
perturbU.C:86: error: ‘endl’ was not declared in this scope
perturbU.C:91: error: ‘args’ was not declared in this scope
perturbU.C:91: error: ‘FatalErrorIn’ was not declared in this scope
perturbU.C:94: error: ‘FatalError’ was not declared in this scope
perturbU.C:94: error: ‘exit’ was not declared in this scope
perturbU.C:99: error: ‘args’ was not declared in this scope
perturbU.C:99: error: ‘FatalErrorIn’ was not declared in this scope
perturbU.C:104: error: ‘FatalError’ was not declared in this scope
perturbU.C:104: error: ‘exit’ was not declared in this scope
perturbU.C:109: error: ‘direction’ was not declared in this scope
perturbU.C:109: error: expected ‘;’ before ‘heightDir’
perturbU.C:110: error: ‘heightDir’ was not declared in this scope
perturbU.C:114: error: ‘heightDir’ was not declared in this scope
perturbU.C:120: error: ‘IOobject’ was not declared in this scope
perturbU.C:120: error: expected ‘;’ before ‘Uheader’
perturbU.C:128: error: ‘volVectorField’ was not declared in this scope
perturbU.C:128: error: expected ‘;’ before ‘U’
perturbU.C:130: error: expected ‘;’ before ‘transportProperties’
perturbU.C:142: error: ‘dimensionedScalar’ was not declared in this scope
perturbU.C:142: error: expected ‘;’ before ‘nu’
perturbU.C:146: error: ‘dimensionedVector’ was not declared in this scope
perturbU.C:146: error: expected ‘;’ before ‘Ubar’
perturbU.C:152: error: ‘nu’ was not declared in this scope
perturbU.C:153: error: ‘Ubar’ was not declared in this scope
perturbU.C:155: error: ‘scalar’ does not name a type
perturbU.C:156: error: ‘utau’ was not declared in this scope
perturbU.C:160: error: ‘scalar’ does not name a type
perturbU.C:162: error: ‘scalar’ does not name a type
perturbU.C:163: error: ‘scalar’ does not name a type
perturbU.C:165: error: ‘scalar’ does not name a type
perturbU.C:166: error: ‘scalar’ does not name a type
perturbU.C:169: error: ‘Random’ was not declared in this scope
perturbU.C:169: error: expected ‘;’ before ‘perturbation’
perturbU.C:171: error: expected initializer before ‘&’ token
perturbU.C:173: error: ‘centres’ was not declared in this scope
perturbU.C:173: error: ‘celli’ was not declared in this scope
perturbU.C:173: error: ‘forAll’ was not declared in this scope
perturbU.C:174: error: expected ‘;’ before ‘{’ token
perturbU.C:218: error: expected ‘}’ at end of input
make: *** [perturbU] Error 1

Regards,
Dhruv

Quote:

Originally Posted by sen.1986 (Post 348906)

Quote:

Originally Posted by dhruv (Post 348920)

Hi,

Can you tell me how did you compile it. I am using wmake perturbU, and it gives in the following error.

Regards,
Dhruv

What do you write on the terminal? 'wmake perturbU'? I did the same, and it flashed me the same error.

What you can or rather should do is write 'wmake' only on the terminal. Make sure you are in the 'perturbU' folder, while doing that. It should work, I guess. After that, come out of the perturbU folder and write 'perturbU' on the terminal. The turbulence will be generated I guess.

I found the source of my problem, somewhat though. The modified 'U' field, after I run perturbUCyl is quite unreasonable. Before running perturbUCyl, my internal field is defined uniformly as (1,0,0). After running perturbUCyl, the non uniform internal field varies somewhere in the range of (10e6 - 10e7, 0, 0). Apart from the unusually high Ux, the 0 field for Uz is not expected. Uy is not altered, that is fine, but why Uz?

Anyone with any suggestions?

PerturbU Compilation error

Hi sen.1986

Thanks for the input. i tried to compile it. However it again throws up this error.

Quote:

SOURCE=perturbU.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-100 -I/soft/OpenFOAM/OpenFOAM-2.1.x/src/meshTools/lnInclude -I/soft/OpenFOAM/OpenFOAM-2.1.x/src/finiteVolume/lnInclude -IlnInclude -I. -I/soft/OpenFOAM/OpenFOAM-2.1.x/src/OpenFOAM/lnInclude -I/soft/OpenFOAM/OpenFOAM-2.1.x/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/perturbU.o
perturbU.C: In function ‘int main(int, char**)’:
perturbU.C:162: error: ‘physicalConstant’ has not been declared
perturbU.C:165: error: ‘physicalConstant’ has not been declared
make: *** [Make/linux64GccDPOpt/perturbU.o] Error 1

I took a look in the perturbU.C file, where there is a mention of physical constant. How can we specify this constant? What is the significance?

Regards,
Dhruv.

Quote:

Originally Posted by sen.1986 (Post 349091)

Quote:

Originally Posted by dhruv (Post 349124)

Hi sen.1986

I took a look in the perturbU.C file, where there is a mention of physical constant. How can we specify this constant? What is the significance?

Regards,
Dhruv.

No idea. Check the perturU.c file and your initialisations. (0 directory). Sorry for not being of much help.

Ok, so I found this. The perturbUCyl is functional when I keep the inlet values at zeroGradient. But when I try to put them as cyclic (which is what I need), the following error message is flashed.

Quote:

/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.1.0 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.1.0-0bc225064152
Exec : perturbUCyl
Date : Mar 13 2012
Time : 14:32:25
Host : "fwss116"
PID : 6645
Case : /home/sen04/OpenFOAM/sen04-2.1.0/testMesh
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

--> FOAM FATAL ERROR:
face 0 area does not match neighbour by 23.4543% -- possible face ordering problem.
patch:INLET_half0 my area:2.35009 neighbour area:2.97451 matching tolerance:0.0001
Mesh face:534768 fc:(0 -16.2802 18.383)
Neighbour fc:(0 24.4505 1.86661e-05)
If you are certain your matching is correct you can increase the 'matchTolerance' setting in the patch dictionary in the boundary file.
Rerun with cyclic debug flag set for more information.

From function cyclicPolyPatch::calcTransforms()
in file meshes/polyMesh/polyPatches/constraint/cyclic/cyclicPolyPatch.C at line 220.

FOAM exiting

What could have been causing this? All ideas are welcome.

perturbU compilation

Hi

I got the correct answer from this link. Now it works.

http://www.cfd-online.com/Forums/ope...m-2-0-0-a.html

Quote:

Originally Posted by sen.1986 (Post 349149)

No idea. Check the perturU.c file and your initialisations. (0 directory). Sorry for not being of much help.

Quote:

Originally Posted by dhruv (Post 349162)

Hi

I got the correct answer from this link. Now it works.

http://www.cfd-online.com/Forums/ope...m-2-0-0-a.html

Nice! So if you don't mind telling, what conditions are you using for 'inlet' and 'outlet' in the, /0/U file, Boundary field?

Hi sen,

I was a little late in posting, but the above post is related to the compilation and the problem I was facing with physicalConstant. The link given in my post addresses that.

Secondly, I am using cyclic condition for my inlet and outlet. I ran perturbU but did not encounter these errors. However, I did have error like this, when I tried to run my case having cyclic patches in parallel. The only thing I can recommend you is to try to use createPatch to generate your cyclic patches. I hope it helps.

Quote:

Originally Posted by sen.1986 (Post 349164)

Nice! So if you don't mind telling, what conditions are you using for 'inlet' and 'outlet' in the, /0/U file, Boundary field?

Hello Dhruv,

I got rid of the previous problem. I redid my meshing and modeling, this time using blockmeshdict. The reported problems are mainly caused due to orientation problem of faces.

Anyway, my problem with perturbU is far from being over. The 'U' field that perturbU generates, is very unreasonable. The Ux are in the range of ~4000, Uy is 0 (understandably so), Uz is also 0 (Why?).

Do you have any idea, what might be causing this? Also, it would be helpful if you could attach three files, your 'transportproperties', 'U' after you run perturbU and the script, perturbU.c. Sorry for sounding too demanding.

Hi Sen,

Sorry for the late reply. Can you tell me the following:

1. What is the velocity that you impose at the beginning of the channel?
2. How did you calculate the expected U_tau and Re_tau?

I am also having the problems with perturbU, that it does not generate the fields in my whole geometry. I am pretty sure, that I am not wrong in giving the dimensions for the channel case, that I have. I am attaching the pictures of the fields getting generated. As you can see, Uz is being generated only in a part of the channel, and the whole thing.

My transport properties are

Code:

/*--------------------------------*- C++ -*----------------------------------*\

| =========                 |                                                 |

| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |

|  \\    /   O peration     | Version:  2.1.x                                 |

|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |

|    \\/     M anipulation  |                                                 |

\*---------------------------------------------------------------------------*/

FoamFile

{

    version     2.0;

    format      ascii;

    class       dictionary;

    location    "constant";

    object      transportProperties;

}

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //



Ubar            Ubar [ 0 1 -1 0 0 0 0 ] ( 0.8 0 0 );



Retau           Retau [ 0 0 0 0 0 0 0 ] 5;



transportModel  Newtonian;



nu              nu [ 0 2 -1 0 0 0 0 ] 1.52e-06;



//Retau           Retau [ 0 0 0 0 0 0 0 ] 500;



CrossPowerLawCoeffs

{

    nu0             nu0 [ 0 2 -1 0 0 0 0 ] 1e-06;

    nuInf           nuInf [ 0 2 -1 0 0 0 0 ] 1e-06;

    m               m [ 0 0 1 0 0 0 0 ] 1;

    n               n [ 0 0 0 0 0 0 0 ] 1;

}



BirdCarreauCoeffs

{

    nu0             nu0 [ 0 2 -1 0 0 0 0 ] 1e-06;

    nuInf           nuInf [ 0 2 -1 0 0 0 0 ] 1e-06;

    k               k [ 0 0 1 0 0 0 0 ] 0;

    n               n [ 0 0 0 0 0 0 0 ] 1;

}





// ************************************************************************* //

My perturbUDict file is

Code:

/*---------------------------------------------------------------------------*\

| =========                 |                                                 |

| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |

|  \\    /   O peration     | Version:  1.0                                   |

|   \\  /    A nd           | Web:      http://www.openfoam.org               |

|    \\/     M anipulation  |                                                 |

\*---------------------------------------------------------------------------*/



FoamFile

{

    version         2.0;

    format          ascii;



    root            "/home/penfold/mattijs/foam/mattijs2.1/run/icoFoam";

    case            "cavity";

    instance        "system";

    local           "";



    class           dictionary;

    object          perturbUDict;

}



// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //





// Expected turbulent Re(tau) Reynolds number with respect to utau

Retau 395;



// Streamwise component of flow. 0=x, 1=y, 2=z

streamwise 0;



// Spanwise component of flow. 0=x, 1=y, 2=z

spanwise 2;



// Halfheight of channel. This is the direction normal to both streamwise and

// spanwise directions.

h 0.0024;



// Set (overwrite) velocity to laminar profile

setBulk false;



// Perturb velocity with some cosine like perturbations

perturb true;



// Perturbation properties

//wall normal circulation as a fraction of Ubar/utau

duplus 0.25;

//spanwise perturbation spacing in wall units

betaPlus 200;

//streamwise perturbation spacing in wall units

alphaPlus 500;

//transverse decay

sigma 0.00055;

//linear perturbation amplitude as a fraction of Ubar

epsilon 0.005;





// ************************************************************************* //

Quote:

Originally Posted by sen.1986 (Post 349568)

Quote:

Originally Posted by sen.1986 (Post 349568)

Hi Sen,

I am replying here on a post of already more than five years ago but I hope that you can help me out.

I have a similar problem with using PerturbU to generate a U initial field for a cylinder with cyclic boundary conditions. The values for Ux (streamwise direction) are very large ~11000 and Uy and Uz are zero. I tried different Retau but the results are the same.

I was wondering if you have found a way to generate a U initial field, either with PerturbU or with another tool? Something that works for pipe flow with periodic conditions.

Thank you very much for any suggestions!

I was searching the forums for something different entirely, but came across this post. In case someone else is searching and looking for an answer to the above problem, I believe it is because the Retau and diameter values are hard-coded in perturbCylinder. You have to edit the perturbU.C file and either change the const scalar Retau and d values to what is correct for your case, or edit the code to read in these values from somewhere (such as the transportProperties file, like the code does for Ubar).

I have seen that perturbCylinder only works for flow in the x direction, is it rght? And how can I calculate Ra_tau rightly?