[Mark JIN]

Dear friends,

I'm a new openfoam user (also has few experience in C++) but have to use openfoam due to my job requirement.

Can any experienced expert help me figure out what was the error as I attached below? This error occurred when I wanted to adjust and apply ABL boundary condition from 'turbinesiting' to my own case. I have ran snappyHexmesh successfully but failed to ran simpleFoam.

Really appreciate for any suggestive guidance!


markjin@markjin-VirtualBox:~/OpenFOAM/markjin-4.1/run/Pavillion$ simpleFoam
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 4.1 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 4.1
Exec : simpleFoam
Date : Feb 06 2017
Time : 17:46:35
Host : "markjin-VirtualBox"
PID : 5988
Case : /home/markjin/OpenFOAM/markjin-4.1/run/Pavillion
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

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

Create mesh for time = 0


SIMPLE: convergence criteria
field p tolerance 0.001
field U tolerance 0.001
field "(k|epsilon|omega)" tolerance 0.001

Reading field p

Reading field U

#0 Foam::error:rintStack(Foam::Ostream&) at ??:?
#1 Foam::sigFpe::sigHandler(int) at ??:?
#2 ? in "/lib/x86_64-linux-gnu/libc.so.6"
#3 log in "/lib/x86_64-linux-gnu/libm.so.6"
#4 Foam::log(Foam::Field<double>&, Foam::UList<double> const&) at ??:?
#5 Foam::log(Foam::tmp<Foam::Field<double> > const&) at ??:?
#6 Foam::atmBoundaryLayer::U(Foam::Field<Foam::Vector <double> > const&) const at ??:?
#7 Foam::atmBoundaryLayerInletVelocityFvPatchVectorFi eld::atmBoundaryLayerInletVelocityFvPatchVectorFie ld(Foam::fvPatch const&, Foam:imensionedField<Foam::Vector<double>, Foam::volMesh> const&, Foam::dictionary const&) at ??:?
#8 Foam::fvPatchField<Foam::Vector<double> >::adddictionaryConstructorToTable<Foam::atmBounda ryLayerInletVelocityFvPatchVectorField>::New(Foam: :fvPatch const&, Foam:imensionedField<Foam::Vector<double>, Foam::volMesh> const&, Foam::dictionary const&) at ??:?
#9 Foam::fvPatchField<Foam::Vector<double> >::New(Foam::fvPatch const&, Foam:imensionedField<Foam::Vector<double>, Foam::volMesh> const&, Foam::dictionary const&) at ??:?
#10 Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh>::Boundary::readField(Foam:imensio nedField<Foam::Vector<double>, Foam::volMesh> const&, Foam::dictionary const&) at ??:?
#11 Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh>::readFields(Foam::dictionary const&) at ??:?
#12 Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh>::readFields() at ??:?
#13 Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh>::GeometricField(Foam::IOobject const&, Foam::fvMesh const&) at ??:?
#14 ? at ??:?
#15 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
#16 ? at ??:?
Floating point exception (core dumped)
markjin@markjin-VirtualBox:~/OpenFOAM/markjin-4.1/run/Pavillion$

[Antimony]

Hi,

What are the values you used for z0, zGround in the ABL definition? And what is the minimum vertical direction coordinate in your simulation?

The output posted seems to indicate a problem with the log function - you are probably taking the log of a non-positive value.

Cheers,
Antimony

[Mark JIN]

Originally Posted by Antimony

Hi,

What are the values you used for z0, zGround in the ABL definition? And what is the minimum vertical direction coordinate in your simulation?

The output posted seems to indicate a problem with the log function - you are probably taking the log of a non-positive value.

Cheers,
Antimony

Dear Antimony,

Thanks for your reply. Please see my ABL as follow. Should I set zGround to be 0? In my case, minimum vertical direction is 0.


/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 4.1 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/

Uref 10.0;
Zref 20;
zDir (0 0 1);
flowDir (1 0 0);
z0 uniform 0.1;
zGround uniform 935.0;
value $internalField;

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

[Antimony]

Hi,

Yes, if your minimum vertical direction coordinate is 0, then zGround should be that.

If you look at the formulation of the ABL velocity, you will see it is log(z+z0-zGround).

If you don't set zGround according to your geometry, it is clear that you will get log of a negative number, which isn't real.

Hope this clarifies.

Cheers,
Antimony

[Mark JIN]

Originally Posted by Antimony

Hi,

Yes, if your minimum vertical direction coordinate is 0, then zGround should be that.

If you look at the formulation of the ABL velocity, you will see it is log(z+z0-zGround).

If you don't set zGround according to your geometry, it is clear that you will get log of a negative number, which isn't real.

Hope this clarifies.

Cheers,
Antimony

Dear Antimony,

Many thanks for the clarification, it has been solved thanks to your guide!

Best,
MarkJIN

[MaySea]

Hi,

Does anyone know if it's somehow possible to run atmBoundaryLayer package with negative vertical coordinates?

I am trying to impose the logarithmic profile over a bathymetric surface, where z represents depth, hence the lowest point is negative. My ABL conditions file:

kappa                0.40;          
Cmu                  0.09;          
flowDir              (0.382683432 -0.923879533 0);
zDir                 (0 0 1);       
Uref                 0.87;       
Zref                 -0.1;        // near the water surface    
z0                   uniform 0.009525; 
d                    uniform 0.0; 
zGround	     -58.4583;  //  minimum seabed depth [m] at the inlets

I keep getting this error:

Time = 0
--> FOAM Warning : 
    From function Foam::Field<Type>::Field(const Foam::word&, const Foam::dictionary&, Foam::label) [with Type = double; Foam::label = int]
    in file /opt/OpenFOAM/OpenFOAM-6/src/OpenFOAM/lnInclude/Field.C at line 324
    Reading "/home/jan/0/k.boundaryField.north" from line 33 to line 35
    expected keyword 'uniform' or 'nonuniform', assuming deprecated Field format from Foam version 2.0.
#0  Foam::error::printStack(Foam::Ostream&) at ??:?
#1  Foam::sigFpe::sigHandler(int) at ??:?
#2  ? in "/lib64/libc.so.6"
#3  log in "/lib64/libm.so.6"
#4  Foam::log(Foam::Field<double>&, Foam::UList<double> const&) at ??:?
#5  Foam::log(Foam::tmp<Foam::Field<double> > const&) at ??:?
#6  Foam::atmBoundaryLayer::atmBoundaryLayer(Foam::Field<Foam::Vector<double> > const&, Foam::dictionary const&) at ??:?
#7  Foam::atmBoundaryLayerInletKFvPatchScalarField::atmBoundaryLayerInletKFvPatchScalarField(Foam::fvPatch const&, Foam::DimensionedField<double, Foam::volMesh> const&, Foam::dictionary const&) at ??:?
#8  Foam::fvPatchField<double>::adddictionaryConstructorToTable<Foam::atmBoundaryLayerInletKFvPatchScalarField>::New(Foam::fvPatch const&, Foam::DimensionedField<double, Foam::volMesh> const&, Foam::dictionary const&) at ??:?
#9  Foam::fvPatchField<double>::New(Foam::fvPatch const&, Foam::DimensionedField<double, Foam::volMesh> const&, Foam::dictionary const&) at ??:?
#10  Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>::Boundary::readField(Foam::DimensionedField<double, Foam::volMesh> const&, Foam::dictionary const&) at ??:?
#11  Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>::readFields(Foam::dictionary const&) at ??:?
#12  Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>::readFields() at ??:?
#13  Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>::GeometricField(Foam::IOobject const&, Foam::fvMesh const&) at ??:?
#14  ? at ??:?
#15  ? at ??:?
#16  __libc_start_main in "/lib64/libc.so.6"
#17  ? at ??:?

Do I need to shift the z coordinates to positive values or is there a workaround?