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Old   January 16, 2013, 11:24
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  #281
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Ed Ransley
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Hi Niels,

Thanks for the info. I've done as you said and copied my waves2Foam folder from my desktop to the cluster but I'm having some problems making it on the cluster. Is there a specific place the folder needs to be to run the Allwmake command? I tried having waves2Foam in opt/OpenFoam/ as I want the libraries to be available to multiple users but I get lots of 'no rule to make target issues? Any tips on how to resolve this?

Thanks a lot

Ed

The terminal read out I got is below:

[root@fotcluster1 waves2Foam]# ./Allwmake > w2f.txt
make[1]: Entering directory `/opt/OpenFOAM/waves2Foam/applications/utilities/misc'
make[2]: Entering directory `/opt/OpenFOAM/waves2Foam/applications/utilities/misc/matlab'
make[3]: Entering directory `/opt/OpenFOAM/waves2Foam/applications/utilities/misc/matlab/postprocessing'
make[3]: Nothing to be done for `application'.
make[3]: Leaving directory `/opt/OpenFOAM/waves2Foam/applications/utilities/misc/matlab/postprocessing'
make[3]: Entering directory `/opt/OpenFOAM/waves2Foam/applications/utilities/misc/matlab/preprocessing'
make[3]: Nothing to be done for `application'.
make[3]: Leaving directory `/opt/OpenFOAM/waves2Foam/applications/utilities/misc/matlab/preprocessing'
make[2]: Leaving directory `/opt/OpenFOAM/waves2Foam/applications/utilities/misc/matlab'
make[1]: Leaving directory `/opt/OpenFOAM/waves2Foam/applications/utilities/misc'
make[1]: Entering directory `/opt/OpenFOAM/waves2Foam/applications/utilities/postProcessing'
make[2]: Entering directory `/opt/OpenFOAM/waves2Foam/applications/utilities/postProcessing/surfaceElevation'
make[2]: Leaving directory `/opt/OpenFOAM/waves2Foam/applications/utilities/postProcessing/surfaceElevation'
make[1]: Leaving directory `/opt/OpenFOAM/waves2Foam/applications/utilities/postProcessing'
make[1]: Entering directory `/opt/OpenFOAM/waves2Foam/applications/utilities/preProcessing'
make[2]: Entering directory `/opt/OpenFOAM/waves2Foam/applications/utilities/preProcessing/relaxationZoneLayout'
make[2]: Leaving directory `/opt/OpenFOAM/waves2Foam/applications/utilities/preProcessing/relaxationZoneLayout'
make[2]: Entering directory `/opt/OpenFOAM/waves2Foam/applications/utilities/preProcessing/setWaveField'
make[2]: Leaving directory `/opt/OpenFOAM/waves2Foam/applications/utilities/preProcessing/setWaveField'
make[2]: Entering directory `/opt/OpenFOAM/waves2Foam/applications/utilities/preProcessing/setWaveParameters'
make[2]: Leaving directory `/opt/OpenFOAM/waves2Foam/applications/utilities/preProcessing/setWaveParameters'
make[1]: Leaving directory `/opt/OpenFOAM/waves2Foam/applications/utilities/preProcessing'

make: *** No rule to make target `lnInclude/sampledSurfaceElevation.H', needed by `sampling/sampledSurfaceElevationFunctionObject/sampledSurfac$
./Allwmake: line 47: cd: applications/solvers/solvers200: No such file or directory
make[2]: *** No rule to make target `../../../../src/lnInclude/IOsampledSurfaceElevation.H', needed by `surfaceElevation.dep'.
make[2]: *** No rule to make target `../../../../src/lnInclude/sampledSurfaceElevation.H', needed by `surfaceElevation.dep'.
make[2]: *** No rule to make target `/opt/OpenFOAM/OpenFOAM-2.0.x/src/OSspecific/POSIX/lnInclude/sigWriteNow.H', needed by `surfaceElevation.de$
make[2]: *** No rule to make target `/opt/OpenFOAM/OpenFOAM-2.0.x/src/OSspecific/POSIX/lnInclude/sigStopAtWriteNow.H', needed by `surfaceElevat$
make[2]: *** No rule to make target `../../../../src/lnInclude/sampledSurfaceElevationTemplates.C', needed by `surfaceElevation.dep'.
make[2]: *** No rule to make target `../../../../src/lnInclude/readWaveProperties.H', needed by `surfaceElevation.dep'.
make[2]: Failed to remake makefile `surfaceElevation.dep'.
make[2]: Target `/root/OpenFOAM/root-2.0.x/platforms/linux64Gcc45DPOpt/bin/surfaceElevation' not remade because of errors.
make[1]: *** [surfaceElevation] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [postProcessing] Error 2
make[2]: *** No rule to make target `/opt/OpenFOAM/OpenFOAM-2.0.x/src/OSspecific/POSIX/lnInclude/sigWriteNow.H', needed by `relaxationZoneLayou$
make[2]: *** No rule to make target `/opt/OpenFOAM/OpenFOAM-2.0.x/src/OSspecific/POSIX/lnInclude/sigStopAtWriteNow.H', needed by `relaxationZon$
make[2]: *** No rule to make target `../../../../src/lnInclude/relaxationShape.H', needed by `relaxationZoneLayout.dep'.
make[2]: *** No rule to make target `../../../../src/lnInclude/relaxationWeight.H', needed by `relaxationZoneLayout.dep'.
make[2]: *** No rule to make target `../../../../src/lnInclude/relaxationWeightCourantCorrection.H', needed by `relaxationZoneLayout.dep'.
make[2]: *** No rule to make target `../../../../src/lnInclude/readWaveProperties.H', needed by `relaxationZoneLayout.dep'.
make[2]: Failed to remake makefile `relaxationZoneLayout.dep'.
make[2]: Target `/root/OpenFOAM/root-2.0.x/platforms/linux64Gcc45DPOpt/bin/relaxationZoneLayout' not remade because of errors.
make[1]: *** [relaxationZoneLayout] Error 2
make[2]: *** No rule to make target `/opt/OpenFOAM/OpenFOAM-2.0.x/src/OSspecific/POSIX/lnInclude/sigWriteNow.H', needed by `setWaveField.dep'.
make[2]: *** No rule to make target `/opt/OpenFOAM/OpenFOAM-2.0.x/src/OSspecific/POSIX/lnInclude/sigStopAtWriteNow.H', needed by `setWaveField.$
make[2]: *** No rule to make target `../../../../src/lnInclude/setWaveField.H', needed by `setWaveField.dep'.
make[2]: *** No rule to make target `../../../../src/lnInclude/convexPolyhedral.H', needed by `setWaveField.dep'.
make[2]: *** No rule to make target `../../../../src/lnInclude/localFace.H', needed by `setWaveField.dep'.
make[2]: *** No rule to make target `../../../../src/lnInclude/localCell.H', needed by `setWaveField.dep'.
make[2]: *** No rule to make target `../../../../src/lnInclude/localCellNeg.H', needed by `setWaveField.dep'.
make[2]: Failed to remake makefile `setWaveField.dep'.
make[2]: Target `/root/OpenFOAM/root-2.0.x/platforms/linux64Gcc45DPOpt/bin/setWaveField' not remade because of errors.
make[1]: *** [setWaveField] Error 2
make[2]: *** No rule to make target `/opt/OpenFOAM/OpenFOAM-2.0.x/src/OSspecific/POSIX/lnInclude/sigWriteNow.H', needed by `setWaveParameters.d$
make[2]: *** No rule to make target `/opt/OpenFOAM/OpenFOAM-2.0.x/src/OSspecific/POSIX/lnInclude/sigStopAtWriteNow.H', needed by `setWaveParame$
make[2]: *** No rule to make target `../../../../src/lnInclude/setWaveProperties.H', needed by `setWaveParameters.dep'.
make[2]: Failed to remake makefile `setWaveParameters.dep'.
make[2]: Target `/root/OpenFOAM/root-2.0.x/platforms/linux64Gcc45DPOpt/bin/setWaveParameters' not remade because of errors.
make[1]: *** [setWaveParameters] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [preProcessing] Error 2
make: Target `application' not remade because of errors.
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Old   January 16, 2013, 12:05
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  #282
ngj
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Niels Gjoel Jacobsen
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Hi Ed,

Did you make a

Code:
wclean all
in the waves2Foam directory before compiling? If not it could have carried some settings from your private computer, and it typically confuses the compilation process.

Kind regards,

Niels
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Old   January 19, 2013, 06:59
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  #283
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Mohammad Ghandali
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Quote:
Originally Posted by ngj View Post
Dear Mohammed,

Please execute the "Allrun" script as
Code:
./Allrun
This script does (as the name suggests ) all what is needed to run the tutorial. It is a simple text file, so you can see, what happens ``inside''.

Kind regards,

Niels
Hi again dear Niels

i try to run waveflume tutorials and i execute ./Allrun script and then i run blockMesh and its ok and then run setWaveField and it runs ok when i run the solver waveFoam in terminal it says command not found
and also i try with interFoam in terminal then i get this error
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.0.1 |
| \\ / A nd | Web: www.OpenFOAM.com |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.0.1-51f1de99a4bc
Exec : interFoam
Date : Jan 20 2013
Time : 14:36:42
Host : mohammad-desktop
PID : 3570
Case : /home/mohammad/Desktop/waveFlume
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

// using new solver syntax:
pcorr
{
solver GAMG;
tolerance 1e-07;
relTol 0;
smoother DIC;
nPreSweeps 0;
nPostSweeps 2;
nFinestSweeps 2;
cacheAgglomeration true;
nCellsInCoarsestLevel 10;
agglomerator faceAreaPair;
mergeLevels 1;
}

// using new solver syntax:
p_rgh
{
solver GAMG;
tolerance 1e-07;
relTol 0;
smoother DIC;
nPreSweeps 0;
nPostSweeps 2;
nFinestSweeps 2;
cacheAgglomeration true;
nCellsInCoarsestLevel 10;
agglomerator faceAreaPair;
mergeLevels 1;
}

// using new solver syntax:
p_rghFinal
{
solver GAMG;
tolerance 1e-08;
relTol 0;
smoother DIC;
nPreSweeps 0;
nPostSweeps 2;
nFinestSweeps 2;
cacheAgglomeration true;
nCellsInCoarsestLevel 10;
agglomerator faceAreaPair;
mergeLevels 1;
}

// using new solver syntax:
U
{
solver PBiCG;
preconditioner DILU;
tolerance 1e-09;
relTol 0;
}

// using new solver syntax:
UFinal
{
solver PBiCG;
preconditioner DILU;
tolerance 1e-09;
relTol 0;
}

// using new solver syntax:
gamma
{
solver PBiCG;
preconditioner DILU;
tolerance 1e-07;
relTol 0;
}


PIMPLE: Operating solver in PISO mode

Reading field p_rgh

Reading field alpha1



--> FOAM FATAL IO ERROR:
Unknown patchField type waveAlpha for patch type patch

Valid patchField types are :

69
(
advective
alphaFixedPressure
atmBoundaryLayerInletEpsilon
buoyantPressure
calculated
codedFixedValue
constantAlphaContactAngle
cyclic
cyclicSlip
directMapped
directMappedField
directMappedFixedInternalValue
directMappedFixedPushedInternalValue
directionMixed
dynamicAlphaContactAngle
empty
epsilonWallFunction
fan
fanPressure
fixedFluxPressure
fixedGradient
fixedInternalValue
fixedPressureCompressibleDensity
fixedValue
freestream
freestreamPressure
inletOutlet
inletOutletTotalTemperature
kappatJayatillekeWallFunction
kqRWallFunction
mixed
nonuniformTransformCyclic
nuSgsUSpaldingWallFunction
nutLowReWallFunction
nutTabulatedWallFunction
nutURoughWallFunction
nutUSpaldingWallFunction
nutUWallFunction
nutkRoughWallFunction
nutkWallFunction
omegaWallFunction
oscillatingFixedValue
outletInlet
outletMappedUniformInlet
partialSlip
processor
processorCyclic
rotatingTotalPressure
selfContainedDirectMapped
sliced
slip
symmetryPlane
syringePressure
timeVaryingAlphaContactAngle
timeVaryingMappedFixedValue
timeVaryingTotalPressure
timeVaryingUniformFixedValue
totalPressure
totalTemperature
turbulentHeatFluxTemperature
turbulentInlet
turbulentIntensityKineticEnergyInlet
turbulentMixingLengthDissipationRateInlet
turbulentMixingLengthFrequencyInlet
uniformDensityHydrostaticPressure
uniformFixedValue
waveTransmissive
wedge
zeroGradient
)


file: /home/mohammad/Desktop/waveFlume/0/alpha1::boundaryField::inlet from line 21450 to line 21518.

From function fvPatchField<Type>::New(const fvPatch&, const DimensionedField<Type, volMesh>&, const dictionary&)
in file /home/opencfd/OpenFOAM/OpenFOAM-2.0.1/src/finiteVolume/lnInclude/fvPatchFieldNew.C at line 135.

FOAM exiting

please help me
like always i thank you for your best helping
king regards
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Old   January 19, 2013, 09:11
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  #284
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Niels Gjoel Jacobsen
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Hi Mohamad,

It appears that the solvers in waves2Foam has not been compiled correctly. Otherwise, the executable should be known.

Try to recompile waves2Foam and identify, whether any errors are reported.

The error using waves2Foam is related to the fact that the boundary condition waveAlpha is distributed along with libwaves2Foam.so, which interFoam does not know.

Kind regards,

Niels

P.S. I have just seen that you are using 2.0.1. No solvers are distributed with waves2Foam for that version. Please follow the guidelines on the wiki for creating the waveFoam solver.

Link: http://openfoamwiki.net/index.php/Contrib/waves2Foam
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Old   January 25, 2013, 00:19
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Hello Niels,

Months ago I started to learn OpenFOAM v2.1.1 and I'm interested in wave generation and further wave-structure interaction within the framework of OF. It's great to see that you have developed a toolbox. I am trying to learn it by first running the tutorials within the wave2foam package.

Currently as you said, the SVN is currently down (see: http://openfoamwiki.net/index.php/Main_Page). I downloaded the package from a source I have forgotten, but I copied the code into the my home directory and it seems that it's compiled successfully, as I can run all the tutorials except periodicSolitary and 3Dwaves. I reported part of the info below, could you please take some time to help me check what's going wrong? Thanks in advance.

1. periodicSolitary
In blockMesh...

Reading patches section
--> FOAM Warning :
From function blockMesh::createTopology(IOdictionary&)
in file blockMesh/blockMeshTopology.C at line 129
Old-style cyclic definition. Splitting patch cyclic1 into two halves cyclic1_half0 and cyclic1_half1
Alternatively use new 'boundary' dictionary syntax.

In setWaveField...
Reading field alpha

--> FOAM FATAL IO ERROR:
Cannot find patchField entry for cyclic cyclic1_half0
Is your field uptodate with split cyclics?
Run foamUpgradeCyclics to convert mesh and fields to split cyclics.

2. 3Dwaves
faceSet
/opt/openfoam211/bin/tools/RunFunctions: line 47: faceSet: command not found
====
Converting faces on zone "f0" into baffles.

--> FOAM FATAL ERROR:
Cannot find faceZone "f0"
Valid zones are
0
(
)

From function createBaffles
in file createBaffles.C at line 175.
====
setsToZones

Create polyMesh for time = 0

--> FOAM FATAL ERROR:
Cannot find file "" in directory "polyMesh/sets" in times 0 down to constant

From function Time::findInstance(const fileName&, const word&, const IOobject::readOption, const word&)
in file db/Time/findInstance.C at line 140.

Last edited by jasonchen; January 25, 2013 at 00:36.
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Old   January 25, 2013, 00:43
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  #286
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Hello Niels,

Another question about the breaking wave validation case in your paper, 3.3

As there is slope in the computational domain, fig 8, did you use snappyHexMesh to generate the meshes? The geometry is rather simple, but by using snappyHexMesh, I have to prepare a STL file, and input a large number of parameters in snappyHexMeshDict. Have you got any idea to easily prepare the required files?

Regards,
Jason
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Old   January 27, 2013, 16:37
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  #287
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Niels Gjoel Jacobsen
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Hi Jason,

With respect to the cyclic and the baffles, apparently the syntax has changed to your version of OF from the version I originally developed waves2Foam in. When you have figured out how to solve it, please write me, so I can modify the tutorials.

Secondly, I used my own small matlab-script to create the mesh. I will upload the mesh files here as soon as possible.

Kind regards,

Niels
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Old   January 28, 2013, 16:48
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Hi Niels,
Thanks for your quick reply. Now i managed to creat a mesh using blockMesh. I modified the waveProperties file for waveFlume to simulate the spilling breaker case.
The file is copied below. Is it ok to specify initializationName as inlet in this case.

// A list of the relaxation zones in the simulation. The parameters are given
// in <name>Coeffs below.
relaxationNames (inlet);
initializationName inlet;
pName p_rgh;
inletCoeffs
{
// Wave type to be used at boundary "inlet" and in relaxation zone "inlet"
waveType cnoidalFirst;
Tsoft 2;
depth 0.400000;
period 2;
direction (1 0 0);
height 0.125;

// Specifications on the relaxation zone shape and relaxation scheme
relaxationZone
{
relaxationScheme Spatial;
relaxationShape Rectangular;
beachType Empty;

relaxType INLET;
startX (-8 0.0 0);
endX (-4 0.0 0.1);
orientation (1.0 0.0 0.0);
}
};

Another big problem is that when i run the case using Allrun script, either w/ or w/t setWaveParameters, the waveProperties file under constant directory is automatically replaced with one using stokeFirst, which is exactly the file for waveFlume case. And for the run with setWaveParameters step, it complains that period is not specified for stokeFirst. Do you have any idea about this? Could you please help me check the file or send me your version of input file for this case? Thanks.

Jason
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Old   January 28, 2013, 17:04
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  #289
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Niels Gjoel Jacobsen
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Hi Jason,

With respect to the initializationName, you can use whatever sub-dictionary, which you have defined.

With respect to the setWaveParameters, then you have to specify input in waveProperties.input. Then a correct waveProperties file is generated, if all input is given correctly in waveProperties.input (look at section 4.1.1. on the wiki: http://openfoamwiki.net/index.php/Co...WaveParameters or the 3Dwaves tutorial).

Also, please note that the Allrun script is tailored for the specific tutorial, thus since setWaveParameters is not used in that tutorial, a tailored waveProperties file is distributed with the tutorial.

Kind regards,

Niels

P.S. Good that you got your mesh working.
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Old   January 28, 2013, 17:54
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Dear Niels,

I am working with a modification of the square pile tutorial. The idea is replacing the pile with a boat stl, so I have added the snappy and the dynamic mesh, so I use waveDyMFoam. I have tried many diferent meshes, the last a millon + cels that checkMesh OK.
No wonder what I do it always ends very soon with FPE. I wander if you could give me a clue as to where to look for the problem, as the courant nš is ok, tried different speeds, etc.
I attach the log file and the terminal output.
Thanks in advance,
Carlos.
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File Type: txt log.txt (10.6 KB, 14 views)
File Type: txt Terminal.txt (12.4 KB, 6 views)
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Old   January 29, 2013, 04:40
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  #291
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Niels Gjoel Jacobsen
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Hi Carlos,

Since it crashes so soon, it is probably related to the mesh motion and VOF coupling. Have you tried running it without waves? I would guess that is still crashes.

@Jason: You can find the mesh I used here: http://www.student.dtu.dk/~ngja/mesh.tar.gz

Kind regards,

Niels
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Old   January 29, 2013, 07:07
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Hi Niels, thanks for answering so soon.

The case has only current, no other wave type but potential current.
Attached a jpg of a run that lasted longer but ended the same way. Since it runs with no mesh motion, it could be related to some issue with the mesh, it may need more room on top to deform freely, I do not know.
Thanks for your attention,
Carlos.
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Old   January 29, 2013, 08:04
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  #293
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Niels Gjoel Jacobsen
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You say it runs without mesh motion, but the ship you have depicted, isn't that being moved? Or have you meshed it in that skewed position?

- Niels
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Old   January 29, 2013, 09:41
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Hi Neils, The picture is the case "with mesh motion" that has run for a short while, allowing me to have a look at what happens. (Short in real time, but it took hour running)
The goal of the simulation is to predict the keel angle and position on the generated wave. I am not much interested in the forces (by now) there fore laminar should be adequate.
Regards,
Carlos.
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Old   January 29, 2013, 18:08
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  #295
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OK. Mesh motion can produce some results from time to time, which are really hard to debug.

A couple of thoughts, which might help:

1. Use a really long ramping time (Tsoft), so the ship motion is not subject to shocks.

2. Use a solution from a potential flow solver with free surface capabilities (do not know of any, though) to initialise the flow field around the ship. Again, avoiding too many shocks.

3. Try with a simple geometry first, e.g. a simplified ship being made of a box and a prism with a triangular cross section. Try to begin with a stationary geometry, i.e. no mesh motion.

4. Look up shipFoam in the forum and couple it with waves2Foam. Unfortunately, the svn/git for the OpenFoam-extend branch is still down, but maybe you can find another source.

5. Some time ago navalPack was released. I have never used it, but the name suggests that it can prove useful.

Good luck,

Niels
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Old   January 30, 2013, 15:52
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Hi Niels,

Thank you very much for your suggestions. I will try ship-foam, that I have downloaded some time ago but was reluctant to try because it works on OF 1.6 which has some differences with 2.1 I have been using.
In any case I will try some of your ideas to learn and how knows, it may work.

Thank you again for your time and help.
Best regards,
Carlos.
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Old   January 30, 2013, 17:11
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  #297
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Niels Gjoel Jacobsen
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I have seen a thread, where a modification of shipFoam to 2.1 was discussed. Try search for it, i.e. use Google on the cfd-online domain

Good luck,

Niels
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Old   February 2, 2013, 06:35
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  #298
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Dear all,

We are currently working on an extension to waves2Foam (hopefully coming out in the late spring/summer of 2013). The key extension is a large post-processing utility, so one does not need to transform the output data into matlab, python or whatever, but you can work with the post-processing directly in OpenFoam.

I have a small question to you, namely: What type of post-processing are you doing on your data?
This is for us to be inspired of which tools to put into the extension.

To give you a flavour, currently the following type of post-processing is implemented and tested:

1. Read probes/surface elevation gauges into the post-processing utility (e.g. velocity, surfaceElevation, forces and moments, void fraction). This includes a concatenation of data from restarted simulations.

2. Perform interpolation to equidistant time series if needed (e.g. for spectral analysis).

3. Output the data in easily accessible ASCII format, i.e. pure numbers in a rectangular matrix format.

4. Spectral analysis (two versions with one for regular and one of irregular waves). Can be carried out on both scalar and vector quantities.

5. Reflection analysis based on the surface elevation signal. Works currently in 2D with two different methods for regular and irregular waves.

6. Ensemble averaging of regular wave quantities (scalar and vector)

7. Trapezoidal time integration and cumulative trapezoidal time integration (scalar and vector).

Any suggestions beyond these methods are highly appreciated.

If extensive implementation is needed, please also provide me with a test case, a mathematical formulation of the problem and a set of results from the analysis to use as validation. Furthermore, a transparent implementation in any language would be nice.

Kind regards,

Niels
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Old   February 11, 2013, 17:55
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carlos
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Hi Niels,

Very interesting, will keep on waiting!!

I have been trying to apply wave2foam to fast speed boat analysis, and finally manage to make it stable.
Now, on Fr nš over 1, the shock of the initial acceleration is to hight so I have been wandering if there is a possibility of making the speed of the current wave as function of time, at least in two steps.

In your previous answer to my first questions, you pointed this up and suggested a hight tsoft. I could not get results with this or did not do it properly, because I get an elevation of the water surface in the inlet and the simulation crashes. If the default is 0, what could be a number to try?

Thanks you for your work and help!
Carlos.
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Old   February 12, 2013, 06:30
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Niels Gjoel Jacobsen
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Hi Carlos,

You can implement any inlet velocity of your liking. Look into the waveTheory folder in the source, and you will quickly be able to make a time varying current.

With respect to the soft start/ramping time, maybe you will need another shape function in the relaxation zone, but I honestly do not know, since I have never tried such types of simulations.

Kind regards,

Niels
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