More solver, utility and library tutorials how to learn yourself

We will start by searching the source code for information on how to use solvers, utilities and libraries. Then we will learn how to use a small number of useful utilities and libraries. Some of them are described in the UserGuide and ProgrammersGuide, some are described in the OpenFOAM Wiki (e.g. Turbomachinery Working Group) and some of them have been discussed in the Forum. In your home assignment you will be asked to go through some of the written tutorials in the UserGuide and ProgrammersGuide, where you will nd some written tutorials. It is HIGHLY recommended that you dig through ALL of the UserGuide and ProgrammersGuide (before complaining that there is not enough OpenFOAM documentation). If you nd a utility, solver or library that is not described anywhere (or insufciently described), you can include a description of it in your project tutorial. I A would prefer if you then use my L TEX slide template, so that I can easily use it in coming courses (then please proved the raw tex-le and accompanying graphical les).

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

68

How to search for solver tutorials in the source code

Type tut to go to the $FOAM_TUTORIALS directory. Here you nd many case-setups for the solvers in OpenFOAM. Unfortunately, they are not well-described. Describing these tutorials in words and gures may be part of your project. Type: tree -d -L 2 $FOAM_TUTORIALS to get a list of which solvers there are tutorial cases available. Type: tree -d -L 1 $FOAM_TUTORIALS/incompressible/icoFoam to get a list of which tutorial cases are available for the icoFoam solver. All the solver tutorials have Allrun scripts that describe the use of those tutorials. We will now have a look at the Allrun script of the $FOAM_TUTORIALS/incompressible/icoFoam tutorials. This is actually what you will do manually when you do the cavity tutorials in the UserGuide. In other words, you can use the Allrun script as a short summary of the description in the UserGuide.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

69

Run the icoFoam cavity tutorials using the Allrun script (1/7)
(Note that the following description shows the principle. There might be small differences in exactly what is done by the Allrun script between versions.)

In the icoFoam tutorial directory there is an Allrun script. When running this script it is preferred to copy the entire directory to your run directory. Type: cp -r $FOAM_TUTORIALS/incompressible/icoFoam $FOAM_RUN cd $FOAM_RUN/icoFoam ./Allrun >& log_Allrun& Looking in the Allrun script, you can see a list of cases that will be executed: cavityCases="cavity cavityFine cavityGrade cavityHighRe cavityClipped" Some of those cases are actually created by the script. At the end of the script it also runs the elbow case. The script contains Linux commands and calls for OpenFOAM applications in order to set up and run the simulations.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

70

Run the icoFoam cavity tutorials using the Allrun script (2/7)
The Allrun script for the icoFoam cavity tutorials actually rst runs the cavity case #Running blockMesh on cavity: blockMesh #Running icoFoam on cavity: icoFoam

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

71

Run the icoFoam cavity tutorials using the Allrun script (3/7)
The Allrun script for the icoFoam cavity tutorials actually then runs the cavityFine case: #Cloning cavityFine case from cavity: mkdir cavityFine cp -r cavity/{0,system,constant} cavityFine [change "20 20 1" in blockMeshDict to "41 41 1"] [set startTime in controlDict to 0.5] [set endTime in controlDict to 0.7] [set deltaT in controlDict to 0.0025] [set writeControl in controlDict to runTime] [set writeInterval in controlDict to 0.1] #Running blockMesh on cavityFine blockMesh #Running mapFields from cavity to cavityFine mapFields -case cavity -sourceTime latestTime -consistent #Running icoFoam on cavityFine icoFoam

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

72

Run the icoFoam cavity tutorials using the Allrun script (4/7)
The Allrun script for the icoFoam cavity tutorials actually then runs the cavityGrade case: #Running blockMesh on cavityGrade blockMesh #Running mapFields from cavityFine to cavityGrade mapFields -case cavityFine -sourceTime latestTime -consistent #Running icoFoam on cavityGrade icoFoam

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

73

Run the icoFoam cavity tutorials using the Allrun script (5/7)
The Allrun script for the icoFoam cavity tutorials actually then runs the cavityHighRe case: #Cloning cavityHighRe case from cavity mkdir cavityHighRe cp -r cavity/{0,system,constant} cavityHighRe #Setting cavityHighRe to generate a secondary vortex [set startFrom in controlDict to latestTime;] [set endTime in controlDict to 2.0;] [change 0.01 in transportProperties to 0.001] #Copying cavity/0* directory to cavityHighRe cp -r cavity/0* cavityHighRe #Running blockMesh on cavityHighRe blockMesh #Running icoFoam on cavityHighRe icoFoam

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

74

Run the icoFoam cavity tutorials using the Allrun script (6/7)
The Allrun script for the icoFoam cavity tutorials actually then runs the cavityClipped case: #Running blockMesh on cavityClipped blockMesh #Running mapFields from cavity to cavityClipped cp -r cavityClipped/0 cavityClipped/0.5 mapFields -case cavity -sourceTime latestTime [Reset the boundary condition for fixedWalls to:] [ type fixedValue; ] [ value uniform (0 0 0); ] [ We do this since the fixedWalls got ] [ interpolated values by cutting the domain ] #Running icoFoam on cavityClipped icoFoam

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

75

Run the icoFoam cavity tutorials using the Allrun script (7/7)
The Allrun script for the icoFoam cavity tutorials actually nally runs the elbow case

Now, open each case with paraFoam and have a look.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

76

Run ALL the tutorials using the Allrun scripts

We will not do this now! You can also run another Allrun script, located in the $FOAM_TUTORIALS directory. This script will run through ALL the tutorials (calls Allrun in each solver directory). You can use this script as a tutorial of how to generate the meshes, how to run the solvers, how to clone cases, how to map the results between different cases etc.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

77

Finding tutorials for the utilities in OpenFOAM

There are no case tutorials for the utilities, but we can search for examples:
find $WM_PROJECT_DIR -name \*Dict | grep -v blockMeshDict | grep -v controlDict

You will get a list of example dictionaries for the utilities that use a dictionary. Some of those examples can be found next to the source code of each particular utility, and some are also used in the solver tutorials. The ones that dont use a dictionary are usually easier to learn how to use, in particular when using the -help ag.

Now you should be ready to go on exploring the applications by yourself.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

78

More tutorials can be found in

The UserGuide The Programmers guide, chapter 3 The OpenFOAM Wiki (in particular the Turbomachinery Working Group) The OpenFOAM Forum

We will now have a look at some utilities and libraries. Please feel free to improve/expand these descriptions as part of your assignment (e.g. 2.0.x, gures etc.)! Use previously mentioned dictionary hints to nd alternatives for entries.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

79

The mapFields utility

The mapFields utility maps the results of one case to another case. You will use this utility when you do the cavityClipped tutorial in the UserGuide (Allrun: mapFields $1 -case $2 -sourceTime latestTime > $2/log.mapFields 2>&1) Try: mapFields cavity -case cavityClipped -sourceTime latestTime Usage (type mapFields -help, version dependent): mapFields <source dir> [-parallelTarget] [-consistent] [-sourceTime scalar] [-parallelSource] [-case dir] [-help] [-doc] [-srcDoc] The time used for the mapping is specied by startFrom/startTime in the target case. The ag -sourceTime can specify another time directory in the source case. The ag -consistent is used if the geometry and boundary conditions are identical in both cases. This is useful when modifying the mesh density of a case. For non-consistent cases a mapFieldsDict dictionary must be edited, see the icoFoam/cavityClipped tutorial. The ags -parallelSource and -parallelTarget are used if any, or both, of the cases are decomposed for parallel simulations.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

80

The sample utility

The sample utility is used to produce graphs for publication or to extract surfaces. You will use this utility when you do the tutorials of the UserGuide, and when you do the ercoftacConicalDiffuser case-study. Usage (sample -help, version dependent): sample [-latestTime] [-time ranges] [-parallel] [-constant] [-noZero] [-case dir] [-region name] [-help] [-doc] [-srcDoc] Copy and modify sampleDict from the plateHole tutorial:
cd $FOAM_RUN/icoFoam cp $FOAM_TUTORIALS/stressAnalysis/solidDisplacementFoam/plateHole/system/sampleDict cavity/system sed -i s/"leftPatch"/"horizontalLine"/g cavity/system/sampleDict sed -i s/"0 0.5 0.25"/"0.001 0.05 0.005"/g cavity/system/sampleDict sed -i s/"0 2 0.25"/"0.099 0.05 0.005"/g cavity/system/sampleDict sed -i s/"axis y"/"axis distance"/g cavity/system/sampleDict sed -i s/"sigmaxx"/"p"/g cavity/system/sampleDict

Running sample -case cavity, the pressure, p, is extracted along a horizontal line at 100 points, and the results are written in cavity/sets. Plot in gnuplot: plot "cavity/sets/0.5/horizontalLine_p.xy" sample can also sample surfaces...

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

81

The sample utility - surfaces

Additions for extracting surface cuts (an additional example is commented):
surfaceFormat vtk;

surfaces ( outputName { //type patch; //patchName movingWall; //triangulate false; type plane; basePoint (0.05 0.05 0.005); normalVector (0 0 1); } );

Run with sample -case cavity The result is written in cavity/surfaces Visualize the surfaces in paraview (File / Open and nd a vtk le in the surfaces directory).

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

82

The sample utility - interpolationScheme

Use dummy entries to see the alternatives for interpolationScheme (interpolationScheme dummy;): cell cellPoint cellPointFace cellPointWallModified (version dependent) See the source code for exact denitions (and help me expand this information): $FOAM_UTILITIES/postProcessing/sampling/sample/sample.C

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

83

The sample utility - formats

Use dummy entries to see the alternatives for formats (version dependent): setFormat: xmgr jplot gnuplot raw surfaceFormat: foamFile null raw vtk See the source code for exact denitions (and help me expand this information): $FOAM_UTILITIES/postProcessing/sampling/sample/sample.C

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

84

The sample utility - types

Use dummy entries to see the alternatives for types (version dependent): Sets:
uniform midPointAndFace face midPoint cloud curve

Surfaces:
thresholdCellFaces cuttingPlane isoSurfaceCell patch isoSurface distanceSurface plane

See the source code for exact denitions (and help me expand this information): $FOAM_UTILITIES/postProcessing/sampling/sample/sample.C

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

85

The foamCalc utility

This utility calculates new elds from existing ones. This replaces some of the utilities in previous versions of OpenFOAM, such as magU and Ucomponents. Usage (NOTE that foamCalc doesnt accept usual ags, and must be run from within the case directory): foamCalc <calcType> <fieldName1 ... fieldNameN> To get a list of available <calcType>s, write: foamCalc xxx and get the following list (version dependent): randomise, magSqr, magGrad, addSubtract, div, mag, interpolate, components Examples: foamCalc div U #(needs: div(U) Gauss linear; in: system/fvSchemes) foamCalc components U The new elds are written in the time directories. An advanced user could try to nd out how to add a <calcType>

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

86

The setFields utility

The setFields utility is used to set values to the elds in specic regions. You will use this when you do the interFoam/damBreak tutorial in the UserGuide. Usage (setFields -help, version dependent): setFields [-latestTime] [-time ranges] [-parallel] [-constant] [-noZero] [-case dir] [-help] [-doc] [-srcDoc] A setFieldsDict dictionary is used. Find an example in the damBreak tutorial:
cd $FOAM_RUN/cavity cp $FOAM_TUTORIALS/multiphase/interFoam/ras/damBreak/system/setFieldsDict cavity/system/ sed -i s/"alpha1"/"p"/g cavity/system/setFieldsDict sed -i s/"box (0 0 -1) (0.1461 0.292 1)"/"box (0 0 -1) (0.05 0.05 1)"/g cavity/system/setFieldsDict setFields -case cavity

- The defaultFieldValues sets the default values of the elds. - A boxToCell bounding box is used to dene a set of cells where the fieldValues should be different than the defaultFieldValues. - Use a dummy instead of boxToCell to see the topoSetSource alternatives. - An advanced user could describe different topoSetSources

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

87

The funkySetFields, groovyBC and swak4Foam utilities

This are really useful community contributions! funkySetFields is a development of the setFields utility, and it includes the option of specifying mathematical expressions etc.: http://openfoamwiki.net/index.php/Contrib_funkySetFields The groovyBC utility is similar, but for boundaries: http://openfoamwiki.net/index.php/Contrib_groovyBC It should be noted that in 2.0.x, there is a new way of setting boundary conditions similar to groovyBC, but with C++ syntax. The above have now been merged into swak4Foam:
http://openfoamwiki.net/index.php/Contrib/swak4Foam http://www.openfoamworkshop.org/6th_OpenFOAM_Workshop_2011/Program/Training/gschaider_slides.pdf http://www.openfoamworkshop.org/6th_OpenFOAM_Workshop_2011/Program/Training/gschaider_material.tgz

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

88

The foamToVTK, checkMesh, and attenMesh utilities

The foamToVTK utility can be used in many different ways. Example: The two empty sides of a 2D mesh must have the same mesh distribution. Add 0.0001 to the z-position of one of the constant/polyMesh/points of the cavity case. The checkMesh utility can be used to verify this. If not, it will complain:
***Number of edges not aligned with or perpendicular to non-empty directions: ???? Writing ???? points on non-aligned edges to set nonAlignedEdges

The point labels are written to constant/polyMesh/sets/nonAlignedEdges Take the opportunity to visualize the point set in paraFoam: First open the cavity case in paraFoam, then use File/Open <case>.OpenFOAM to read in the same case again. This time mark Include Sets, mark only Mesh Parts/NonAlignedEdges, and visualize using box glyphs. Another way to view the problematic points in paraview (not paraFoam): foamToVTK -case cavity -pointSet nonAlignedEdges The result appears in the VTK directory. The flattenMesh utility can sometimes x the problem, like in this case.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

89

The transformPoints utility

Moves, rotates and scales the mesh. Usage (transformPoints -help, version dependent): transformPoints [-translate vector] [-yawPitchRoll (yaw pitch roll)] [-rotateFields] [-parallel] [-rotate (vector vector)] [-rollPitchYaw (roll pitch yaw)] [-scale vector] [-case dir] [-help] [-doc] [-srcDoc] Example: run cp -r cavity cavityMoved transformPoints -case cavityMoved -translate "(0.1 0 0)" Have a look in paraFoam: run touch cavityMoved/cavityMoved.OpenFOAM paraFoam -case cavity Click Accept and then use File/Open to open the cavityMoved.OpenFOAM le at the same time.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

90

The mergeMeshes utility

Takes the meshes from two different cases and merges them into the master case. mergeMeshes reads the system/controlDict of both cases and uses the startTime, so be careful if you have a moving mesh for example. The rst case that you specify will be the master, and a new time (startTime+deltaT) will be written in which a new polymesh is located. Move it to the correct position (constant/polyMesh), and you have a case with the merged mesh. Example (start from clean cases): run cp -r $FOAM_TUTORIALS/incompressible/icoFoam/cavity cavityMerged cp -r $FOAM_TUTORIALS/incompressible/icoFoam/cavity cavityTransformed blockMesh -case cavityMerged blockMesh -case cavityTransformed transformPoints -case cavityTransformed -translate "(0.1 0 0)" mergeMeshes . cavityMerged . cavityTransformed #No dots in 2.0.x! mv cavityMerged/0.005/polyMesh/* cavityMerged/constant/polyMesh Note that the two meshes will keep all their original boundary conditions, so they are not automatically coupled. Try icoFoam! To couple the meshes, use stitchMesh...

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

91

The stitchMesh utility

Couples two uncoupled parts of the mesh that belong to the same case. You should have a patch in one part of the mesh (masterPatch) that ts with a corresponding patch on the other part of the mesh (slavePatch). If you have that, then the command is: stitchMesh masterPatch slavePatch masterPatch and slavePatch are important, as the face and cell numbers will be renamed after the masterPatch. After stitchMesh, masterPatch and slavePatch are still present in the new polymesh/boundary, but they are empty so just delete them. The same thing can be done as well for the boundary conditions in the 0 folder. We have to re-organize the patches for this to work with our cavityMerged case. See www.openfoamwiki.net for more details:
http://openfoamwiki.net/index.php/Sig_Turbomachinery_/_ERCOFTAC_centrifugal_pump_with_a_vaned_diffuser#stitchMesh

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

92

The decomposePar utility

decomposePar makes a domain decomposition for parallel computations. This is described in the UserGuide. Usage: decomposePar [-fields] [-force] [-copyUniform] [-cellDist] [-filterPatches] [-ifRequired] [-case dir] [-region name] [-help] [-doc] [-srcDoc] A decomposeParDict species how the grid should be decomposed. An example can be found in the interFoam/damBreak tutorial: system/decomposeParDict. There are some different alternatives for which method to use for the decomposition. See the UserGuide. numberOfSubdomains species the number of subdomains the grid should be decomposed into. Make sure that you specify the same number of subdomains in the specic decomposition method you will use, otherwise your simulation might not run optimal. We will discuss parallel processing later on.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

93

The reconstructPar utility

reconstructPar is the reverse of decomposePar, reassembling the grid and the results. Usage: reconstructPar [-zeroTime] [-fields "(list of fields)"] [-latestTime] [-time ranges] [-constant] [-noZero] [-noLagrangian] [-case dir] [-region name] [-help] [-doc] [-srcDoc] This is usually done for post-processing, although it is also possible to post-process each domain separately by treating an individual processor directory as a separate case when starting paraFoam. We will discuss parallel processing later on.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

94

functionObjects
functionObjects are general libraries that can be attached run-time to any solver, without having to re-compile the solver. An example can be found in the incompressible/pisoFoam/les/pitzDaily tutorial. A functionObject is added to a solver by adding a functions entry in system/controlDict You can nd functionObjects in the source code, in the OpenFOAM Wiki (www.openfoamwiki.net), and in the OpenFOAM-extend project (www.sourceforge.net). Search the tutorials for examples using: grep -r functionObjectLibs $FOAM_TUTORIALS The implementations can be found in: $FOAM_SRC/postProcessing/functionObjects I need your help documenting this.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

95

The probes and eldAverage functionObjects

The probes functionObject probes the development of the results during a simulation, writing to a le in the directory probes. The eldAverage functionObject calculates the time-average of specied elds and writes the results in the time directories. Copy and modify the functions part at the end of the controlDict of the incompressible/pisoFoam/les/pitzDaily tutorial to your case and run it. Visualize the output le of sample in Gnuplot: plot "probes/0/p" using 1:2,"probes/0/p" using 1:3 Visualize the output from eldAverage in paraFoam.

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

96

The surfaces functionObjects

The surfaces functionObject writes out surface interpolated results to disk. If the surfaceFormat is VTK, those can be viewed in paraview. Two examples (see the commented lines for the second one):
functions( pressure{ type surfaces; functionObjectLibs ("libsampling.so"); outputControl timeStep; outputInterval 1; surfaceFormat vtk; fields ( p ); surfaces ( walls { //type patch; //patchName movingWall; //triangulate false; type plane; normalVector (0 0 1); basePoint (0 0 0.005); } ); } );

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

97

The forceCoeffs functionObject

The forceCoeffs functionObject prints out the lift and drag coefcients. See the sonicFoam/ras tutorial: system/controlDict Note that you must specify realistic reference values! See the source code for the details!

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

98

More functionObjects
http://openfoamwiki.net/index.php/Contrib_simpleFunctionObjects
http://openfoamwiki.net/index.php/Sig_Turbomachienry_/_ERCOFTAC_centrifugal_pump_with_a_vaned_diffuser#Optional_tools

Hakan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics

99