CFD with OpenSource Software, 2016

Examples of how to use some utilities and functionObjects

(and some Gnuplot, Python, Matplotlib)

©Håkan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics 1

 CFD with OpenSource Software, 2016

Some utilities and functionObjects

• We will now learn how to use a small number of useful utilities and functionOb-
jects. 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.

• It is HIGHLY recommended that you dig through ALL of the UserGuide and
ProgrammersGuide (before complaining that there is not enough OpenFOAM
documentation).

©Håkan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics 2

 CFD with OpenSource Software, 2016

Postprocessing
• Some functionality that was earlier available as utilities for post processing have been
reorganized using functionObjects (discussed more later).
• We will have a look at how to extract data for plotting and visualization in the coming
slides.
• You can list the available options by typing

postProcessing -list

Use the -help flag for more information, as usual.

• You can figure out how to do other kinds of postProcessing by looking at info and exam-
ples in $WM_PROJECT_DIR/etc/caseDicts/postProcessing/

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 CFD with OpenSource Software, 2016

postProcess -func singleGraph

• postProcess -func singleGraph is used to produce graphs for publication.
• Copy the singleGraph dictionary from the plateHole tutorial:
cd $FOAM_RUN/icoFoam/cavity
cp $FOAM_TUTORIALS/stressAnalysis/solidDisplacementFoam/plateHole/system/singleGraph cavity/system

• Modify the singleGraph dictionary to make it match the cavity case:

sed -i s/"0 0.5 0.25"/"0.001 0.05 0.005"/g cavity/system/singleGraph
sed -i s/"0 2 0.25"/"0.099 0.05 0.005"/g cavity/system/singleGraph
sed -i s/"axis y"/"axis distance"/g cavity/system/singleGraph
sed -i s/"sigmaxx"/"p U"/g cavity/system/singleGraph

Running postProcess -func singleGraph -case cavity, the variables p and U

are extracted along a horizontal line at 100 points, and the results are written in
cavity/postProcessing/singleGraph.
• Plot in gnuplot (first type gnuplot in a terminal window):
plot "cavity/postProcessing/singleGraph/0.5/line_p.xy"
exit
• Some info about plotting, in the two next slides...

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 CFD with OpenSource Software, 2016

Plotting with Gnuplot

• Read more about Gnuplot at http://www.gnuplot.info/
• Example of Gnuplot script (copy to myPlot.gplt, run with gnuplot myPlot.gplt,
show plot with display myPlot.png):
set title "Velocity components"
set xlabel "Y-position"
set ylabel "Velocity"
set yrange [-0.3:0.3]
set xtics 0.02
set grid xtics noytics
set terminal png
set output "myPlot.png"
plot "cavity/postProcessing/singleGraph/0.5/line_U.xy"\
using 1:2 every ::5 with lines title "U_X",\
"cavity/postProcessing/singleGraph/0.5/line_U.xy"\
using 1:3 every ::5 with lines title "U_Y"

• using 1:2 means plot column 2 against 1

• every ::5 means start at line 5

• Short format: u 1:2 ev ::5 w l t "U_X"

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 CFD with OpenSource Software, 2016

Plotting with Python and Matplotlib

• You can also use Python and Matplotlib to plot your results

• See http://openfoamwiki.net/index.php/Sig_Turbomachinery_/_Timisoara_Swirl_Generator#Post-processing_using_Python
and http://www.scipy.org/Plotting_Tutorial
• Copy the text below to plotPressure.py (make sure the indentation is correct), type
python plotPressure.py
#!/usr/bin/env python
description = """ Plot the pressure samples."""
import os, sys
import math
from pylab import *
from numpy import loadtxt
def addToPlots( timeName ):
fileName = "cavity/postProcessing/singleGraph/" + timeName + "/line_p.xy"
i=[]
time=[]
abc =loadtxt(fileName, skiprows=4)
for z in abc:
time.append(z[0])
i.append(z[1])
legend = "Pressure at " + timeName
plot(time,i,label="Time " + timeName )
figure(1);
ylabel(" p/rho "); xlabel(" Distance (m) "); title(" Pressure along sample line ")
grid()
hold(True)
for dirStr in os.listdir("cavity/postProcessing/singleGraph/"):
addToPlots( dirStr )
legend(loc="upper left")
savefig("myPlot.jpeg")
show() #Problems with ssh

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 CFD with OpenSource Software, 2016

Plotting with xmgrace

• You can plot the pressure with xmgrace:
xmgrace cavity/postProcessing/singleGraph/0.5/line_p.xy

• and the velocity components:

xmgrace -block \
cavity/postProcessing/singleGraph/0.5/line_U.xy -bxy 1:2 -bxy 1:3 -bxy 1:4

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 CFD with OpenSource Software, 2016

postProcess -func surfaces

• postProcess -func surfaces is used to extract surfaces in VTK format.
• Find a surfaces dictionary file example in
$WM_PROJECT_DIR/etc/caseDicts/postProcessing/visualization/surfaces
A modified version for the cavity case follows on the next slide, to be put in the system
directory and executed by
postProcess -func surfaces -case cavity
• The results are written in
cavity/postProcessing/surfaces.
• Open the VTK files in Paraview / paraFoam

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 CFD with OpenSource Software, 2016

surfaces dictionary for postProcess -func surfaces

/*--------------------------------*- C++ -*----------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Web: www.OpenFOAM.org
\\/ M anipulation |
-------------------------------------------------------------------------------
Description
Writes out surface files with interpolated field data in VTK format, e.g.
cutting planes, iso-surfaces and patch boundary surfaces.

This file includes a selection of example surfaces, each of which the user
should configure and/or remove.

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

#includeEtc "caseDicts/postProcessing/visualization/surfaces.cfg"

fields (p U);

surfaces
(
zNormal
{
$cuttingPlane;
pointAndNormalDict
{
basePoint (0.05 0.05 0.005); // Overrides default basePoint (0 0 0)
normalVector $z; // $y: macro for (0 0 1)
}
}
p0
{
$isosurface;
isoField p;
isoValue 0;
}
movingWall
{
$patchSurface;
patches (movingWall);
}
);

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

©Håkan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics 9

 CFD with OpenSource Software, 2016

postProcess -func ’div(U)’ (and ’components(U)’)

• Use postProcess to calculate new fields from existing ones.

• First add to cavity/system/fvSchemes, under divSchemes:

div(U) Gauss linear;
This is needed to specify how the div operator should operate.

• Execute by:
postProcess -func 'div(U)' -case cavity

• Try also extracting the components of U:

postProcess -func 'components(U)' -case cavity

• The new fields are written in the time directories.

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 CFD with OpenSource Software, 2016

The mapFields utility

• The mapFields utility maps the results of one case to another case. We already did the
procedure while running the icoFoam/Allrun script, but let’s do it again by hand:
cd $FOAM_RUN/icoFoam/cavity
#Assumes that you copied all icoFoam tutorials before:
#cp -r $FOAM_TUTORIALS/incompressible/icoFoam $FOAM_RUN
• Run the cavity case:
blockMesh -case cavity
icoFoam -case cavity >& log_cavity
• Prepare the cavityClipped case and map the cavity/0.5 results to it:
blockMesh -case cavityClipped
cp -r cavityClipped/0 cavityClipped/0.5
mapFields cavity -case cavityClipped -sourceTime latestTime
• We first copied the 0 directory to 0.5, since mapFields applies the mapping to the
startFrom/startTime directory of the cavityClipped case, which is by default set
to 0.5. Try setting startTime 0; to map to that time directory.
• The flag -sourceTime latestTime sais that the cavity/0.5 results should be used.

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 CFD with OpenSource Software, 2016

The mapFields utility

• Type mapFields -help to get the optional flags
• The flag -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, while preserving
the geometry and patch names.
• For non-consistent cases a mapFieldsDict dictionary must be edited, see
cavityClipped/system/mapFieldsDict:

patchMap ( lid movingWall );

cuttingPatches ( fixedWalls );

The first line sais that the name of the top patch has different names in the cases.
The second line sais that the fixedWalls patch is cutting through the cavity case.
• The flags -parallelSource and -parallelTarget are used if any, or both, of the
cases are decomposed for parallel simulations.

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 CFD with OpenSource Software, 2016

The setFields utility

• The setFields utility is used to set values to the fields in specific regions. You use this
if you do the interFoam/damBreak tutorial in the UserGuide.

• Type setFields -help for optional flags

• A setFieldsDict dictionary is used. Find an example in the damBreak tutorial.

• We here copy the setFieldsDict from damBreak, and modify and run it for cavity:
cd $FOAM_RUN/icoFoam/cavity
cp $FOAM_TUTORIALS/multiphase/interFoam/ras/damBreak/damBreak/system/setFieldsDict cavity/system/
sed -i s/"alpha.water"/"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

• Have a look at the cavity/system/setFieldsDict:

- The defaultFieldValues sets the default values of the fields.

- A boxToCell bounding box is used to define a set of cells where the fieldValues
should be different than the defaultFieldValues.

- Use a dummy instead of boxToCell to see the topoSetSource alternatives.

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 CFD with OpenSource Software, 2016

The funkySetFields, groovyBC and swak4Foam utilities

(related to setFields)
These 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 from 2.0.x, there is a new way of setting boundary conditions
similar to groovyBC, but with C++ syntax (codedFixedValue - google it!).

• The above have now been merged into swak4Foam (Swiss Army Knife For Foam):

http://openfoamwiki.net/index.php/Contrib/swak4Foam

See also the OpenFOAM Workshop training material:

www.openfoamworkshop.org

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 CFD with OpenSource Software, 2016

The foamToVTK, checkMesh, and flattenMesh 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 fix the problem, like in this case.

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 CFD with OpenSource Software, 2016

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:
cd $FOAM_RUN/icoFoam/cavity; blockMesh -case cavity
cp -r cavity cavityMoved
transformPoints -case cavityMoved -translate "(0.1 0 0)"

• Have a look in paraFoam:

touch cavityMoved/cavityMoved.OpenFOAM
paraFoam -case cavity
Click Apply and then use File/Open to open the cavityMoved.OpenFOAM file at the
same time.

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 CFD with OpenSource Software, 2016

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 first 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/cavity cavityMerged
cp -r $FOAM_TUTORIALS/incompressible/icoFoam/cavity/cavity cavityTransformed
blockMesh -case cavityMerged
blockMesh -case cavityTransformed
transformPoints -case cavityTransformed -translate "(0.1 0 0)"
mergeMeshes cavityMerged cavityTransformed
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...

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 CFD with OpenSource Software, 2016

The stitchMesh utility

• Couples two uncoupled mesh regions, belonging to the same case.

• You should have a patch in one region of the mesh (masterPatch) that fits with a cor-
responding patch in the other region of the mesh (slavePatch). If you have that, then
the command is:
stitchMesh masterPatch slavePatch

• 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, so we
will do it for another case.

First let’s run and have a look at the original interFoam/ras/damBreak/damBreak

tutorial
(not in slides)

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 CFD with OpenSource Software, 2016

Example: mergeMeshes and stitchMesh

Create two fresh interFoam/ras/damBreak cases:
run
cp -r $FOAM_TUTORIALS/multiphase/interFoam/ras/damBreak/damBreak damBreakLeft
cp -r $FOAM_TUTORIALS/multiphase/interFoam/ras/damBreak/damBreak damBreakRight
Change the right wall name of damBreakLeft to rightWallLeft, and the left wall name of
damBreakRight to rightWallRight, since they are to be stitched (make sure to do this only
once!):
sed -i s/rightWall/rightWallLeft/g damBreakLeft/system/blockMeshDict
sed -i s/leftWall/leftWallRight/g damBreakRight/system/blockMeshDict
Modify the number of cells in damBreakRight and create the meshes of both parts.:
sed -i s/" 42 "/" 43 "/g damBreakRight/system/blockMeshDict
blockMesh -case damBreakLeft
blockMesh -case damBreakRight

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 CFD with OpenSource Software, 2016

Example: mergeMeshes and stitchMesh

Move the damBreakRight case so that its leftWallRight coincides with the rightWallLeft
patch of damBreakLeft, and merge the meshes into damBreakLeft:
transformPoints -translate "(0.584 0 0)" -case damBreakRight
mergeMeshes damBreakLeft damBreakRight
rm -r damBreakRight
rm -r damBreakLeft/constant/polyMesh
mv damBreakLeft/0.001/polyMesh damBreakLeft/constant
rmdir damBreakLeft/0.001
Change the patch names in the 0-directory, using regex(7) POSIX expressions (make sure to do
this only once!):
sed -i s/"leftWall"/'"leftWall.*"'/g damBreakLeft/0/*
sed -i s/"rightWall"/'"rightWall.*"'/g damBreakLeft/0/*
Run the case:
setFields -case damBreakLeft
interFoam -case damBreakLeft >& log
paraFoam -case damBreakLeft
Clean up:
rm -r damBreakLeft/{0.*,[1-9]*}

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 CFD with OpenSource Software, 2016

Example: mergeMeshes and stitchMesh

Stitch the damBreakLeft case:
• Check that you have two regions:
checkMesh -case damBreakLeft #=> *Number of regions: 2

• Stitch the two regions into a single region:

stitchMesh -case damBreakLeft rightWallLeft leftWallRight
rm -r damBreakLeft/constant/polyMesh
mv damBreakLeft/0.001/polyMesh damBreakLeft/constant
rm -r damBreakLeft/0.001 #Also the variables have been saved, but we
#keep the original in the 0 directory!

• Check that you have one region:

checkMesh -case damBreakLeft #=> Number of regions: 1 (OK).

• Run and visualize (use Surface With Edges representation to see the stitching):
setFields -case damBreakLeft
interFoam -case damBreakLeft >& log
paraFoam -case damBreakLeft

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 CFD with OpenSource Software, 2016

The decomposePar utility

• decomposePar makes a domain decomposition for parallel computations. This is de-
scribed in the UserGuide.

• Type decomposePar -help to see optional flags

• A decomposeParDict specifies how the mesh should be decomposed. An example can

be found in the interFoam/damBreak tutorial: system/decomposeParDict.
numberOfSubdomains specifies the number of subdomains the grid should be decom-
posed into. Make sure that you specify the same number of subdomains in the specific
decomposition method you will use, otherwise your simulation might not run optimal.
• Try running in parallel:
rm -r damBreakLeft/{0.*,[1-9]*}
decomposePar -case damBreakLeft
mpirun -np 4 interFoam -case damBreakLeft -parallel >& log&
top

• Use flag -force if you have already decomposed, but want to do it again.

• Try also changing to scotch (does not require a scotchCoeffs)

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 CFD with OpenSource Software, 2016

The reconstructPar utility

• reconstructPar is the reverse of decomposePar, reassembling the mesh and the re-
sults.

• Type reconstructPar -help to see optional flags

• 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, or using the paraFoam flag \verb-builtin+.
• Try reconstructing our case:
reconstructPar -case damBreakLeft

It will do the time directories that are available until now.

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 CFD with OpenSource Software, 2016

Modifying dictionaries with changeDictionary

In system/changeDictionaryDict (test on clean cavity case):
FoamFile
{
version 2.0;
format ascii;
class dictionary;
object changeDictionaryDict;
}
boundary
{
frontAndBack
{
type symmetryPlane;
}
}
U
{
internalField uniform (0.01 0 0);
boundaryField
{
frontAndBack
{
type symmetryPlane;
}
".*Wall.*" // ".*" is for RegExp
{
type fixedValue;
value uniform (0.01 0 0);
}
}
}

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 CFD with OpenSource Software, 2016

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 find functionObjects in the source code, in the OpenFOAM

Wiki (www.openfoamwiki.net), and in the OpenFOAM-extend project
(www.sourceforge.net).

• The implementations can be found in:

$FOAM_SRC/functionObjects
Have a look in the *.H files for descriptions of how to use them (see
e.g. forces/forces/forces.H). This information can also be found in
Doxygen. In some cases there are also controlDict examples in those
directories.

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 CFD with OpenSource Software, 2016

The fieldMinMax functionObject

• Add to damBreakLeft/system/controlDict:
functions
{
minMaxU
{
type fieldMinMax;
libs ("libfieldFunctionObjects.so");
enabled true;
log false;
write true;
fields
(
U
);
mode magnitude;
writeControl timeStep;
writeInterval 1;
}
}

• Run the case:

interFoam -case damBreakLeft >& log&

• Output in (time directory according to when it was initialized):

damBreakLeft/postProcessing/minMaxU/0/fieldMinMax.dat

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 CFD with OpenSource Software, 2016

Plot the output of fieldMinMax

• The output of fieldMinMax is a bit complex:
# Field minima and maxima
# Time field min position(min) max position(max)
0.00119048 U 0 (0 0.00299993 0.0073) 0.0553571 (0.146 0.296857 0.0073)
0.00258503 U 0 (0 0.00299993 0.0073) 0.124416 (0.171391 0.00299994 0.0073)
0.00422003 U 0 (0 0.00299993 0.0073) 0.238544 (0.171391 0.00299994 0.0073)

• Use sed and gnuplot to plot, removing headerline and unwanted char-
acters (U, (, and )):
plot '<sed "s/U//g;s/(//g;s/)//g" damBreakLeft/postProcessing/minMaxU/0/fieldMinMax.dat'\
using 1:7 every ::2 with lines title "X-position of maximum velocity magnitude"

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 CFD with OpenSource Software, 2016

The probes functionObject

• The probes functionObject probes the development of the results during a
simulation, writing to a file in the directory postProcessing/probes.
• Be inspired by incompressible/pisoFoam/les/pitzDaily and add
to the functions dictionary in controlDict:
probes
{
type probes;
functionObjectLibs ("libsampling.so");
enabled true;
writeControl timeStep;
writeInterval 1;
fields
(
U
);
probeLocations
(
( 0.1778 0.0253 0 )
);
}

• Plot with gnuplot as for fieldMinMax

• Note that the values are the cell center values, i.e. not interpolated!

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 CFD with OpenSource Software, 2016

The fieldAverage functionObject

• The fieldAverage functionObject calculates the time-average of speci-
fied fields and writes the results in the time directories.
• Be inspired by incompressible/pisoFoam/les/pitzDaily and add
to the functions dictionary in controlDict:
fieldAverage1
{
type fieldAverage;
libs ("libfieldFunctionObjects.so");
enabled true;
writeControl outputTime;
fields
(
U
{
mean on;
prime2Mean on; //RMS
base time;
}
);
}

• There are now also files fieldAverage1Properties in [0-9]*/uniform.

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 CFD with OpenSource Software, 2016

The surfaces functionObject

The surfaces functionObject writes out surface interpolated results to disk.
If the surfaceFormat is VTK, those can be viewed in paraview.

First example:
surfaceSampling
{
type surfaces;
libs ("libsampling.so"); Two more examples:
enabled true;
atmosphere
writeControl outputTime;
{
interpolationScheme cellPoint;
type patch;
surfaceFormat vtk;
patches ( atmosphere );
fields ( U );
triangulate false;
surfaces
}
(
plane
nearWall
{
{
type plane;
type patchInternalField;
normalVector (0 0 1);
patches ( leftWall );
basePoint (0 0 0.005);
distance 1E-6;
}
interpolate true;
triangulate false;
}
);
}

The VTK files end up in postProcessing/surfaceSampling for each outputTime.

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 CFD with OpenSource Software, 2016

The forces functionObject

• The viscous and pressure forces and moments (about a center of rotation)
is reported by the forces functionObject (try with damBreakLeft):
forces
{
type forces;
libs ("libforces.so");
patches ( lowerWall );
rhoName rho;
pName p;
UName U;
CofR (0 0 0);
rhoInf 1000;
name forces;
uitype forces;
writeControl timeStep;
writeInterval 1;
format ascii;
}

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 CFD with OpenSource Software, 2016

The forceCoeffs functionObject

• The lift and drag coefficients are reported by the forceCoeffs func-
tionObject (try with damBreakLeft), see sonicFoam/ras:
forceCoeffs
{
type forceCoeffs;
libs ( "libforces.so" );
writeControl timeStep;
writeInterval 1;
patches ( lowerWall );
pName p;
UName U;
log true;
rhoInf 1;
CofR ( 0 0 0 );
liftDir ( -0.239733 0.970839 0 );
dragDir ( 0.970839 0.239733 0 );
pitchAxis ( 0 0 1 );
magUInf 618.022;
lRef 1;
Aref 1;
}

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 CFD with OpenSource Software, 2016

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

• http://openfoamwiki.net/index.php/Contrib/swak4Foam

©Håkan Nilsson, Chalmers / Applied Mechanics / Fluid Dynamics 33