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Gerristutorial

TheGerrisTutorial
Version1.3.2
StphanePopinet
[email protected]

March23,2011
Contents
1Introduction
1.1Simulationfile
2Asimplesimulationfile
2.1Afewcommentsonsyntax
2.2Topologydescriptionofthesimulationdomain
2.3Controllingthesimulation
2.3.1Spatialdiscretisation
2.3.2Initialconditions
2.3.3Writingresults
3Amorecomplexexamplewithsolidboundaries
3.1Domaingeometryandboundaryconditions
3.1.1Boundaryconditions
3.1.2Solidboundaries
3.2Savingthewholesimulation
3.3Visualisation
3.3.1GfsView
3.3.2Somepostprocessingusinggfs2oogl
3.4Usingdynamicadaptivemeshrefinement
4Goingfurther
4.1Moreonboundaryconditions
4.2Addingtracers
4.3Addingdiffusionterms
4.3.1Boundaryconditionsfordiffusionterms
4.4Outputs
4.5Boundaryconditions
5RunningGerrisinparallel
6Learningmore
7Doyouwanttohelp?

1Introduction
ThistutorialisastepbystepintroductiontothedifferentconceptsnecessarytouseGerris.Itisspecificallydesignedfor
aenduserandisnotatechnicaldescriptionofthenumericaltechniquesusedwithinGerris.Ifyouareinterestedbythat,
youshouldconsultthebibliographysectionontheGerriswebsite.
Variousversionsofthistutorialareavailable:
Printableformat:PDF.
HTML:directlinkorcompressedarchive.
InthistutorialIwillassumethatyouarefamiliarwiththeUnixshell(andthatyouarerunningsomeversionofaUnix
system).SomeknowledgeofCprogrammingwouldalsobeveryhelpfulifyouintendtoextendGerriswithyourown
objects.
IfGerrisisnotalreadyinstalledonyoursystem,havealookattheinstallationinstructionsontheGerriswebsite.
Wearenowreadytostart.Justtocheckthateverythingisokaytry:
%gerris2DV
http://gfs.sourceforge.net/tutorial/tutorial/tutorial1.html

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1.1Simulationfile
Gerrisisaconsolebasedprogram.Ittakesaparameterorsimulationfileasinputandproducesvarioustypesoffilesas
output.Everythingneededtorunthesimulationisspecifiedintheparameterfile,thisincludes:
Layoutofthesimulationdomain
Initialconditions
Boundaryconditions
Solidboundaries
Whattooutput(andwhen)
Controlparametersforthenumericalschemes

2Asimplesimulationfile
InthissectionwewillseehowtowriteasimulationfilefortheinitialrandomvorticityexampleintheGerriswebsite
gallery.Firstofall,itisalwaysagoodideatorunsimulationsintheirowndirectory.Typethisatyourshellprompt:
%mkdirvorticity
%cdvorticity
Asastartingpointwewillusethefollowingsimulationfile:vorticity.gfs
12GfsSimulationGfsBoxGfsGEdge{}{
GfsTime{end=0}
}
GfsBox{}
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Thisisavalidsimulationfilebutitdoesnotdomuchasyoucanseebytyping
%gerris2Dvorticity.gfs
Itisagoodstartingpointhowevertoexplainthegeneralstructureofasimulationfile.

2.1Afewcommentsonsyntax
Firstofall,therearetwotypesofparametersinasimulationfile:compulsoryandoptionalparameters.Optional
parametersarealwaysspecifiedwithinabracedblock(i.e.ablockoftextdelimitedbybraces({likethis}).They
alsooftentaketheform
parameter=value
whereparameterisanuniqueidentifier(withinthisbracedblock).Alltheotherparametersarecompulsoryparameters.
Forexample,invorticity.gfsboth
GfsTime{end=0}
and
end=0
areoptionalparameters.
Thesecondimportantsyntaxpointregardsthewayvariousfieldsaredelimited.Newline(orcarriagereturn)characters
aregenerallyusedtodelimitatedifferentobjectsinthesimulationfile.Theonlycasewherethisruledoesnotapplyis
withinbracedblocksdefiningoptionalargumentsoftheform

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parameter=value
Forexample,invorticity.gfsthefollowingblocksoftextareallobjects:
12GfsSimulationGfsBoxGfsGEdge{}{
GfsTime{end=0}
}

GfsTime{end=0}

GfsBox{}

11right

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Followingthisrule,vorticty.gfscouldhavebeenwrittenequivalentlyas:
12GfsSimulationGfsBoxGfsGEdge{}{GfsTime{
end=0}
}
GfsBox{}
11right
11top

2.2Topologydescriptionofthesimulationdomain
Ok,sowhatarealltheseobjectsfor?Thefirstlineofthesimulationfiledefinesagraphrepresentingthegenerallayout
ofthesimulationdomainandfollowsthissyntax:
1stfield
numberofnodesinthegraph(1)
2ndfield
numberofedgesconnectingthenodes(2)
3rdfield
objecttypeforthegraph(GfsSimulation)
4thfield
defaultobjecttypeforthenodes(GfsBox)
5thfield
objecttypefortheedges(GfsGEdge)
6thfield
1stoptionalparameters(bracedblock)
7thfield
2ndoptionalparameters(bracedblock)
Wethenjumptotheendofthe2ndoptionalparameterstoline
GfsBox{}
whichdescribesthefirst(anduniqueinthiscase)nodeofthegraph.Thefirstfieldistheobjecttypeofthenode
(GfsBox),thesecondfieldcontainsoptionalparameters.Thefollowingtwolines
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11top
definetheedgesofthegraphasfollows:
1stfield
indexofthestartingnode(1)
2ndfield
indexoftheendingnode(1)
3rdfield
spatialdirectioninwhichthetwonodesareconnected(rightandtop)
Thenodesarealwaysindexedstartingfromone.Thespatialdirectionsaredefinedonfigure1.Fromthis,weseethat
thisfiledefinesasimulationdomaincontainingonenode(aGfsBox)connectedwithitselfinboththehorizontal(right)
andvertical(top)directions.

Figure1:Definitionofspatialdirections

Bydefault,aGfsBoxisasquare(in2D)oracube(in3D)ofsizeunity.Thefirstnodeofthegraphisalwayscenteredon
theoriginandisusedasthereferencetopositiontheothernodes.Wehaveconsequentlydefinedasquaresimulation
domainofsizeunity,centeredontheoriginandusingperiodicboundaryconditions.

2.3Controllingthesimulation
Nowthatwehavedefinedthesimulationdomainandtheboundaryconditions,weneedtospecifytheinitialconditions,
numericalschemesparametersandsoon.Thisisalldonewithinthesecondoptionalparametersblockofthegraph
definition.
Inourfilewehaveforthemomentonlyoneobjectinthisblock:
GfsTime{end=0}
Asitsnameindicate,thisobjectdefinesthephysicalandthecomputationaltime.BycomputationaltimeImeanthe
numberoftimestepsperformed.Bydefaultboththephysicaltimeandthetimestepnumberarezerowhentheprogram
starts.Itispossibletosetdifferentvaluesusingforexample
GfsTime{t=1.4i=32end=0}
whereiisthetimestepnumberandtisthephysicaltime.Theendidentifierspecifiesthatthesimulationshouldstop
whenthephysicaltimereachesthegivenvalue.Itisalsopossibletostopthesimulationwhenaspecifiednumberof
timestepsisreached,usingtheiendidentifier.Ifbothendandiendarespecified,thesimulationstopswheneitherof
thesearereached.Bydefault,bothendandiendvaluesareinfinite.
Ok,letsthenchangethisobjectto
GfsTime{end=50}
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2.3.1Spatialdiscretisation
Thenextstepistospecifywhatspatialresolutionwewantforthediscretisation.Forthemoment,theonlythingwehave
definedistherootofthequad/octree.Thewholedomainisthusdiscretisedwithonlyonegridpoint
Weneedtospecifyhowwewanttorefinethisinitialrootcell.ThisisdonebyusinganGfsRefineobject.Wecandothis
byaddingtheline
GfsRefine6
tothesecondoptionalparameterblock.Thisisthesimplestpossiblewaytorefinetheinitialrootcell.Wetelltheprogram
thatwewanttokeeprefiningthecelltree(bydividingeachcellinfourchildrencells(in2D,eightin3D))untilthelevelof
thecellisequaltofive.Theleveloftherootcelliszero,thelevelofallitschildrencellsisoneandsoonrecursively.
AfterthisrefinementprocesscompleteswehavecreatedaregularCartesiangridwith26=64cellsineachdimensionon
thefinestlevel(6).

2.3.2Initialconditions
Wenowneedtospecifytheinitialconditionsandthevariousactions(suchaswritingresults,informationmessages
etc)wewanttoperformwhenthesimulationisrunning.AllthesethingsaretreatedbyGerrisasvarioustypesof
events,allrepresentedbyobjectsderivedfromthesameparentobjectGfsEvent.
Initialconditionsareaparticulartypeofeventhappeningonlyonceandbeforeanyothertypeofevent,theyareall
derivedfromthesameparentobjectGfsInit.
Gerriscomeswithafewdifferentobjectsdescribingvariousinitialconditions.AsthereisnowayGerriscouldprovideall
thedifferentinitialconditionsuserscouldthinkof,Gerrismakesiteasyforuserstocreatetheirowninitialisationobjects
byextendingtheGfsInitobjectclass.Inordernottohavetorecompile(ormoreexactlyrelink)thewholecode
everytimeanewclassisadded,Gerrisusesdynamicallylinkedmoduleswhichcanbeloadedatruntime.Wewillsee
laterhowtowriteyourownmodules.
Forthemoment,wewillusethedefaultGfsInitobject.Justaddthefollowinglinestovorticity.gfs:
12GfsSimulationGfsBoxGfsGEdge{}{
GfsTime{end=50}
GfsRefine6
GfsInit{}{
U=(0.5rand()/(double)RAND_MAX)
V=(0.5rand()/(double)RAND_MAX)
}
}
GfsBox{}
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UsingGfsInititispossibletosettheinitialvalueofeachofthesimulationvariables.Bydefaultallvariablesaresetto
zeroinitially.InourcasewetellGerristodefinethetwocomponentsofthevelocityfieldUandVasCfunctions.The
standardrandfunctionoftheClibraryreturnsa(pseudo)randomnumberbetween0andRAND_MAX.Thetwofunctions
wedefinedthussetthecomponentsofthevelocitiesineachcellasrandomnumbersbetween0.5and0.5.
Thisisapowerfulfeatureoftheparameterfile.InmostcaseswhereGerrisrequiresanumber(suchastheGfsRefine6
line,afunctionofspaceandtimecanbeusedinstead.Forexample,avalidparameterfilecouldinclude:
...
GfsRefine6.*(1.sqrt(x*x+y*y))
...
whichwoulddefineameshrefinedinconcentriccircles.
Usingthisfeature,itispossibletodefinemostinitialconditionsdirectlyintheparameterfile.

2.3.3Writingresults
Thevorticity.gfsfilewehavenowisallGerrisneedstorunthesimulation.However,forthisruntobeanyuse,we
needtospecifyhowandwhentooutputtheresults.Thisisdonebyusinganotherclassofobjects:GfsOutput,derived
http://gfs.sourceforge.net/tutorial/tutorial/tutorial1.html

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fromGfsEvent.Gerriscomeswithanumberoftheseobjectsallowingtooutputvariousaspectsofthesimulation.
ThegeneralsyntaxforanGfsEventobjectisasfollows:
GfsEvent{
start=0.5step=1e2end=3.4
istart=10iend=46
}
thisdefinesanevent:
startingwheneverthephysicaltimeislargerthan(orequalto)0.5orthetimestepnumberislargerthan(orequal
to)10,
endingwheneverthephysicaltimeisstrictlylargerthan3.4orthetimestepnumberisstrictlylargerthan46,
andoccurringevery102physicaltimeunits.
Itisalsopossibletospecifyaneventstepasanumberoftimestepsusingtheistepidentifier.Note,however,thatyou
cannotspecifybothstepandistepforthesameevent.Bydefault,startandistartarezeroandend,iend,step
andistepareinfinite.
AnGfsOutputobjectisderivedfromGfsEventandfollowsthissyntax:
GfsOutput{}filename%d%f%ld
ThefirstpartofthelineGfsOutput{}definestheGfsEventpartofGfsOutputandfollowsthesyntaxabove.Inthe
remainderofthistutorial,Iwillusethefollowingnotationtoexpressthisinheritanceofsyntax:
[GfsEvent]filename%d%f%ld
toavoidrepeatingthewholethingforeveryderivedobjects.
Thesecondpartfilename%d%f%ldspecifieswheretooutputthings.The%d,%fand%ldcharactersareformatting
stringswhichfollowtheClanguagesyntaxandwillbereplacedeverytimetheeventtakesplaceaccordingto:
%d
%f
%ld

integerreplacedwiththecurrentprocessnumber(usedwhenrunningtheparallelversionofGerris).
floatingpointnumberreplacedwiththecurrentphysicaltime.
(long)integerreplacedwiththecurrenttimestepnumber.

Ofcourse,youarefreenottospecifyanyofthese,inwhichcasetheoutputwilljustbeappendedtothesamefileevery
timetheeventtakesplace.Therearealsotwofilenameswhichhaveaspecialmeaning:stdoutandstderr,forthe
standardoutputandstandarderroroftheshellrespectively.
Wenowaddthefollowingtooursimulationfile:
12GfsSimulationGfsBoxGfsGEdge{}{
GfsTime{end=50}
GfsRefine6
GfsInit{}{
U=(0.5rand()/(double)RAND_MAX)
V=(0.5rand()/(double)RAND_MAX)
}
GfsOutputTime{istep=10}stdout
GfsOutputProjectionStats{istep=10}stdout
}
GfsBox{}
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Thefirstlineweaddedtellstheprogramtooutputinformationaboutthetimeevery10timestepsonthestandardoutput.
Thesecondlineoutputsstatisticsabouttheprojectionpartofthealgorithm.
http://gfs.sourceforge.net/tutorial/tutorial/tutorial1.html

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Youcannowrunthecodelikethis:
%gerris2Dvorticity.gfs
andyoushouldgetanoutputinyourconsolelookinglikethis(youcanstoptheprogramusingCtrlC):
step:0t:0.00000000dt:0.000000e+00
MACprojectionbeforeafterrate
niter:0
residual.bias:0.000e+000.000e+00
residual.first:0.000e+000.000e+000.0
residual.second:0.000e+000.000e+000.0
residual.infty:0.000e+000.000e+000.0
Approximateprojection
niter:0
residual.bias:0.000e+000.000e+00
residual.first:1.050e141.050e140.0
residual.second:1.612e141.612e140.0
residual.infty:7.105e147.105e140.0
step:10t:0.02190704dt:2.801016e03
MACprojectionbeforeafterrate
niter:5
residual.bias:3.053e161.403e16
residual.first:3.365e+012.949e0516.3
residual.second:4.274e+014.676e0515.6
residual.infty:1.954e+023.285e0414.3
Approximateprojection
niter:5
residual.bias:9.714e172.874e16
residual.first:3.322e+012.548e0516.7
residual.second:4.250e+014.062e0516.0
residual.infty:1.880e+023.380e0414.1
step:20t:0.05278371dt:3.531551e03
MACprojectionbeforeafterrate
niter:5
...
Thelinesstartingwithstep:arewrittenbyGfsOutputTime.Theygivethetimestepnumber,correspondingphysical
timeandthetimestepusedforthepreviousiteration.
TheotherlinesarewrittenbyGfsOutputProjectionStatsandgiveyouanideaofthedivergenceerrorsand
convergencerateofthetwoprojectionsteps(MACandapproximate)performedduringthepreviousiteration.Thevarious
normsoftheresidualofthesolutionofthePoissonequationaregivenbeforeandaftertheprojectionstep.Therate
columngivestheaverageamountbywhichthedivergenceisreducedbyeachiterationofthemultigridsolver.
Well,numbersaregreatbutwhataboutsomeimages?Whatwewanttodo,forexample,isoutputsomegraphical
representationofagivenscalarfield.In2D,asimplewaytodothatistocreateanimagewhereeachpixeliscoloured
accordingtothelocalvalueofthescalar.Gerrisprovidesanobjecttodojustthat:GfsOutputPPMwhichwillcreatea
PPM(PortablePixMap)image.Thisobjectisderivedfromamoregeneralclassusedtodealwithscalarfields:
GfsOutputScalarfollowingthissyntax:
[GfsOutput]{v=Umin=1max=2.5}
whereasbeforethesquarebracketsexpressinheritancefromtheparentclass.Thevidentifierspecifieswhatscalarfield
wearedealingwith,oneof:
U,V(andWin3D)
:componentsofthevelocity.
P
C

:pressure.
:passivetracer.

Vorticity
:vorticity(normofthevorticityvectorin3D).
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Velocity
:normofthevelocity.
Theminandmaxvaluesspecifytheminimumandmaximumvaluesthisscalarcantake.Iftheyarenotgiven,theyare
computedeverytimetheeventtakesplace.
Wecannowusethisinoursimulationfile:
12GfsSimulationGfsBoxGfsGEdge{}{
GfsTime{end=50}
GfsRefine6
GfsInit{}{
U=(0.5rand()/(double)RAND_MAX)
V=(0.5rand()/(double)RAND_MAX)
}
GfsOutputTime{istep=10}stdout
GfsOutputProjectionStats{istep=10}stdout
GfsOutputPPM{step=1}vorticity%4.1f.ppm{v=Vorticity}
}
GfsBox{}
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Thecodewilloutputevery1timeunitsaPPMimagerepresentingthevorticityfield.Theresultwillbewritteninfiles
named:vorticity00.0.ppm,vorticity01.0.ppm(ifthe%4.1fthingisnotfamiliar,consultaCbookortry%man
3printf).
Ifyoureruntheprogramusingthisnewsimulationfile,youwillgetanumberofPPMfiles(51tobeprecise)youcan
thenvisualisewithanyimageeditingorviewingtool.IwouldrecommendtheverygoodImageMagicktoolbox.Ifyourun
aLinuxbox,thesetoolsareverylikelytobealreadyinstalledonyoursystem.Trytypingthisinyourworkingdirectory:
%display*.ppm
Ifitworks,youshouldseeasmall(64x64)imagerepresentingtheinitialvorticityfield.Ifyouclickonit,amenuwill
appear.SelectFileNextandlookattheevolutionofthevorticityfieldwithtime(youcanalsousethespacebarand
backspacekeytochangebackandforth).Youmightalsowanttotrytheanimate*.ppmcommand.Readtheman
pagesofImageMagickifyouwanttoknowmore.NotethatyoucanusethesetoolsalsowhileGerrisisrunning(and
creatingnewimages).Withabitofpatienceyouwillgettheimageonfigure2att=18(resolutionhasbeenincreasedto
128128).

Figure2:Vorticityfieldfortheinitialrandomvorticityproblematt=18.

Beforewecarryon,wearegoingtomaketwomodificationstothesimulationfile.Firstofall,itisnotreallyhandyto
generateonefileforeveryimagegenerated.ImageMagick(andmostotherprograms)candealwithmultiplePPMimages
containedwithinthesamefile.Secondly,inthesequenceofimageswegenerate,agivenvalueofthevorticitydoesnot
alwayscorrespondtothesamecolour(becausetheminimumandmaximumvaluesofthevorticitycanvaryintime).We
canfixthatlikethis:
http://gfs.sourceforge.net/tutorial/tutorial/tutorial1.html

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12GfsSimulationGfsBoxGfsGEdge{}{
GfsTime{end=50}
GfsRefine6
GfsInit{}{
U=(0.5rand()/(double)RAND_MAX)
V=(0.5rand()/(double)RAND_MAX)
}
GfsOutputTime{istep=10}stdout
GfsOutputProjectionStats{istep=10}stdout
GfsOutputScalarStats{istep=10}stdout{v=Vorticity}
GfsOutputPPM{step=0.1}vorticity.ppm{
v=Vorticity
min=10
max=10
}
}
GfsBox{}
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11top
Wehavenowspecifiedfixedboundsforthevorticity(usingtheminandmaxidentifiers).EachPPMimagewillbe
appendedtothesamefile:vorticity.ppm.
HowdidIchoosetheminimumandmaximumvaluesforthevorticity?ThelineGfsOutputScalarStats{istep=10
}stdout{v=Vorticity},writestheminimum,average,standarddeviationandmaximumvaluesofthevorticity.
Byrerunningthesimulationandlookingatthesevaluesitiseasytofindasuitablerange.

3Amorecomplexexamplewithsolidboundaries
Inthissectionwewillseehowtosetupasimulationfortheflowpastasolidbody(ahalfcylinder)inanarrowchannel.
Whiledoingthatwewillalsoencounternewwaysofdisplayingsimulationresults.

3.1Domaingeometryandboundaryconditions
Whatwewantisanarrowchannel(41forexample).Fromthepreviousexample,weknowthatwecanbuilditlikethis:
43GfsSimulationGfsBoxGfsGEdge{}{
GfsTime{end=0}
}
GfsBox{}
GfsBox{}
GfsBox{}
GfsBox{}
12right
23right
34right
i.e.fourboxes,box1connectedtobox2horizontally(totheright),box2connectedtobox3horizontallyandbox3
connectedtobox4horizontally.Box1iscenteredontheoriginandisofsizeone.Alltheotherboxesarepositioned
accordingly.Wenowhaveour41rectangulardomain.

3.1.1Boundaryconditions
Whataboutboundaryconditions?BydefaultGerrisassumesthatboundariesaresolidwallswithslipconditionsforthe
velocity(i.e.thetangentialstressonthewalliszero).Forthemomentwethenhavedefinedarectangularboxclosedon
allsidesbysolidwalls.
Whatwereallywantistospecifyaninputvelocityontheleftsideoftheboxandsomesortofoutputconditiononthe
rightside.Wecandothatlikethis:
43GfsSimulationGfsBoxGfsGEdge{}{
GfsTime{end=0}
}
GfsBox{left=GfsBoundaryInflowConstant1}
GfsBox{}
GfsBox{}
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GfsBox{right=GfsBoundaryOutflow}
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Thewholeleftsideofthefirst(leftmost)boxisnowdefinedtobeaGfsBoundaryInflowConstantobjectandthewhole
rightsideofthelast(rightmost)boxaGfsBoundaryOutflowobject.Again,boundaryconditionsobjectsareallderived
fromtheGfsBoundaryobjectand,asinitialconditions,newobjectscanbeeasilywrittenbytheuser(seealsosection
4.1).
WeseethatGfsBoundaryInflowConstanttakesoneargumentwhichisthevalueofthe(constant)normalvelocity
appliedtothisboundary.Alltheothervariables(pressure,tracerconcentrationetc...)followazerogradientcondition.
GfsBoundaryOutflowimplementsasimpleoutflowboundaryconditionwherethepressureissettozeroaswellasthe
gradientofallotherquantities.

3.1.2Solidboundaries
Wenowhaveanemptywindtunnelwithaconstantinletvelocityofnormunity.Gerriscandealwitharbitrarilycomplex
solidboundariesembeddedinthequad/octreemesh.ThegeometryofthesolidboundariesisdescribedusingGTS
triangulatedsurfaces.In2D,using3Dtriangulatedsurfacesseemsoverkill,as2Dcurveswouldbeenough.However,
Gerrisbeingbotha2Dand3Dcodeitdealswith2Dsolidboundariesexactlyaswith3Dones,evenifthesimulationis
doneonlyona2Dcrosssection.
Creating3Dpolygonalsurfacesisnotaneasyjobandisclearlyoutsidethescopeofthistutorial.Thereareanumberof
utilitiesyoucanusetodothat,includingbigcommercialCADpackages.Ingeneral,onceyouhavecreatedapolygonal
surfacewithoneofthesetoolsitshouldberelativelyeasytoconvertittothefileformatusedbyGTS.Inparticular,most
CADpackagescanexporttotheSTL(stereolithography)formatwhichiseasilyconvertedtotheGTSfileformatusing
thestl2gtsutilitywhichcomeswiththelibrary.
Thistutorialcomes(handily)withonesuchfile:halfcylinder.gts.Youcanvisualisethesurfaceitdescribesusinga
programcalledGeomview.Todothis,youfirstneedtoconverttheGTSfiletoaformatGeomviewunderstands.Thiscan
bedoneusingthegts2ooglutilitylikethis:
%gts2oogl<halfcylinder.gts>halfcylinder.oogl
(OOGListhefileformatusedbyGeomview).gts2ooglhasanumberofoptions.Youcanhaveashortexplanationof
whattheydobytyping:
%gts2ooglh
Ifyounowstartgeomviewlikethis:
%geomviewhalfcylinder.oogl
andplayaroundwiththepan/rotate/zoomfunctionsofGeomview(readthemanualfordetails),youshouldseesomething
liketheimageonfigure3.

Figure3:Geomviewrepresentationofhalfcylinder.gts

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Youcannoticethatthisisaproper3Dobject,evenifweareonlygoingtosimulatetheflowina2Dcrosssection.Itis
alsoimportantthattheobjectistallenoughsothatitspanstheentireheightofthe2Ddomain,asifweweregoingto
simulatetheflowarounditinaproper3Dchannelwithasquarecrosssection.Theorientationofthesurfaceisalso
importanttodefinewhatisinside(thesolid)andwhatisoutside(thefluid).
Wecannowinsertthisobjectinthesimulationdomainlikethis:
43GfsSimulationGfsBoxGfsGEdge{}{
GfsTime{end=0}
GfsSolidhalfcylinder.gts
}
GfsBox{left=GfsBoundaryInflowConstant1}
GfsBox{}
GfsBox{}
GfsBox{right=GfsBoundaryOutflow}
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addwhatmeshrefinementwewantandafewthingstooutput:
43GfsSimulationGfsBoxGfsGEdge{}{
GfsTime{end=9}
GfsRefine6
GfsSolidhalfcylinder.gts
GfsInit{}{U=1}
GfsOutputBoundaries{}boundaries
GfsOutputTime{step=0.02}stdout
GfsOutputProjectionStats{step=0.02}stdout
GfsOutputPPM{step=0.02}vorticity.ppm{
min=100max=100v=Vorticity
}
GfsOutputTiming{start=end}stdout
}
GfsBox{left=GfsBoundaryInflowConstant1}
GfsBox{}
GfsBox{}
GfsBox{right=GfsBoundaryOutflow}
12right
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IhaveaddedanewGfsOutputobjectwehaventseenyet:GfsOutputTiming.Thisobjectwritesasummaryofthetime
takenbyvariouspartsofthesolver.Youmightalsohavenoticedtheunusualstart=endbitthisjustspecifiesthat
thiseventwillonlyhappenonceattheendofthesimulation.
AnothernewoutputobjectisGfsOutputBoundaries.Thisobjectwritesageometricalsummary(inOOGL/Geomview
format)ofthemeshused,includingboundaryconditions,solidboundariesandsoon.
Wealsoinitialisethevelocityfieldonthewholedomaintoaconstantvalue(1,0,0).Wecouldhaveleftthevelocityfield
toitsdefaultvalueof(0,0,0)but,giventhatweimposeinflowboundaryconditions,itwouldhavemeantthattheinitial
velocitywouldhavebeenstronglydivergent.Gerrisalwaysstartsasimulationbyaprojectionstep(tofixproblemslike
this)butitisalwaysagoodideatostartwiththebestpossiblevelocityfield.
Wecannowrunthecode:
%gerris2Dhalfcylinder.gfs
Itisgoingtotakeawhiletocomplete,butrememberthatyoucanlookatfileswhiletheyarebeinggenerated.Thefirst
filewhichwillbegeneratedisboundaries.IfyouloaditinGeomview,youshouldgetsomethinglikefigure4(you
probablywanttodisableautomaticnormalizationinGeomviewbyselectingInspectAppearanceNormalizeNone).

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Figure4:Representationofboundaryconditionsandsolidboundaries

Theblacklinesrepresenttheboundariesbetweensolidcellsandfluidcells.Ifyouzoominonthehalfcylinder,youwill
seethatitisrepresentedbylinesfollowingthegrid(itislegolooking).Thisdoesnotmeanthatthereal(i.e.
computational)solidboundaryisalsolegolookingbecausefluidcellscanbecutbythesolidboundaries,inwhichcase
thealgorithmproperlytakesintoaccountthecorrespondingcellgeometry.
EachGfsBoundaryobjectiscolourcoded.Fromthecoloursinthepictureweseethatwehaveindeedaninflow
boundaryconditionontheleftside(blue)andanoutflowboundaryconditionontherightside(green).
Youcanalsoloadinthefullhalfcylindergeometrywecreatedbefore:halfcylinder.ooglorvisualisethePPMfiles
usinganimateanddisplayasinthepreviousexample.Bytheway,ausefulfeatureofdisplayisthatyoucanzoom
inbyclickingonthemiddlebuttonintheimagebeingdisplayed.

3.2Savingthewholesimulation
Hmm,thissimulationistakingquiteawhileWhatifwewanttostopthesimulation,makesomemodificationstothe
simulationfileandrestartwhereweleftfrom?Orequivalently,savethewholesimulationatregularintervalsforlatter
postprocessing?
YoucandothisusingtheGfsOutputSimulationobject.Likethisforexample:
GfsOutputSimulation{step=0.1}halfcylinder%3.1f.gfs{
variables=U,V,P
}
wherevariablesdefineswhichvariablesyouwanttosave.Bydefaultallthevariablesaresaved.
Ifyounowrerunthesimulation,youwillgetanewfileevery0.1timeunits.Thisfileisavalidsimulationfile(likehalf
cylinder.gfs)andyoucanuseitdirectlytorestartthesimulationfromthispointonward.Ifyoueditit,youwillseethat
thegeneralstructureisthesameasusualbutforfiveprettybigchunksofdata.
ThefirstchunkstartswithGfsSolidandisjustthedatacontainedinhalfcylinder.gtsbutthistimeembedded
directlyintothesimulationfile.Thegoalthereistohavefullyselfcontainedsimulationsfileswhichyoucanjustmove
aroundwithouthavingtokeeptrackoftwentydifferentfiles.
ThefourotherchunksareeachassociatedwithaGfsBoxandcontainboththetopologyofthecorrespondingcelltreebut
alsotheassociatedphysicaldata,solidboundarydefinitionsetc...
Youcanofcourseeditthisfile,addnewoutputsandsoonandrestartthesimulationfromwhereyouleftit.

3.3Visualisation
3.3.1GfsView
GfsViewisatoolwrittenspecificallytovisualiseGerrissimulationfiles.Itisstillyoungbutfullyusablebothfor2Dand
3Dsimulations.Itsmainadvantageoverotheroptionsandthereasonforitsexistenceisthatitmakesfulluseofthe
adaptivenatureoftheoctreerepresentationatthevisualisationlevel.TheoctreestructureisusedwithinGfsViewto
dynamicallyselecttheappropriatelevelofrefinementdependingontheviewpoint,zoomandrenderingspeed.Itisalso
usedtoefficientlycomputecomplexgeometricalentitiessuchasisosurfacesorcutplanes.
ThemoreclassicalviewerssuchasopenDXorMayaViaredesignedforeitherregularCartesiangridsorfully
unstructuredmeshesanddonottakeadvantageoftheoctreerepresentation(worsestill,theoctreerepresentationfirst
needstobeconvertedtoCartesianorfullyunstructuredmeshesbeforebeingimportedintotheseprograms).
ToinstallGfsView,youneedtohavetheGtk+toolkitinstalledonyoursystem.IfyouarerunningaLinuxmachine,Gtk+
ismostprobablyalreadyinstalled.YouwillalsoneedtheGtkGlExtOpenGLextensiontoGtk+.
IfyouarerunningaDebianbasedsystem,youcaninstallthesepackagesusing
http://gfs.sourceforge.net/tutorial/tutorial/tutorial1.html

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%aptgetinstalllibgtkglext1dev
IfyouthendownloadarecentversionofGfsViewfromtheGerriswebsite(eitheranofficialreleaseorasnapshot)anddo
thenowclassical:
%gunzipgfsview.tar.gz
%tarxvfgfsview.tar
%cdgfsview
%./configureprefix=/home/joe/local
%make
%makeinstall
youwillbeabletostartGfsViewusing:
%gfsview2Dhalfcylinder0.5.gfs
NotethatyoucanalsoinstallthemostrecentGfsViewversionusingdarcsand
http://gfs.sourceforge.net/darcs/gfsview/gfsviewmainlineassourcerepository(youwillalsoneedtoinstall
Gerristhisway,seesection??fordetails).
ClickingonLinear,VectorsandSolidinthetoolbarandchangingthevectorlengthbyeditingthepropertiesofthe
Vectorsobject(selecttheobjectthenchooseEditProperties)youshouldbeabletogetsomethinglookinglikefigure
5.Youcanpanbydraggingtherightmousebutton,zoombydraggingthemiddlebuttonandrotatebydraggingtheleft
button.

Figure5:ScreenshotofaGfsViewsession.

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Whilebynomeanscomplete,youcanalreadydomanythingswithGfsView.Ihopeitisfairlyuserfriendlysojustplay
withitanddiscoverforyourself.

3.3.2Somepostprocessingusinggfs2oogl
Gerriscomeswithautilitycalledgfs2ooglwhichconvertssimulationfilestovariousrepresentationsinOOGLformat.
Wearejustgoingtolookattwotypesofrepresentationsgfs2ooglcando:scalarfieldcrosssectionsandvectorfields.
Firstofall,youcanaccessasmallsummaryoftheoptionsofgfs2ooglbytyping:
%gfs2oogl2Dh
Bydefaultgfs2ooglwillgeneratethesameoutputasGfsOutputBoundarieslikethis:
%gfs2oogl2D<halfcylinder0.1.gfs>boundaries.oogl
TogenerateanOOGLrepresentationofascalarfield(acolouredsquareforeachdiscretisationcell)dothis:
%gfs2oogl2DSz0cVorticity<halfcylinder0.5.gfs>squares.oogl
whichtellsgfs2oogltodoacrosssectionforz=0(z0)representedbysquares(S)andcoloredaccordingtothe
localvorticity(cVorticity).Togenerateavectorfieldrepresentingthevelocitytry:
%gfs2oogl2DV2z0<halfcylinder0.5.gfs>vectors.oogl
whereV2specifiesthatthemaximumlengthofthevectoristwicethedimensionofthesmallestcellinthedomain.
IfyounowloadallthesefilesinGeomviewanddoabitofpanningandzoomingaround(andpossiblytunethingslike
faceshading)youshouldgetanimagelookinglikefigure6.

Figure6:Scalarandvectorrepresentationgeneratedusinggfs2oogl.

3.4Usingdynamicadaptivemeshrefinement
Forthemomentoursimulationisnotverywellresolved.WecouldalwayschangetheGfsRefine6linetosomething
biggerbutitwouldnotmakereallygooduseofthequadtreeapproachusedinGerris.Acodeusingasimpleregular
Cartesiangridapproachwouldbefasterandwouldproducethesameresults.Insteadwearegoingtousedynamic
adaptivemeshrefinement,wherethequadtreestructureofthediscretisationisusedtoadaptivelyfollowthesmall
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structuresoftheflow,thusconcentratingthecomputationaleffortontheareawhereitismostneeded.
Thisisdoneusingyetanotherobjectclass:GfsAdapt,alsoderivedfromGfsEvent.Variouscriteriacanbeusedto
determinewhererefinementisneeded.Inpractice,eachcriteriumwillbedefinedthroughadifferentobjectderivedfrom
GfsAdapt.IfseveralGfsAdaptobjectsarespecifiedinthesamesimulationfile,refinementwilloccurwheneveratleast
oneofthecriteriaisverified.
Forthisfirstexample,wewilluseasimplecriteriumbasedonthelocalvalueofthevorticity.Acellwillberefined
whenever

|v|x
max|v|

>,

wherexisthesizeofthecellandisauserdefinedthresholdwhichcanbeinterpretedasthemaximumangular
deviation(causedbythelocalvorticity)ofaparticletravelingatspeedmax|v|acrossthecell.Thiscriteriumis
implementedbytheGfsAdaptVorticityobject.
ThegeneralsyntaxforanGfsAdaptobjectis:
[GfsEvent]{mincells=1maxcells=100000minlevel=1maxlevel=10cmax=1e2}
wheremincellsspecifiestheminimumnumberofcellsinthedomain,maxcellsthemaximumnumberofcells,
minlevelthelevelbelowwhichitisnotpossibletocoarsenacell,maxlevelthelevelabovewhichitisnotpossibleto
refineacellandcmaxthemaximumcellcost.Thedefaultvaluesare0forminlevelandmincellsandinfinitefor
maxlevelandmaxcells.Animportantpointisthat,forthemoment,itisnotpossibletodynamicallyrefinesolid
boundaries.Asimplesolutiontothisrestrictionistoalwaysrefinethesolidboundarywiththemaximumresolutionatthe
startofthesimulationandtorestricttherefinementusingthemaxlevelidentifierinGfsAdapt.
Whathappensifthemaximumnumberofcellsisreached?Therefinementalgorithmwillkeepthenumberofcellsfixed
butwillminimizethemaximumcostoverallthecells.Thiscanbeusedforexampletorunaconstantsizesimulation
wherethecellsareoptimallydistributedacrossthesimulationdomain.Thiswouldbedonebysettingmaxcellstothe
desirednumberandcmaxtozero.
Followingthiswecanmodifyoursimulationfile:
43GfsSimulationGfsBoxGfsGEdge{}{
GfsTime{end=9}
GfsRefine7
GfsSolidhalfcylinder.gts
GfsInit{}{U=1}
#GfsOutputBoundaries{}boundaries
GfsAdaptVorticity{istep=1}{maxlevel=7cmax=1e2}
GfsOutputTime{step=0.02}stdout
GfsOutputBalance{step=0.02}stdout
GfsOutputProjectionStats{step=0.02}stdout
GfsOutputPPM{step=0.02}vorticity.ppm{
min=100max=100v=Vorticity
}
GfsOutputSimulation{step=0.1}halfcylinder%3.1f.gfs{
variables=U,V,P
}
GfsOutputTiming{start=end}stdout
}
GfsBox{left=GfsBoundaryInflowConstant1}
GfsBox{}
GfsBox{}
GfsBox{right=GfsBoundaryOutflow}
12right
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34right
Wehaveaddedtwolinesandcommentedout(using#)thelineoutputtingtheboundaries(wedontneedthatanymore,
wehavethesimulationfiles).
ThefirstlineweaddedsaysthatwewanttorefinedynamicallythemeshthroughtheGfsAdaptVorticityobjectapplied
everytimestep(istep=1).Theparameter(cmax)issetto102.
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ThesecondlineweaddedisanewGfsOutputobjectwhichdisplaysthebalanceofthedomainsizesacrossthe
differentprocesses(whenGerrisisraninparallel).Wewillusethistomonitorhowthenumberofcellsevolveswithtime
asthesimulationrefinesorcoarsensthemeshaccordingtoourvorticitycriterium.
Wecannowrunthisnewsimulation.Iftheprevioussimulationdidnotcompleteyet,dontbeafraidtoabortit(CtrlC),
thisoneisgoingtobebetter(andfaster).
%gerris2Dhalfcylinder.gfs
IfwenowlookatthebalancesummarywrittenbyGfsOutputBalance,weseethatinitially(step:0)thetotalnumberof
cells(onalllevels)is86966,whichcorrespondstoaconstantresolutionof42727=512128.Atstep10thenumber
ofcellsisdownto990withacorrespondingincreaseincomputationalspeed.Ifwenowlookatthefirstsimulationfilewe
saved,using:
%gfs2oogl2D<halfcylinder0.1.gfs>boundaries
%gfs2oogl2DSz0cVorticity<halfcylinder0.1.gfs>squares.oogl
weobtainfigure7showingnotonlythedomainboundariesasusual,butalsotheboundaries(thinblacklines)between
differentlevelsofrefinement.

Figure7:Dynamicadaptivemeshrefinementt=0.1

Weseethatthemeshisveryrefinedaroundthesolidandaroundthetwovorticesdevelopingatthetrailingedgeand
verycoarse(onecellperboxonly)onthedownstreampartofthedomain.Ifyouarenotsurewhatthesethinblacklines
represent,justswitchontheedgerepresentationinGeomview(usingtheInspectAppearancemenu).Youwillgeta
picturelookinglikefigure8,showingallthecellsusedforthediscretisation.

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Figure8:Dynamicadaptivemeshrefinementt=0.1.Detailofthecells.

Asthesimulationgoeson,youcanseethenumberofcellsinthedomainincreaseasthetrailingvorticesdevelop.With
abitofpatienceyouwillgettofigure9showingthefullydevelopedVonKarmanvortexstreetwithpatchesofincreased
resolutionfollowingeachvortex.Evenwhentheflowisfullydevelopedusingadaptivemeshrefinementstillsavesa
factorof~6intimeandmemoryuse.Theadvantageofadaptivemeshrefinementisevenmoreobviousinsituations
whereitisnecessarytouseverylargedomainstoavoidanycontaminationofthesolutionbytheboundaryconditions.

Figure9:Dynamicadaptivemeshrefinementt=9.

Youshouldalsotrytoanimatevorticity.ppmwhichbynowshouldgiveyouaniceanimationofthedevelopingtrailing
vorticesbecomingunstableandgeneratingtheVonKarmanstreet.IfImageMagickisproperlyinstalledonyoursystem
youcanalsotry:
%convertvorticity.ppmvorticity.mpg
whichwillproduceamuchsmallerMPEGvideofile,suitablefordistributionthroughthenetwork.

4Goingfurther
4.1Moreonboundaryconditions
UptonowwehaveonlydealtwithprepackagedboundaryconditionssuchasGfsBoundaryInflowConstantand
GfsBoundaryOutflow.Whatifyouneedmorespecificboundaryconditions?
Formostpracticalproblems,boundaryconditionscanbereducedtotwomaincategories:Dirichletboundaryconditions
forwhichthevalueofthevariableissetandNeumannboundaryconditionsforwhichthevalueofthederivativeofthe
variableisset.Aswehaveseenearlier,thedefaultboundaryconditioninGerrisisDirichlet(zero)forthenormal
componentsofthevelocityandNeumann(zero)forallothervariables.
LetussaythatwewanttoimposeaPoiseuille(parabolic)profileratherthanaconstantinflowvelocityforthehalf
cylinderproblemi.e.wewantaDirichletboundaryconditiononthenormalcomponentofthevelocity(U)withanimposed
parabolicprofile.ThiscaneasilybedoneinGerrislikethis:
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...
GfsBox{left=GfsBoundary{
GfsBcDirichletU{return1.4.*y*y;}
GfsBcDirichletV0
}
}
GfsBox{}
GfsBox{}
GfsBox{right=GfsBoundaryOutflow}
...
SimilarlyaNeumannboundaryconditiononvariableXwoulduseGfsBcNeumannX...

4.2Addingtracers
Inthehalfcylinderexample,itwouldbenicetobeabletovisualisetheflowusingforexampleapassivetracerinjected
attheinlet.Thisisverysimple,justmodifythehalfcylinder.gfsparameterfilelikethis:
43GfsSimulationGfsBoxGfsGEdge{}{
GfsTime{end=9}
GfsRefine7
GfsSolidhalfcylinder.gts
GfsVariableTracer{}T
...
GfsOutputPPM{step=0.02}tracer.ppm{
min=0max=1v=T
}
GfsOutputSimulation{step=0.1}halfcylinder%3.1f.gfs{
variables=U,V,P,T
}
...
}
GfsBox{left=GfsBoundary{
GfsBcDirichletU1
GfsBcDirichletV0
GfsBcDirichletT{returny>0.?1.:0.;}
}
}
...
whichwillinjecttracerTattheinletonlyintheupperhalfofthechannel.
Theadaptiverefinementalgorithmshoudalsotakeyourtracerintoaccount.Trythis
...
GfsAdaptVorticity{istep=1}{maxlevel=7cmax=1e2}
GfsAdaptGradient{istep=1}{maxlevel=7cmax=1e2}T
...
whichwilladaptusingboththegradientoftracerTandthevorticity.
Youcanhaveanynumberoftracersyouwant,theyaredynamicallyallocated.

4.3Addingdiffusionterms
Uptonow,wehaveonlyconsideredinviscid,incompressibleflows.Withoutgoingintothedetails,thistypeofproblems
requirethesolutionoftwomainsubproblems:solvingaPoissonequationforthepressureandanadvectionequationfor
themomentumandtracerswiththecorrespondingboundaryconditions.
Gerriscanalsosolveathirdclassofsubproblems:diffusionequations.DiffusionequationsaresimilartoPoisson
equations(theybothinvolveLaplacianoperators)andcanbesolvedefficientlyusingthesamemultigridsolverweusefor
thepressure.
Inpracticeaddingdiffusiontoagiventracerisassimpleasadding:

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...
GfsSourceDiffusion{}T0.01
...
totheparameterfile,where0.01isthevalueofthediffusioncoefficient.

4.3.1Boundaryconditionsfordiffusionterms
Whatifwewanttomodifythetracerexampleabovesothatnowthehalfcylinderitselfisa(diffusive)sourceoftracer
ratherthantheinlet?Weneedtobeabletoimposethisboundaryconditionontheembeddedsolidsurface.On
embeddedsolids,thedefaultboundaryconditionsforthediffusionequationisNeumann(zeroflux)fortracersand
Dirichlet(noslip)forthevelocitycomponents.Tochangethatuse
...
GfsVariableTracerT
GfsSourceDiffusion{}T0.001
GfsSurfaceBcTDirichlet1
...
andchangetheinletboundaryconditionbackto
...
GfsBox{left=GfsBoundary{
GfsBcDirichletU1
GfsBcDirichletV0
}
}
...

4.4Outputs
4.5Boundaryconditions

5RunningGerrisinparallel
6Learningmore
WhilethistutorialshouldgiveyouagoodoverviewofGerris,itisbynomeansacompletedescription.Tolearnmoreyou
shouldfirstconsulttheGerrisFrequentlyAskedQuestionsandtheGerrisobjecthierarchywhichdescribeseachobject
andthecorrespondingfileparametersinmoredetail.
YoushouldalsohavealookattheGerrisExamplespageforexamplesofhowtouseGerrisforarangeofproblems.The
parameterfilesarecrosslinkedwiththereferencemanual.
AnothersourceofmoreadvancedexamplesistheGerristestsuite.
Ifthingsarestillunclearyoucanaskforhelponthegfsusersmailinglist.Pleasenotethatyoufirstneedtosubscribe
tothelisttobeabletopostmessages.

7Doyouwanttohelp?
TheideabehindGerrisandotherfreesoftwareprojectsisthattransparency,freeexchangeofinformationand
cooperationbenefitindividualsbutalsosocietyasawhole.Ifyouareascientist,youknowthatthesesameprinciples
arealsokeystotheefficiencyofScience.
HelpingwithGerrisdevelopmentcanbedoneinvariouswaysandasidefromgivingyouthisaltruistic,warmfuzzyfeeling
ofhelpingotherswillalsobenefityoudirectly.Afewconcretesimplewaysofhelpingare(inapproximateorderof
difficulty):
Usethecode,commentontheproblemsyoufind,whatyoulike,dontlikeaboutit.
ShareyourresultswithotherGerrisusers,writeawebpageabouttheproblemyousolvedusingGerrisetc
IfyoupublishpapersusingGerris,sendmethereference.Itisveryusefultobeabletoshowevidenceofwider
usagewhenseekingcontinuedfundingfortheproject.
Also,ifGerriscapabilitiesarecentraltoyourarticlefeelfreetoaskmetobeacoauthoronyourpaper
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HavealookattheGerrisinternals(writeyourownmodules)andsharethemwithus.
ThinkofwaystoextendGerrisforyourownproblems,implementthemandsharethemwithus(youcancounton
myandotherdevelopershelp).
ThisdocumentwastranslatedfromLATEXbyHEVEA.

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