Table Of ContentMem.S.A.It.Vol.,1
(cid:13)c SAIt 2013 Memoriedella
The CO5BOLD Analysis Tool
S. Wedemeyer
InstituteofTheoreticalAstrophysics,UniversityofOslo,P.O.Box1029Blindern,N-0315
Oslo,Norwaye-mail:[email protected]
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0 Abstract. The interactive IDL-based CO5BOLD Analysis Tool (CAT) was developed to
2 facilitateaneasyandquickanalysisofnumericalsimulationdataproducedwiththe2D/3D
radiationmagnetohydrodynamicscodeCO5BOLD.Thebasicmodeofoperationisthedis-
n
playandanalysisofcross-sectionsthroughamodeleitheras2Dslicesor1Dgraphs.Awide
a
rangeofphysicalquantitiescanbeselected.Furtherfeaturesincludetheexportofmodels
J
into VAPOR format or the output of images and animations. Ashort overview including
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scientificanalysisexamplesisgiven.
]
R Keywords.Sun:photosphere;Radiativetransfer
S
.
h 1. Introduction andanalysisofslicesthrough3D(or2D)mod-
p
els. CAT can handle files with multiple snap-
- The growing computational resources allow
o shots(.full).
for increasingly larger and more detailed nu-
r
t mericalsimulationsofstellaratmospheres,re-
s
a sultinginaconsiderablylargeamountofdata. Settings and sessions. After the installa-
[ The production of advanced comprehensive tion, adjustments such as the default window
modelsmustthereforebeaccompaniedbythe size and paths can be made and saved. These
1 development of efficient analysis and visual- standard settings will be restored every time
v
izationsoftwarethatiscapableofhandlingthe CATisstarted.Settingsthatareconnectedtoa
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9 producedlargedatasets.Here,theCO5BOLD particularanalysissessioncanbesavedandre-
4 AnalysisTool(abbreviatedCAT,Fig.1)isde-
1 scribed. It is designed for an interactive anal-
. ysis of 2D and 3D model atmospheres, which
1
areproducedwithCO5BOLD –awidelyused
0
3 state-of-the-artcodeforthesimulationofstel-
1 laratmospheres(Freytagetal.2012).
:
v
i 2. Programoverview
X
r CAThasaninteractivegraphicaluserinterface,
a which is is programmed in IDL (see Fig. 2).
The primary mode of operation is the display
Sendoffprintrequeststo:S.Wedemeyer Fig.1.LogooftheCO5BOLD AnalysisTool.
2 Wedemeyer:TheCO5BOLDAnalysisTool
Fig.2. Screen shot showing the data tab of the graphical user interface and the color-coded horizontal
2Dslicethroughthephotosphereofa3Dmodelofthesolaratmosphere.Theselectedphysicalquantity,
heretheverticalvelocity,clearlyshowsthegranulationpattern.Thelinesmarkthecurrentpositionofthe
interactivecursor.
storedassessionfiles.Itispossibletodefinea magnitudeinthedisplayedslice(e.g.,themass
default session, which is automatically loaded density in the x-z plane). By default, a color-
whenCATstarts. coded2Dsliceisdisplayed.Alternatively,the
data in the current projection plane can be
shown as surface plot, contour plot or line
Slice display The projection plane can be plot. Color-coded slices can be overlaid with
chosen perpendicular to the axes, resulting in contours (incl. a reference contour at optical
the three planes x-y, x-z, and y-z in a 3D depth unity) and/or a vector field. For the lat-
model. The position within a plane can be ter the spatial components of the velocity or
changedeitherbyclickinginthedisplayedim- the magnetic field in the selected projection
ageorthroughthewidgetsinthecontrolpanel. plane can be drawn as vectors or streamlines,
CAT now also provides a zoom function in a whiletheperpendicularcomponentisnotcon-
separate tab, in which the magnification and sidered.Thelengthofthevectorscanbecho-
the currently displayed region can be selected sen directly inthe data tab with more options
(seeFig.3foraclose-upregion). beingavailableintheoptionsmenu.
Different physical quantities can be cho-
sen in the data tab (see Fig. 2), ranging from
thebasicquantitiescontainedinthemodelfile Measurements. Thenewmeasuretabpro-
tomoreadvancedquantitieslike,e.g.,thespa- videsdifferenttoolsfor(i)measuringdistances
tialcomponentsoftheelectriccurrent density between two points or along a polygon path,
(e.g., Schaffenberger et al. 2005). The chosen (ii) defining markers, and (iii) producing and
quantity can then be combined with a mathe- exporting contour paths. The markers, which
maticaloperation,e.g.thelogarithm,whichis aresetsofcoordinates,andthecontourscanbe
usefulforquantitiesthatcovermanyordersof interactively selected, modified and exported
Wedemeyer:TheCO5BOLDAnalysisTool 3
Fig.3.Screenshotshowingthemeasuretabofthegraphicaluserinterfaceanda2Dslicewiththecolor-
codedhorizontalvelocity.Thedisplayedsliceisaclose-upregion(zoomfactor3)inthechromosphereof
the3DMHDmodelofthesolaratmospherebyWedemeyer-Bo¨hmetal.(2012).Thecolorshadesandthe
arrows,whichfollowthehorizontalvelocityfield,bothexhibitaringofincreasedvelocity,whichiscaused
bytherotationofthemagneticfieldstructures.Adiameterof1058kmisdeterminedwiththemeasurement
tool(seeupperleftcorner).
forfurtherprocessing.Thesetoolscanbeused CAT can be used to extract the last time step
for,e.g.,defining3Dstructuresorformanually fromthecorresponding.fullfileforusingitas
trackingfeaturesinspaceandtime. startmodelforthenextsimulationrun.Model
snapshots can also be saved as plane-parallel
models.Inacomingversion,itwillbepossible
Images and animation. Thedisplayedim-
to save only parts of the model and to extract
ages can be output in various image formats.
dataintoIDLsavefilesforfurtheranalysis.
Theanimationtoolprovidesaninteractiveway
The 3D visualization tool, which is inte-
toproduceMPEGvideosorimagesequences.
grated in CAT, can give a first 3D impression
It can either be a time animation for a series
but has limited functionality (see Fig. 4). The
of model snapshots contained in one or more
VAPORtool(Clyneetal.2007;Clyne&Rast
multi-snapshotfile(s)oraspatialscanthrough
2005) allows for a more comprehensive anal-
aselectedmodelsnapshotalongoneofthespa-
ysis of the 3D structure, in particular for vec-
tialaxes.
tor fields like velocity and magnetic field. For
thatreason,CAToffersthepossibilitytoexport
Export. CAT offers several options to ex- CO5BOLD dataintoVAPORformat.
portmodeldata.Thecurrentlyloadedsimula-
tionsnapshotcanbewrittenoutinUIOformat,
3. Dataanalysisexamples
evenwhenitispartofamulti-snapshot(.full)
file.Thisfeatureisusefulifasimulationtermi- CAT has been repeatedly proved useful in the
nated without producing an .end file or if this past. It provides an easy way of monitoring
file is corrupted for some reason. In this case the evolution of an ongoing simulation. CAT
4 Wedemeyer:TheCO5BOLDAnalysisTool
magnetic fields with different field strengths
and different topologies (e.g., homogeneous
vertical or mixed polarities) will be analysed
inmoredetailinforthcomingpublications.
4. Outlook
Sincethefirstversionin2002,thedevelopment
of CAT has been driven by the need for addi-
tionalfunctionalityfortheanalysisofincreas-
inglycomplexmodels.Alsointhefuture,CAT
will be continuously extended. The feedback
of users is therefore very welcome. Possible
Fig.4. 3DvisualizationofaMHDmodelofaM- extensionsinfuturereleasescouldincludethe
type dwarf star (Wedemeyer et al.2012) with IDL ability to read the data formats of other MHD
aspartofCAT.Plasma-betaisdisplayedasreddish codesandtodisplayandanalyseslicesatarbi-
slicesandupperbluishsurface.Thelowerbluesur- traryangles.
faceencloseregionsofhighmagneticfieldstrength.
Acknowledgements. The author likes to thank the
organisersofthe2ndCO5BOLD Workshop(CW2),
can also help to quickly reveal what is wrong whichwasheldinHeidelberg,Germany,in2012.
in cases where a simulation terminates due to
problems at a specific grid cell. Next to these
References
“care-taking”tasks,CATasbeenessentialfor
thedetailedscientificanalysisinmanycases. Clyne, J., Mininni, P., Norton, A., & Rast, M.
2007,NewJ.Phys,9,1
Clyne, J. & Rast, M. 2005, in Proceedings of
Swirls and tornadoes. Oneexampleisthe
Visualization and Data Analysis 2005, ed.
discoveryofring-likestructureswithincreased
J. C. G. M. T. B. K. Edited by Erbacher,
horizontal velocity at chromospheric heights
RobertF.;Roberts,284–294
in 3D magnetohydrodynamic (MHD) mod- Freytag, B., Steffen, M., Ludwig, H.-G., et al.
els of the Sun. Similar rings were previ-
2012, Journal of Computational Physics,
ously observed as so-called “chromospheric
231,919
swirls”withtheSwedish1-mSolarTelescope Schaffenberger, W., Wedemeyer-Bo¨hm,
(Wedemeyer-Bo¨hm & Rouppe van der Voort
S., Steiner, O., & Freytag, B. 2005,
2009). The rings of enhanced velocity, which
in ESA Special Publication, Vol. 596,
appearedprominentlyinCAT(seeFig.3),sug-
Chromospheric and Coronal Magnetic
gested that chromospheric swirls are the ob-
Fields, ed. D. E. Innes, A. Lagg, & S. A.
servationalsignatureofrotatingmagneticfield
Solanki
structures. This finding finally led to a more
Wedemeyer, S., Ludwig, H.-G., & Steiner, O.
comprehensivestudyofthisphenomenon,then
2012,ArXive-prints
known as “magnetic tornadoes” (Wedemeyer-
Wedemeyer-Bo¨hm, S. & Rouppe van der
Bo¨hmetal.2012).
Voort,L.2009,A&A,507,L9
Wedemeyer-Bo¨hm, S., Scullion, E., Steiner,
O.,etal.2012,Nature,486,505
M-type dwarf stars. CAT has been exten-
sively used for the development of 3D MHD
atmospheremodelsofM-typedwarfstarsthat
extendfromtheupperconvectionzoneintothe
chromosphere (Wedemeyer et al. 2012). The
resulting set of models with different initial
