A Graphical User Interface of Particle-In-Cell Finite Element Analysis of Lithospheric Deformation and Mantle Convection in Two Dimension

This paper describes a graphical user interface (GUI) that has been developed for two-dimensional (2-D) simulations of lithospheric deformation and mantle convection. It was originally developed for the ellipsis simulation software (Moresi et al.,
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  Computers & Geosciences 33 (2007) 1088–1093 Short note A graphical user interface for particle-in-cell finite elementanalysis of lithospheric deformation and mantle convection intwo dimensions $ S. Dyksterhuis a, Ã , R.D. Mu ¨ller a , P. Rey a , L. Moresi b a School of Geosciences and The Earthbyte Research Group, Baxter Building H11, The University of Sydney, NSW 2006, Australia b Rm 301, Building 28, Monash University Clayton Campus, Vic. 3800, Australia Received 14 June 2006; accepted 2 November 2006 1. Introduction This paper describes a graphical user interface (GUI)that has been developed for two-dimensional (2-D)simulations of lithospheric deformation and mantleconvection. It was srcinally developed for the ellipsissimulation software (Moresi et al., 2003), but could alsobe adapted to other codes with similar objectives.Ellipsis is an open-source particle-in-cell finite elementmodelling system used in the geophysics and mechan-ical engineering community for research and teaching.The system has, in the past, required a considerableamount of expertise, as setting up simulations requiredediting complex parameter files. This work can often befrustrating, especially for novice users and students,and is prone to error. To resolve these problems, a GUIand documentation for use with the programme ellipsishas been created that facilitates more user-friendlyentry into setting up ellipsis simulations.Ellipsis simulates large deformations of materialsusing a finite element method where the problemdomain is represented using an Eulerian mesh, inwhich Lagrangian integration points are embedded.Ellipsis is used primarily for simulations in whichcontinuum solids display behaviour similar to thatof fluids.Moresi et al. (2003)describe ellipsis indetail, especially the implementation of visco-elasticity, and provide details of several applica-tions. Ellipsis has been applied to a number of problems including 2-D (Boschetti et al., 2003;Wijns et al., 2003;Dyksterhuis et al., 2007) and three-dimensional (O’Neill et al., 2006) lithosphericextension, mantle convection modelling with avisco-elastic/brittle lithosphere (Moresi et al.,2002), folding in finely layered visco-elastic rockstructures (Muhlhaus et al., 2002), and the investi-gation of continental geotherms, heat flow and thesurvival of cratonic lithosphere through geologicaltime (Lenardic, 1998;Lenardic et al., 2000, 2003; O’Neill et al., 2003). 2. A user friendly GUI for 2-D geodynamicmodelling Simulations using ellipsis must be set up bycreating a text file, called an ellipsis input file. These ARTICLE IN PRESS www.elsevier.com/locate/cageo0098-3004/$-see front matter r 2007 Elsevier Ltd. All rights reserved.doi:10.1016/j.cageo.2006.11.004 $ Code available from server at http://www.iamg.org/CGEditor/index.htm or www.earthbyte.org. Ã Corresponding author. Tel.:+61293514257;fax: +61293510184. E-mail addresses: scottd@geosci.usyd.edu.au(S. Dyksterhuis),dietmar@geosci.usyd.edu.au (R.D. Mu ¨ller),prey@geosci.usyd.edu.au (P. Rey),louis.moresi@sci.monash.edu.au (L. Moresi).  files contains a long list of parameters, in theformat parameter name ¼  parameter value . Theseparameter settings control all aspects of the simula-tions, ranging from the types and locations of different materials in the simulation, the rheologicalproperties of those materials, parameters control-ling how much information ellipsis should provideabout the simulation as it executes as well as thetypes and specifications of graphical output files.The parameter values can be numeric, or they canconsist of a text string. In addition, some para-meters require lists of numbers or strings to bespecified.Often groups of these parameters work together,so that it is necessary to ensure that they areconsistent with one another. For example, severalparameters are used to define the materials presentat the start of the simulation, and this is done byspecifying regions of various shapes. For rectangu-lar regions, we have to define the locations of thetop left and bottom right of each region, and whichmaterial the region consists of. Because we willnormally have more than one such region in aparticular simulation, we must enter lists of coordinates, so that we have one entry for eachregion (seeFig. 1). It is difficult to determine thelayout of the regions from such lists, and whenediting them, the user has to be careful to edit thecorrect number in each list. This becomes increas-ingly complex as more regions, and more differentregion shapes are used. Clearly, it would bepreferable if such lists could be replaced with aGUI that would plot the regions graphically andallow new regions to be drawn using a mouse.Ellipsis GUI incorporates such a system, not onlyfor material regions, but also for boundary condi-tions and tracer regions, as well as providingsupport for rectangular, triangular and circularregions. It also comes with a set of documentationoutlining use of the GUI as well as description of the various ellipsis input parameter variables.Fig. 2shows the regions given inFig. 1when they areloaded into the GUI, and displayed with the GUI’svisual editor. Besides allowing ellipsis parameters tobe edited visually, the GUI also allows annotationsto be drawn in the visual editor window, and imagefiles showing photographs or other graphicalrepresentations of the area being modelled can alsobe displayed in the window. This can help indeciding where to place regions, as they can bealigned with a photograph or with annotationsdrawn in the window.The GUI, however, does not just manipulatethose parameters that can be displayed graphically.Other parameters can be edited using a variety of window controls. This reduces the steepness of theinitial learning curve for novice users, as they do nothave to remember the names and required formatfor the relevant parameters. Furthermore, in manycases, the GUI restricts the range of values that canbe entered for any parameter, therefore preventinginvalid entries. For example, ellipsis allows instruc-tions for creating graphical output files to be defined(PPM files), each of which can sample one of fivepossible fields, such as temperature or pressure.Ellipsis requires that the desired field be specifiedusing a code number, and users editing ellipsis inputfiles directly therefore had to consult a referencetable translating between field types and their codenumbers. However, in the GUI, the possible fieldsoccur in a list, and the user simply has to choosebetween them. The GUI will then automaticallyconvert the user’s chosen field into the appropriatecode number. Besides making the setting up of theseparameters much easier, this also prevents errors, asit is now impossible to specify an invalid parametersetting, or to specify a parameter using incorrectsyntax.Another advantage of using the GUI is that itorganises the multitude of over 150 parameters intoa number of windows, so that the user can easilyfind them. This also makes clear what aspects of thesimulation can be controlled, and prompts users to ARTICLE IN PRESS Material_rect=4Material_rect_property=0,1,2,3Material_rect_x1=0.0,0.0,0.0,0.0Material_rect_x2=450000,450000,450000,450000Material_rect_z1=0,10000,25000,40000Material_rect_z2=10000,25000,40000,150000 Fig. 1. Parameters defining four rectangular material regions inellipsis. First number in each list corresponds to first rectangle,second to second rectangle, etc.. Material_rect_property ¼ 0,1,2,3means that first rectangle is made from material number 0,second from material 1, third material 2 and final from material3. (Materials can also be defined and not used in simulation.) Material_rect_x1 and Material_rect_z1 define x and z coordi-nates of top left of the regions, while Material_rect_x2 and Material_rect_z2 define those of their bottom rights. Material_ rect ¼ 4 is also needed to specify that there are four materialrectangles. S. Dyksterhuis et al. / Computers & Geosciences 33 (2007) 1088–1093 1089  set parameters that they might otherwise haveforgotten about. In addition, the GUI containsembedded instructions in the form of tool tips formany parameters, reducing the need to refer toseparate documentation.There are two windows that control eachmaterial’s rheology, one for general para-meters, shown inFig. 3, and another for thermo-dynamic and melt properties, shown inFig. 4.Each material also has a window in which thecolours used to display it in output files can bechosen, and there is another window controllingthe general parameters affecting all materials.There is one window for each of general settings,controlling initial conditions and boundarycondition settings. Two more windows are showninFigs. 5 and 6. Those windows control whatinformation ellipsis will output, and in whatformat. Previously, users would have to remembercodes for all the variables that they wanted tooutput, so simply being able to select variablesfrom a list, as inFig. 5, greatly simplifiesthe task of setting up simulations. The samplingtracers which can now be specified using the windowshown inFig. 6, previously had to be specifiedusing a list for each settings, in a similar way tothe material region parameters shown inFig. 1.Editing such lists is extremely difficult when there isa large number of sampling tracers specified, sobeing able to display and edit sampling tracersettings using the GUI eliminates much potentialfor error. ARTICLE IN PRESS Fig. 2. The visual editor pane of the GUI, showing the four rectangular regions defined by the parameters given inFig. 1. The colour orgrey-level in which each material appears in the GUI can be specified. Here material 0 (air) is assigned a light blue colour, material 1 (uppercrust) appears in gold, material 2 (lower crust) appears in orange and material 3 (mantle) appears in red. On the left, rectangle controls areshowing, but these can be switched to show circle or triangle controls instead. On the right are controls for defining and choosingmaterials, together with a list of all material regions. There are also controls, which allow individual material regions to be selected andthen edited, or deleted. S. Dyksterhuis et al. / Computers & Geosciences 33 (2007) 1088–1093 1090  3. Scaling of model parameters Perhaps the most difficult aspect of setting upan ellipsis simulation concerns scaling of theparameters. Some of the parameters used byellipsis can have values with very great or very tinymagnitudes, and once calculations are performedon those parameters by ellipsis, the magnitudesof the resulting values can become even moreextreme, which can result in the number be-coming too big or too small to be representedaccurately. This can lead to a loss of precision in theresults of the simulation, and can prevent thesimulation from concluding successfully. Therefore,it is desirable to scale some parameter values beforethey are entered into an ellipsis input file. Theparameters controlling the simulations can bespecified in any units, so long as all the unitsare consistent. The ellipsis GUI offers two choiceswith respect to scaling of the model parameters,although since the code is open source it ispossible to add extra scaling methods to the GUI.Currently, the user can choose to leave allinput unscaled, or to have the GUI automati-cally scale all parameters based on the usersselection of five independent scaling factors(Fig. 7). If an ellipsis input template previouslycreated without using the GUI is loaded into theGUI, no scaling is carried out and the automaticscaling is set to off, unless the input templatecontains information informing the GUI aboutthe five independent scaling parameters. Further,information regarding the GUI scaling methodscan be found the documentation accompanyingthe GUI. 4. Code availability The source code for the GUI as well as ellipsishave been released under the gnu public licence, and ARTICLE IN PRESS Fig. 3. The GUI’s material rheology window, in which most of rheological components of materials can be controlled. Thiswindow shows settings for upper crust (material 1), used insimulations shown inFigs. 1 and 2. Windows used to choosecolour in which material should be displayed, both within GUIand in output PPM files, can be opened by clicking onappropriate buttons, as can a window used to set thermodynamicand melt properties.Fig. 4. The GUI’s thermodynamic and melt properties window,in which parameters controlling materials thermal behaviour canbe defined. This window shows settings for upper crust material. S. Dyksterhuis et al. / Computers & Geosciences 33 (2007) 1088–1093 1091  are available for download atwww.earthbyte.org.Ellipsis can currently be compiled and run underany Unix-based operating system and also Windowsoperating systems (using Cygwin) while the GUIwill run on any platform for which Java 1.4.2 orhigher is available. Acknowledgements We would like to thank the Australian ResearchCouncil and ExxonMobil for supporting this work.We thank Mike Dowman and James Clark for theirhelp with the code. The development of this GUIwas inspired by a prototype GUI written by CraigO’Neill. ARTICLE IN PRESS Fig. 5. Output settings pane of the GUI. On this pane, user can decide which variables ellipsis should output, as well as how often. It isalso possible to specify how many graphical output files should be created, what each one should measure, and how large each one shouldbe. Other controls allow user to control name and format of files themselves, and a button allows a window controlling sampling tracers tobe opened.Fig. 6. Sampling tracers window. This window allows samplingtracers, which are used in producing output of results of simulations, to be defined. Users can define any number of thesetracers, each of which can sample a range of different variables,and do so at different points in simulation area. S. Dyksterhuis et al. / Computers & Geosciences 33 (2007) 1088–1093 1092
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