USER MANUAL - Quark Nova Project
Contents
1. ans ina 1 3 3 DEALS DAP eem 11 3 4 Parameters 12 E a ot ue de 12 Dp TEE ERE NE ER 12 SR TTC BYE LES ARR RE a 19 3 5 CS ESS UC DOE EUN 16 Graphine MOULE M 16 2 52 Render Modu ss ann De dA T DRM M M 19 dB e Modulen a Dod AD ER o 2 3 6 Pub dU 22 Burn UD User Manual Page iv Burn UD User Manual 1 0 GENERAL INFORMATION 1 0 GENERAL INFORMATION 1 1 What is Burn UD The theory of strong interactions Quantum Chromodynamics predicts that hadronic nucleated matter subjected to high densities and or temperatures will de confine into a quark gluon plasma QGP This transition has already been realized in the low density high temperature regime both in heavy ion collision experiments and in Nature during the first few moments after the Big Bang where the reverse transition is expected to have occurred The high density low temperature regime is also expected to occur in Nature at the centers of compact stars Although asymptotic freedom would suggest otherw2. Thu Sep 11 11 31 46 PDT 2014 Time 5 0049999999999155 Thu Sep 11 11 31 55 PDT 2014 DONE Time 10 0000000000001 63 Thu Sep 11 11 31 55 PDT 201 4 Thu Sep 11 11 31 55 PDT 2014 Burn Time 18 438345288 s Thu Sep 11 11 31 55 PDT 2014 Thu Sep 11 11 32 08 PDT 2014 BEGIN Diagnostics Thu Sep 11 11 32 08 PDT 2014 dt dx is supposed to be less than 0 5 or so gt dt dx 0 09999999999999999 Thu Sep 11 11 32 08 PDT 2014 dt dx 2 is supposed to be less than 0 3 or so dt dx 2 1 9999999999999998 Thu Sep 11 11 32 08 PDT 2014 Numerical diffusion 4 933178987678397E 13 x V1 Thu Sep 11 11 32 08 PDT 2014 dx 0 05dt 0 005 Thu Sep 11 11 32 08 PDT 2014 END Diagnostics rex Thu Sep 11 11 33 41 PDT 2014 Time 50 00000000000713 Thu Sep 11 11 35 08 PDT 2014 Time 100 00499999998154 Thu Sep 11 11 35 08 PDT 2014 DONE Time 100 00499999998154 Thu Sep 11 11 35 08 PDT 201 4 Thu Sep 11 11 35 08 PDT 2014 Burn Time 180 6737315 s Thu Sep 11 11 35 08 PDT 201 4 Figure 12 Message Module Burn UD User Manual Errors Page 21 3 6 Animations Burn UD has the capability to output graphs and camera rendering at certain intervals throughout the calculation The number of time steps between an output event 15 controlled via the Atow field of the main Output panel To run an animation it is necessary to Make sure Atout 15 a reasonable value in the Output panel Enable the animatio
3. VERSION 2 0 SEPTEMBER 2014 USER MANUAL QUARK NOVA PROJECT 2 QUARKNOVA UCALGARY CA Burn UD User Manual BURN UD USER MANUAL Quark Nova Project O Quark Nova Project 2500 University Drive N W Calgary Alberta Canada T2N 1N4 http quarknova ucalgary ca Page ii Revision Sheet Release No Revision Description 09 11 2014 User Manual Created 800 9 O Wo o O o Burn UD User Manual Page iii USER MANUAL TABLE OF CONTENTS Page 1 0 GENERAL INFORMATION Reina deu DN bU EN 2 1 1 A hatis BOr UD 2 1 2 Acronyms and ADDbrEeviatiOnS 3 2 0 INSTALLATION x lerede 5 2 1 rccte E FD 5 2 2 115 1 8 ao a 5 2 3 S 5 3 0 GRAPHICAL USER INTERFACE needs eee dede 7 3 1 DESKTOP 7 SUC 1 P Sm ei 8 2 153 Recent EO CO ireo ao e a a a a Eno 9 SUMMA COMM ANS ies costs Dmm 9 SP he beata cac 9 3 2 Ouick Lawnch
4. D gt N P E D gt E vtt Graphs test2 burn test burn Progress Messages Render burnud burn Figure 1 The Burn UD desktop Burn UD User Manual Page 7 3 1 1 System The system icons are responsible for project management New The new icon closes the current project and opens a new blank one Open The open icon opens a pre existing project saved as a file on the drive Save Saves the current project If this is the first time saving the project the user will be asked for a filename and location to save the project to Save as Saves the current project under a different name 3 1 2 Modules The module icons allows one to navigate between different Burn UD modules Desktop This icon returns the user to the main desktop view Graphs Opens the graphing module where the user can plot various quantities from the calculation CR Render Opens the render module where the user can visualize certain calculated quantities Burn UD User Manual Page 8 Messages Opens the messages module which displays various information including any error messages 3 1 3 Recent Projects Once a project is saved its location and name is added to the list of recent projects This group of icons on the main desktop make it easy to open old projects without searching the file system Up to five projects are stored in the recent list Opens the project named bel
5. control the grid fidelity and the physics involved whereas the output parameters control where the output is stored Each numerical field will turn red when a key is pressed indicating that the value has not yet been stored Pressing ENTER will store the value and the field will return to normal 3 4 1 Input Setup tmax The maximum time to run the simulation to Cells Number of cells in the simulation grid Grid Width The width in cm or the simulation grid dt The size of each time step dx The width of one cell in the grid grid width cells This field is not editable dt dx A field indicating the value of dt dx For the solutions to be stable this value should be less than 0 5 If the background is red this criteria is not satisfied if it 15 green then everything is ok This field is not editable dt dx A field indicating the value of dUdx For the solutions to be stable this value should be less than 0 3 If the background is red this criteria is not satisfied if it is green then everything is ok This field is not editable Physics 6 Opens a function dialog see 3 4 3 Function Dialog where the user can specify the total density as a function of position Units of MeV njnia Opens a function dialog see 3 4 3 Function Dialog where the user can specify the strange quark density as a function of position Ne Ntotal Electron fraction Hos The initial chemical potential of the stra
6. the desktop for easy access 2 2 Mac OSX Run the dmg installer file and follow the prompts from the installer dialog Java is bundled with the installer so there is no need to install Java if it is not on your system Once installed you can move the Burn UD icon from the installation directory to the desktop for easy access 2 3 Linux Run the sh script to bring up the installer dialog Follow the prompts Java is not bundled with the Linux version of Burn UD so make sure Java v1 7 or greater is installed on the system Once installed you can move the Burn UD icon 1 from the installation directory to the desktop for easy access 2 4 Known Issues On some Linux machines with a dual monitor setup the main Burn UD window will disappear immediately after the splash window is hidden The workaround for this is to either use one monitor or switch which monitor is the primary Burn UD User Manual Page 5 3 0 GRAPHICAL USER INTERFACE Burn UD User Manual Page 6 3 0 GRAPHICAL USER INTERFACE The Graphical User Interface or GUI is a user friendly way to manipulate parameters and generate output Otherwise the change will not be registered within Burn UD 3 1 Desktop The desktop Figure 1 is the starting point for all projects It consists of icons from five different categories System Modules Recent projects Commands and Information odynamical Combustion Code Modules Recent projects Commands Information E
7. the interface Thus one cannot define a typical speed from analytic considerations alone the one considered in Burn UD therefore uses a numerical approach to this problem Burn UD User Manual Page 2 Burn UD solves the equations of hydrodynamical combustion It solves the equations explicitly in time using a fourth order Runge Kutta scheme spatial derivatives are treated separately as per the Method of Lines The spatial derivatives include advection which is treated with a third order upwinded flux limited finite volume scheme and diffusion and pressure terms which are second order not upwinded and treated separately from the advection terms ie not flux limited While it may seem that Flux Corrected Transport would be well suited to this problem it provides only a negligible increase in accuracy at the cost of excessive overhead 1 2 Acronyms and Abbreviations GUI Graphical User Interface JVM Java Virtual Machine CFL Colour Flavour Lock EOS Equation of state SOM Strange quark matter QGP quark gluon plasma Burn UD User Manual Page 3 Burn UD User Manual 2 0 INSTALLATION 2 0 INSTALLATION 2 1 Windows Simply double click on the exe provided either 32 or 64 bit depending on your system to open the installer program Java 15 bundled with the installer so there is no need to install Java if it is not on your system Once installed you can move the Burn UD icon from the installation directory to
8. the main Output panel must be selected for the graph to write output The name of the output file will be defined by the animation name see main Output panel and the title of the graph If two graphs have the same title the animation output of the first will be overwritten by the second e Save Image Saves the graph image with each animation step The image type is defined in the main output panel 9 Save ASCII Saves the contents of the graph as a text file Burn UD User Manual Page 17 Parameters Parameters General General Strange Point AXES n Up Point X Axis X pos Li n Down Point Y Axis n Strange n Up Down Add Delete n rn Properties Name n Strange Type Connected Color 5 n Down M visible v 2 Selected v TURA Misc Point Size 10 5 j a Auto Range ral Line Width 215 Shape Circle p Animation Stroke Solid Save image scale X Y scale X Save ASCII Normalize Control Points Bin sort Edit Figure 9 Graph general parameters Figure 10 Graph data parameters 3 5 1 2 Graph Appearance The appearance of each graph can be customized through its properties To access the graph properties right click on the graph and select properties A dialog box containing many customizable options for the Axes General Appearance Ticks Labels and Data is then presented to the user Axes Tab Each axis has the following option
9. will attempt to equilibrate chemically by producing more S quarks which will diffuse into the hadronic regions forming even more SQM The situation is then an interface where hadronic matter is on one side and SQM on the other with the interplay between reactions and diffusion governing the speed at which the interface spreads This scenario is of a type similar to that of non premixed combustion with the important difference being that the reactions in question are not activated above a certain temperature as is often the case for combustion processes Instead the presence of S quarks activates the burning and the process is governed by particle diffusion rather than heat diffusion During the combustion an interface is created with cold unburnt fuel on one side and hot burnt ash on the other Subsequent cooling of the ash will result in pressure gradients that induce fluid like motion of the matter in and around the interface To conserve energy fluid velocities across the interface would then differ causing compression or rarefaction in the burning region which can enhance or quench the combustion Thus a fluid dynamical treatment of the problem is essential to determine the interface speed There is large uncertainty in the typical speed of the interface values proposed in the literature range from 10 to 10 cm s This variation stems from the strong dependence of the reaction rate on temperature and density both of which vary throughout
10. black Bottom left x position versus velocity Bottom right x position versus neutrino emissivity Burn UD User Manual Page 24 Parameters General Name evalocity Enabied La Variable X Velocity Camera Image 525 12 Modifiers Edit Animation Enable Figure 14 Render module example of a Burn UD calculation Top left x velocity with a perspective view camera rotation of xrot 45 yrot 45 and relative camera position of 3 Top right strange quark density Bottom left neutrino emission Bottom right up quark density with a perspective view and a relative camera position of 2 Burn UD User Manual Page 25
11. d scale blurring color adjustments etc xRot Rotation of the camera in the x axis yRot Rotation of the camera in the y axis zRot Rotation of the camera in the z axis 6 Animation Enable If selected the rendered image will be output to a file at each Atout time step defined in the main Output panel 3 5 3 Message Module The message module displays to the user any information provided by the Burn UD calculation as well as any errors that it may have encountered It is wise to check the message module from time to time to make sure everything 1s running smoothly Use the refresh toolbar icon to erase all messages DITIIUO Y gt gt E Refresh Messages Thu Sep 11 11 31 37 PDT 2014 BEGIN Diagnostics rer Thu Sep 11 11 31 37 PDT 2014 dt dxis supposed to be less than 0 5 or so dt dx 0 09999999999999999 Thu Sep 11 11 31 37 PDT 2014 dt dx 2 is supposed to be less than 0 3 or so gt dt dx 2 21 9999999999999998 Thu Sep 11 11 31 37 PDT 2014 Numerical diffusion gt 4 933178987678397E 13 x V1 Thu Sep 11 11 31 37 PDT 2014 dx 0 05dt 0 005 Thu Sep 11 11 31 37 PDT 2014 END Diagnostics
12. e current usage of computer resources Progress Displays a progress dialog showing any tasks currently running and there level of completion It is possible to cancel certain tasks using this dialog Figure 3 Help Displays this manual Burn UD User Manual Page 10 Progress x Task status Progress Running pipeline Running 2 Cancel All Figure 3 The Progress dialog shows information about currently running tasks 3 2 Quick Launch Toolbar The quick launch toolbar is provided along the top of the program and provides an easy to access location for all the icons one uses most Simply drag an icon from the desktop to the quick launch bar to add it The user can drag icons around to position them most conveniently To remove an icon from the quick launch bar drag the icon from the bar to somewhere on the desktop I BurnUD v2 0 New project gt o9 m 22 2 wt CI Figure 4 Quick launch toolbar 3 3 Status bar The status bar Figure 5 displays the current memory usage the total memory usage and the top most task currently running Pressing the orange x icon cancels the task and pressing the question mark icon opens the progress dialog Used Mb Total Mb Running pipeline Complete E3 7 Figure 5 The status bar Burn UD User Manual Page 11 3 4 Parameters Many parameters for the Burn UD calculation can be controlled through the GUI The input parameters
13. ing Module The graphing module is responsible for displaying the output from the Burn UD calculation in various graphs Graphs E m 1 2 0 89 Q Re plot Variable Time Clear Th Cascade Graph 1 Graph 2 x Parameters Data Axes X Axis X pos Y Axis n Stange n Down n Up nUp 4 00E x Save ASCII x 54520 y 1 2963E6 f 0 0000 L Figure 8 Graphing module 3 5 1 1 Graph Toolbar The graph module contains a toolbar which allows the user to manipulate the content E Re plot Re plots all graphs within the module 2 Variable Adds a new variable graph to the project The variable graph is capable of graphing quantities within a cell e g densities temperatures etc Time Adds a new time graph to the project The time graph plots quantities that vary from one time step to another such as interface position and velocity The interface velocity is calculated by using the interface position at the current stored time step and the interface at the previous stored time step The time steps are stored with every output defined by Atout in the output panel Burn UD User Manual Page 16 ao m Clear Clears all graphs within module This removes all data including that stored within the graph Tile Arranges the graphs in a tile pattern Cascade Arranges the graphs in a cascading fashion 4 Each graph currently open in the module is displayed 85 8 sequence of icons at the end of
14. ise even at ultra high densities higher than that of a nucleus hadrons do not spontaneously dissolve into their constituent u amp d quarks because overall the energy per baryon would be higher But if a significant number of S quarks are included then the extra quantum number flavor allows more quarks to share the same energy state thus lowering the overall energy per baryon This phase of matter is referred to as strange quark matter SQM Since the probability of converting many amp d quarks into S quarks at the same time is effectively zero a conversion from hadronic to SQM can only proceed readily if a substantial number of S quarks are already present The situation considered here is inside a compact star where the central density has reached that of nuclear de confinement Subsequently a seed of SOM is instantiated at the star s center It has been speculated that such a situation could occur during the core collapse phase of a supernova or if the nucleation timescale is slower in an older neutron star whose central density has increased due to spin down The details of the seeding mechanism are not considered here but it is assumed to proceed via either clustering of lambdas higher order neutrino sparking reactions or seeding from the outside In the boundary region surrounding the SQM seed hadrons will then overlap with S quarks allowing the hadrons to dissolve into their constituent u amp d quarks Such a region
15. n via the Output panel Enter a name for the animation via the Output Panel Press ENTER to register the change Set the output directory Set the type of image that is output Enable animation in each graph and camera within their respective modules Burn UD User Manual Page 22 4 0 EXAMPLES Burn UD User Manual Page 23 4 0 EXAMPLES In this section we present several example outputs generated by Burn UD ax 24 24 22 Re plot New Clear Th Cascade neurino emi velocity deruies chemical pou chemical potentials ox Z densities ax Parameters E X pos Xpos General 400 00 n Strange Point n Down Poing n Up Point EEE ee 300 00 4 00E6 Add Delete mm 2 200 00 2 Properties 2 00 8 Name J n Electrons a 100 00 E Type Connected v os Visible 0 00 0 00 Selected v Point Size 1022 0 00 20 00 40 00 Line Width 289 Shape Circle Stroke Solid v EE lt N Xi Y scale x Xpos X pos Normalize 030 Control Points 0 01 0 01 020 000 3 2 010 2 0 00 0 00 0 00 0 00 20 00 40 00 0 00 20 00 40 00 Bin sot Ed F igure 13 Graph module example of a Burn UD calculation Top left x position versus chemical potential for U blue D red LA and S green quarks Top right x position versus density for U blue D red and S green quarks and electrons
16. nge quarks MeV To The initial temperature in units of MeV EOS A drop down box allows the user to specify the equation of state EOS Currently the MIT Bag model and a Colour Flavour Lock CFL version of the MIT Bag EOS are available Each allows the user to enter the bag constant B Control Diffusion Enable disable diffusion 1n the Burn UD calculations Advection Enable disable advection 1n the Burn UD calculation Reactions Enable disable reactions in the Burn UD calculation Neutrino Enable disable neutrino cooling in the Burn UD calculation 3 4 2 Output Status Burn UD User Manual Page 12 9 Current time A non editable field showing the current time of the simulation This value is updated every second regardless of the Ato field see below Below the field is a status bar to visually show how far along the calculation is Animation e Enable Enables the output of data every Atou time steps Atow Number of time steps before output is updated written e Name The name of the animation This name will be appended to each filename output by Burn UD Example BurnUD 5 10 2014 In order to register the name the user must press ENTER e Directory The directory where the output files are to be stored A browse button allows the user to search the file directory e Image Type A drop down box giving several options for the type of image to store for image outputs 3 4 3 Function Dialog The func
17. ound numbers Labels Tab e Label Color Defines the color of the label e Size The font size in pixels of the label text e Format A string containing the format of the numbers For example 0 000 will force the number to be drawn to 3 decimal places whereas 0 will round each number to the nearest integer e Font Drop down box containing a list of available fonts for the labels Data Tab The data tab provides a list of all data sets within the graph Each data set is customizable and data sets can be added or removed 3 5 2 Render Module The render module displays the output from the Burn UD calculation as a brightness distribution representing a real image The brightness of each pixel depends on the quantity selected e g ns nu nd etc and the location of each pixel is proportional to the distance from the grid origin It is possible to rotate the camera around the scene by using the mouse or by adjusting the rotation parameters individually in the parameters panel on the right Burn UD User Manual Page 19 x 10 Parameters General scam 1008 Name Camera 2 Grid Width Enabled et s ariabie X Valocih Cut 1 amera Ovid Image Diffus v ntho Advect v Modifers Ed Reactons v Position 1 Neutri x Rot yRot nuu MEN Ed zRot 05 r En De etat 0 04 Animation T meV 01 0X Enabie 505 839 v EOS Properties B 4 42050625E8 d Mb Total Mb 1 354 Running pipeline Comple
18. ow the icon 3 1 4 Commands The commands group contains icons responsible for starting pausing and restarting the Burn UD calculation 7 Calculate Runs the calculation from the current time to the max time Once the calculation is complete the time step is reset to 0 I Pause Pauses the calculation at the current time step To resume simply press the calculate button 3 1 5 Information The information group on the desktop provides the user with a means to monitor certain aspects of the program as well as view the user manual Burn UD User Manual Page 9 Memory Opens a dialog containing information about the current memory usage Figure 2 TEMA the dialog The right panel contains memory usage including used memory average usage total memory and maximum memory The maximum memory is the total amount available to the Java Virtual Machine JVM whereas the total memory is the amount allocated to Burn UD Memory Information x X Memory Information Title Ia ajg x 2 s uL i Used Memory MB 538 Avg Usage MB 599 231 Time step Total Memory MB 1244 Max Memory MB 12444 Usage Rate MB s 0 006 Update Interval ms 2000 5 1200 00 GC on each step Dump Heap Im 1000 00 D j o x 800 00 D 600 00 0 00 5 00 10 00 x 5 2051 y 1730 4504 f x LE Start Stop GC Clear Done Figure 2 The memory usage dialog displays information about th
19. s e Min The minimum value of the axis e Max The maximum value of the axis e Lock If this is enabled the axis range does not change during a zoom operation or during an auto range call Label The label of the axis that is displayed on the graph e Log If selected the axis values will be displayed on a LOGIO scale Make sure the range does not contain and negative values or else the graph will not display any data e Label Location A drop down box containing different screen locations for the axis label Burn UD User Manual Page 18 General Tab Name The title of the graph Show Title Displays hides the title on the graph ToolBar Displays hides the individual graph s toolbar Coordinates Displays hides the coordinate panel at the bottom of the graph Crosshairs Displays hides the cross hairs that follow the mouse location Panel Color The fill color of the graph exterior to the axes Area Color The fill color of the graph within the axes Line Color The color of the graph boarder Crosshairs The color of the cross hairs Margins Sets the margins of the graph Plot Area Fixed Size The graph is constrained to the width height provided Ticks Tab Number The number of tick marks to display on each axis Length The length in pixels of each tick mark Width The width in pixels of each tick mark Grid Display hide the grid Nice Numbers If enabled the graph will attempt to place tick marks at r
20. te 100 a Figure 11 Render module 3 5 2 1 Render Toolbar The render module contains a toolbar which allows the user to manipulate the content Refresh Refreshes all cameras M New Adds a new camera to the project 1 Clear Removes all cameras from the project Tile Arranges the cameras in a tile pattern Cascade Arranges the cameras in a cascading fashion EN Each camera currently open in the module is displayed as a sequence of icons at the end of the toolbar The camera title is displayed underneath the icon Pressing the icon brings the camera to the forefront Burn UD User Manual Page 20 3 5 2 1 Camera Parameters Each camera in the render module has a set of parameters Variable A drop down box containing various quantities to display The brightness of each pixel Image size The size in pixels of the rendered image The larger the image the more time it will Ortho If this is selected an orthographic projection will be used Otherwise a perspective Modifiers Displays a dialog where the user can control properties of the output image including Position Position of the camera for perspective projections ortho checkbox is unselected e Name The name of the camera e g nS Front e Enabled If selected this camera will be rendered on each output in the rendering will be proportional to the value of this quantity e take to render projection will be use
21. the toolbar The graph title is displayed underneath the icon Pressing the icon brings the graph to the forefront 3 5 1 2 Graph Parameters Each graph has a set of parameters that are displayed in a panel on the right These parameters fall under two categories Data and General Data Tab The data tab displays all of the data contained within the graph the different series Selecting a data set allows the user to edit its properties including its name type connected or scatter the color of the data when plotted whether it is visible the size of the data points the width of the connected line the shape of the data points and the stroke of the connected line General Tab The general tab controls what is plotted on the graph The user can select a single x axis variable but can select a number of y axis variables in order to show several quantities Axes e X axis Drop down box where the user can select the variable used for the x values 9 Y Axis List of currently plotted quantities along with a drop down box showing the possible variables to plot To add a new variable to the y axis simply click on the plus icon below the drop down box To remove a y axis variable select it and then press the x icon below the drop down box Misc e Auto Range If selected the range of the x and y axes will be adjusted in order to fit all the data within view Animation Please be aware that the Enable parameters in
22. tion dialog allows a user to enter a function which is then parsed by Burn UD and applied to the parameter of interest The user can select from either an analytic function Figure 6 or a point function Figure 7 through the drop down box The analytic function allows the user to enter a function string in the accompanying text field All functions are a function of x With a point function the user can directly control the function via control points The graph displays the function for a given range of x and y If the function is out of viewable range it is possible to adjust the graph range through the graph properties Right click anywhere on the graph and select properties from the popup menu The user is then presented with options to adjust the graph properties Please section 3 5 1 2 Graph for more information about customizing graphs Burn UD User Manual Page 13 me Hx ews 0 0004 fo 0 0003 Function AnaMic 0 11 Templates Constraints Variables 001 1 0 expi ix 1 0 8 0 1 0 0 00105 1 07 3 0 Figure 6 The function dialog window showing an example of an analytic function Burn UD User Manual Page 14 me aale else ma 6 1964 y 00004 f x 0 0003 Function nint Load Ascil Edit Figure 7 The function dialog showing an example of a point function Burn UD User Manual Page 15 3 5 Modules 3 5 1 Graph
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