USER MANUAL - Quark Nova Project
Contents
1. 2700 0 T 4 273 Iteration 2600 0 T 4 5 Iteration 2500 0 T 4 81555456108 iteration 2400 0 T 5 241381451431368E9 Iteration 2300 0 T 5 810754781449967E9 Iteration 2200 0 T 6 193311123849593E9 Iteration 2100 0 T 6 556727029435853E9 iteration 2000 0 T 7 775 Iteration 1900 0 T 9 82922 Iteration 1800 0 T 1 282810 Iteration 1700 0 T 1 6 iteration 1600 0 T Iteration 1500 0 T iteration 1400 0 T 2 42765899970 iteration 1300 0 T 2 534068047677073E10 iteration 1200 0 T 2 6918411592022E10 3493087328E10 La Figure 7 The message tab shows information sent from the calculation code including ertors QUARK NOVA PROJECT Parameters Panel The parameters panel is located at the bottom of the main window You can expand and collapse the panel by clicking on the minus or plus icon in the far right of the title bar The panel consists of four tabs e Project Parameters This panel allows you to set the layout for the Graphs panel in the main panel You can specify the number of rows and columns for your display In addition there is an MF Cutoff field that specifies the minimum isotope mass fraction needed to be included in the graphs e Code Parameters This panel allows you to select the type of code to run and input the parameters for the calculation e Animation Parameters This panel sets up an animation run It allows you to spe2. Closes r java Toolbar CA Fx dd lo Figure 2 Main toolbar The toolbar provides a graphical interface to some common commands in r Java The icons represent Calculate Icon This is the main icon which starts off any abundance calculation When pressed r Java will calculate the resulting abundances of isotopes and create the necessary graphs Open Icon Opens a saved project Save Project Icon Saves the current project Add Graph Icon Adds a new graph to the graph panel Remove Graph Icon Removes the selected graph from the graph panel Animate Icon Runs an animation based on the Animation Parameters in the Parameters panel Clear Icon Clears the data from all graphs Maximize Restore Icon Maximizes or restores the currently selected graph Main Panel Graphs Table Periodic Table Messages Figure 3 Tabs located on the main panel QUARK NOVA PROJECT The main panel is located directly below the Toolbar and consists of three tabs e Graphs This panel displays all of the graphs You can add as many graphs as you like to this panel see Add Graph Icon above and can arrange them using the Project Parameters tab in the Parameters Panel Graphs Table Periodic Table Messages Time step Graph 12087 3 10087 4 Bos 6008 Mass Fraction 4006 8 4 2 00 8 F Figure 4 Example of graphs layed out in the
3. 01 Click the red Import button to calculate the necessary input parameters These will be displayed in the left section of the panel Input Parameters Of course you can enter the general input parameters without importing them from the QN parameters section Set Z0 26 and Duration 1 0 in the Input Parameters section Click the Calculate button in the main toolbar to start the calculation This will take a few seconds to complete and you can see how the graph changes during the calculation Adjusting the Update field will add more or less animation steps To save the graph right click anywhere on the graph and choose Save Ascii or Save Image depending on if you want to save the text data or the image respectively To change the scale of the graph right click anywhere on the graph and choose Graph Properties Under the Axes tab default set the Scale to log10 x in the Y axis section and set the Min to 20 and the Max to 0 Save the project by clicking the Save icon in the main toolbar or selecting Save Project in the File menu You can then open this project at a future time by using the Open icon in the toolbar or the Open Project entry in the File menu The above steps should get you started in exploring the user interface Feel free to change parameters and options to see what the program can do QUARK N
4. graph tab e Table This panel displays a list of isotopes currently loaded in the project Several of these fields are editable including the color of the isotope which is useful for some types of graphs Also available in the table view is the ability to select isotopes Selected isotopes are used in some graphs such as Isotope Graph Mass Fraction the animation graphs and time step graphs Graphs Table I Periodic Table Messages 0 00 50 00 100 00 150 00 200 00 250 00 300 00 350 00 A Isotope Graph 10 00 F Mass Fraction 1200 F 1400 F 16 00 F 18 00 F 20 00 0 00 50 00 100 00 150 00 200 00 250 00 300 00 350 00 A Z A N Mass amu Partition Function Beta Decay Rate s Q Value Solar MF Mass Fraction 0 1 1 1 009 0 0 o O 0 1 1 o 1 008 o D o 0 706 o 1 2 1 2 014 2 225 0 o 0 0 1 3 2 3 016 8 482 0 o 0 0 003 1 4 3 4 028 5 501 0 o 0 o 1 5 4 5 041 1 082 ly o 0 o 1 6 5 6 045 5 782 0 0 0 o 2 3 1 3 016 7 718 0 o 0 oj 2 4 2 4 003 28 296 0 o 0 275 ol 2 5 3 5 012 27 406 o o 0 oj 2 6 4 6 019 29 269 0 859 o i ol 2 7 5 7 028 28 824 0 o 0 oj 2 8 6 8 034 31 408 5 82 0 0 o 2 9 7 9 044 30 259 O o 0 o 3 4 1 4 027 4 618 0 o 0 o 3 5 2 5 013 26 331 0 o 0 oj 3 6 3 6 015 31 995 0 ol 0 oj 3 7 4 7 016 39 245 0
5. the Table tab in the main window you will be presented with a table of all the isotopes imported from the file Several of these fields are editable including the color of the isotope which is useful for some types of graphs 9 Click on the Graphs tab in the main window and then click on the green Plus icon in the toolbar to open a dialog of possible graph types 10 Choose Isotope from the dialog and click Accept 11 Click on the Code Parameters tab in the Parameters panel at the bottom of the main window 12 Choose NSE Nuclear Statistical Equilibrium as the code type and enter the following values press Enter after you input the values for each T 3 5E9 p 1E7 Ye 0 5 QUARK NOVA PROJECT 13 14 15 16 17 18 19 20 21 22 Click on the Calculator icon in the main toolbar The abundances will then be calculated and displayed on the graph you created in step 10 Click on the Graph Parameters tab in the Parameters panel at the bottom of the main window Set the x axis to A You will notice that you do not have to re calculate for the changes to be displayed on the graph Click on the Code Parameters tab and select Dynamic as the code type Enter the following values in the QN Parameters section again remember to press Enter after each entry M star 1 4 R star 10 M ejecta 1E 2 Zeta 0
6. 1 40792300 JNPIANOO v Lambda 1 5 HODODODODOPRDODO 00000000 00000000 00000000 00000000 78187000E 9 00000000 00000000 00000000 00000000 00000000 85923786 00000000 81987557 Figure 9 Example input file for r Java Each column is tab separated Q value 0 00000000 0 00000000 0 00000000 0 00000000 0 00000000 0 00000000 0 0 0 0 o 0 0 00000000 00000000 00000000 00000000 00000000 00000000 00000000 10 BE Mev 00013973 72600800E 5 22474349 48213612 50170232 08242395 78256880 71826722 28 29602201 27 40616746 29 26973036 28 82504062 31 40884087 NUR UONWoO SN Mev 0 00000000 0 00000000 2 22470623 6 25739263 2 98043380 4 41927836 4 70014485 0 00000000 20 57775479 0 88985455 1 86356290 0 44468974 2 58380025 solar MF 0 00000000 0 70600000 4 80000000E 5 0 00000000 0 00000000 0 00000000 0 2 0 0 0 0 0 00000000 93000000E 5 27500000 00000000 00000000 00000000 00000000 Mass Fraction DONAANJIAWONDO 00000000 02851269E 8 50918463E 10 00402482 03216566E 19 06784776E 39 75181392E 36 30969737E 63 00260323E 20 24163925E 31 71154826E 35 23173162E 45 25332971E 47 QUARK NOVA PROJECT Codes sotope abundances are the main output from r Java calculations There exists however three different types of underlying code to perform these calculations Eac
7. OVA PROJECT Graphical User Interface Java is graphical user interface to the r process code Navigating the toolbars menus and graphs is meant T to be intuitive This section will briefly cover the function of each interface component An important point to note is that when you enter a value in a text box you must press Enter for the change to be recorded t java does not monitor key presses and will not update unless Enter is pressed Main Menu New Project Open Project Save Project Save ProjectAs Import Export Exit Figure 1 File menu The main menu consists of one sub menu the File menu This menu allows you to open and save projects as well as import and export isotope data e New Project This creates a new blank project When r java is first started a new project is automatically created This menu item is useful if you have a project loaded and you want to start a new one e Open Project Opens a saved project e Save Project Saves the current project to the current filename of the project If the project has not yet been saved a dialog will be displayed asking for the name of the file you wish to save to e Save Project As Saves the project to a filename of your choice QUARK NOVA PROJECT Import Imports isotope data from a text file A dialog is displayed requesting information about the file Export Writes the current isotope information to a text file Exit
8. Version t Process code for the Java platform USER MANUAL QUARK NOVA PROJECT r Java User Manual Quark Nova Project University of Calgary 2500 University Dr NW Calgary Alberta Canada T2N 1N4 http quarknova ucalary ca Table of Contents IMtTOdUcI Masa di cade 1 Quick STA on 2 Graphical User Interface oooonoonicicnciccccnnconncnnnncnnnnnncnnncnninnanas 4 MEN Maia 4 A A EAA AAN AA AE ER A 5 MaM RANE a dia 5 Parameters Pla eats it A A AAA 8 Importing Data aa 9 5 A otebecaabdenennanebvanaenb ease 11 No A DS 11 O O 12 A tata echt aR cdi a a tabi mi tte a tata tcad 13 A A art ASE tae 14 QUARK NOVA PROJECT Ci Introduction T He r process is needed to explain the origin of many heavy neutron rich nuclei The astrophysical site where the r process occurs however has not been positively identified One fruitful avenue of research involves the study of decompressing neutron matter from the surface of neutron stars Several mechanisms may play a role in this decompression include the quark nova Code has been developed at the Quark Nova Project QNP to simulate the ejection of neutron matter from the surface of a neutron star and calculate the abundance of elements via the r process that results r Java is a graphical user interface to this code that makes exploring the parameter space simple and intuitive This manual describes the functionality of this graphical interface and assists in the use of the soft
9. cify what variable is animated and which isotopes participate in the animation e Graph Parameters This panel allows you to edit the attributes of the currently selected graph including the axis variables QUARK NOVA PROJECT Importing Data ince r Java calculates abundances of isotopes certain isotope data is needed before the calculations can commence This data is loaded into t Java via the Import command in the File menu Clicking on the Import command will display the import dialog Figure 8 E e Parameters Filename ADesktopir java_inputasciil Comment String Clear Isotopes co Column Separator Space Tab Other Input Columns af A Neutrons Mass amu Partition Function Als Q Value Sol Mass Fraction Import Close Figure 8 The import dialog is the interface through which isotope data is loaded into r java fal fal aly ap e e ato aly QUARK NOVA PROJECT This dialog provides the interface for loading isotope data into r Java There ate several inputs that need to be defined before any data can be loaded e Filename The name of the input file This is a text file separated into columns by some delimiting character such as a tab or a space e Comment String Often data files have comments that should not be read as data This field allows you to specify the string of characters at the beginning o
10. f a line that signals a comment Usually this is the FP character e Clear Isotopes When selected all isotopes previously loaded into r Java will first be removed If this is not selected the list of isotopes is appended to by the import If the isotope already exists in r Java it will be altered to reflect the new values read e Column Separator This is the character that signals a new column in a row of data from the text file Usually this is a space or tab character but can be anything Make sure this is selected properly or the data will not be read correctly The format of the input file does not need to follow any convention It is possible to define which columns of the data file correspond to what attributes of the isotopes The Input Columns section of the dialog allows you to make this assignment The only required values for each isotope are the Z and A values These values define the isotope The other columns ate not necessary but some calculations may not proceed correctly without them i e mass Figure 9 shows an example input file for r Java N M amu 00866485 00782496 01410166 01604913 02791873 04132298 04494221 01602917 00260323 01222352 01888792 02803031 03392151 III A HOH DAHUAWHUEWNHEE p AufWNRPuUbWwNroOr function 00000000 00000000 22457300 48182100 50124200 08182100 78182100 71805800 28 29567300 27 40567400 29 26909200 28 82426700 3
11. f you want a Log scale for the y axis click on the Axes tab and enter logl0 x in the Scale field for the Y Axis Similarly the range of the axes can be set and locked if necessary so they don t change automatically Several types of graphs are available including e Isotope This is the main graph type in r Java Graph Properties Axes Labels Ticks Layout Misc Data X Axis Y Axis min 10 0000 min 10 0000 Max 10 0000 Max 10 0000 Lock lt Lock Scale x Scale x Done Cancel Default Load Save Figure 13 Graph properties available when you right click on a graph and select Graph Properties and plots attributes of all the loaded isotopes The variables plotted on the axes can be selected via the parameters in the Graph Parameters tab in the Parameters panel Attributes you can plot include Z A N Mass Fraction population coefficients and even solar abundances e Time Step This graph allows you to plot values for every time step in the dynamic code calculation The axis variables available to this graph type include time temperature Q heat and neutron density It is also possible to plot isotope attributes for each time step by selecting an appropriate y axis Any isotope that is selected in the Tab panel of the Main Panel will be plotted in this graph 14 QUARK NOVA PROJECT e Animation This graph w
12. h code is suitable for a different scenario Different codes and their inputs can be selected via the Code Parameters tab in the Parameters panel NSE Project Parameters Code Parameters Animation Parameters Graph Parameters Type NSE y TK 0 p a em 0 Ye D Figure 10 Parameters available to the NSE code type NSE is short for Nuclear Statistical Equilibrium and represents a state where the rate of all forward nuclear reactions is equal to the rate of the reverse reactions This code does not represent the conditions existing during the neutron matter decompression that r Java is used to investigate but is included as a benchmark or test of the underlying code This being said it is still useful for NSE work The Code Parameters tab in the Parameters panel displays the options for the NSE code These options include e T The temperature of the system in Kelvin e 0 The density of the system in g cm 11 QUARK NOVA PROJECT e Ye The electron fraction Static Project Parameters Code Parameters Animation Parameters Graph Parameters Type Static Vv TK nt cm Ye Duration sec Vo ooo Z0 0 Figure 11 Parameters available to the static code type The static code is an r process code but does not allow for the expansion and cooling of the system with time This provides a snapshot of isotope
13. i Be B EN Q E Ne ao n oa w as f o ag Na Ma Al si PS Cl Ar 19 20 21 2 23 24 25 20 21 28 29 30 31 32 33 34 35 36 K Ca Sc Ti Y Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr I 38 39 40 41 42 43 44 45 46 49 50 51 52 53 54 Rb Sr Y Zr Nb Mo Tc Ru Rh Pd In Sn Sb Te 1 Xe ssi sel 5 zal ra ml il 7 7 ve so s ea 83 84 es 88 cs Ba La Hf Ta W Re Os Ir Pl Au Ha TI Pb Bl PO Al Rn E se 59 60 Ga 62 63 6 70 71 Fr Ra MB ce pr nd pm Sm Eu Tm Yb Lu 93 94 95 96 97 98 99 100 101 102 103 Np Pu Am Cm Bk Cf Es Fm Md No Lw Figure 6 The periodic table tab gives a visual aid to which elements are being produced in the current calculation e Messages This panel displays all of the messages from the underlying code including possible errors The Clear icon at the top of this panel will clear all messages Graphs Table Periodic Table Messages Error Messages Messages 57 521571011 25473042286375 TIME Time s Actual Run Tim Final neutron density 1 6641570635432544E31 Final temperature 2 0533082475867617E9 iteration 3800 0 T 2 1693141408794537E9 Iteration 3700 0 T 2 508 18456E9 iteration 3600 0 T 2 748 Iteration 3500 0 T 2 92561662 iteration 3400 0 T 3 083311559761069E9 Iteration 3200 0 T 3 385 Iteration 3100 0 T 3 539 8 iteration 3000 0 T 3 6977614978011374E9 Iteration 2900 0 T 3 81 Iteration 2800 0 T 4 055 Iteration
14. ill plot an attribute of one or more isotopes versus temperature density or electron fraction The animation parameters can be defined in the Animation Parameters tab of the Parameters panel 15 QUARK NOVA PROJECT Animations nimations are used to study how specific isotope attributes change with temperature The animations require an animation graph to be created via the Create Graph Icon in the toolbar Once created attributes to plot can be selected via the Graph Parameters tab in the Parameters Panel Project Parameters Code Parameters Animation Parameters Graph Parameters X axis Temperature lv Max 1 5E10 Min 2E9 Num Steps 50 5 Output Dir Save Ascii 9 Save Images e Figure 14 Animation parameters Before an animation is run you will need to adjust the Animation Parameters in the Parameters Panel The options you can adjust are e X axis This defines the axis of the animation plot Values include temperature neutron density and electron fraction e Max The maximum value for the animation to reach i e the max value on the x axis e Min The starting value for the animation Le the min value on the x axis e Num Steps The number of steps in the animation The more steps allow for a smoother the graph but will take longer 16 e Output Dir This directory is where images or data will be stored for each fra
15. me of the animation These images can then be used to create a movie of the run with external software SHAPE is an astrophysical modeling tool that has the capability to create such movies and can be downloaded from http bufadora astrosen unam mx shape e Save Ascii When selected ascii data from the graph will be saved in the output directory for each frame of the animation e Save Images When selected images of the graphs will be saved in the output directory for each frame of the animation In addition to the above options one must specify which isotopes to include in the animation This can be accomplished through the Table tab on the Main Panel Simply click the radio button in the far right column to select the isotope It is useful to note at this point that the color of the isotope can also be changed in the Table tab of the Main Panel This makes identification of the plotted isotope much simpler Once the parameters for an animation are setup clicking on the Animation Icon in the Toolbar will start the animation The animation uses the currently selected Code and the parameters associated with it Animation Graph 2 0069 4 0089 6 0089 8 0089 1 0010 1 20E10 1 40610 1 6010 Temperature Figure 15 Resulting animation graph from a test run The different colors represent different isotopes 17
16. o 0 oj 3 8 5 8 022 41 278 0 825 0 0 0 3 9 6 9 027 45 341 3 888 o 0 oj 3 10 7 10 036 44 922 o o 0 ly 3 11 8 11 044 45 649 80 692 o 0 o 4 6 2 6 02 26 924 o o 0 o 4 7 3 7 017 37 6 0 ly 0 oj 4 8 4 8 005 56 5 0 o 0 ly 4 9 5 9 012 58 165 ly o 0 o 4 10 6 10 014 64 977 o o 0 o 4 11 7 11 022 65 481 0 05 o 0 ly 4 12 8 12 027 68 65 32 542 o 0 oj 4 13 9 13 038 66 639 ly 0 0 0 4 14 10 14 043 69 987 159 344 o O o 5 7 2 7 03 24 72 0 0 0 o 5 8 3 8 025 37 738 O o 0 ly E 9 4 9 013 56 314 O 0 0 0 Color Selected 00D Mo Figure 5 The table tab allows you to view which isotopes are currently loaded in the project QUARK NOVA PROJECT e Periodic Table The periodic table in r Java is used to visually display which elements are created in the calculations At the beginning of the calculation all elements are blue which indicates there are no elements produced As the calculation runs and new elements are created the periodic table will convey this by turning these elements red Hovering your mouse over the element will display the name and current mass fraction of that element Only elements with a mass fraction greater than the cutoff defined in the Parameters panel will be turned red Graphs Table Periodic Table Messages 1 2 H He 3 4 5 6 7 8 9 10 L
17. s are changing but may take longer to calculate Instead of these inputs one can alternatively specify quark nova parameters The input parameters are then calculated based on these values The QN parameters include e Mstar The mass of the neutron star in solar masses e R star The radius of the neutron star in km e M ejecta The mass of the neutron star ejecta o Zeta 13 QUARK NOVA PROJECT Graphs raphs are the main component by which the abundance information is conveyed to the user Several types of graphs are available for plotting The graphs are displayed in the Graphs tab in the Main Panel and can be arranged via the Project Parameters tab of the Parameters Panel Each graph can be selected by clicking on the graph A red line will then appear around the graph indicating its currently selected state Once a graph is selected its parameters will become available in the Graph Parameters tab in the Parameters panel and will be available for removal via the Remove Graph Icon in the toolbar Individual graph properties can be adjusted by right clicking anywhere on the graph Here you can save the graph information as a text file or save it as an image Additionally you can edit the properties of the graph Many aesthetic options are available so that you can customize your graph any ways you like There is also an option to set the scale of the axes For example i
18. s produced under the conditions supplied The parameters for the code include e T The temperature of the system in K e n The number density of the system in cm e Ye The electron fraction e Duration How long the simulation is run for in seconds e Z0 The seed element the neutrons are bombarding 12 QUARK NOVA PROJECT Dynamic Project Parameters Code Parameters Animation Parameters Graph Parameters Type Dynamic v Input Parameters QN Parameters T K 0 00000000 zo El M star Msun 0 p ta cm 0 00000000 Update 500 R star km 0 Ye 0 00000000 M ejecta Msun 0 1 s 0 00000000 Zeta 0 Duration s 100 00000000 Figure 12 Parameters available to the dynamic code type The dynamic code is the main code in r java Itis similar to the static code but allows for the expansion of the system and hence cooling and a reduction in density The dynamic code is like a series of static calculations and as such takes longer to run The parameters for the code include e T The temperature of the system in K e 0 The density of the system in g cm e Ye The electron fraction e tt Expansion timescale in seconds e Duration How long the simulation is run for in seconds e Z0 The seed element the neutrons are bombarding e Update This specifies how many steps in the calculation before the graphs are updating Setting this to a lower number allows you to see how the abundance
19. ware The underlying code and methods for the r process calculation are not described here For an in depth review of the code and its application please see the paper Nucleosynthesis in neutron rich ejecta from Quark Novae Prashanth Jaikumar Bradley S Meyer Kaori Otsuki and Rachid Ouyed This paper is available on the Quark Nova Project QNP website at http quarknova ucalgary ca QUARK NOVA PROJECT Quick Start Java was designed to be user friendly and easy to use As such starting and running a project involves very few steps This chapter will present you with a quick no details list of commands to get started Once started you can explore the interface on your own or read further to understand the full details of the softwate 1 Launch r Java via java webstart on the QNP website 2 Save the isotope data file r java_input ascit from the QNP website to disk 3 In r java choose the menu option File and then Import to load the isotope data file 4 You will be presented with a dialog where you can enter the name of the data file Browse to the location you saved your file in step 2 and select the file 5 The column separator in the file is a tab character so select the Tab option under Column Separator 6 Click import the rest of the options are correct for the input file from the QNP website 7 Click Close to close the import dialog 8 If you now click on
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