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ZEUS-3D USER MANUAL

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1. tslcon discon radcon pgen idirect 1 n0O 400 d0 1 000 e0 1 0 vi0 0 0 b10 0 75 b20 0 6 b30 0 8 pgen idirect 1 n0O 400 d0 0 125 e0 0 8 v10 0 0 b10 0 75 b20 0 6 b30 0 8 EOF focossresssssssssssssssessssssssssssss s gt make the ZEUS executable make f makezeus Note that a in column 1 indicates a comment in a script file In this example two flavors of comment lines are used Comments led with a double dashed line gt indicate portions of the script file which rarely if ever need to be changed by the user Comments with a single dashed line gt indicate portions of the script file that will probably need to be changed with every simulation Below are descriptions of the seven segments found in the script file zeus32 s 3 3 1 Files Copied from AFS The first segment copies the files necessary to create the ZEUS 3D executable from AFS to the user s local directory only if they do not already exist there In the above example the job is to be run on NCSA s Cray Y MP uy This script assumes the user has already conncted to AFS as decribed above note in reality uy cannot connect to AFS ftp is used instead If the job is to be run on another system the compiler and loader names and options that are written to the file inedit would have to be altered 16 appropriately The files retrieved are zeus32 the 45 000 lines of source code divided up into 160 s
2. the following source code is kept provided the macro is not defined by a define statement somewhere in the file 3 if def not macro same as 2 Note that def is an acceptable short form for define 4 if def macrol and macro2 the following source code is kept provided both macros are defined by a def statement somewhere in the file 5 if def macrol or macro2 the following source code is kept provided either macro is defined by a def statement somewhere in the file 6 if alias macro eq phrase the following source code is kept provided the alias macro has been set to the character string phrase by an alias statement somewhere in the file 7 if alias macro ne phrase the following source code is kept provided the alias macro has not been set to the character string phrase by an alias statement some where in the file 8 else the following source code is kept if the source code following the previous if and all the way to this else statement was not kept i e if the truth value of the previous if is false 9 endif closes the previous if else structure All source code following the endif statement is not affected by the previous if or else statements For every if statement there must be an endif statement which follows 36 10 call deckname includes the contents of the common deck deckname at the location of the call statement These precompiler commands can be used
3. 9 bminor bpa cpb eorb port 1 bworb vimin icut pcut pscale 2 incpx incpy units Xirdmn xirdmx 3 x2rdmn x2rdmx x3rdmn_ x3rdmx 27 PGEN Problem GENerator read from subroutine aliased to PROBLEM This namelist is reserved for the problem generator which sets the flow variables to the desired initial conditions Thus the parameters which appear in this namelist depend on which problem is being studied The desired problem is specified by setting the EDITOR alias PROBLEM in the file zeus32 mac to the name of the problem generating subroutine This subroutine should initialize the active zones of all field variables and then call the subroutines bndyflgs bndyall and bndymag to set all the boundary values See the problem generator template in Subsection 6 1 Below is a description of some of the problem generators which are already part of the main source code zeus32 1 ADVECT Sets up an advection test in the 1 2 or 3 direction Periodic boundary conditions are used in XYZ geometry In ZRP geometry reflecting boundary conditions are used at the ijb and either flow in or flow out boundary conditions are used at the ojb depending on the sign of vO In RTP geometry reflecting boundary conditions are used at the iib and either flow in or flow out boundary conditions are used at the oib depending on the sign of vO parameter description default idirect 1 gt 1 direction ie biggest gt 1
4. code there is a statement call START which becomes call mstart after preprocessing using the above example of the file zeus32 mac Note that there is no subroutine called START but there is a subroutine in the source code called mstart Thus the user is free in principle to create his or her own initialization subroutine to be called instead of mstart which can be linked into the code by altering the alias setting for START from mstart to the name of the user s initialising subroutine Note that by setting any of the Module Name Aliases to empty a subroutine in zeus32 which does nothing but return to the calling routine a Module Name Alias can be effectively turned off Aliases can also be used to set parameters in various parameter statements scattered throughout the source code These are the Error Criteria Aliases and Iteration Limits Aliases in the example above Thus the EDITOR statement alias GRAVITYERROR 1 0 e 5 sets the maximum convergence error in the self gravity module to 1075 Somewhere in the code is the statement parameter maxit GRAVITYITER and the preprocessor makes the substitution However the majority of the parameters array dimensions for example are set directly in zeus32 s which is described in the next subsection To better understand the descriptions of the Module Name Aliases which follow the reader should examine the flow chart in Appendix 1 the ZEUS 3D Skeleton This is
5. re quired for the application The most common and often the only changes which must be made to the source code are to the parameter statements which set the size of the arrays needed for the run e runs the EDITOR preprocessor e creates the input deck for the ZEUS 3D run and finally e compiles and loads the source code and libraries using the UNIX make facility 8 A description of the file naming convention may be helpful at this point ZEUS 3D refers in a general way to the package and its capabilities while zeus32 is more specific and is a mnemonic for ZEUS 3D version 3 2 zeus32 is the common denominator for the names of the principle files required to create the executable Thus the source code itself is simply zeus32 the script file is zeus32 s the macro file is zeus32 mac and the executable is xzeus32 However some minor files don t follow this convention The input deck is just inzeus no 32 suffix There are two change decks one is chgzeus the other is chgz32 and the libraries don t even have ZEUS as part of their names The bottom line is that if the only changes to be made to the source code are the values of the parameters which set the array dimensions then there are only three files to be concerned with chgzeus zeus32 mac and inzeus The rest is automatic 3 2 THE MACRO FILE zeus32 mac Below is an example of a zeus32 mac file for use on a Cray Y MP with the calmath library This f
6. read from subroutine NMLSTS This namelist is reserved for a user supplied I O subroutine aliased to USERDUMP see Appendix 1 parameter description default dtusr physical problem time interval between user dumps 0 0 0 0 gt no user dumps namelist usrcon 1 dtusr 23 HDFCON HDF dump CONtrol read from subroutine NMLSTS This namelist controls the HDF dumps HDF is a format for data files developed at NCSA and is becoming widely used throughout the world HDF dumps are necessary for most of the graphics packages available These files are 4 bytes deep and contain the grid coordinates along with other useful information about the data parameter description default dthdf physical problem time interval between hdf 0 0 dumps 0 0 gt no hdf dumps hdfvar niov names of variables to be dumped character 2 Zz Valid names are to total dump gt vi v2 v3 b1 b2 b3 d and e all in the same file bl b2 b3 2d E e an gp 2312 J22 j3 m an 2 le 2 b 2 E SI 5 225 s3 namelist hdfcon 1 dthdf hdfvar 60 24 TSLCON Time SLice history dump CONtrol read from subroutine NMLSTS This namelist controls the time slice data dumps Various scalars such as total mass angular momenta energy extrema of variables etc are periodically written to an ascii file and or a metafile NCAR graphics parameter description default dttsl physical problem time interv
7. 300 CPU seconds for the entire job 1 Mega word of memory and 200 Mbytes of temporary scratch disc space in SCR In this example it was assumed that the environment variables SAVE and SCR were set to ap propriate text strings in the user s login file Idealy files that are to be saved should be transferred to a permanent storage facility To submit this script file to the NQS batch system simply type qsub zeus32 nqs 20 IV OUTPUT FROM ZEUS 3D A variety of methods for dumping data to disc during execution are available in ZEUS 3D Each of these methods has its specific use and often all types are used simultaneously In this section a brief description of each method is given along with a list of the most vital statistics These include the EDITOR definition if any which enables the data dump the logical unit to which the dumps are attached during execution the namelist which controls the data dump Appendix 2 the convention used for naming the disc file for this type of data dump and the format of the data in the disc file created 1 RESTART DUMPS These are full precision dumps of all variables at specified time intervals which can be used to resume a calculation should a job terminate prematurely for whatever reason Execution can be instructed to overwrite the previous even odd numbered dump with the new even odd numbered dump should disc space be at a premium Thus only two restart dumps would exist at any one
8. 8 9 15 17 18 25 35 38 72 73 debugging changes see also zeus32 1 20 numerical attributes 5 scaling grid 45 47 field variables 73 74 size 4 6 skeleton 40 source code see zeus32 staggered grid 5 72 variables 34 71 76 boundary variables 74 75 field variables 31 32 34 73 74 grid variables 72 73 scratch variables 34 75 78 sundry variables 75 76 zeus ngs see NQS zeus3 2 directory 8 11 15 17 18 20 35 38 zeus32 source code 9 12 15 17 30 33 35 36 38 40 42 71 zeus32 f EDITOR precompile of zeus32 38 zeus32 1 compiler messages 9 16 20 zeus32 m EDITOR merge of zeus32 37 zeus32 mac EDITOR macros 8 9 14 17 18 34 35 39 zeus32 n EDITOR listing of zeus32 36 37 zeus32 s 8 9 10 11 12 15 20 39 42 79
9. Appendix 2 3 Put the desired source code changes if any into the file chgz32 Section VI Appen dices 2 and 3 4 Run the script file to create the ZEUS 3D executable by typing zeus32 s assuming you already have execute permission 5 Run the executable by either typing xzeus32 or by submitting the job to the appro priate batch queue Subsection 3 4 38 APPENDIX 1 THE ZEUS 3D SKELETON Modules in upper case are EDITOR aliases set in zeus32 mac Modules in lower case are actual subroutine names in the source code As asterisk in a subroutine name is a wildcard for 1 2 and 3 Exemplary choices for the EDITOR aliases enclosed parenthetically have been made These choices are appropriate for the Sod shock tube problem All the existing choices for the EDITOR module name aliases follow on the next page START mstart lt greeting mget addzx gt alter setup lt gridx gsetx gsetx nmlsts defaults PROBLEMRESTART NEWGRID empty nmlsts empty coolinit PROBLEM shkset DATAQUTPUT dataio GRAVITY empty NEWTIMESTEP nudt BNDYUPDATE empty EXTENDGRID empty GRAVITY empty SPECIAL empty SOURCE srcstep lt pressure SPECIALSRC empty v3tos3 RTP ZRP TRANSPORT transprt lt ct lt moc v2tos2 RTP SPECIALTRN empty vtos or currents nhy nhy 1 tranxl enfs stv time ti
10. Cartesian geometry these zones are rectangular boxes In general the gridding need not be uniform so the ratio of the dimensions of each zone need not be constant across the grid There are eight locations one can associate uniquely with each zone Each of these locations can be tagged with the indices i j k These lo cations are the center of each box the center of three of the six faces the center of three of the twelve edges and one of the eight corners In ZEUS 3D there are two grids which are referred to as the half grid or the a grid and the full grid or the b grid By convention the i j k th point on the a grid is half a grid spacing closer in each dimension to the origin that the i j k th point on the b grid Points on the b grid x1b i x2b j x3b k correspond to zone centers while points on the a grid xla i x2a j x3a k correspond to zone corners Edges and faces have mixed grid coordinates The center of the 1 face has coordinates x1la i x2b j x3b k the cen ter of the 2 face has coordinates x1b i x2a j x3b k and the center of the 3 face has coordinates x1b i x2b j x3a k The center of the l edge has coordinates x1b i x2a j x3a k the center of the 2 edge has coordinates xla i x2b j x3a k and the center of the 3 edge has coordinates x1la i x2a j x3b k For various reasons it is necessary to stagger the grid That is to say not all variables are located at the same pl
11. NCAR graphics dumps 12 14 16 22 23 55 57 75 NQS Batch 20 21 39 parameters 10 17 18 33 34 76 setting values in zeus32 12 15 17 18 39 pixel dumps 12 14 18 23 24 29 57 59 75 precompiling zeus32 see EDITOR problem generators 14 30 33 41 65 70 namelist pgen 16 31 34 RADIO dumps 6 7 10 12 14 18 25 26 27 62 65 76 restart dumps 7 14 15 21 28 29 41 43 45 73 75 TT restarting a run 14 22 41 43 45 46 47 56 58 60 62 63 69 rouse ZEUS 3D declarations 30 33 35 71 scratch arrays in ZEUS 3D see worker arrays script file UNICOS utility see also zeus32 s 8 15 16 20 36 39 comments 16 source code see zeus32 time slice dump 12 14 24 25 29 61 76 UNICOS 6 7 10 12 19 42 USERDUMP 10 14 16 26 29 35 60 61 76 variables see ZEUS 3D voxel dumps 10 14 16 24 29 59 60 75 worker arrays in ZEUS 3D 33 34 75 xzeus32 ZEUS 3D executable 9 15 creating 8 20 39 executing 21 22 41 ZEUS 3D community code 4 contributors 4 data dumps 12 14 22 27 28 29 48 54 64 65 naming conventions 22 27 declarations see rouse features new to version 3 2 6 7 files required for compilation 8 15 17 geometry 5 7 9 11 71 72 73 initialising variables see also problem generator 12 14 30 35 interrupt messages 28 29 limitations 5 6 MHD equations solved 4 5 making changes adding whole subroutines 13 14 18 26 30 35 71 changes to existing code
12. This is where the user should indicate the size of the arrays required for the simulation to be performed The parameters set in the given example of the script file zeus32 s are in number of zones plus 5 in the 1 direction the extra five are ghost zones jn number of zones plus 5 in the 2 direction kn number of zones plus 5 in the 3 direction ijkn the maximum of in jn and kn nxpx maximum number of pixels in the x direction for pixel dumps nypx maximum number of pixels in the y direction for pixel dumps nxrd maximum number of pixels in the x direction for RADIO dumps nyrd maximum number of pixels in the y direction for RADIO dumps The other parameters are discussed in Appendix 3 Section A3 6 Finally the second read statement commented out in this example inserts the file chgz32 which contains other changes to the source code deemed necessary by the 17 user to perform the computation These changes should be specified using the language of EDITOR very similar to HISTORIAN for those who are familiar with the old prepro cessor used under CTSS and would include additional subroutines such as the problem generator which need to be compiled with the rest of the source code Full description of how to do this is found in Section VI In principle one could manually replace the read zeus32 mac command with the contents of zeus32 mac and replace the read chgz32 command with the contents of that file Then zeus32 s would be the only
13. This namelist specifies both the boundary type and the inflow values of all the flow variables for the inner j boundary These variables are not declared if the EDITOR macro JSYM is set See comments for IIB parameter description default nijb k i nflo of inner j boundary on sweep k i 2 ijb1 k i first inner j boundary value of variable floor for sweep k i flow in only ijb2 k i second inner j boundary value of variable floor for sweep k i flow in only ijb3 k i third inner j boundary value for emf s 0 0 for sweep k i flow in only namelist ijb 1 nijb dijbi dijb2 vlijbl viijb2 2 v2ijb1 v2ijb2 v3ijb1 v3ijb2 if def ISO 3 eijb1 eijb2 xendif ISO if def GRAV 4 gpijb xendif GRAV if def MHD 5 blijb1 blijb2 b2ijbi b2ijb2 b3ijbi 6 b3ijb2 emflijbi emf1ijb2 emf1ijb3 emf2ijbl 7 emf2ijb2 emf2ijb3 emf3ijb1 emf3ijb2 emf3ijb3 endif MHD 11 OJB Outer J Boundary control read from subroutine NMLSTS This namelist specifies both the boundary type and the inflow values of all the flow variables for the outer j boundary These variables are not declared if the EDITOR macro JSYM is set See comments for IIB parameter description default nojb k i nflo of outer j boundary on sweep k i 2 kojb1 k i first outer j boundary value of variable floor for sweep k i flow in only kojb2 k i second outer j boundary value of variable floor for sw
14. file that would ever have to be altered However in the interest of modularity the script file zeus32 s is presented here with the change deck divided up into three parts The macros are all delegated to the file zeus32 mac the changes to the parameters statements remain in the zeus32 s file where they are the most accessible and the remaining changes to the source code are delegated to the file chgz32 3 3 4 Preprocessing zeus32 The next segment creates the input deck for the preprocessor EDITOR and then executes it Changes to this segment should be needed rarely If it becomes necessary to change the name of the main source file from zeus32 or to change the name of the change deck from chgzeus or to change the name of the directory created for the precompiled and compiled subroutine files from zeus3 2 or to change the name of the makefile from makezeus or to change the name of the ZEUS 3D executable from xzeus32 or to use a compiler other than cft77 or to use a loader other than ncargf77 these changes should be reflected in the EDITOR input deck inedit In addition various compiler options can be set as necessary For example the compiler options ez o off generate a symbol table required by the debugger and turns all optimization off These options are necessary for full debugging capabilities and can be invoked simply by de commenting deleting the c in column 1 the statement c coptions ez o off Note t
15. input x3rat to compute dx3min dx3min size of last zone in block 2 gt ratioed use input dx3min to compute x3rat dx3min size of first zone in block 2 gt ratioed use input dx3min to compute x3rat dx3min size of last zone in block 3 gt scaled compute x3rat and dx3min from nbl x3rat desired ratio dx3a k 1 dx3a k 1 0 dx3min desired difference x3a kmint1 x3a kmin 0 0 units sets the angular units character 2 ZRP and RTP only rd rd gt radians pi gt pi radians dg gt degrees lgrid false gt read another block namelist card false true gt all blocks are read in Do not look for another ggen3 namelist card namelist ggen3 1 nbl X3min X3max X3scale igrid 46 2 xdrat dx3min units lgrid 6 PCON Problem CONtrol read from subroutine NMLSTS Determines the criteria for terminating the job parameter description default nlim cycles to run 0 tlim physical problem time to stop calculation 0 0 ttotal total seconds of execution time permitted for job 0 0 tsave seconds of execution time reserved for cleanup 0 0 namelist pcon 1 nlim tlim ttotal tsave 7 HYCON HYdro CONtrol read from subroutine NMLSTS Set parameters which control the hydrodynamics Default values are advisable If itote 0 all energy variables should be interpreted as internal energy density per unit volume Evolving the inter
16. is 11 advisable that the macro MOC be set for most applications In some circumstances especially for dynamically unimportant passive magnetic fields stable Alfv n waves are not critical and MOC may be turned off yielding a time savings of 25 to 30 The user should be warned however that without MoC numerical instabilities in passive magnetic fields have been observed to generate local enhancements of many orders of magnitude yielding dynamically important magnetic fields in a relatively short period of time 5 The graphics enabled during a run are set by the graphics macros To enable 2 D pixel dumps set PIX for 3 D voxel dumps set VOX for 1 D NCAR plots set PLT1D for 2 D NCAR plots set PLT2D for HDF dump files set HDF for display dumps set DISP for RADIO dump files set RADIO and for time slice dumps set TIMESL As many as these may be set simultaneously as necessary See Section IV for a discussion of the various ZEUS 3D dump files 6 The operating system is defined by setting only one of the macros UNICOS for the Crays or CONVEXOS for the Convex etc In addition CALMATH should be set for Crays that have the calmath library 3 2 2 The EDITOR Aliases The alias macros allow phrases in the code to be substituted for other phrases during the precompiling step Thus Module Name Aliases give the user control over what subroutines are called during execution As an example in the main program of the source
17. monitoring via another user supplied subroutine to which USERDUMP has been set PROBLEM This macro specifically initializes all the flow variables and is called by the subroutine setup which is called by mstart START It will almost always be set to a user written subroutine unless by some miracle the user can use a problem generator which already exists in the source code The problem generators currently available in zeus32 include jetinit which initializes the variables for the launching of a jet blast which initializes the variables for an explosion advect which initializes the variables for 1 D advection tests and shkset which initializes the variables for 1 D Sod shock tube tests ATMOSPHERE This macro defines the atmosphere for a jet and is called by jetinit For a uniform atmosphere set ATMOSPHERE to empty since a uniform atmosphere is established in jetinit before ATMOSPHERE is called Otherwise the user will have to supply a subroutine to initialize the desired atmosphere PROBLEMRESTART This macro allows the specifications of the problem to be altered should the job be restarted from a restart dump Set the macro to empty if no alteration of the problem is desired as for example to simply extend the evolution time ARTIFICIALVISC This macro specifies which artificial viscosity algorithm should be used Currently the only option is viscous which uses either the von Neumann Richtmyer artificial viscosity algor
18. on each line The numbered file will be called zeus32 n and can be printed with a printer capable of 132 column output Beware that at 60 lines per page there will be some 750 pages of output The third column to the right of the source listing is the number of lines since the most recent EDITOR deck or cdeck statement This is the column needed to perform microsurgery on the master file During preprocessing EDITOR makes two major passes over the code The first pass does the merging of the change deck chgzeus which contains zeus32 mac and chgz32 into the main code EDITOR commands performed during this pass include 1 insert deckname n inserts text immediately following the insert command into the source code directly after line n in deck or cdeck common deck deckname The value of n is determined from the third column to the right of the source code in the numbered listing zeus32 n 2 delete deckname n m deletes lines n through m in deck or cdeck deckname and replaces it with the text immediately following the delete command if any Note that m must be greater than n If m is missing altogether then m n will be assumed That s it An example delete zeus3d 10 20 a b b c xinsert mstart 100 d i j k 1 0 xi zeus3d 100 c d d zeus3d 120 Note that d and i are short forms for delete and insert respectively In addition 35 replace rp for short is a synonym for delete In the example li
19. only namelist iib 1 niib diibi diib2 viiibi viiib2 2 v2iibi v2iib2 v3iib1 v3iib2 if def ISO 3 eiib1 eiib2 xendif ISO if def GRAV 4 gpiib xendif GRAV if def MHD 5 bliibi bliib2 b2iib1 b2iib2 b3iibl 6 b38iib2 emfliibi emf1liib2 emf1iib3 emf2iibl T emf2iib2 emf2iib3 emf3iib1 emf3iib2 emf3iib3 xendif MHD 9 OIB Outer I Boundary control read from subroutine NMLSTS This namelist specifies both the boundary type and the in flow values of all the flow variables for the outer i boundary These variables are not declared if the EDITOR macro ISYM is set See comments for IIB parameter description default noib j k nflo of outer i boundary on sweep j k 2 koib1 j k first outer i boundary value of variable f floor for sweep j k flow in only koib2 j k second outer i boundary value of variable f loor for sweep j k flow in only 0ib3 j k third outer i boundary value for emf s 0 0 for sweep j k flow in only namelist oib 1 noib doibl doib2 vioibi vioib2 2 v2oibi v20oib2 v30ibl v30ib2 if def ISO 3 eoibl e0ib2 xendif ISO if def GRAV 4 gpoib xendif GRAV if def MHD 5 bioibi bioib2 b20ib1 b20ib2 b3o0ibl 49 6 b380ib2 emfloibi emfiloib2 emfioib3 emf2oibi 7 emf20ib2 emf20ib3 emf30ib1 emf30ib2 emf30ib3 xendif MHD 10 IJB Inner J Boundary control read from subroutine NMLSTS
20. pixmax are 0 compute them as if ipixmm were 1 1 gt raw format used for dumps 2 gt HDF used for dumps in which case nlpix pixmin and pixmax are ignored sets the angular units character 2 rd gt radians pi gt units of pi radians dg gt degrees 0 0 253 0 nxpx nypx Zz O oO O O rd minimum x1 for pixel image xla is maximum x1 for pixel image xla ie 1 minimum x2 for pixel image x2a js maximum x2 for pixel image x2a je 1 minimum x3 for pixel image x3a ks maximum x3 for pixel image x3a ke 1 namelist pixcon OP WNF ipixdir lpix gt dtpix nepix iref jref gt npi npj pixvar nlpix pixmin pixmax ipixmm rorhpix units Xipxmn xipxmx x2pxmn x2pxmx x3pxmn x3pxmx 21 VOXCON VOXel graphics CONtrol read from subroutine NMLSTS 58 This namelist controls the voxel dumps of the 3 D data volume These are the 3 D analogues of the 2 D pixel dumps and are snapshots of the entire data volume See comments in namelist pixcon above for discussion on raw format vs HDF bracketing and dumping files logarithmically Voxel dumps are currently available for Cartesian XYZ and cylindrical ZRP ge ometries only The dimensions of the voxel dumps are limited by the parameters in jn and kn In particular the voxel dump may be no larger than in 1 x 2 jn 1 x 2 kn 1 For a uniform Cartesian grid there is no reason to specify
21. the copyright notice and the unit identification Laboratory for Computa tional Astrophysics NCSA along with this permission notice appear in all such copies and supporting documentation that no charge be made for such copies and that the name of the University of Illinois not be used in advertising or publicity pertaining to the distribution of this software without specific prior written permission Any entity desiring permission to incorporate this software into commercial products should contact NCSA at the University of Illinois at Urbana Champaign 217 244 0072 The University of Illinois makes no repre sentations about the suitability of this software for any purpose It is provided as is without expressed or implied warranty It is the intent of the Laboratory for Computational Astrophysics to make its codes available to the widest possible user community for solving and visualizing computation ally complex fluid dynamics problems in a diverse arena of applications We request that everyone who uses ZEUS 3D register with the LCA at lca ncsa uiuc edu so that we may maintain a complete list of our users and a description of the problems to which they are applying our code HI INTRODUCTION 2 1 VERSION 3 2 1 ZEUS 3D is a three dimensional MHD code based on a two dimensional one ZEUS 3D was designed with astrophysical applications in mind although problems in the other physical sciences can be addressed with this software The c
22. to construct the changes to be inserted into zeus32 using the EDITOR delete and insert commands All changes should be placed in the file chgz32 Note that during both passes the deck and cdeck statements are used as reference points and are then expunged from the source code during the second pass If any precompilation syntax errors are detected EDITOR will write the precompiled file as best as could be done given the error s detected into a file named zeus32 f and insert an error message immediately after each offending line EDITOR will abort further processing namely splitting up the source code into separate files for each subroutine substituting namelist statements with subroutine calls autotasking and the user will be told what character pattern to search for in the file zeus32 f in order to find the generated error messages On the other hand if the precompilation is successful EDITOR will update the files in the directory zeus3 2 The makefile makezeus will then compile only those subroutines affected by the changes made and the executable will be created 37 VII QUICK SUMMARY This final section is intended to serve as a quick reference sheet for those who are already familiar with running ZEUS 3D 1 Set the macros in zeus32 mac Subsection 3 2 Appendix 1 2 Make the necessary changes to the parameters in the change deck chgzeus Seg ment 3 3 3 and the input parameters in the input deck inzeus Segment 3 3 5 and
23. type diib1 1 100 1 100 0 1 diib1 20 30 70 80 1 0 This capacity is not supported by the current UNICOS or CONVEXOS version of namelist and so some of the namelist syntax will have to be changed in the input decks inzeus and inedit should the user wish to use the standard namelist In addition error messages from the EDITOR namelist are much more user friendly than from the UNICOS version The most severe drawback of the EDITOR namelist is that it is not supported by Cray nor anyone else In general do not allow any of the namelist lines to extend beyond the 72nd column The first column in each line can be a blank or a c to comment out the line and nothing else The second column may contain a blank or a and nothing else Note that because zeus32 s is a script file the must be protected by a Otherwise the script file will try to interpret the as a control character rather than treating it as a character to be written to a disc file The user will note that a does not precede the in the input deck inzeus once it is written to disc by zeus32 s Text specifying the input parameters may start in column 3 if a character string is too long to fit in the 72 column format e g libs in the input deck inedit subsection 3 3 4 one simply types as much as one can in the first line 7 e up to the 72nd column then 19 resumes typing the character string on the next line beginning in column 3 Note the locatio
24. waid through wz1d where the w stands for worker Similarly if a local 2 D array is required one can avoid requiring extra memory by declaring the 2 D array with dimensions ijkn ijkn and equivalencing it to one of eight 2 D 32 5 T scratch arrays wa2d through wh2d Finally a local 3 D array should be declared with dimensions in jn kn and equivalenced to one of six 3 D scratch arrays wa through wf Note that when one of the symmetry macros ISYM JSYM KSYM has been defined in zeus32 mac wa2d through wf2d are equivalenced to wa through wf in rouse while wg2d and wh2d are not declared Further if ISYM is defined 2 D arrays should be dimensioned jn kn if JSYM is defined 2 D arrays should be dimensioned kn in and if KSYM is defined 2 D arrays should be dimensioned in jn The namelist pgen is reserved for the namelist in the Problem GENerator Of course any name other than pgen could be used so long as it is not already used in the input deck inzeus and the new name for the namelist is substituted for pgen in inzeus Note that default values for the input parameters can be assigned before the namelist is read Loop 30 is a typical way the 3 D field variables d density e internal energy per unit volume etc are assigned values In this very simple case the variables are assigned to the scalars read from the namelist Note that all variables pertaining to the energy e eiib1 etc should be consi
25. x3a k zone corner x3 coordinate in grid units dxta i 1 edge xta it1 xta i dx2a j 2 edge x2a j 1 x2a j dx3a k 3 edge x3a k 1 x3a k g2a i zone corner 1 for Cartesian and cylindrical coordinates xla i for spherical polar coordinates g31a i zone corner g2a i g32a j zone corner 1 for Cartesian coordinates x2a j for cylindrical coordinates sin x2a j for spherical polar coordinates Note that xta i lt x1b i The exact relationship between the two grids is xib i xla i 0 5 dxta i Similarly for the 2 and 3 directions Every grid variable has a corresponding variable representing the quantity at the next time step and half way to the next time step These are denoted by appending an n or an h respectively to the variable name For example x1bn and x1bh contain the values of x1b at the next time step and half time step respectively Note that the three variables x1b x1bn and x1bh will be identical if the grid velocities are set to zero a stationary grid In addition every grid variable has a corresponding inverse variable denoted by appending an i to the variable name Thus dxtai 1 dxla x2bhi 1 x2bh etc Evidently there are numerous grid variables However only the a grid variables x1a x2a and x3a are written to the restart dump All others are re computed when a job be resumed A3 2 FIELD VARIABLES 3 D ARRAYS There is very little internal scaling of variables in ZEUS 3D t
26. 1 of plot window xta is maximum x1 of plot window xla ie 1 minimum x2 of plot window x2a js maximum x2 of plot window x2a je 1 minimum x3 of plot window x3a ks maximum x3 of plot window x3a ke 1 namelist plt2con eUWUNEe iplt2dir lplt2 dtplt2 plt2var nlplt2 plt2min plt2max iplt2mm vscale incvx incvy numcl units xlp2mn xip2mx X2p2mn x2p2mx x3p2mn x3p2mx 20 PIXCON PIXel graphics CONtrol read from subroutine NMLSTS This namelist controls the pixel dumps Pixel dumps are 2 D raster images of slices through the data volume and are rebinned to a uniform square Cartesian grid During a run as many as nios slices may be specified for each variable plotted A single pixel dump is created for every variable and every slice specified The extent of the pixel slice 56 can be limited by setting x1pxmn x1pxmx etc The normal to the pixel slice is parallel to one of the axes of the computational grid and is specified by ipixdir The index at the base of the normal is given by 1pix Pixel dumps are designed to provide a format for generating smooth qualitative temporal animations of the flow variables Aim for about 500 dumps for each animation They may be written in either raw format rorhpix 1 one byte per datum or HDF rorhpix 2 four bytes per datum Raw format files are small and so numerous images may be generated with a rela tively small amount of disc space However the low dyn
27. 2 gt 2 direction je biggest gt 2 3 gt 3 direction ke biggest gt 3 advvar nvmx variable names to be initialized Valid ZZ names are d e vil v2 v3 b1 b2 and b3 NOTE v and b can not be advected in the direction where 1 2 or 3 ishp nvmx integer flag describing the shape of the pulse 1 1 gt square 2 gt triangular 3 gt ramps 4 gt Gaussian 5 gt co sinusoidal 6 gt coordinate amp nvmx amplitude of pulse 1 0 floor nvmx amplitude outside of pulse 0 1 mO nvmx grid zone at which pulse center is located nx z 2 nO nvmx ishp 1 2 3 gt initial width of pulse in zones nx z 5 ishp gt number of zones per FWHM ishp 5 gt number of zones per wavelength ishp 6 gt irrelevant do background density if density pulse not advected 1 0 vO velocity of advection 1 0 For XYZ geometry vi vO v2 vO v3 v0 65 For ZRP geometry vi vO v2 vO x2 v3 v0 For RTP geometry vi vO x1 v2 vO x1 sin x2 v3 vO namelist pgen 1 idirect advvar ishp amp floor 2 m0 nod dd gt VO 2 BLAST Sets up an overpressured region centered at the specified point on the grid x10 x20 x30 with the specified radius r The pressure and density ratios of the compressed region relative to the ambient are prat and drat respectively parameter description default r initial radius of overpressured region 1 0 x10 x20 x30 coordi
28. 3 d e gt gp j ar cee laser j2 53 m ao p ar gt pb pt 2S 7 s2 s3 rge y r ei eae V2 v3 vv nlvox niov 0 gt store data 0 gt 0 gt store logi0 data concentrating colors at low end Dynamic range nlvox 1 gt 100 lt 0 gt store logi0 data concentrating colors at high end Dynamic range nlvox 1 gt 100 voxmin niov value of data to be assigned the minimum color 0 0 voxmax niov value of data to be assigned the maximum color 0 0 ivoxmm 1 gt compute voxmin and voxmax for images 1 0 gt use input voxmin voxmax for images If voxmin and voxmax are 0 compute them as if ivoxmm were 1 rorhvox 1 gt raw format used for dumps 1 2 gt HDF used for dumps in which case nlvox voxmin and voxmax are ignored 59 units sets the angular units character 2 rd rd gt radians pi gt units of pi radians dg gt degrees xivxmn minimum x1 for voxel image xla is xivxmx maximum x1 for voxel image xla ie 1 x2vxmn minimum x2 for voxel image x2a js x2vxmx maximum x2 for voxel image x2a jet 1 x3vxmn minimum x3 for voxel image x3a ks x3vxmx maximum x3 for voxel image x3a ket1 namelist voxcon 1 dtvox ncvox nvi gt nvj nvk 2 Voxvar nlvox gt voxmin voxmax ivoxmm 3 rorhvox units Xivxmn xivxmx x2vxmn 4 x2vxmx x3vxmn x3vxmx 22 USRCON USeR dump CONtrol
29. An EDITOR alias FINISH which represents a subroutine called after the main loop of the main program zeus3d gives the user a slot in which to perform various tasks at the end of the run The code can be microtasked automatically for Crays Tests indicate that for typical runs a real time speed up of 3 9 can be achieved with 4 dedicated processors The code will now run efficiently i e it vectorizes as a unitasked process on Con vex C Series machines This is done by defining the EDITOR definition CONVEXOS Multitasking on a Convex using the 03 option can be done but yields a real time speed up of only about 2 5 on a four processor machine More combinations of dimension and geometry have now been tested against analyti cal solutions The list includes Cartesian XYZ with two one or no symmetry flag s set cylindrical ZRP with either JSYM KSYM or KSYM set spherical polar RTP with either JSYM KSYM or KSYM set Other combinations should be used with caution One can select an isothermal equation of state An EDITOR definition ISO causes the code to take advantage of the reduction in memory and computation required for isothermal systems Yu Zhang NCSA has implemented a 3 D self gravity module using the so called DADI Dynamical Alternating Direction Implicit scheme The EDITOR definition GRAV must be set if self gravity is to be invoked One has the choice of solving either the total energy equation to globally conserve the to
30. DDING AN ENTIRE SUBROUTINE Adding source code to the ZEUS 3D package is not as difficult as one might anticipate especially if all of the changes are restricted to the addition of entirely new subroutines Below is a template for a subroutine called myprob which can be used to create a problem generator An electronic copy of this template resides in the AFS directory afs ncsa projects lca codes zeus3d source The style is that which is used for all subroutines currently in zeus32 xinsert zeus3d 9999 deck myprob CHS SSS SS S SS SS SS SS SS SS SS SS SS SS SS SS SS SSS SS SS SSS SS SS SS FS SS SS SS SSS SS SS SS SSS SS c c BEGIN SUBROUTINE c MYPROB c CHS SS SS SS S SS SS SS SS SS SS SSS SS SS SS HS SS SS SS SS SS SSS SS SS SS FS SS SS SS SS SF SS SS SS SSS SS c subroutine myprob c c abcd zeus3d myprob lt initializes my problem c september 1990 c c written by A Busy Code Developer c modified 1 c c PURPOSE Initializes all the flow variables for my problem More c description of my problem can go here c c LOCAL VARIABLES c c EXTERNALS BNDYFLGS BNDYALL BSETMAG c GAA Nc E E E EE E E EES c call rouse integer i yj j real da db ea eb via 1 vib v2a v2b vea vb 1 bla bib b2a b2b bea 1 b3b c real arrayid ijkn real array2d ijkn ijkn real array3d in jn kn c 29 Q aa qgqgqgeQqgnaaqaaqaaaa Q Q equivalence equivalence equivalence extern
31. OBLEMRESTART or FINISH see Subsection 3 2 2 and the ZEUS 3D skeleton in Appendix 1 in zeus32 mac to the subroutine name 6 2 MICROSURGERY USING EDITOR It is possible for the user to alter individual lines of code in zeus32 without actually changing the original source code In this way the changes made can be kept separate from the code and thus not lost in the abyss of zeus32 In addition the user s changes could in principle be incorporated into the master code at a later date and become part of the next release To do this there are two things required an EDITOR listing of the code and a short tutorial on how to use EDITOR For those who have worked with HISTORIAN all this should seem very familiar For those who haven t take heart the structure is very intuitive However one must ensure that the changes made don t break something else in the code To get an EDITOR listing of the code run the following script file call it number s by typing csh v number s 34 esSSsssssssssssss gt Create the input deck for EDITOR and execute rm f inedit cat lt lt EOF gt inedit editpar inname zeus32 ibanner 1 job 1 inumber 3 itable 1 ixclude 1 EOF xedit21 An electronic copy of this and other useful scripts reside on landrew in afs ncsa projects codes zeus3d editor source This script file will run EDITOR in its numbering mode and produce a listing with a table of contents and various labels
32. Representations 4 Variable Dumps 4 Variable Dumps ai 1 vector potential P v_ velocity norm speed PVH a2 2 vector potential P vi l velocity PVH a3 3 vector potential P v2 2 velocity PVH bi l magnetic field PVH v3 3 velocity PVH b2 2 magnetic field PVH vv velocity divergence PV b3 3 magnetic field PVH A po n position angle d density PVH AV pola with pol n vectors e_ internal energy PVH F_ fractional pol n gp gravitational potential PVH FV fpol with pol n vectors R j current density norm V I total intensity R j1 1 current density PVH IV toti with pol n vectors j2 2 current density PVH P_ polarized intensity j3 3 current density PVH PV poli with pol n vectors m Mach number PVH V po n vectors black p thermal pressure PVH VR pol n vectors white pb magnetic pressure PVH D density R pt thermal magnetic pres PVH E_ internal energy pres R si 1 momentum PVH PB magnetic pressure R s2 2 momentum PVH SE sp int energy temp s3 3 momentum PVH SH scalar velocity shear se specific internal energy PVH VV velocity divergence to all field arrays H 26 V INTERACTING WITH ZEUS 3D During interactive execution as opposed to batch execution the user may probe ZEUS 3D for its status change a few input parameters and even submit instructions to create a dump stop pause resume etc This is done by typing one of many recognized three character interrupt messages followed by a carriage return Once every cycle or
33. ZEUS 3D USER MANUAL Version 3 2 1 David A Clarkes Michael L Norman and Robert A Fiedler Laboratory for Computational Astrophysics National Center for Supercomputing Applications University of Illinois Revised August 17 1994 1994 The Board of Trustees of the University of Illinois Current address St Mary s University Department of Astronomy Halifax NS B3HC3H Canada TABLE OF CONTENTS I Copyright Notice II Introduction Il Running ZEUS 3D 3 1 Overview 3 2 The Macro File zeus32 mac 3 2 1 The EDITOR Definitions 3 2 2 The EDITOR Aliases 3 3 The Script File zeus32 s 3 3 1 Files Copied from AFS 3 3 2 Creating the zeus3 2 Directory 3 3 3 Creating the Change Deck chgzeus 3 3 4 Preprocessing zeus32 3 3 5 Creating the Input Deck inzeus 3 3 6 Making the Executable xzeus32 3 3 7 Cleaning up Compiler Listings 3 4 Executing ZEUS 3D IV Output from ZEUS 3D V Interacting with ZEUS 3D VI Adding Source Code to ZEUS 3D 6 1 Adding an Entire Subroutine 6 2 Microsurgery Using EDITOR VII Quick Summary Appendix 1 ZEUS 3D Skeleton Appendix 2 The Namelists Appendix 3 The ZEUS 3D Variables Index Page 11 12 14 16 17 17 18 19 20 20 20 22 28 30 30 35 39 40 42 71 TT I COPYRIGHT NOTICE Permission to use copy modify and distribute this software and its documenta tion for education research and non profit purposes is hereby granted provided that
34. a flow chart of the code and indicates in which order the Module Name Aliases are called Some subroutines are charged with reading the input data from the input deck inzeus A description of all the input parameters is given in Appendix 2 12 1 10 START This module is called just once before the computations begin It should initialize all the variables to be used in the simulation and perform all the initial I O Currently the only choice available for START is mstart BNDYUPDATE This module is called at the beginning of each time step and allows inflow boundary conditions to be evolved in time should this be necessary for the simulation Examples of evolving inflow boundary conditions include helically perturbing the inflow at a jet orifice to break the symmetry wiggle generating magnetic field at the boundary bgen or empty if no inflow boundary update is desired The user can of course supply a subroutine for this alias See Section VI for discussion on how to add a subroutine to the code EXTENDGRID This module will allow the grid to be extended as a disturbance shock propagates into initially quiescent zones Currently the only options are extend and empty The subroutine extend will prevent quiescent zones from being updated until the disturbance comes within five zones potentially saving significant amounts of computational time Care should be exercised in its use however If the subroutine is unsuccessful
35. a voxel dump larger than the flow variable array However for non uniform gridding in either or both of the 2 and 3 directions in XYZ coordinates or in ZRP coordinates in general the factor of 2 in both of these dimensions will allow the voxel dumps to represent better the regions in the computational grid with the highest resolution 250 voxel dumps with four million voxels from a one million zone computation will require 1 Gbyte of disc space Thus temporal sequences of 3D voxel dumps are possible but only in a limited fashion N B For restarted runs in which the computation is resumed on a larger or smaller grid and where the default values for x1vxmn x1vxmx etc were used in the initial run it will be necessary to set xivxmn x1vxmx etc in the input deck for the restarted run to the extrema of the new grid if the dumps are to extend to the bounds of the new grid Otherwise the dumps will be bound by the old grid parameter description default dtvox problem time interval between voxel dumps 0 0 0 0 gt no voxel dumps ncvox number of color contour levels in image 253 nvi number of voxels in 1 direction le in 1 0 0 gt in 1 nvj number of voxels in 2 direction le 2x jn 1 0 0 gt increment in 2 dir same as 1 dir nvk number of voxels in 3 direction le 2 kn 1 0 0 gt increment in 3 dir same as 1 dir voxvar niov names of variables to be plotted character 2 Zz Valid names are bi b2 b
36. ace Scalars density and internal energy are zone centered quantities while the components of the flow vectors velocity and magnetic field 70 are face centered quantities penetrating the face upon which they are centered Vectors derived from vector quantities such as the current density V x B and the emf v x B have edge centered components parallel to the edges while scalars derived from vector quantities such as V v are zone centered Thus the two grids play equally important roles and the user needs to be careful about which grid should be used and where the variables are located while making any changes to the code A3 1 GRID VARIABLES Limits for do loops Variable Location Description is ie beginning and ending i index for active zones js je beginning and ending j index for active zones ks ke beginning and ending k index for active zones Corresponding to each variable is ie etc are the limiting variables ismn iemx etc which indicate the extreme values possible for the do loop indices should the grid extending option be used see the description of the namelist extcon in Appendix 2 In addition the variables ism2 ism1 isp1 isp2 and isp3 exist which are set to is 2 is 1 ist1 is 2 and is 3 respectively If the computation is symmetric in the i direction ism2 ism1 isp1 isp2 and isp3 are simply set to is Similar variables exist for ie js je ks and ke The b grid Variable Location Descriptio
37. agnetic in 1 direction in 2 direction in 3 direction field in 1 direction field in 2 direction field in 3 direction Input parameters for wiggling the jet at the orifice iwiggle omega thetaj thetak rmode Note that if omega is specified it is not necessary to specify BWRrRRPR RE 0 gt do not wiggle jet orifice 1 gt wiggle jet orifice frequency of sinusoidal perturbation in units of external sound speed divided by the jet radius maximum ratio of v2 to vi at inlet maximum ratio of v3 to vi at inlet resonant frequency mode namelist pgen gt rjet eta pore bijet E betapol ibpol i betaran damb gt Vodamb biamb P omega thetaj 69 kappa betator zsigma eamb b2amb thetak v v v v v v rmode mjet rpeak rnode viamb b3amb rmode Default of 0 9 v_ v v v v ere O O huge Ore oo oOoo0oo0oo0oo0ooO oOoo0oo0o0o0oO e OoOO O N ojet rsigma znode v2amb iwiggle APPENDIX 3 THE ZEUS 3D VARIABLES This Appendix contains a glossary of the variables used in zeus32 and is meant to aid the user in writing subroutines and making changes to the source code itself It is by no means complete but should contain the variables needed for most purposes All these variables are declared in the common deck rouse Thus adding the EDITOR command call rouse before the local declarations makes all these variables accessible from within the subroutine The
38. al Input parameters da db values for ea eb values for via vib values for v2a v2b values for v3a v3b values for bia bib values for b2a b2b values for b3a b3b values for namelist pgen 1 da 1 vib 1 bla 1 b3b Default values da db ea eb via vib v2a v2b v3a v3b bla bib b2a b2b b3a b3b rea d DODCVCOORFRORFRORFROOOCOF oOo0oo0o0000000000 0 0reO ioin pgen write iolog pgen Set field arrays do 30 k ksmn kemx do 20 j jsmn jemx do 10 i ismn iemx d i j k da arrayid wald array2d wa2d array3d wa density bndyflgs bndyall bsetmag internal energy 1 velocity 2 velocity 3 velocity 1 magnetic field 2 magnetic field 3 magnetic field db v2a bib 30 ea eb via v2b v3a v3b b2a b2b ba vi i j k vila v2 i j k v2a v3 i j k v3a if def ISO e i j k ea xendif ISO if def MHD bi i j k bla b2 i j k b2a b3 i j k b3a endif MHD 10 continue 20 continue 30 continue if def ISYM c c Set inflow boundary values c do 50 k ksmn kemx do 40 j jsmn jemx niib j k 3 diib1 j k db viiibl j k vib v2iib1l j k v2b v3iib1l j k v3b if def ISO eiib1 j k eb xendif ISO if def MHD biiibi j k bib b2iib1 j k b2b b3iib1 j k b3b endif MHD 40 continue 50 continue xendif ISYM c c Set all boundary values c call bndyflgs call bndyall i
39. al between time slice 0 0 ascii dumps 0 0 gt no ascii time slices dttslp physical problem time interval between time slice 0 0 plot dumps 0 0 gt no metacode time slices tslpmn problem time for beginning of plot 0 0 tslpmx problem time for end of plot 0 0 gt maximum time 0 0 namelist tslcon 1 dttsl dttslp tslpmn tslpmx 25 DISCON DISplay dump CONtrol read from subroutine NMLSTS This namelist controls the display dumps of 2 D slices During a run as many as nios slices may be specified for each variable displayed All display dumps generated during a run are dumped to the same ascii data file The extent of the display slice can be limited by setting idismn idismx etc The normal to the display slice is parallel to one of the axes of the computational grid and is specified by idisdir The index at the base of the normal is given by ldis The display format allows the user to view a small portion of the data quantitatively in a matrix format The maximum amount of data that can be visualized at once from each specified variable and slice is 38 by 38 The data are scaled and converted to integers with a dynamic range anywhere from 100 to 10 depending on the amount of data being displayed The data are arranged in a 2 D matrix and labelled with the grid indices and the scaling factor used to scale the data The functionality is similar to that of the task PRTIM in AIPS N B For restarted runs in which the comp
40. amelists were fraught with inconveniences and so the preprocessor EDITOR was built with a namelist emulator which resembles the namelist under the now all but extinct CTSS operating system The following discussion therefore reflects some of the syntactic rules appropriate to the EDITOR namelist and not necessarily those of the UNIX UNICOS namelist In order to specify an input parameter one merely needs to set it to the desired value as done in the input deck inzeus found in the sample script file zeus32 s Subsection 3 3 The order in which the variables are declared in the namelist declaration need not be adhered to in the input deck nor must all of the variables be set So long as the variable specified in the input deck is an element of the namelist then the namelist facility will set the variable to the specified quantity There are a few rules to bear in mind The namelists in the input deck must be in the same order as they are encountered during execution If no parameters are to be set an empty namelist one with the namelist name between two sentinels must be put in the correct place There is no problem with namelists appearing that are never read but a read to a non existent namelist will generate a namelist error message and abort execution In this catalogue the order of the namelists is the same as the order in which they appear in inzeus and the order in which they are encountered in zeus32 The syntactic rules of setting the
41. amic range of the images 256 dictates that the data be bracketed and perhaps even dumped logarithmically in order to render the salient features visible The data may be bracketed automatically ipixmm 1 in which case differences from one image to the next will be caused by both the evolution of the flow and the fluctuations of the extrema which are used to bracket the data Al ternatively one may bracket the data manually ipixmm 0 by setting values for pixmin and pixmax This can be done by running the simulation until 10 to 20 pixel dumps have been generated for each variable with ipixmm set to 1 The extrema used to bracket the data are reported in the log file zlnnid and these can be used to set the extrema pixmin and pixmax Now run the job from the beginning with ipixmm set to 0 If a log dump is desired some experimentation may have to be done in order to set the value of nlpix the dynamic range properly However the default value of 100 should be fine for most applications Basically the higher the absolute value for a positive negative nlpix the more concentrated the colors will be at the low high end HDF files are four times as big and thus may cause disc and storage problems However because these images are four bytes deep bracketing and converting to log are not necessary In fact these files may be used quantitatively as well as qualitatively For HDF the parameters ncpix ipixmm pixmin pixmax and nlpix are all ignor
42. at one byte per datum or HDF four bytes per datum see below The raw format files can be read by NCSA IMAGETOOL and are not intended for quantitative analysis since the dynamic range 256 is too small for most purposes other than qualitative rendering The HDF files may be read by IMAGETOOL1 1 NCSA IMAGE open windows or any other software package capable of reading HDF files and may be used quantitatively In this version polar plots are rebinned to a Cartesian plane and dumped as Cartesian pixel plots Thus POLAR IMAGETOOL is no longer necessary Because the data files are so small especially the raw format enough images can be written to disc during the simulation to create a smooth temporal animation of the calculation for a number of variables Multiple slices can be specified for each variable and in a post processing session using NCSA DATAVU a program which formats and annotates frames for an animation reassembled in their proper 3 D perspective Note that raw pixel dumps have no header Thus the dimensions of the dumps needed to read the raw dumps correctly are noted in the message log file see below each time a dump is created EDITOR definition PIX logical unit iopix namelist pixcon filename zix nnnid mm h where zi is the common prefix to all 2 D pixel dumps is a two character representation of the variable see Table 4 1 at the end of this section nnn is a 3 digit integer dis tinguishing the multiple d
43. dary values using the namelists iib oib etc see Appendix 2 Note the use of the EDITOR if define endif construct to prevent this loop from being compiled in the event that ISYM is defined If ISYM has been defined the variables niib etc are not declared in rouse Variables that are conditionally declared depending on which EDITOR definitions are set are noted in Appendix 3 After loop 50 all the boundary values of the 3 D field arrays can be initialized by calling the subroutines bndyflgs which sets all the secondary boundary flags according to the values set for the primary flags niib etc bndyall which sets all the hydrodynamical variable boundaries and bsetmag which sets all the magnetic 33 variable boundaries The boundaries are set depending on the values of the boundary flags niib etc which indicate the boundary type Appendix 2 Note that the user s problem generator must initialize the boundary zones in addition to the active zones If the subroutines bndyall and bsetmag are insufficient for this purpose the boundary zones should be set explicitly 9 Finally if desired the user can write various messages to the terminal logical unit iotty or to the message log file logical unit iolog Both iotty and iolog are declared in rouse and set by the subroutine mstart Once the subroutine is written it should be placed in its entirety into the change deck chgz32 Upon its first pass the merge step the pre
44. de tailored specifically for the problem to be solved Therefore in order to customize the code for the problem at hand it is necessary to set the EDITOR definitions and aliases generically referred to as macros found in zeus32 mac The combined effect of the macros is two fold First they determine what parts of the code are activated and what parts are ignored Thus it is possible to eliminate the computations and the memory requirements necessary to evolve the magnetic fields for example by not defining the MHD macro this can be done by commenting out double asterisk the define MHD statement in the example above The preprocessor will then remove all coding pertaining to magnetic fields including the declarations of the magnetic field arrays during the preprocessing step The compiler never sees the magnetic stuff and the executable is streamlined for the hydrodynamics problem Of course the original source code is not altered by preprocessing it Rather the preprocessor creates a precompiled version of the code and stores each subroutine into its own file to facilitate debugging and make in the directory zeus3 2 which was created by the script file zeus32 s Second the alias macros can be used to substitute any character string in the code during the preprocessing step 8 2 1 The EDITOR Definitions A description of the definition macros called Conditional Compilation Switches in the example f
45. ded in the integration Finally the variables lower and upper allow each variable to be masked by its own distribution These can be set in addition to the density and or magnetic field masks dsw btsw For example if only the compressive portions of the flow are to be integrated then setting xupper 0 0 will mean that only negative values of V v will be included in the integration All values excluded by the various masks will be given zero weight In all cases the default is no mask Reversing the palette nlrad lt O is useful for raster images in which radmin lt 0 and radmax lt 0 e g negative velocity divergences In these cases it may be desirable to have the maximum color correspond to the minimum pixel value which has the greatest absolute value Note that the parameters which set the dimensions of the arrays for the RADIO 62 pixel plots nxrd nyrd are independent of the parameters which set the dimensions of the flow variables in jn kn and of the regular pixel slices nxpx nypx N B For restarted runs in which the computation is resumed on a larger or smaller grid and where the default values for xirdmn x1rdmx etc were used in the initial run it will be necessary to set xirdmn x1rdmx etc in the input deck for the restarted run to the extrema of the new grid if the dumps are to extend to the bounds of the new grid Otherwise the dumps will be bound by the old grid parameter dtrad thetamin thetamax
46. dered as energy per unit volume and not energy per unit mass Appendix 3 has a list of all the variable names and their dimensions The do loop indices declared in rouse are all assigned values in the subroutine nmlsts see Appendix 1 and so they can be used explicitly in any user supplied subroutine called thereafter Thus the index for loop 30 k ranges from ksmn k start minimum to kemx k end maximum Similarly for the indices of loops 20 j and 10 i Note the use of the EDITOR if define endif if def ei for short structure which conditionally includes or excludes a segment of coding depending on whether in this case MHD was defined during precompilation Similar conditionals can be based on the truth of any EDITOR definition and on how aliases are set For example one could place an EDITOR if alias PROBLEM eq myprob just after the subroutine statement and the matching endif just before the return statement In this way the subroutine would be empty nothing between the subroutine and return statements unless the EDITOR alias PROBLEM were set to myprob This would prevent it from being compiled when it is not needed Loop 50 illustrates how inflow boundary values to be applied only to those boundary zones where matter is flowing into the grid in a known fashion can be easily set In this case the inner i boundary iib values of the flow variables are being initialized Alternatively one could set the inflow boun
47. dtheta ntheta phimin phimax dphi nphi itype alpha freq ncrad radvar niov xlower xupper dsw btsw description default problem time interval between RADIO dumps 0 0 gt no RADIO dumps minimum angle between xi axis and plane of sky maximum angle between xi axis and plane of sky desired increment in theta between successive dumps number of values for theta between specified limits overrides choice for dtheta minimum azimuthal angle for lines of sight maximum azimuthal angle for lines of sight desired increment in phi between successive dumps number of values for phi between specified limits overrides choice for dphi O gt emissivities are not computed 1 gt Smith et al emissivity p 2 2 gt CNB emissivity function of d p B spectral index itype 2 only frequency of RADIO observation Hz O number of color contour levels in images 253 names of variables to be plotted character 2 Currently valid names are A pol n position angle AV pol n position angle with pol n vectors superposed F P I FV P I with pol n vectors superposed I total intensity IV total intensity with pol n vectors superposed P pol d intensity PV pol d intensity with pol n vectors superposed V pol n vectors black on white VN pol n vectors white on black D density E internal energy SE specific internal energy PB magnetic pressu
48. e grid or the EDITOR macros leave the values of igetmn etc to their defaults and make sure that the parameters in etc are set to the same values as in the run which generated the restart dump 42 Example 2 If the first run was on a 64 grid and the user wishes to read only the inner eighth of the data and position the data at the center of a larger 100 grid and if the new portion of the grid is to be determined from the existing grid then the following settings are necessary igetmn jgetmn kgetmn 17 iaddz 1 igetmx jgetmx kgetmx 48 jaddz 1 iputmn jputmn kputmn 35 kaddz 1 The desired portion of the restart dump will be read and loaded into the 100 grid between i 35 66 j 35 66 k 35 66 In addition x1a 35 66 see Appendix 3 for a discussion of the naming convention for the grid variables will be filled by the values of x1a 17 48 in the restart dump The code will detect that the grids x1a x2a x3a are now incomplete and will call the appropriate modules to add zones to the x1 x2 and x3 grids If the user wishes addz 1 i j k the new portion of the grid may be determined automatically from the existing grid In this example x1a 1 34 would be determined i e dximin x1rat etc see namelist ggen1 from x1a 35 37 Similarly x1a 67 100 would be determined from x1a 64 66 Alternatively the user may opt to set the new portion of the grid manually In this case one should set addz 0 and p
49. e last block There are two types of gridding The first is ratioed gridding where the distance across a zone is a fixed multiple of the distance across the previous zone If this multiple is 1 then the zones are uniform If the multiple is 1 1 then each zone is 10 larger than the previous one If the multiple is 0 9 then each zone is 10 smaller than the previous one To determine a block of ratioed zones uniquely one must specify the number of zones in the block nb1 the minimum and maximum extent of the block in coordinate units ximin x1max and EITHER the smallest zone size in the block dximin OR the ratio to use between zones x1rat Specifying either dx1min or xtrat will allow the other to be computed The second type of gridding is scaled gridding where the coordinate value is some fixed multiple of the previous coordinate value For ratioed grids dx n mult dx n 1 For scaled grids x n mult x n 1 For example scaled gridding would be appropriate for the r direction in spherical polar coordinates if the zones were all to have the same shape To determine a block of scaled zones uniquely one must specify the number of zones in the block nb1 and the minimum and maximum extent of the block in coordinate units ximin x1max Neither dx1min nor xirat are needed The grid can be scaled to physical units most conveniently by setting the multiplica tive factor x1scale to the desired scaling value For restarted jobs t
50. e log for the execution This file was formerly called zeus1p EDITOR definition logical unit namelist filename format none iolog formerly iolp none zl1llid where zl is the common prefix to all log files ll is as de fined for time slice dumps and id is as defined for restart dumps ascii 11 USERDUMP This is an EDITOR alias available for the user to include their own special type of I O which may be desired in addition to those currently available See Section VI for details on how to add subroutines to the code EDITOR definition logical unit namelist filename format none iousr usrcon zunnid where zu is the common prefix to all user dump files nn and id are as defined for restart dumps chosen by the user 25 The following table lists the two character variable representations corresponding to the double asterisks above used for generating the filenames for pixel P voxel V HDF H and RADIO R dumps These two character representations are identical to those used to specify the variables to be dumped see pixvar in namelist pixcon voxvar in namelist voxcon hdfvar in namelist hdfcon and radvar in namelist radcon Appendix 2 with the exception that variables specified by a single character e g d appear with a trailing underscore e g d_ in the dump file name The third column indicates the I O types in which the variable may be dumped Table 4 1 Two Character Variable
51. e various integral quantities such as total mass angular momenta magnetic monopoles energy etc as well as extrema of quantities such as density pressure divergence of magnetic field etc The user may wish to add other scalars to this format subroutines tslice and tslplot EDITOR definition TIMESL logical units iotsl and iotslp namelist tslcon filenames ztllid ascii file where zt is the common prefix to all time slice ascii files Il is incremented by one each time the job is restarted and id is as defined for restart dumps ztpllid metafile where ztp is the common prefix to all time slice metafiles etc formats ascil metacode 8 DISPLAY DUMP FILE This is a single ascii file maximum of 80 characters per line which contains a quantitative display matrix format of a specified portion of various 2 D slices through any of many variables at evenly spaced time slices during a simulation The data are scaled and converted to integers before being written to the ascii file The dynamic range of the scaled data depends on the specified width of the field of view no more than 38 and ranges from 10 to 10 For very small widths lt 8 the data are not scaled and written as real numbers with three or four significant figures This utility is much like PRTIM in AIPS for those familiar with the Astronomical Image Processing System Its primary use is in debugging or when one needs to view a small portion of data
52. ed Both Cartesian slices and polar slices are treated in the same way With this release Polar IMAGETOOL is no longer necessary If a polar grid includes very small zones near the origin it may be best to request two pixel slices for each slice to be visualized One slice would include the entire grid and mimic the resolution near the mid radial regions i e oversample the outer grid but undersample the inner grid The second slice would include only the inner radial regions and would mimic the resolution of the inner grid In this way the main advantage of polar IMAGETOOL and the previous format for polar pixel dumps may be recovered The parameters which set the dimensions of the arrays for the pixel plots nxpx nypx are independent of the parameters which set the dimensions of the flow variables in jn kn Thus in the case of a non uniform grid pixel dumps may be written with enough pixels to preserve the highest resolution on the grid N B For restarted runs in which the computation is resumed on a larger or smaller grid and where the default values for x1pxmn x1pxmx etc were used in the initial run it will be necessary to set x1pxmn x1pxmx etc in the input deck for the restarted run to the extrema of the new grid if the dumps are to extend to the bounds of the new grid Otherwise the dumps will be bound by the old grid parameter description default 57 ipixdir nios lpix nios dtpix ncpix iref jref npi n
53. ed use input x2rat to compute dx2min dx2min size of first zone in block 1 gt ratioed use input x2rat to compute dx2min dx2min size of last zone in block 2 gt ratioed use input dx2min to compute x2rat dx2min size of first zone in block 2 gt ratioed use input dx2min to compute x2rat dx2min size of last zone in block 3 gt scaled compute x2rat and dx2min from nbl x2rat desired ratio dx2a j 1 dx2a j 1 0 dx2min desired difference x2a jmint1 x2a jmin 0 0 units sets the angular units character 2 RTP only gt rd rd gt radians pi gt pi radians dg gt degrees lgrid false gt read another block namelist card false true gt all blocks are read in Do not look for another ggen2 namelist card namelist ggen2 1 nbl gt X2min x2max x2scale igrid 2 x2rat ax2min units lgrid 5 GGEN3 Grid GENerator for x3 read from subroutine GRIDX3 See comments for GGEN1 parameter description default nbl number of active zones in block being generated 1 x3min x3a kmin bottom position of block 0 0 x3max x3a kmax top position of block 0 0 x3scale arbitrary scaling factor for x3min and x3max 1 0 igrid method of computing zones 1 0 gt block has already been set restarted runs only 1 gt ratioed use input x3rat to compute dx3min dx3min size of first zone in block 1 gt ratioed use
54. ed that the user is familiar with the fundamentals of MHD and has come up with a complex problem to solve which is described by equations 1 through 4 It is 4 also assumed that the user has a working knowledge of some flavor of UNIX such as Cray UNICOS SGI Irix etc In this spirit this manual is designed to instruct the user on the mechanics of using ZEUS 3D ZEUS 3D has the following features e finite differencing on an Eulerian mesh possibly moving in an average sense with the fluid e fully explicit in time and therefore subject to the Courant condition e operator and directional splitting of the equations governing the hydrodynamic vari ables e can be used efficiently for 1 D and 2 D simulations with any of the coordinates reduced to symmetry axes e Cartesian cylindrical and spherical coordinates for 1 D 2 D and 3 D simulations e written in a covariant fashion to minimize the effects of the different coordinate systems on the structure of the code e fully staggered grid with scalars density and internal energy zone centerd and vec tor components velocity and magnetic field face centered Derived vector compo nents current density and emf s are edge centered e von Neumann Richtmyer artificial viscosity to smear shocks e upstream weighted monotonic interpolation using one of donor cell first order van Leer second order or piecewise parabolic advection third order schemes e Co
55. eep k i flow in only ojb3 k i third outer j boundary value for emf s 0 0 for sweep k i flow in only 50 namelist ojb 1 2 if def ISO 3 xendif ISO if def GRAV 4 xendif GRAV if def MHD 5 6 7 xendif MHD nojb dojbi dojb2 R V2ojb1 v2ojb2 v3ojb1 eojb1 eojb2 gpojb biojbl blojb2 b2ojbl b3ojb2 emflojb1 emflojb2 emf20jb2 emf20jb3 emf3o0jbi viojbi v30jb2 b20jb2 emfiojb3 emf3o0jb2 12 IKB Inner K Boundary control read from subroutine NMLSTS viojb2 b30jb1 emf2o0jb1 emf30jb3 This namelist specifies both the boundary type and the inflow values of all the flow variables for the inner k boundary These variables are not declared if the EDITOR macro KSYM is set See comments for IIB parameter nikb i j kikb1 i j ikb2 i j ikb3 i j namelist 1 2 if def ISO 3 xendif ISO if def GRAV 4 xendif GRAV if def MHD 5 6 7 xendif MHD description nflo of inner k boundary on first inner k boundary value for sweep i j flow in only second inner k boundary value for sweep i j flow in only sweep i j of variable of variable third inner k boundary value for emf s for sweep i j flow in only ikb nikb dikb1 dikb2 vlikbi v2ikb1 v2ikb2 v3ikbi v3ikb2 eikb1 eikb2 gpikb blikb1 blikb2 b2ikbi b2ikb2 b3ikb2 emflikbi emfiikb2 emf1ikb3 emf2
56. es in the HDF format developed at NCSA and differs from the voxel HDF dumps in that these dumps are not rebinned The data are stored in four byte words which is more than adequate for quan titative graphical study Most graphical software packages at NCSA use this format for data dumps HDF files are useful because they contain header information which includes array dimensions extrema of data and the grid coordinates It is highly recommended that this format be used if any post processing of the data is to be performed using soft ware developed outside NCSA The size of an HDF file containing a single variable is the number of active zones times 4 bytes For a total dump all primary variables to the same HDF file the size is the number of active zones times 32 bytes for MHD runs or times 20 bytes for HD runs EDITOR definition HDF logical unit none namelist hdfcon filename zh nnnid where zh is the common prefix to all HDF files nnn and id are as defined for pixel dumps format HDF four bytes per datum 7 TIME SLICE DUMPFILES There are two types of time slice dumps and either both or neither may be selected The first is a single ascii file which contains values of various scalars at specified time intervals The second is a metafile containing 1 D plots of 23 these scalars plotted as a function of time The user selects the time interval for the ascii and metafile dumps independently The scalars includ
57. f def MHD call bsetmag xendif MHD write iotty 2010 write iolog 2010 2010 format MYPROB Initialization complete c return end c CHS SS SS S SS SS SS SS SS SS SS SSS SS SS SS SS SS SSS SS SS SS SS SS SS SS SSS SS SS SS SS SS SS SSS SS 31 o D o DE g a a aa There are many ingredients to this template which warrant discussion In order of appearance these are 1 Ignoring for the moment the EDITOR statement insert zeus3d 9999 the first line of each subroutine must be an EDITOR deck dk for short statement Without this statement the precompiler won t put the subroutine into a separate file inhibiting the debugger should it be necessary It is easiest although not necessary to give the deck the same name as the subroutine 2 Note that there is no parameter list in the subroutine statement A parameter list is unnecessary since all variables that need to be used and or set are accessible via the common blocks In fact using a parameter list would inhibit the inclusion of a user supplied subroutine using the present structure of the code 3 All of the important variables declared in zeus32 are in common blocks and can be included into a subroutine simply by inserting the EDITOR statement call rouse just before the local declarations are made The EDITOR call ca for short statement is much like the VMS INCLUDE facility whereby a section of code known as a common deck called rouse in this ca
58. gt 1 2 3 direction iplti1 nios i index of 1 D plot in 2 or 3 direction istie 2 jplt1 nios j index of 1 D plot in 3 or 1 direction jstje 2 kplt1 nios k index of 1 D plot in 1 or 2 direction ks ke 2 dtplti physical problem time interval between 1 D 0 0 54 plot dumps 0 0 gt no plots pltivar niov names of variables to be plotted character 2 Zz Valid names are d density e internal energy se specific internal energy p thermal pressure pb magnetic pressure gt pt thermal plus magnetic pressure vil v2 v3 velocity components s1 s2 s3 momentum components m Mach number gp gravitational potential b1 b2 b3 magnetic field components bd magnetic field density 417 j2 j3 current density components nlplti niov 0 gt plot data 0 1 gt plot log10 of data positive definite quantities only pltimin niov minimum value to be plotted 0 0 pltimax niov maximum value to be plotted 0 0 ipltimm 1 gt compute pltimin and pltimax for plots 1 0 gt use input pltimin pltimax for plots If pltimin and pltimax are 0 compute them as if ipltimm were 1 corl 1 gt use open Circles one per zone 2 2 gt use Line segments to connect zone values namelist plticon 1 ipltidir iplti jplti kpltl dtplt1 2 pltivar nlplti pltimi
59. h wf For 2 D problems in which one of the EDITOR definitions ISYM JSYM KSYM is set the 2 D arrays are dimensioned jn kn kn in in jn respectively and are equivalenced to wa through wf The scratch arrays wg2d and wh2d are not declared when one of the symmetry flags is set A3 5 SUNDRY VARIABLES AN ABBREVIATED LIST Variable Description ioin logical unit attached to input deck iolog logical unit attached to message log file iotty logical unit attached to terminal TTY or CRT iodmp logical unit attached to restart dumps ioplt1 logical unit attached to 1 D NCAR graphics dumps iop1t2 logical unit attached to 2 D NCAR graphics dumps iopix logical unit attached to 2 D pixel dumps iovox logical unit attached to 3 D voxel dumps iousr logical unit attached to user dumps iotsl logical unit attached to time slice ascii dump iotslp logical unit attached to time slice plot dump 74 iodis iorad nhy nwarn time dt logical unit attached to display dump logical unit attached to RADIO dump number of cycles time steps completed in simulation running total of warnings issued problem time elapsed in simulation increment of problem time that solution is being advanced In addition all of the namelist variables except from namelist pgen are declared in rouse Parameter niov nios ntsl pi tiny huge A3 6 PARAMETERS OTHER THAN ARRAY DIMENSIONS Description maximum number of variables plotted dumped maximum n
60. hat lines commented out in a namelist will be echoed on the CRT as the input deck is read This is a feature of the EDITOR namelist See Segment 3 3 5 and Appendix 2 for a discussion of the EDITOR namelist feature If the code is to be microtasked set iutask third line of the namelist editpar to 1 and invoke cf77 rather than cft77 with the compiler options c Zp Wf M0726 66 99 This is done by commenting out putting a c in column 1 the statement compiler cft77 M0726 and de commenting the statements c compiler cf77 c coptions c Zp Wf M0726 Finally additional libraries may be linked to the ZEUS 3D executable by adding them to the list libs With this input deck the preprocessor will merge the change deck chgzeus with zeus32 carry out the precompiler commands according to the aliases and definitions 18 in the macro file zeus32 mac split up the precompiled source code now containing nothing but FORTRAN syntax into separate files for each subroutine search the direc tory zeus3 2 and write to disc only those files which do not already exist or have been changed and finally create the makefile makezeus described in Segment 3 3 6 3 3 5 Creating the Input Deck inzeus The fifth segment is where the input deck for the ZEUS 3D executable is created inzeus and so the user should set all input parameters here In this example inzeus is set up for a 1 D MHD Sod shock t
61. hat the user must consider Density energy and velocity all may be scaled according to the needs of the user simply by setting the initial conditions as appropriate For example the user may wish to set the density and the sound speed at infinity to unity This along with some canonical length scale will set the scale for the calculation The only scaling implicit to ZEUS 3D 72 is the permeability of free space 47 x 1077 in mks 47 in cgs is set to 1 Thus the total pressure thermal plus magnetic is given by ptot Pthermal B 2 Having set the scale of the hydrodynamical variables the user should set the magnetic fields with this additional scaling in mind Variable d i j k vi i j k v2 i j K v3 i j k e i j k gp i j k b1 i j k b2 i j k b3 i j k Location zone center 1 face 2 face 3 face zone center zone center 1 face 2 face 3 face Description density velocity in the 1 direction grid units velocity in the 2 direction grid units velocity in the 3 direction grid units internal energy density x pressure gravitational potential magnetic field in the 1 direction uo 1 magnetic field in the 2 direction wo 1 magnetic field in the 3 direction uo 1 If the EDITOR macro ISO is defined the energy variable e is not declared The gravi tational potential variable gp and the magnetic field variables b1 b2 b3 are declared only if the EDITOR macros GRAV and MHD are defined respect
62. here is a third gridding option Setting igrid to zero will cause the grid generator to skip over the nb1 zones specified for this block Thus in the second example in the discussion for namelist rescon one could set the new zones for the x1 direction manually with three ggen1 namelist cards The first card would set zones 1 34 in whatever manner desired with the condition that the last zone of the new grid ends where the first zone of the old grid begins The second card would set igrid 0 and nb1 32 This would leave zones 35 66 alone since they were set when the restart dump 44 was read Finally the third card would set zones 67 100 in whatever manner desired with the condition that the first zone of the new grid begins where the last zone of the old grid ends Other than remaining within the memory limits of the machine there are two prac tical considerations when choosing the number of zones for each of the three dimensions First if at all possible the greatest number of zones should be along the 1 direction so that the vector length of the vectorized loop is as long as possible Second if the code is to be multitasked specify nN 1 active zones in the 3 direction where n is a positive integer and N is the number of parallel processors available on the machine This will yield the best overall degree of parallelism parameter description default nbl number of active zones in block being generated 1 ximin xla imin bo
63. ialized do input density tiny e0 input specific internal energy e d tiny v10 input velocity in 1 direction 0 0 v20 input velocity in 2 direction 0 v30 input velocity in 3 direction 0 0 b10 input magnetic field in 1 direction 0 0 b20 input magnetic field in 2 direction 0 0 b30 input magnetic field in 3 direction 0 0 namelist pgen 1 idirect nO gt dd 0 vid 2 v20 gt v30 b10 b20 b30 5 ZPINCH Sets up a Bennett pinch equilibrium Jackson second edition section 10 5 p 479 in ZRP geometry parameter description default do input density none e0 input internal energy proportional to pressure none namelist pgen 1 do gt 0 6 MHDROT Sets up the aligned rotator problem which tests the MoC algorithm in ZRP coordinates parameter description default re radius of the cylinder 1 0 omegac initial constant angular velocity of the cylinder 1 0 e 6 dc density of the cylinder 1 0 da density of the ambient medium 1 0 ec internal energy of the cylinder 1 0 ea internal energy of the ambient medium 1 0 bi axial magnetic field 1 0 67 namelist pgen 1 rc omegac dc da ec 2 ea bi 7 JETINIT Sets up the initial ambient medium and the jet orifice at the inner i boundary An entire equilibrium jet may be established across the entire grid if desired The orifice is centered on the origin which must lie on the inner i boundary and is rounded as well as is possible in Cartesian coord
64. ias alias xalias alias OK START BNDYUPDATE EXTENDGRID GRAVITY SPECIAL SOURCE SPECIALSRC TRANSPORT SPECIALTRN NEWTIMESTEP NEWGRID DATAOUTPUT FINISH PROBLEM ATMOSPHERE PROBLEMRESTART ARTIFICIALVISC USERDUMP HER RR RR KR k kkk k KKK k k xalias xalias xalias xalias GRAVITYERROR GRIDERROR PDVCOOLERROR NEWVGERROR FKK KKK K KK K 2K K K K K FK K K K 3K K K K K xalias xalias xalias xalias GRAVITYITER GRIDITER PDVCOOLITER NEWVGITER ITERATION LIMITS ALIASES mstart empty empty empty empty srcstep empty transprt empty nudt empty dataio empty shkset empty empty viscous empty ak RR A RR ak 2k RR 2K KK KOK xk ERROR CRITERIA ALIASES 6 e 6 6 10 ek FOR RA Kk Kk K 5 20 20 20 These are all preprocessor commands the preprocessor used here is called EDITOR and was developed by David Clarke and become part of the change deck chgzeus created by the script file zeus32 s A change deck is a file which is merged with the source code during the preprocessing step of zeus32 s Both the source code and the change deck can contain preprocessor commands which are interpreted carried out and 10 then deleted from the code by EDITOR before the code is compiled by the FORTRAN compiler All preprocessor commands have an asterisk in column 1 Double aster isks indicate a comment When the preprocessor has finished the result is a purely FORTRAN source co
65. ikb2 emf2ikb3 emf3ikb1 emf3ikb2 13 OKB Outer K Boundary control read from subroutine NMLSTS default 2 floor floor 0 0 viikb2 b3ikb1 emf2ikbi emf3ikb3 This namelist specifies both the boundary type and the inflow values of all the flow variables for the outer k boundary These variables are not declared if the EDITOR 51 macro KSYM is set See comments for IIB parameter nokb i j kokb1 i j kokb2 i j kokb3 i j namelist okb 1 nokb dokbi dokb2 2 V2okb1 v2okb2 v3o0kbl if def ISO 3 eokbi eokb2 xendif ISO if def GRAV 4 gpokb xendif GRAV if def MHD 5 biokbi biokb2 b2okbi 6 b3okb2 emflokbi emfiokb2 7 emf20kb2 emf2okb3 emf3o0kbl xendif MHD 14 GRVCON GRaVity CONtrol read from subroutine NMLSTS description nflo of outer k boundary on first outer k boundary value for sweep i j flow in only second outer k boundary value for sweep i j flow in only third outer k boundary value for sweep i j flow in only of variable of variable default 2 floor floor 0 0 viokb2 b3okb1 emf2okb1 emf3o0okb3 This namelist specifies the parameters which control the gravitational force from a point mass In addition the parameters to specify the type of boundary conditions for the self gravity module are in this namelist parameter description g gravitational constant ptmass fixed central poin
66. ile is much less general than the on line version but it still cantains all the macros and runs the same test problem Another example provided on line is the 3 D blast wave test problem set up by the version of zeus32 s called blast s which can be downloaded from landrew ncsa uiuc edu as described earlier from directory afs ncsa projects lca codes zeus3d tests 3d blast The on line versions of zeus32 s are designed to create the ZEUS 3D executable on various systems besides Cray UNICOS xk oR k kk kk kkk kkk CONDITIONAL COMPILATION SWITCHES 27K KKK xk k 1 symmetry axes ISYM JSYM KSYM xk xdefine KSYM JSYM xk 2 geometry XYZ or ZRP or RTP xx xdefine XYZ xk k 3 physics MHD ISO GRAV xk xdefine MHD xk k 4 algorithms MOC xk xdefine MOC xk xx 5 data output modes PLT1D PLT2D PIX VOX HDF DISP RADIO TIMESL xdefine xk PLT1D k 6 operating system xk xdefine FKK KKK K KK K FK K K K FK K K K K FK K K 2K K K OK The modules BNDYUPDATE UNICOS CALMATH UNICOS CALMATH CONVEXOS SUNOS IRIX FER RRR KK k k k kk k k kkk k kkk k MODULE NAME ALIASES SPECIAL SPECIALSRC SPECIALTRN k USERDUMP and FINISH are slots available to the user to help k adapt the code to the problem being solved OK alias alias alias alias alias alias alias alias alias alias alias alias alias OK alias al
67. in determining when the disturbance gets close to an edge of the current computational domain the results can be disastrous GRAVITY This module updates the self gravitational potential Currently the only choices are empty and gravity The latter invokes the DADI algorithm developed for ZEUS 3D by Yu Zhang and should still be considered experimental In most applications the DADI algorithm will consume a similar amount of cpu time as the hydrodynamics SPECIAL This is a simplistic solution to the potentially complex problem of the user desiring to add a whole new type of physics to the code It assumes that changes do not need to be intertwined into existing modules which in practice often will be necessary The two accompanying plugs SPECIALSRC for special source terms and SPECIALTRN for special transport considerations allow for some flexibility in installing new physics within the current structure but this still may not be enough for any type of sophisticated addition By default all three are set to empty SOURCE This is the module in which source terms are incorporated For full dynamics this should be set to srcstep or the user s module if need be while for problems of pure advection this should be set to empty SPECIALSRC See SPECIAL TRANSPORT This is the module for the transport of variables across zone boundaries and should be set to transprt or to the user s equivalent module It is unlikely
68. inates The inflow boundary conditions are set at all grid points inside the orifice This overwrites any parameters that may have been set for these zones by the namelist iib Thus should a jet run be restarted it is necessary to prevent the namelist iib from reseting all the inner i boundary parameters in the orifice zones The jet orifice can be wiggled helically to break the pseudo azimuthal symmetry by setting iwiggle to 1 and by setting the EDITOR alias BNDYUPDATE to wiggle For a circular helical perturbation set thetaj thetak For an elliptical helical perturbation set thetajAthetak For a sinusoidal perturbation set one of thetaj or thetak to zero To generate a magnetic field at the jet orifice set BNDYUPDATE to bgen If both wiggle and bgen are required set BNDYUPDATE to jetbndy which calls both subroutines in succession If a non uniform atmosphere is required the user may use the EDITOR alias ATMO SPHERE to include a user supplied subroutine describing the desired atmosphere parameter description default Input parameters for the jet hydrodynamical variables rjet radius of jet in coordinate units 1 0 eta ratio between jet density and ambient medium density 0 1 effective at the inflow boundary kappa ratio between jet pressure and ambient medium pressure 1 0 effective at the inflow boundary mjet Mach number of the jet with respect to its own sound 6 0 speed at the jet inlet ojet initial angular velocity of jet about ax
69. ios npj nios pixvar niov nlpix niov pixmin niov pixmax niov ipixmm rorhpix units xipxmn nios xipxmx nios x2pxmn nios x2pxmx nios x3pxmn nios x3pxmx nios direction of normal to image slice 0 gt no dumps 1 2 3 gt 1 2 3 direction 0 level of 2 D pixel dump value of 1 2 or istie 2 3 index problem time interval between pixel dumps 0 0 gt no pixel dumps number of color contour levels in image 0 gt no reflection 1 gt q reflected across x axis on output generates twice the y pixels requested 0 gt no reflection 1 gt q reflected across y axis on output generates twice the x pixels requested number of x pixels in image slice number of y pixels in image slice names of variables to be plotted character 2 Valid names are al a2 a3 vector potential components b1 b2 b3 2d 26 7 2 eps goa ar a ae j3 m en p Ze pb aoa aa Ys12 52 53 gt see vi yD v3 yy 0 gt store data gt 0 gt store log10 data concentrating colors at low end Dynamic range nlpix 1 gt 100 lt 0 gt store log10 data concentrating colors at high end Dynamic range nlpix 1 gt 100 value of data to be assigned the minimum color value of data to be assigned the maximum color 1 gt compute pixmin and pixmax for images 0 gt use input pixmin pixmax for images If pixmin and
70. is solid body 0 0 rotation pore 1 gt propagating jet 1 2 gt equilibrium jet Phil Hardee s stability runs bijet initial magnetic field in 1 direction pore 2 only 0 0 toroidal magnetic field generator betator gt 0 gt minimum plasma beta of toroidal magnetic field huge lt 0 gt average plasma beta of toroidal magnetic field rpeak radial distance from the jet axis to the peak of the 0 5 toroidal magnetic field profile rsigma FWHM of the toroidal magnetic field profile in radial 0 5 direction poloidal magnetic field generator 68 betapol ibpol zsigma rnode znode gt 0 gt minimum plasma beta of poloidal magnetic field huge lt 0 gt average plasma beta of poloidal magnetic field 1 gt semi infinite flux loop of axial magnetic field 1 ramped up using zsigma 2 gt flux loops of axial magnetic field HWHM of the magnetic field profile in the axial direction to ramp up the magnetic field radial distance between flux loop nodes axial distance between flux loop nodes random magnetic field generator betaran effective plasma beta of the random magnetic field component 0 gt huge lt huge gt toroidal and poloidal generators turned off Input parameters for the ambient medium damb eamb viamb v2amb v3amb biamb b2amb b3amb density specific internal energy e d implies an external sound speed of 1 0 velocity velocity velocity magnetic magnetic m
71. istp steepener switch third order only for variable 1 lt 0 gt istp is set to istp 47 floor smallest value desired for variable d e tiny rest 0 0 icool O gt use PDV in SRCSTEP 0 1 gt use PDVCOOL in SRCSTEP for pdv work with arbitrary cooling function itote 0 gt solve the internal energy equation 0 1 gt solve the total energy equation namelist hycon 1 qcon gt qlin courno dtrat iord 2 iordd iordsi iords2 iords3 iorde 3 iordb1 iordb2 iordb3 istp istpd 4 istpsl istps2 istps3 istpe istpbl 5 istpb2 istpb3 dfloor efloor vifloor 6 v2floor v3floor bifloor b2floor b3floor 7 icool itote 8 IIB Inner I Boundary control read from subroutine NMLSTS This namelist specifies both the boundary type and the inflow values of all the flow variables for the inner i boundary These variables are not declared if the EDITOR macro ISYM is set Any one of 6 MHD boundary conditions nflo may be specified independently at every boundary zone These boundary conditions are nflo 1 gt reflecting v normal b normal 0 1 gt reflecting with inversion of 3 components 2 gt flow out 3 gt flow in 4 gt periodic 5 gt reflecting v normal b tangential 0 The boundary values for the variables are used only in the event that a zone along the boundary is inflow nflo 3 Otherwise the boundary value is determined from the flo
72. ithm or a form which is linear in velocity USERDUMP See DATAOUTPUT 3 3 THE SCRIPT FILE zeus32 s Below is a stripped down version of the zeus32 s script Download the much more eloborate version from landrew ncsa uiuc edu via ftp as described earlier 14 It is assumed below that the user s Cray is on AFS Andrew File System and that the command klog zeus3d cell ncsa uiuc edu has been issued to allow access to files on landrew The script file is run by typing chmod 700 zeus32 s zeus32 s bin csh v SCRIPT FILE TO CREATE THE ZEUS 3D EXECUTABLE set ZEUS3D afs ncsa projects lca codes zeus3d if e zeus32 cp ZEUS3D source zeus32 if e zeus32 mac cp ZEUS3D xeq uy zeus32 mac if e chgz32 cp ZEUS3D xeq uy chgz32 if e xedit21 cp ZEUS3D editor xeq uy xedit21 if e namelist lib cp ZEUS3D namelist xeq uy namelist lib if e cfiles lib cp ZEUS3D cfiles xeq uy cfiles lib if e ncar libo cp ZEUS3D ncar xeq uy ncar libo Hsssssssssssssssssss gt If necessary create the directory zeus3 2 if e zeus3 2 mkdir zeus3 2 RSS St ee SSS a gt Create the change deck rm f chgzeus cat lt lt EOF gt chgzeus read zeus32 mac d par 14 15 parameter in 805 jn 1 kn 1 ijkn 805 parameter nxpx 1 nypx 1 nxrd 1 nyrd 1 kread chgz32 EOF gt Create the input deck for EDITOR and execute rm f inedi
73. ity for advection tests for explosions for shock tube tests Bennett pinch problem aligned magnetic rotator test initializes jet simulations user defined module to initialize flow variables sets all magnetic field variables to zero user defined module to alter variables for restarted job 40 APPENDIX 2 THE NAMELISTS There are nearly 500 namelist parameters and one might be overwhelmed at the prospect of setting values for every one Take heart many of the defaults can be used for most applications As a good start use the input deck given in the zeus32 s template Subsection 3 3 and then alter or add the appropriate parameters On the next page begins a complete catalogue of all the input parameters in zeus32 The parameters are grouped together in namelists and discussion for each namelist is contained within a segment headed by the name of the namelist and the subroutine in which the namelist is called For example the first namelist is iocon input output control and is called by the subroutine mstart After each heading is a discussion of what the namelist controls a list of all the parameters which are elements of the namelist and finally the syntax used in zeus32 to declare the namelist For the uninitiated a namelist is a standard feature of FORTRAN9X and a non standard feature of most FORTRAN77 compilers which provides a very convenient way to specify input data Historically however the UNIX UNICOS n
74. ively A3 3 BOUNDARY VARIABLES 2 D ARRAYS First inner i boundary Variable niib j k diib1 j k viiib1 j k v2iib1 j k v3iib1 j k eiib1 j k gpiib j k bliib1 j k b2iib1 j k b3iib1 j k Location zone center at i is 1 l face at i is 2 face at i is 1 3 face at i is 1 zone center at i is 1 zone center at i is 1 1 face at i is 2 face at i is 1 3 face at i is 1 Second inner i boundary Variable diib2 j k viiib2 j k v2iib2 j k v3iib2 j k Location zone center at i is 2 1 face at i is 1 2 face at i is 2 3 face at i is 2 Description indicates boundary type for all variables see discussion on namelist iib in Appendix 2 density 1 velocity normal to the boundary 2 velocity tangential to the boundary 3 velocity tangential to the boundary internal energy density x pressure gravitational potential 1 magnetic field normal to the boundary 2 magnetic field tangential to the boundary 3 magnetic field tangential to the boundary Description density 1 velocity normal to the boundary 2 velocity tangential to the boundary 3 velocity tangential to the boundary 73 eiib2 j k zone center at i is 2 internal energy density pressure biiib2 j k l face at i is 1 1 magnetic field normal to the boundary b2iib2 j k 2 face at i is 2 2 magnetic field tangential to the boundary b3iib2 j k 3 face at i is 2 3 magnetic field tangential to the boundary Analogous boundary
75. king of the flow be required This feature has only been partially tested in this release parameter xifac x2fac x3fac ia ja ka igcon 1 description x1 motion factor lt 0 gives Lagrangian tracking in x1 lines x2 motion factor lt 0 gives Lagrangian tracking in x2 lines x3 motion factor lt 0 gives Lagrangian tracking in x3 lines i lt ia zone ratio is preserved in x1 lines j lt ja zone ratio is preserved in x2 lines k lt ka zone ratio is preserved in x3 lines selects grid treatment gt separate motion gt averaged motion tracking x1 x2 and x3 boundary averaged boundary tracking input grid boundary speeds vgi io xifac central sound speed vg2 jo x2fac central sound speed vg3 ko x3fac central sound speed Vv Vou uw eu PUNEO namelist gcon xifac x2fac x3fac la 53 default 0 0 0 0 2 Ka igcon 17 EXTCON grid EXTension CONtrol read from subroutine NMLSTS This namelist controls the grid extension feature of the code This is useful only for problems in which a shock separates quiescent material which does not require updating from material requiring computations As the shock propagates across the grid more zones are added to the computational domain until the entire domain has been included Because quiescent zones are not being updated a substantial savings in computation time could be realized Use this feature with caution I
76. me dt momx1 bvalv1 NEWTIMESTEP nudt tranx2 stv2 NEWGRID empty momx2 bvalv2 DATAOUTPUT dataio lt intchk tranx3 stv3 plotid momx3 bvalv3 o plot2d stov ARTIFICIALVISC no stop pixdmp bndyall viscous voxdmp bvalv USERDUMP empty pdv or pdvcool yes hdfdmp bvale tslice tslplot FINISH empty disdmp radio msave 39 START EXTENDGRID BNDYUPDATE GRAVITY SPECIAL SOURCE SPECIALSRC TRANSPORT SPECIALTRN NEWGRID NEWTIMESTEP DATAOUTPUT FINISH USERDUMP ARTIFICIALVISC PROBLEM PROBLEMRESTART mstart empty extend empty breset wiggle bgen jetbndy empty gravity empty empty srcstep empty empty transprt empty resetv empty newgrid nudt advectdt empty dataio empty empty empty viscous advect blast homol shkset zpinch mhdrot jetinit empty resetb to reset flow in boundary values used in test problems to wiggle jet inlet to generate magnetic field at jet inlet calls both subroutines wiggle and bgen no self gravity DAD I algorithm to update self gravitational potential user defined module for additional physics for advection tests user defined module for additional source terms for advection tests user defined module for additional transport terms no grid velocity full dynamics for advection tests user defined module called once at the end of execution user defined I O module von Neumann Richtmyer artificial viscos
77. mproper use can be disastrous parameter description default istretch 1 le 0 gt perform computations over entire i domain 0 gt 0 gt i index of first zone in initial i domain istretch 2 i index of last zone in initial i domain 0 le 1 gt istretch 2 istretch 1 istretch 3 1 istretch 3 le 0 gt 10 0 istretch 4 le 0 gt istretch 3 0 is is decremented by istretch 3 and or ie is incremented by istretch 4 whenever the quiescent density increases by 3 within 5 zones of the current domain boundary Note that is will not be permitted to fall below ismn and ie will not be permitted to rise above iemx jstretch 1 2 3 4 same as istretch but for the 2 direction kstretch 1 2 3 4 same as istretch but for the 3 direction namelist extcon 1 istretch jstretch kstretch 18 PLT1CON PLoT 1 D CONtrol read from subroutine NMLSTS This namelist controls the 1 D NCAR graphics During a run as many as nios 1 D slices may be specified for each variable plotted where nios is a parameter set before compilation currently nios 20 For every slice chosen a metafile is created with a plot generated for each variable specified Each 1 D slice continues across the entire data volume parallel to one of the axes of the computational grid To uniquely specify the slice two of iplt1 jplt1 and kplt1 must be set parameter description default ipltidir nios axis parallel to slice 0 gt no plots 0 1 2 3
78. n pltimax ipltimm 3 corl 19 PLT2CON PLoT 2 D CONtrol read from subroutine NMLSTS This namelist controls the 2 D NCAR graphics During a run as many as nios 2 D slices may be specified for each variable plotted For every slice chosen a metafile is created with a plot generated for each variable specified The normal to each slice is parallel to one of the axes of the computational grid and is specified by iplt2dir The extent of the slice is limited by x1p2mn x1p2mx etc while the index at the base of the normal to the slice is given by 1p1t2 2 D graphics are in the form of contours scalars and vector components normal to the image plane vectors poloidal vector components or both for combined plots N B For restarted runs in which the computation is resumed on a larger or smaller grid and where the default values for x1p2mn x1p2mx etc were used in the initial run it will be necessary to set x1p2mn x1p2mx etc in the input deck for the restarted run to the extrema of the new grid if the plots are to extend to the bounds of the new grid Otherwise the plots will be bound by the old grid parameter description default iplt2dir nios direction of normal to image plane 0 0 gt no plots 1 2 3 gt 1 2 3 direction lplt2 nios level of 2 D plot value of 1 2 or istie 2 55 dtplt2 plt2var niov nlplt2 niov plt2min niov plt2max niov iplt2mm vscale incvx incvy numcl units xi
79. n x1b i zone center x1 coordinate in grid units x2b j zone center x2 coordinate in grid units radians in spherical polar coordinates x3b k zone center x3 coordinate in grid units radians in both cylindrical and spherical polar coordinates dx1b i 1 face xib i x1b i 1 dx2b j 2 face x2b j x2b j 1 dx3b k 3 face x3b k x3b k 1 In order to make the grid covariant metric factors have been introduced which carry all the dependence of the geometry In general the metric appears in the expression for a differential in volume dV g dz g2d 2 g3dx3 In Cartesian coordinates gj g2 g3 1 In cylindrical coordinates g go 1 93 2 In spherical polar coordinates g 1 g2 1 g3 z Sinx2 Note that if one is limited to XYZ ZRP and RTP coordinates there is no need for g and g3 can be split into two variables one dependent just on x1 the other just on z2 In this way g3 can be represented by two 1 D arrays rather than one 2 D array Thus three 1 D metric factors 71 are used in ZEUS 3D g2b i zone center 1 for Cartesian and cylindrical coordinates x1b i for spherical polar coordinates g31b i zone center g2b i g32b j zone center 1 for Cartesian coordinates x2b j for cylindrical coordinates sin x2b j for spherical polar coordinates The a grid Variable Location Description xila i zone corner x1 coordinate in grid units x2a j zone corner x2 coordinate in grid units
80. n of the single quotes A detailed description of all the namelist parameters is contained in Appendix 2 3 3 6 Making the Executable xzeus32 The sixth segment executes the makefile makezeus created by the preprocessor ED ITOR The makefile will compile only those FORTRAN files in the directory zeus3 2 which have been written since the last time they were compiled then link all the object files together with the specified libraries using the loader ncargf77 actually a locally available script to create the executable xzeus32 3 4 EXECUTING ZEUS 3D Once the script file has successfully completed simply type xzeus32 followed by a carriage return and ZEUS 3D will begin running Alternatively the executable can be run in batch mode using the NQS system A sample NQS file called zeus32 nqs follows QSUB 1T 300 QSUB 1M 1Mw QSUB 1F 200Mb QSUB HSS SSS PSS Se re tee eee oe gt enable job accounting gt copy executable and input deck from SAVE to batch scratch SCR cd SCR cp SAVE xzeus3d SAVE inzeus i ae ig E gt execute xzeus32 PoR r r n a a ee ay err ne gt create libraries for data dumps tar cvf plt2d tar zq tar cvf pixel tar zi tar cvf voxel tar zv fap Rae re asa aa ee oe gt copy data dumps to SAVE cp plt2d tar pixel tar voxel tar SAVE fis Ae SSeS ase gt report job accounting information and disable accounting date echo job complete ja csft The QSUB directives request a maximum of
81. nal energy density will ensure positive definite pressures but will introduce numerical deviations from total energy conservation which may become severe at steep gradients such as strong shocks If itote 1 all energy variables should be interpreted as total energy per unit volume and thus is the sum of internal kinetic and gravitational energy densities Evolving the total energy density will ensure energy conservation to within machine round off but may yield negative pressures in extreme cases where the internal energy is a small fraction of the total energy Using 64 bit words should prevent this from ever being a problem To date little has been done with the total energy option and so it may be advisable to set itote 0 unless one expects particularly strong shocks Mach numbers gt 100 say Also if either MHD or ISO is defined itote will be reset to 0 parameter description default qcon quadratic artificial viscosity q constant 2 0 qlin linear artificial viscosity q constant 0 0 courno Courant number 0 5 dtrat ratio of dtmin to initial value of dt 0 001 iord order of advection scheme used by all variables 2 Legal values are 1 donor cell 2 van Leer or 3 ppa iord order of advection scheme to be used for variable 0 O gt iord is set to iord istp steepener switch third order only for all variables 0 0 gt always off 1 gt always on 2 gt on only at contact discontinuity and only for density
82. nates of center of overpressured region 3 0 0 drat ratio of density across blast front 1 0 prat ratio of pressure across blast front 1 0e6 do density in ambient medium 1 0 po pressure in ambient medium 0 6 b10 1 magnetic field in ambient medium 0 0 b20 2 magnetic field in ambient medium 0 0 b30 3 magnetic field in ambient medium 0 0 m drs dr parameters for specifying a sphere whose surface 0 is sinusoidally perturbed spherical coordinates 0 0 only For an unperturbed sphere set all values 0 0 to zero namelist pgen 1 r X10 X20 X30 drat 2 prat dd pO b10 b20 3 b30 gt m drs arc 3 HOMOL Sets up a homologous contraction or expansion test problem in one of the three directions parameter description default idirect 1 gt 1 direction 1 2 gt 2 direction 3 gt 3 direction vO velocity of contraction or expansion 1 0 nn exponent of velocity field v vO r nn 1 do density at xla i 1 d d0 r nn 1 0 e0 internal energy density at xla i 1 0 1 0 e e0 r nn namelist pgen 1 idirect nn gt VO dd e0 66 4 SHKSET Sets up a Sod shock tube in one of the three directions parameter description default idirect 1 gt 1 direction ie biggest gt 1 2 gt 2 direction je biggest gt 2 3 gt 3 direction ke biggest gt 3 no number of zones to be initialized Namelist nx1z cards are read from logical unit ioin until ie ist1 or je jst1 or ke ks 1 zones are init
83. nes 10 through 20 in the main program zeus3d are replaced with the two lines which set a and b a single line setting d i j k is inserted after line 100 in subroutine mstart a single line setting c is inserted after line 100 in zeus3d and line 120 in zeus3d is simply deleted These statements should be placed in the file chgz32 and would be incorporated into the master code during the first pass of the preprocessing To aid the user in deciding what changes to make and where to make them a flow chart showing the sequence of subroutine calls in ZEUS 3D is given in Appendix 1 This will be particularly useful once faced with the task of comprehending the source code listing zeus32 n If EDITOR detects any merge syntax errors or conflicts during the merge it will write the merged file as best as could be done given the error s detected into a file named zeus32 m and insert an error message immediately after each offending line A merge error will prevent the second pass of preprocessing i e precompilation from being executed and the user will be told what character pattern to search for in the file zeus32 m in order to find the generated error messages Should the merge step be successful EDITOR goes through a second pass and performs all the precompilation commands These include 1 if define macro the following source code is kept provided the macro is defined by a define statement somewhere in the file 2 if define macro
84. ngle radians measured counter clockwise between major axis and x axis cells per beam E vectors gt B vectors vector length proportional to poli vector length proportional to fpol black and white pixel vectors gt black pixel vectors only vectors with length lt vlmin max vector not plotted vectors are not plotted if toti lt icut max toti vectors are not plotted if poli lt pcut max poli scaling factor for polarization vectors plot every incpx th vector in x direction plot every incpy th vector in y direction sets the angular units character 2 rd gt radians pi gt units of pi radians dg gt degrees minimum x1 for maximum x1 for minimum x2 for maximum x2 for minimum x3 for maximum x3 for lt 0 gt value value 1 gt RADIO RADIO RADIO RADIO RADIO RADIO integration integration integration integration integration integration namelist radcon oono ewr ntheta dphi radvar slower oupper nlrad icnvlv dtrad phimin alpha elower dupper xupper radmax thetamax nphi ncrad olower tupper thetamin phimax freq tlower eupper dsw iradmm btsw rorhrad v v v v v v v_ v v v v v v v v v v v v v v v v v v v 64 1 gt 100 dtheta itype dlower xlower supper radmin bmajor 0 0 0 0 1 oO rPrROOO ooo 001 001 001 rd xla is xla ie 1 x2a js x2a je 1 x3a ks x3a ke 1
85. nsistent Advection Michael Norman used to evolve internal energy and mo menta and e Constrainted Transport Evans and Hawley modified with the Method of Char acteristics Jim Stone is used to evolve the magnetic fields NEW FEATURES FOR VERSION 3 2 1 COMPARED TO 3 2 e A much more powerful zeus32 s script makes installing and customizing ZEUS 3D much easier e ZEUS 3D and EDITOR have been modified to work properly on Cray Convex Sun and SGI systems all over the world FORTRAN source code for the standard library routines ISMIN ISMAX and SASUM are provided in zeus32 s for systems without them e The EDITOR aliases UY and U2 have been replaced by the CALMATH alias which should be defined only for UNICOS systems that have the Cray calmath math library NEW FEATURES FOR VERSION 3 2 COMPARED TO 3 0 Line of sight integrations through the data volume for a variety of variables including the Stokes parameters see Section IV may be output in both XYZ and ZRP coordi nates The EDITOR definition RADIO must be set to invoke this display option An option for generating time slice data that is values of certain global quantities as a function of time The EDITOR definition TIMESL must be set in order to get time slice output Rather than generating polar pixel dumps ZEUS 3D converts polar slices to Carte sian slices on the fly before writing them to disk 1 D and 2 D NCAR graphical output
86. ode uses algorithms and structures developed over the past 20 years by David Clarke Philip Colella Chuck Evans John Hawley Michael Norman Larry Smarr Jim Stone Bram van Leer Jim Wilson Karl Heinz Winkler Paul Woodward and others It is therefore appropriate that this code should become a community tool available to anyone with a complex fluid dynamics problem to solve ZEUS 83D is a three dimensional ideal non resistive non viscous adiabatic non relativistic magnetohydrodynamical MHD fluid equation solver which numerically in tegrates the following coupled partial differential equations as a function of time and space Op Be 0 1 L V pv 1 Os a V SV Vp pV J xB 2 o S V ev pV v 3 OB Ot v x B 4 where p matter density v velocity flow field S pv momentum vector field p thermal pressure gravitational potential J current density B magnetic induction e internal energy density per unit volume This code is strictly Newtonian Relativistic astrophysics cannot be simulated in any way with this version No explicit account for relativistic particles is incorporated either The code assumes strict charge neutrality at all times it is not a plasma code It is assumed that the fluid is thermal and is coupled to the magnetic field via collisions with an ionized component which never undergoes charge separation The thermal pressure is assumed to be isotropic It is assum
87. ollows 1 The code can be streamlined optimized for 1 D and 2 D problems by setting the appropriate symmetry macros If symmetry along any of the i x1 j x2 or k x3 axes is desired then set the ISYM JSYM or KSYM macros If the macros are not set and a 1 D or 2 D calculation is initialized by the input deck ZEUS 3D will still carry out the sub 3 D computation correctly but will do so less efficiently 2 The geometry is set by setting ONE of the XYZ Cartesian ZRP cylindrical or RTP spherical polar macros These macros are mutually exclusive so set only one of them 3 By setting the MHD macro the algorithm for evolving the magnetic fields is activated With MHD on additional field arrays are declared and the code pertaining to updating the magnetic field is compiled The ISO macro should be set if an isothermal equation of state is desired With ISO defined the internal energy variables are not declared saving both computational time and memory Finally defining GRAV and setting the EDITOR alias GRAVITY to gravity see below will turn on the DADI self gravity module developed by Yu Zhang at NCSA 4 The MoC algorithm Method of Characteristics developed by Jim Stone and Michael Norman of NCSA John Hawley at the University of Virginia and Chuck Evans at the University of North Carolina is the most robust algorithm developed for evolving magnetic fields and is essential for stable propagation of Alfv n waves Thus it
88. p2mn nios xip2mx nios x2p2mn nios x2p2mx nios x3p2mn nios x3p2mx nios 3 index physical problem time interval between 2 D 0 0 plot dumps 0 0 gt no plots names of variables to be plotted character 2 zz Valid names are d e se p pb gt pt vp poloidal velocity vn normal velocity vv divergence of velocity sp poloidal momentum sn normal momentum m gp an normal vector potential bp poloidal magnetic field bn normal magnetic field jp poloidal current density jn normal current density dv density plus poloidal velocity ds density plus poloidal momentum db density plus poloidal magnetic field dj density plus poloidal current density 0 gt plot data 0 1 gt plot log10 of data positive definite quantities only Minimum value to be contoured 0 0 maximum value to be contoured 0 0 1 gt compute plt2min and plt2max for plots 1 0 gt use input plt2min plt2max for plots If plt2min and plt2max are 0 compute them as if iplt2mm were 1 scaling factor for vectors 0 8 index increment in x direction for vector plots 1 index increment in y direction for vector plots 1 number of contour levels 20 sets the angular units character 2 rd rd gt radians pi gt units of pi radians dg gt degrees minimum x
89. processor will in this case insert the user s subroutine into zeus32 immediately after line 9 999 of the main program zeus3d by virtue of the EDITOR statement insert zeus3d 9999 appearing at the top of the subroutine template Since zeus3d doesn t have 9 999 lines EDITOR will simply stick the subroutine after the last line of the main program It doesn t matter where in zeus32 the subroutine gets inserted so long as it isn t in the middle of an existing deck Immediately after the main program is as good of a place as any Upon the second pass the precompiler will find the user s deck and treat it as it would any other it encounters Thus if there are any EDITOR commands in the user s deck such as call rouse if define MHD they will be carried out and then expunged from the working copy of the source code The user s subroutine will then be placed in its own file in the directory zeus3 2 and the name of the subroutine will be included in the makefile makezeus which will then compile the subroutine and link it with the rest of the object files and libraries Provided the EDITOR alias PROBLEM has been set to myprob in the macro file zeus32 mac the user s problem generator will be called at the appropriate time during execution Similarly if the subroutine should be called at the location of any of the other available plugs in the code set the appropriate alias i e SPECIAL SPECIALSRC SPECIALTRN USERDUMP PROBLEM PR
90. quantitatively and simultaneously EDITOR definition DISP logical unit iodis namelist discon filename zdllid where zd is the common prefix to all display files Il is as defined for time slice dumps and id is as defined for restart dumps format ascii 9 2 D RADIO DUMPS These files are similar to the 2 D pixel dumps but contain line of sight integrations of various quantities rather than 2 D slices through the data volume In this release RADIO dumps are possible in both Cartesian XYZ and cylin drical ZRP coordinates The integrands are all scalars density pressure internal energy magnetic pressure velocity shear velocity divergence and three Stokes emissivities and are integrated using a very fast binning algorithm as opposed to the slower by a factor of 50 direct ray tracing algorithm used in the original RADIO code Files may be dumped in either raw format one byte per datum or HDF four bytes per datum EDITOR definition RADIO logical unit iorad namelist radcon 24 filename formats zR nnnid h where zR is the common prefix to all RADIO dumps nnn id and h are as defined for pixel dumps raw one byte per datum HDF four bytes per datum 10 MESSAGE LOG FILE This file contains all the messages that are written to the terminal by the code during execution In addition the grid and all the values of the namelist parameters specified in the file inzeus are dumped here It serves as th
91. re SH velocity shear VV velocity divergence variable is integrated along los provided it is greater than lower where is any one of d e se pb sh and vv variable is integrated along los provided it is less than upper 1 0 gt dlower and dupper determine integration limits for all variables 0 0 gt not 1 0 gt B field extent determines integration limits for all variables 63 ooo ooo ooo ooo O 5 0e9 0 5 0 9277 huge huge 0 0 0 0 nlrad niov radmin niov radmax niov iradmm rorhrad icnvlv bmajor bminor bpa cpb eorb porf bworb vimin icut pcut pscale incpx incpy units xirdmn xirdmx x2rdmn x2rdmx x3rdmn x3rdmx 0 0 gt not 0 gt store data gt 0 gt store logi0 data concentrating colors at low end Dynamic range nlrad 1 gt 100 store logi0 data concentrating colors at high end Dynamic range nlrad of data to be assigned the minimum color of data to be assigned the maximum color compute radmin and radmax for images use input radmin radmax for images If radmin and radmax are 0 compute them as if iradmm were 1 raw format used for dumps HDF used for dumps in which case nlrad radmin and radmax are ignored 0 gt do not apply convolution 1 gt apply convolution to Stokes parameters major axis of convolving beam minor axis of convolving beam beam position a
92. roceed with setting the namelists ggen1 ggen2 ggen3 See discussion in ggeni Note that if the user selects the manual option addz 0 it is imperative that the portion of the new grid that overlaps the old grid be in fact identical to the old grid Next all arrays will be padded with values at the edges of the portion read Thus d 1 34 j k d 35 j k d 67 100 j k d 66 j k where d is the density array see Appendix 3 etc Of course the user is free to overwrite the padded portion of the arrays with whatever is necessary by linking the appropriate user supplied subroutine to the EDITOR macro PROBLEMRESTART subsection 3 2 2 Finally a job may be resumed from a restart dump with different EDITOR macros defined or not Thus if a job that began with magnetic fields is to be resumed without them the user may recompile zeus32 without magnetic fields MHD not defined and then blindly read the restart dump which contains magnetic field arrays There is enough information in the restart dump that the code can selectively read the non magnetic part of the dump and resume the calculation as though there were never any magnetic fields Of course what happens dynamically once the flow no longer feels the magnetic fields may be another matter parameter description default dtdmp problem time interval between restart dumps 0 0 0 gt no restart dumps probably a bad idea gt 0 gt write each dump to a new file lt 0 gt over
93. se is inserted at the location of the call statement Every variable of any possible interest is declared in rouse including many that the user would never need A description of the most widely used variables is given in Appendix 3 At the beginning of rouse is an implicit none statement which requires that the attributes of all variables used in the subroutine be declared Note that should the user inadvertently try to use a variable name already declared in rouse the compiler will flag the repetition and abort compilation While the implicit none statement no longer requires that all externals called by the program unit be declared in an external statement cft77 5 0 and later it is still good practice to do so In fact if undeclared externals appear inside a nested do loop construct this may inhibit EDITOR s autotasking feature which microtasks zeus32 for parallel processing on either of the Crays 4 Should one dimensional arrays be required to store data at each grid point along one of the axes it is best to declare the 1 D vector with dimension ijkn as done in the template The parameter ijkn is declared in rouse and is defined as the largest of in jn and kn the dimensions of the 3 D arrays also declared in rouse So that no additional memory is occupied by this local array it can be equivalenced to one of the 26 1 D scratch arrays declared in rouse as done in the template The names of the 1 D scratch arrays are
94. t cat lt lt EOF gt inedit editpar inname zeus32 ibanner 0 idump 1 job 3 safety 0 20 ipre 1 inmlst 1 iupdate 1 iutask 0 chgdk chgzeus branch zeus3 2 makename makezeus xeq xzeus32 loader ncargf77 compiler cft77 M0726 ve v v v v v v v v v c coptions ez o off c compiler cf77 c coptions c Zp Wf M0726 libs lcalmath namelist lib cfiles lib ncar libo ldf EOF xedit21 farsa SST SaaS anaes ora ees gt Create the input deck for ZEUS 3D rm f inzeus cat lt lt EOF gt inzeus iocon iotty 6 iolog 2 rescon dtdmp 80 0 id xd resfile zr00xd ggen1 nb1 800 xilmin 0 0 ximax 800 0 igrid 1 xlrat 1 0 15 lgrid t ggen2 nb1 001 x2min 0 0 x2max 1 0 igrid 1 x2rat 1 0 lgrid t ggen3 nb1 001 x3min 0 0 x8max 1 0 igrid 1 x3rat 1 0 lgrid t pcon nlim 999999 tlim 80 0 ttotal 900 0 tsave 10 0 hycon qcon 2 0 qlin 0 0 courno 0 5 iord 2 istp 0 itote 0 iib niib 1 1 1 1 2 oib noib 1 1 1 1 2 ijb nijb 1 1 1 805 2 ojb nojb 1 1 1 805 2 ikb nikb 1 805 1 1 2 okb nokb 1 805 1 1 2 grvcon eqos gamma 2 0 Sgcon extcon plticon ipltidir 1 dtplt1 80 0 pltivar d se p vl v2 v3 bl b2 i b3 bd plt2con pixcon voxcon usrcon hdfcon
95. t mass izero i index of x1 0 jzero j index of x2 0 kzero k index of x3 0 igpiib O gt symmetric Dirichlet boundary conditions igpoib 1 gt non symmetric boundary conditions value igpijb calculated using multipole expansion igpojb igpikb igpokb namelist grvcon wye g ptmass izero gpiib igpoib igpijb igpokb 52 default igpikb 15 EQOS EQuation Of State control read from subroutine NMLSTS This namelist specifies the parameters which control the equation of state Using all the defaults is recommended unless a different adiabatic constant gamma is required This version of ZEUS 3D does not permit multi material calculations and so the param eter mn should always be set to 1 Note that if an isothermal equation of state is desired setting the EDITOR definition ISO in addition to setting niso 1 will allow execution to take advantage of the reduced computations necessary for isothermal systems parameter description nmat number of materials gamma mn ratio of specific heats rgas mn gas constant niso mn 0 gt adiabatic eos 1 gt isothermal eos ciso mn isothermal sound speed rmetal mn metallicity gt cooling strength M MML namelist eqos 1 nmat gamma rgas niso 2 rmetal 16 GCON Grid motion CONtrol read from subroutine NMLSTS Ciso default 1 5 3 1 0 0 1 0 0 0 This namelist sets the parameters for grid motion should a partial trac
96. tains the 1 D plots along one of the specified 1 D slices through all of the selected variables If for example m slices are specified for n variables then each time 1 D plots are required m metafiles will be created each containing n plots Note place the command setenv NCARG_GKS_OUTPUT GMETA in your login file to ensure that the default name for metacode files is GMETA EDITOR definition PLT1D 21 logical unit ioplt1 namelist plticon filename zpnnid mm where zp is the common prefix to all 1 D plot files nn and id are as defined for restart dumps and mm is an exten sion indicating the slice number format metacode use cgmtrans or plt to read the metafiles 3 2 D NCAR PLOT FILES These are metacode files each of which contains the 2 D plots contours and or vectors on one of the specified 2 D slices through all of the selected variables If for example m slices are specified for n variables then each time 2 D plots are required m metafiles will be created each containing n plots EDITOR definition PLT2D logical unit ioplt2 namelist plt2con filename zqnnid mm where zq is the common prefix to all 2 D plot files nn and id are as defined for restart dumps and mm is an exten sion indicating the slice number format metacode 4 2 D PIXEL DUMPS Each file contains a binned 2 D slice through the data volume of a single variable designed for visualization They can be written in either raw form
97. tal energy or the internal energy equation The toggle itote in the namelist hycon specifies which of these formalisms is to be used Byung I Jun NCSA Pixel Voxel and RADIO dumps may be made in HDF format This avoids the cumbersome process of bracketing the images but at the cost of more than four times the disc space requirements It is possible to read a restart dump for example that was generated by a compiled version of the code with different EDITOR macro settings and different values for the array parameters e Boundaries must be regular Users of version 3 0 will be happy to note that there are no major changes in the way ZEUS 3D is compiled or executed and the namelist parameters have remained more or less fixed Still there are enough subtle changes that it might do the experienced user some good to review these notes before attempting to run a job with this new version Also note that version 3 2 cannot read restart dumps created by version 3 0 and vice versa III RUNNING ZEUS 3D 3 1 OVERVIEW ZEUS 3D version 3 2 1 runs on most Cray Convex SGI and Sun systems The examples in this manual are written assuming that the user will run the code on a Cray while providing some additional notes for running the code on other systems The user may obtain assistance with porting the code by contacting the Laboratory for Computational Astrophysics LCA at lca ncsa uiuc edu In order to obtain the ZEUS 3D executable do
98. that empty should ever be used here SPECIALTRN See SPECIAL NEWTIMESTEP This module determines how the next time step is computed Since ZEUS 3D is an explicit code all algorithms should incorporate the Courant condition CFL Current choices are nudt for full M HD problems and advectdt for pure advection problems 13 11 12 13 14 15 16 17 18 NEWGRID This is the module which adjusts the grid should grid velocities be desired to partially follow the flow Current choices are newgrid and empty In practice users will probably have to provide their own prescriptions for evaluating the grid velocities as most of the available methods are untested This will require replacing or adding to the subroutine newvg See Section VI for discussion on how to add or modify a subroutine in the code DATAOUTPUT This module is responsible for data I O Setting this macro to dataio will cause restart dumps NCAR plot files pixel dumps voxel dumps hdf files display files RADIO dumps time slice dumps and any other format as specified by the macro USERDUMP to be created at time intervals set by the user Section IV Setting the macro to empty will prevent all data I O probably not a good idea FINISH This is a plug available to the user to have any user supplied subroutine called once at the end of execution It could for example be used to generate NCAR plots of certain variables that the user has been
99. time Anticipate that the size of the restart dumps will be about 10 x in x jn x kn words for MHD runs and 6 5 x in x jn x kn words for HD runs The first data written to a restart dump are the array dimensions and parameters which indicate which EDITOR macros are defined Values of EDITOR aliases are not stored These then are the first data read from a restart dump and are used to allow a restart dump to be read regardless of the differences between the array dimensions and EDITOR definition settings in the new executable that which is reading the restart dump and the old executable that which created the restart dump Thus it is possible for example to resume an MHD run without the MHD definition set and thus resume the calculation hydrodynamically or to read the inner eighth of a 64 data volume into any part of a new 100 grid or whatever This added flexibility of the restart dump format is new to this version of the code Note that restart dumps generated by previous versions of the code cannot be read by zeus32 and vice versa EDITOR definition none logical unit iodmp namelist rescon filename zrnnid where zr is the common prefix to all restart dumps nn is a two digit integer distinguishing the multiple dumps created during a run and id is a two character user specified problem tag format binary one word 8 bytes Cray 4 bytes Convex per datum 2 1 D NCAR PLOT FILES These are metacode files each of which con
100. time step ZEUS 3D glances at the terminal buffer If an interrupt message has been typed followed by a carriage return ZEUS 3D will carry out the instruction to the best of its ability If no interrupt message is found execution will proceed without pause Below is a list of the interrupt messages currently recognized by ZEUS 3D along with a brief description of their function Only the first three characters of each command those in typewriter font need be entered Note that there are several synonyms for a number of the commands which are separated by commas Controlling execution e time cycle status t n prints a time and cycle report then resumes execution e quit abort crash break immediate emergency termination no final dumps are made e stop end exit finish terminate clean stop all final dumps are made e halt pause wait interrupt halt execution and wait for a message from the crt or controller e restart go restarts execution after a halt e tlimit tfinish followed by a real number resets the physical problem time e nlimit nfinish followed by an integer resets the cycle limit e ttotal tcpu followed by an integer number of seconds resets maximum cpu time to consume e tsave treserve followed by an integer number of seconds resets the save time reserved for cleanup and termination Controlling data output e dump creates a restart dump at current time e dtdmp followed b
101. ttom position of block 0 0 ximax xta imax top position of block 0 0 xiscale arbitrary scaling factor for xlmin and ximax 1 0 igrid method of computing zones 1 0 gt block has already been set restarted runs only 1 gt ratioed use input xlrat to compute dximin dximin size of first zone in block 1 gt ratioed use input xlrat to compute dximin dximin size of last zone in block 2 gt ratioed use input dximin to compute xirat dximin size of first zone in block 2 gt ratioed use input dximin to compute xirat dximin size of last zone in block 3 gt scaled compute xtrat and dximin from nbl xirat desired ratio dxia it1 dxia i 1 0 dximin desired difference xla imint1 xla imin 0 0 lgrid false gt read another block namelist card false true gt all blocks are read in Do not look for another ggeni namelist card namelist ggen1 1 nbl X min ximax xlscale igrid 2 xirat dximin lgrid 4 GGEN2 Grid GENerator for x2 read from subroutine GRIDX2 See comments for GGEN1 parameter description default nbl number of active zones in block being generated 1 x2min x2a jmin bottom position of block 0 0 x2max x2a jmax top position of block 0 0 x2scale arbitrary scaling factor for x2min and x2max 1 0 igrid method of computing zones 1 0 gt block has already been set restarted runs only 45 1 gt ratio
102. uantities integrated along the lines of sight through the data volume at arbitrary viewing angles theta and phi The volume integrated can be limited by setting x1rdmn x1rdmx etc RADIO dumps are currently available for Cartesian XYZ and cylindrical ZRP geometries See discussion in namelist pixcon regarding raw format vs HDF bracketing images and dumping images logarithmically There are two types of integrated quantities flow variables and emissivities Many of the parameters listed below are for controlling the latter For example the Stokes parameters once integrated can be convolved with a beam polarization vectors may be plotted directly rather than raster images polarization vectors may be superposed on total intensity raster images and so on The masks lower upper btsw and dsw are useful in limiting which portion of the grid is included in the integration of the non emissivity scalars For example if there is a contact discontinuity CD enclosing the region of interest then there will be a jump in the density d along this interface Thus if d for example jumps from about 0 1 to about 1 0 across the CD setting dsw 1 0 and dupper 0 5 would allow only the low density region be it interior or exterior to the CD to contribute to the line of sight integration Alternatively if the magnetic field is found only in the material of interest setting btsw 1 0 would allow only material with magnetic field to be inclu
103. ube problem Note that the aliases in the example of zeus32 mac previous subsection are also set for this problem ZEUS 3D uses namelists to specify input parameters but does not use the standard namelist utility Historically the first versions of namelist available under UNICOS were horrid character variables could not be set vectors could only be set one element at a time error messages were unreadable and so a more useful namelist utility was incorporated into the preprocessor EDITOR Thus as one of its duties EDITOR can be instructed to replace all references to namelists with calls to subroutines found in the library namelist 1ib which is linked to the executable during the make process This step is entirely transparent to the user Namelists can be used as always with the usual more or less syntax bearing in mind that once defined a namelist must be read before the next namelist is defined Since this time the namelist utility under Cray UNICOS has been significantly improved and should the user prefer to use the UNICOS namelist then the input parameter inmlst in the EDITOR input deck inedit should be set to 0 Segment 3 3 4 One primary difference between the UNICOS namelist and the EDITOR namelist is the latter allows for rank 2 arrays to be specified in an extremely intuitive fashion So for example to set diib1 i j i 20 30 j 70 80 to 1 0 while setting the rest of the 100 by 100 array to 0 1 one merely needs to
104. ubroutines zeus32 mac file containing all the EDITOR macros Section 3 2 chgz32 the change deck containing changes to the source code that the user deems necessary for the simulation Segment 3 3 3 This line is commented out because we are not making any changes here xedit21 the preprocessor executable namelist lib the library of subroutines which emulate the namelist feature Seg ment 3 3 5 cfiles lib the library of C subroutines ncar libo the library of subroutines containing calls to NCAR graphics routines 3 3 2 Creating the zeus3 2 directory The second segment creates the directory zeus3 2 on condition that it does not already exist The precompiled source files one subroutine per file the compiled object files and all the compiler listing files will be put here 38 8 8 Creating the Change Deck chgzeus The third segment creates the change deck chgzeus which is merged with the source code zeus32 during the preprocessing step The first line in chgzeus reads the EDITOR macros in zeus32 mac using the EDITOR command read This command replaces the statement with the contents of the named file Thus the macros in zeus32 mac become part of the change deck chgzeus and get merged with the source code Next the EDITOR command delete or d for short is used to replace lines 14 and 15 in the common deck par in the main source code zeus32 with parameter statements which set the parameters to the desired values for the simulation
105. umber of slices for each variable plotted dumped maximum number of time slices to be collected for plots 3 14159 1 0 x 10799 smallest greater than zero number available on machine 1 0 x 10 99 largest number available on machine The parameter nios is used by the following I O formats 1 D NCAR plots 2 D NCAR plots pixel dumps and display dumps The parameter niov is used by all these I O formats plus voxel dumps HDF dumps and RADIO dumps They are both currently set to 20 in the common deck par and can be altered as needed 79 INDEX Page numbers in bold face indicate primary references Batch see NQS boundaries 13 32 34 35 41 49 53 74 75 CDBX UNICOS utility 11 change decks chgz32 9 15 17 18 35 38 chgzeus 9 10 15 17 18 19 36 39 compiler messages see zeus32 1 compilers CF77 Cray 15 18 CFT77 Cray 11 15 18 33 FC Convex 11 Convex C2 and C3 7 8 11 12 17 22 CONVEXOS 7 10 12 19 Courant condition 5 14 Cray 2 and Cray YMP 8 9 11 12 19 20 21 22 33 DADI algorithm see garvity directory created see zeus3 2 display dumps 12 14 16 25 29 61 62 76 e mail address of the Laboratory for Computational Astrophysics LCA 3 EDITOR 10 17 18 19 35 38 alias al 10 37 xcall ca 30 33 37 72 deck dk cdeck cd 30 33 36 38 xdefine def 9 10 11 37 xdelete d 15 17 36 38 if else el endif ei 32 34 37 xinsert i 35 36 38 xread r 15 17 18
106. umps created during a run id is the character 2 problem tag specified in rescon mm is an extension indicating the slice number and h is an extension added only for 22 HDF files formats raw one byte per datum HDF four bytes per datum 5 3 D VOXEL DUMPS Each file contains a 3 D dump of a single variable rebinned to a Cartesian grid using either raw format one byte per datum or HDF four bytes per datum These are the 3 D analogues of the 2 D pixel dumps and can be used by a variety of software packages including DATAVU and Spyglass DICER In this release voxel dumps may be generated in both Cartesian XYZ and cylindrical ZRP coordinates Storing enough of these images to create a smooth 3 D animation of a run is possible but strains the current disc space limitations As much as 4 Megabytes per raw format image may be required for a one million zone simulation Note that the maximum dimensions of a voxel dump are in 1 2 jn 1 2 kn 1 Since raw voxel dumps have no header software reading these dumps will require their dimensions as input These are noted in the message log file as the voxel dumps are created EDITOR definition VOX logical unit iovox namelist voxcon filename zv nnnid h where zv is the common prefix to all 3 D voxel dumps nnn id and h are as defined for pixel dumps formats raw one byte per datum HDF four bytes per datum 6 HDF FILES These files contain 3 D data of one or more variabl
107. user should be aware of the index convention used A 3 D array such as the density is denoted d i j k where i is the index for the x1 coordinate j is the index for the x2 coordinate and k is the index for the x3 coordinate The coordinates x1 x2 and x3 are intentionally generic since an attempt has been made to write the code in a covariant fashion In Cartesian cylindrical and spherical polar coordinates x1 x2 x3 corresponds to x y z z r and p 0 respectively In FORTRAN the index which changes the fastest is the first one Thus in triple do loops which manipulate the 3 D arrays it is best to have the outer loop run on k the middle loop run on j and the inner loop run on i If one of the directions is divided into more zones than the other two then it is best that this direction be the 1 direction with index i since it is the inner loop which vectorizes In Cartesian coordinates this can always be arranged The indices strictly follow a right hand rule Thus the array nijb k i is a 2 D array which has k as its first index and i as its second In the list below arrays are given with their indexing to remind the user of the ZEUS 3D convention The user should also be aware of the gridding The computational domain is di vided into in by jn by kn zones In each direction five of these zones are ghost or boundary zones while the remaining zones are active zones where the equations of MHD are solved In
108. utation is resumed on a larger or smaller grid and where the default values for idismn idismx etc were used in the initial run it will be necessary to set idismn idismx etc in the input deck for the restarted run to the extrema of the new grid if the dumps are to extend to the bounds of the new grid Otherwise the dumps will be bound by the old grid parameter description default idisdir nios direction of normal to display slice 0 0 gt no dumps 1 2 3 gt 1 2 3 direction ldis nios level of 2 D display value of 1 2 or istie 2 3 index dtdis physical problem time interval between display 0 0 dumps 0 0 gt no display dumps disvar niov names of variables to be displayed character 2 ZZ 61 Valid names are d e se p pb 2 t v1 2722 V3 yy Ia4 Is 933 3 gt gt gt a m ri gp bl b2 b3 j1 RJA J3 idismn nios bottom i index of display window is idismx nios top i index of display window ie jdismn nios bottom j index of display window js jdismx nios top j index of display window je kdismn nios bottom k index of display window ks kdismx nios top k index of display window ke namelist discon 1 idisdir ldis dtdis disvar idismn 2 idismx jdismn jdismx kdismn kdismx 26 RADCON RADio dump CONtrol read from subroutine NMLSTS This namelist controls the RADIO dumps which are 2 D pixel dumps of q
109. variables can be gleaned from the input deck inzeus Subsection 3 3 Column 1 is reserved for a c to comment out a namelist line Namelist lines commented out will be echoed on the CRT when encountered in the input deck Column 2 is reserved for the leading sentinel The specification of the namelist may start in column 3 and must terminate with a second sentinel Until the second sentinel is found all lines will be interpreted as part of the same namelist All characters appearing after the 72nd column will be ignored including the closing sentinel should it inadvertently be placed there Al 1 IOCON 1 0 CONtrol read from subroutine MSTART This namelist sets the logical units to be used during execution Typically these parameters will not need to be set to anything other than their default values These parameters are not written to the restart dump Therefore all non default values for any of the parameters in this namelist must be set each time the job is resumed parameter description default iotty logical unit for terminal standard output 6 ioplti logical unit for 1 D plots using NCAR graphics 99 ioplt2 logical unit for 2 D plots using NCAR graphics 99 iolog logical unit for message log dump 30 iodmp logical unit for restart dumps 31 iopix logical unit for pixel dumps 32 iousr logical unit for user dumps 33 iotsl logical unit for time slice history ascii dumps 34 iotslp logical unit for time slice histor
110. variables exist at the outer i boundary oib inner j boundary ijb outer j boundary ojb inner k boundary ikb and outer k boundary okb Note that the i boundary variables use indices j k and are declared so long as the EDITOR macro ISYM is not defined Similarly the j boundary variables use indices k i and are declared so long as JSYM is not defined Finally the k boundary variables use indices i j and are declared so long as KSYM is not defined In addition all energy boundary variables eiib1 etc are not declared if ISO is defined and the gravity and magnetic boundary variables gpiib etc bliib1 etc are declared only if GRAV and MHD are defined respectively Note that the boundary variables are used only for regions of the boundary specified as flow in niib j k 3 For all other boundary types discussed in Appendix 2 the boundary values of the flow variables are determined from the values in the neighboring active zones A3 4 SCRATCH VARIABLES As discussed in Subsection 6 1 point 4 there are a multitude of scratch arrays available which can be used to minimize the additional memory required by the user s subroutines These should be used wherever possible especially for 3 D arrays There are 26 1 D arrays dimensioned ijkn and named wald through wzid There are eight 2 D arrays dimensioned ijkn ijkn and named wa2d through wh2d Finally there are six 3 D arrays dimensioned in jn kn and named wa throug
111. w variables on the active portion of the computational grid The flow variables are d density e internal energy per volume v1 1 velocity v2 2 velocity v3 3 velocity bi 1 magnetic field b2 2 magnetic field b3 3 magnetic field emf1 1 emf emf2 2 emf and emf3 3 emf Note that the emf s are used to compute the magnetic fields and their boundary values may be specified by the user Instead however it is often easier just to specify the magnetic field and velocity components along the boundary and then let the code determine the emf s Note that there are two sets of boundary values for most variables and three for the tangential emf s Set all boundaries for every variable whose boundaries are to be set Finally while the boundary values for the gravitational potential gpiib etc may be set here the boundary type igpiib etc is actually set in the namelist grvcon Normally the code will determine the values for gpiib etc from the boundary type specified and so it is not usually necessary or even desirable to set gpiib etc man ually 48 parameter description default niib j k nflo of inner i boundary on sweep j k 2 kiib1 j k first inner i boundary value of variable floor for sweep j k flow in only iib2 j k second inner i boundary value of variable f loor for sweep j k flow in only 1ib3 j k third inner i boundary value for emf s 0 0 for sweep j k flow in
112. wnload a script called zeus32 s from landrew ncsa uiuc edu Establish an ftp connection not telnet using the signon zeus3d and the current password available from the LCA to registered users and cd to the directory afs ncsa projects lca codes zeus3d source The on line version of zeus32 s is much more eloborate than the one shown below for illustrative purposes Running this script will automatically download everything else needed to create the EDITOR executable build the namelist and other libraries and perform the test problem discussed here To customize ZEUS 3D for applications of your own you need to modify the EDITOR changedeck chgzeus which consists of the macro definition file zeus32 mac instructions to set various array sizes and any supplimental source code modules Rerunning the script will then produce the corresponding ZEUS 3D executable The next two subsections describe these modifications in more detail The zeus32 s script is run by typing chmod 700 zeus32 s To make sure it is executable zeus32 s This script performs sequentially the following tasks e retrieves all the files necessary to compile the code e creates a directory called zeus3 2 within the user s current directory to store all the source and object files created during compilation e creates a change deck for the ZEUS 3D code containing preprocessor macros and aliases zeus32 mac next subsection and changes to the source code if any
113. write old even odd numbered dump with new even odd numbered dump id character 2 problem tag appended to filenames aa resfile restart dump filename gt zr00aa igetmn minimum x1 index i to be read from restart dump 1 igetmx maximum x1 index i to be read from restart dump in iputmn i index at which xta igetmn is stored 1 43 iaddz lt 0 gt no new zones are generated i 0 gt call GRIDX1 to redo entire grid gt O0 gt new zone spacing determined from existing grid The variables jgetmn jgetmx jputmn jaddz and kgetmn kgetmx kputmn kaddz are analogous to igetmn igetmx iputmn iaddz for the 2 and 3 directions respectively namelist rescon 1 dtdmp id resfile igetmn igetmx 2 jgetmn jgetmx kgetmn kgetmx iputmn 3 jputmn kputmn iaddz jaddz Kaddz 3 GGEN1 Grid GENerator for x1 read from subroutine GRIDX1 This namelist controls how the grid is determined in the 1 direction All the pa rameters in this namelist as well as those in namelists ggen2 ggen3 and those read by subroutine nmlsts are written to the restart dump These values therefore will be the default values of the parameters for any run resumed from the restart dump The grid can be created all at once or in several blocks Each block requires a separate read of this namelist specifying how that portion of the grid is to be computed The parameter lgrid should be set to true only for th
114. xreplace rp 36 aliases 13 14 19 34 40 choices for aliases 12 14 36 comments 9 11 definitions 11 12 22 26 34 75 error messages 37 38 inedit input deck 15 18 19 20 36 listing files 35 36 merging files 10 17 19 35 36 precompiling files 11 12 19 37 38 setting definitions and aliases 9 10 76 EDITOR macros see zeus32 mac energy units of 34 equation of state 54 isothermal EDITOR definition ISO 7 9 11 32 48 50 53 54 74 75 total energy equation 7 16 48 49 executable see xzeus32 gravity 7 11 12 13 41 53 75 GRAV EDITOR definition 7 9 11 50 53 74 75 GRAVITY EDITOR alias 10 11 13 40 41 grid extension 10 13 55 grid generation 13 14 16 45 49 72 74 HDF dumps 7 12 14 16 23 24 25 29 62 HISTORIAN 18 35 implicit none statement 33 interrupt messages see ZEUS 3D inzeus input deck 9 16 19 20 34 39 42 listing zeus32 see EDITOR loaders NCARGF77 15 18 make UNICOS utility 9 11 16 20 makezeus makefile 15 16 18 20 35 38 merging zeus32 see EDITOR message log file zlnnid 26 35 75 MHD EDITOR macro 9 11 32 34 48 50 53 equations 4 5 multitasking microtasking 7 18 19 33 46 namelist lib 15 17 19 namelists 19 20 22 26 34 42 column reserved for key characters 19 42 comments 18 19 42 comparison between EDITOR and UNICOS versions 19 42 error messages 19 setting rank 2 arrays 19 namelist parameters in ZEUS 3D 16 42 70 76
115. y plot dumps 99 iovox logical unit for voxel dumps 35 iodis logical unit for display dumps 36 iorad logical unit for RADIO dumps 37 WARNING AVOID LOGICAL UNIT 3 APPARENT CONFLICT WITH NCAR NOTE IOTTY MAY BE SET TO 6 TO GET CRT OUTPUT OR O NO OUTPUT namelist iocon 1 iotty lopltl ioplt2 iolog iodmp 2 lopix iousr iotsl iotslp iovox 3 iodis lorad 2 RESCON REStart dump CONtrol read from subroutine MSTART This namelist determines if the job is to be started from initial conditions or if it is to be restarted from a previous run These parameters are not written to the restart dump Therefore all non default values for any of the parameters in this namelist must be set each time the job is resumed The default values are set for starting from initial conditions which occurs when the third and fourth characters in resfile are 00 To restart a job one can usually use the same input deck as was used for the original run with resfile set to the desired restart dump name In addition parameters in the namelist pcon may have to be changed The parameters getm i j k n x are designed so that only a portion of the restart dump may be read and or so that the data may be read into a larger grid That is it is no longer necessary for the field arrays in a restarted job to be dimensioned the same as those in the run which generated the restart dump Example 1 For a straight restart without altering th
116. y a real time interval resets the problem time interval between restart dumps 27 pli creates a 1 D plot at current time dt1 followed by a real time interval resets the problem time interval between 1 D plots p12 creates a 2 D plot at current time dt2 followed by a real time interval resets the problem time interval between 2 D plots pixel creates a pixel dump at current time dtpix followed by a real time interval resets the problem time between pixel dumps voxel creates a voxel dump at current time dtvox followed by a real time interval resets the problem time between voxel dumps usr creates a user dump calls USERDUMP at current time dtusr followed by a real time interval resets the problem time between user dumps hdf creates an HDF dump at current time dth followed by a real time interval resets the problem time between HDF dumps tslice adds a time slice dump at current time to time slice file dttslice followed by a real time interval gt 0 resets the problem time between time slice ascii dumps lt 0 resets the problem time between time slice plot dumps display adds a display dump at current time to display dump file dtdisplay followed by a real time interval resets the problem time between display dumps radio creates a radio dump at current time dtradio followed by a real time interval resets the problem time between radio dumps 28 VI ADDING SOURCE CODE TO ZEUS 3D 6 1 A

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