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CO5BOLD User Manual

1. 2 2 2 00 00 eee ee 53 12 Time step Control sg Kn eee ee Re a ab Ei ee ee eee eG 5 3 13 Input Output Control cow toe Gow Gk ae ee ee ee a aa 5 3 14 Additional Information Obsolete and Test Parameters 5 4 Additional Control and Status Files rhd stop rhd cont and rhd done 6 1 Quickstart How to Run COSBOLDJ 0 0 0 20 02 2000 0008 6 2 Running CO5BOLD on a Machine with Batch System 7 Data Analysis with IDL 7 1 Preparations 12 COSBOLD Data in IDLI a a SERTE Pt Bam EE re Se ee PETA lu 7 2 2 Loading COSBOLD Data Full sta end a0 vb cue Be ew eee Ce poke Mette Bo oe ee ee ee Tt ute oh eae ee Bee ee ee ka A eh eas ee ee ee See BS 1 3 IDL Data Structure 7 4 More IDL routines Glossary 50 51 52 54 57 57 58 60 62 63 68 70 73 76 79 80 80 81 82 82 82 82 82 83 83 83 83 85 86 4 1 INTRODUCTION 1 Introduction CO5BOLD nickname COBOLD is the short form of COnservative COde for the COmputa tion of COmpressible COnvection in a BOx of L Dimensions with 1 2 3 It is used to model solar and stellar surface convection For solar type stars only a small fraction of the stellar surface layers are included in the computational domain In the case of red supergiants the computational box contains the entire star CO5BOLD solves the coupled non linear equations of compressible hydrodynamics in an ex ternal gravity
2. Number density of CO amp u 1 cm 3 rreal rhovb_xmean d 1 1 1 1 1 121 f E13 6 p 4 b 4 amp n Mass flux amp u g cm amp ds 0 0 0 0 0 1 real frhovi3b_xmean d 1 1 1 1 1 121 f E13 6 p 4 b 4 n Momentum x1 flux x3 direction amp u erg cm 3 amp ds 0 0 0 0 0 1 real frhov23b_xmean d 1 1 1 1 1 121 f E13 6 p 4 b 4 n Momentum x2 flux x3 direction amp u erg cm 3 amp ds 0 0 0 0 0 1 real frhov33b_xmean d 1 1 1 1 1 121 f E13 6 p 4 b 4 n Momentum x3 flux x3 direction u erg cm 3 amp ds 0 0 0 0 0 1 real feipb xmean d 1 1 1 1 1 121 f E13 6 p 4 b 4 amp n Enthalpy Flux amp 50 5 CONTROL AND DATA FILES u erg cm 2 s amp ds 0 0 0 0 0 1 real fekb_xmean d 1 1 1 1 1 121 f E13 6 p 4 b 4 amp n Kinetic Energy Flux amp u erg cm 2 s amp ds 0 0 0 0 0 1 real fegb_xmean d 1 1 1 1 1 121 f E13 6 p 4 b 4 amp n Gravitational Energy Flux amp u erg cm 2 s amp ds 0 0 0 0 0 1 real fepb_xmean d 1 1 1 1 1 121 f E13 6 p 4 b 4 amp n Pressure Energy Flux amp u erg cm 2 s amp ds 0 0 0 0 0 1 real fevb_xmean d 1 1 1 1 1 121 f E13 6 p 4 b 4 amp n Viscous Energy Flux amp u erg cm 2 s amp ds 0 0 0 0 0 1 real ferb_xmean d 1 1 1 1 1 121 f E13 6 p 4 b 4 amp n Radiative Energy Flux amp u erg cm 2 s amp ds 0 0 0 0 0 1 label endbox The above list was slightly edited by adding blanks to improve readabi
3. Sections and 5 3 4 respectively e effective temperature control s_inflow teff luminositypervolume C_radHtautop e gravity grav_mode grav mass star e abundances eosfile opafile check the paths 6 If the gravity of the new model and therefore the characteristic time scale signifi cantly deviates from the old one the time specifications controlling the output frequency dtime_out_full dtime_out_mean the total length of the simulation if specified as stel lar time endtime plustime and absolute boundaries specifications for the time step dtime_min dtime_min_stop dtime_max dtime_start have to be scaled Look for pa rameters with units u s see Sections 5 3 12 and 5 3 13 7 The rest of the parameters controls additional details Most of the constants are specified in dimensionless form and keep their value in a class of related simulations The previously used values will probably be reasonable for the new simulation too Of course a complete control of CO5BOLD is only possible after studying of the meaning of the parameters in detail e g by reading the following pages AND unfortunately an accompanying look into the source code itself 5 3 2 Header The header of the parameter file contains information about the file format and contents The description array can be used to specify the goal of the simulation special model characteristics or important parameter changes compared to a pr
4. case a central potential is assumed with an origin at x 0 The stellar mass as well as inner and outer smoothing radius have to be specified real grav In the case of a constant gravity the amount of the acceleration has to specified with real grav f E15 8 b 4 n Gravity u cm s 2 27500 0 Setting this value to zero switches off gravity oh wonder real mass_star In the case of a central the mass in cgs units of the star has to be specified with real mass_star f E15 8 b 4 n Stellar Mass u g 9 94500e 33 real r0_grav To avoid the central singularity in a 1 r potential it is smoothed in the center to give a central potential of 1 r0_grav specified with real r0_grav f E15 8 b 4 n Inner Smoothing Radius u cm 9 45833e 12 This parameter should always be non zero for a central potential real ri_grav The density in an atmosphere in hydrostatic equilibrium can decline to very low values To artificial enlarge the pressure and density scale height in the outer layers of the star the corners of the box the gravity can be reduced by defining the potential at infinity to be 1 ri_grav specified with real rl grav f E15 8 b 4 n 0uter Smoothing Radius u cm amp c0 0 0 Not used 11 35000e 13 Setting this parameter to zero gives the usual 1 r behavior of the potential in the outer layers but also chooses another smoothing formula in the central part where real r0_grav is relevant But a value somewh
5. 0 5 time centered 1 0 fully implicit 0 0 Allowed values are o 0 0 Fully explicit radiation transport possible with all modules o 0 0 lt C lt 1 0 Partly implicit radiation transport o 0 5 Radiation transport time centered o 1 0 Fully implicit radiation transport Values outside this range do not have much meaning The implicit transport does not work efficiently yet It does not yield significantly larger time steps than possible with a sequence of purely explicit sub time steps Additionally it turns out that the hydrodynamics runs into trouble if a too large time step still well within the Courant condition is requested e real c_raditereps With activated implicit radiation transport LHDrad module only the requested convergence accuracy of the iteration can be set e g with real c_raditereps f E15 8 b 4 amp n Relative accuracy for radiation iteration u 1 amp c0O Typical value 1 0E 03 2 0E 03 e real c_raditerstep With activated implicit radiation transport LHDrad module only the step size of the iter ation can be restricted with e g real c_raditerstep f E15 8 b 4 amp n Step size of radiation iteration u 1 2 c0O Typical values 0 7 0 81 1 0 Allowed values are o 0 0 lt 1 0 Restricted step size o 1 0 No restriction standard step size o gt 1 0 Extra large steps This value has to be chosen carefully to get optimal performance Is the step size too small the c
6. 0PT Olimit 0 General optimization e IPA plimit 5500 Even more optimization 3 8 10 Sun SunFire CO5BOLD has been used on the SunFire machines firel fire2 and fire3 in Uppsala with compiler version Sun WorkShop 6 update 2 Fortran 95 6 2 2001 05 15 an later An older version was not able to compile CO5BOLD properly Information about Fortran and the Sun compiler can be found on the Sun Forte pas under documentation Important switches are e openmp Enable OpenMP e fast xvector yes no General optimization On the Sun the fast option switches on more or less all optimization features of the compiler That works reasonable well However during the compilation of gasinter_routines f90 and only there the switch xvector no is requiered e inline Optimization Routines that should be inlined file rhd_hyd_module F90 rhd_hyd_avg rhd_hyd_upwind rhd hyd pred0 rhd hyd predm rhd_hyd_predp rhd_hyd_alpha rhd hyd constanteg rhd hyd minmodeg rhd hyd minmod rhd hyd vanleereg rhd hyd vanleer rhd hyd superbeeeg rhd hyd superbee rhd hyd ppeg rhd hyd pp rhd hyd hdflux file rhd Ihdrad module F90 rhd rad3d raylhd rhd rad3d solve rhd rad3d solveeg file rhd shortrad module F90 rhd shortrad operator rhd shortrad dtauop e Drhd shortrad formal 101 1 Optimization split loop for exp dtau computation into two loops See Sect e Drhd shortrad dirl 101 1 Optimization Transpose array
7. Directories amp Paths All UIO routines are located in subdirectories of a common directory called e g uio which also contains a Readme file The subdirectories and their contents are bin shell scripts uiolook uiocat uioinfo 90 Fortran90 source codes object files executables idl IDL routines man man1 manual pages for shell scripts uiolook uiocat uioinfo tex Old description files in ATX the most recent version is part of this document To use the UNIX scripts and the makefile you need a global system variable UIOPATH pointing to this directory The path to the shell scripts and to the man pages should be added to your shell path variables e g in one of the login scripts C shell cshrc uio setenv UIOPATH HOME uio setenv PATH PATH UIOPATH bin setenv MANPATH MANPATH UIOPATH man xxxk Korn shell kshrc uio UIOPATH HOME uio export UIOPATH PATH PATH SUIOPATH bin export PATH MANPATH MANPATH UIOPATH man export MANPATH xxx 4 5 Fortran90 4 5 1 Files The Fortran UIO package is a collection of Fortran90 modules and programs described in Table 8 The file uio_base_module f90 contains the basic set of modules see Table 9 The files uio_mac _module f90 contain possibly machine dependent routines collected in the module uio_mac_module It comes in various flavors The machine independent version is uio mac module f90
8. 1 The program fragment with the tau coupling operator is included No inlining necessary e rhd_shortrad_formal_101 in rhd_shortrad_module F90 rhd short characteristics radiation formal loop 01 Category performance enhancement Select version of loop splitting for exp dtau computation Values o 0 default dtauhalf exp_mdtauhalf exp12t_mdtauhalf are computed in single loop o 1 dtauhalf exp_mdtauhalf exp12t_mdtauhalf are computed in separate loops This prevents the SUN1 machine Sunfire Solaris Forte 6 2 from doing some perfor mance degrading optimization e rhd shortrad dirl 101 in rhd shortrad module F90 rhd short characteristics radiation direction 1 loop 01 Category performance enhancement Choose routine version for rays in x1 direction Values o 0 default Use routine with permuted indices for rays in x1 direction In this case the innermost loop index is the third array index The transposition of arrays is not needed but some machines e g SUN1 do not like this index arrangement o 1 Transpose arrays and use routine rhd_shortrad_dir3 for rays in xl direction The extra step for the transposition of some arrays and the reverse procedure needs some time But now the routine with the optimum index ordering can be used e rhd_shortrad_dir_102 in rhd_shortrad_module F90 rhd short characteristics radiation direction loop 02 Category performance enhancement Determine position
9. 63 63 63 63 63 63 f E13 6 p 4 b 4 n Velocity 1 u cm s real v2 d 63 63 63 63 63 63 f E13 6 p 4 b 4 n Velocity 2 u cm s real v3 d 63 63 63 63 63 63 f E13 6 p 4 b 4 n Velocity 3 u cm s label endbox label enddataset date 02 01 2002 16 17 43 322 The UIO format is described in some detail in Sect Each entry has a type e g label real character an identifier e g box time description and ad ditional information about array size e g d 63 63 63 63 63 63 data format e g f E13 6 p 4 b 4 and properties of the quantity e g n Density u g cm 3 Each start rhd sta or final rhd end model file has a structure as shown above The rhd full file usually contains a sequence of these data sets which of course can also be used as start model of a simulation 5 2 File with Additional Data rhd mean File A rhd mean file contains derived data averaged fluxes other averaged quantities surface intensities in addition to the complete data sets in rhd full files It has more entries than a full model file However they are much smaller Therefore one can afford a higher output sampling rate Its format is usually Fortran unformatted binary 5 2 1 Organization of rhd mean File A mean file usually consists of several datasets The overall structure is fileform uio form unformatted convert ieee_4 character
10. EOSPATH f 90 export EOSSRCPATH Opacity OPTAPATH FORTRANDISK opa opta export OPTAPATH OPTASRCPATH OPTAPATH export OPTASRCPATH hydrostatic HSTPATH FORTRANDISK hd qf15 export HSTPATH HSTSRCPATH HSTPATH export HSTSRCPATH rad RADPATH FORTRANDISK rad hdrad export RADPATH RADSRCPATH RADPATH export RADSRCPATH RHD RHDPATH FORTRANDISK hd rhd export RHDPATH RHDSRCPATH RHDPATH export RHDSRCPATH RHDB RHDBPATH FORTRANDISK hd rhdb export RHDBPATH RHDBSRCPATH RHDBPATH export RHDBSRCPATH HDW HDWPATH FORTRANDISK hd hdw export HDWPATH HDWSRCPATH HDWPATH export HDWSRCPATH DUST DUSTPATH FORTRANDISK hd dust export DUSTPATH DUSTSRCPATH DUSTPATH export DUSTSRCPATH MHD MHDPATH FORTRANDISK hd mhd export MHDPATH MHDSRCPATH MHDPATH export MHDSRCPATH mean MEANPATH FORTRANDISK hd mean export MEANPATH MEANSRCPATH MEANPATH export MEANSRCPATH 11 12 3 PROGRAM FILES INSTALLATION COMPILATION Architecture dependent directories for object file and executables TIMEEXEPATH TIMEPATH MAC export TIMEEXEPATH CONEXEPATH CONPATH MAC export CONEXEPATH UIOEXEPATH ULOSRCPATH MAC export UIOEXEPATH STREXEPATH STRPATH MAC export STREXEPATH MATEXEPATH MATSRCPATH MAC export MATEXEPATH GASEXEPATH
11. GASPATH MAC export GASEXEPATH EOSEXEPATH EOSSRCPATH MAC export EOSEXEPATH OPTAEXEPATH OPTAPATH MAC export OPTAEXEPATH HSTEXEPATH HSTPATH MAC export HSTEXEPATH RADEXEPATH RADPATH MAC export RADEXEPATH RHDEXEPATH RHDPATH MAC export RHDEXEPATH RHDBEXEPATH RHDBPATH MAC export RHDBEXEPATH HDWEXEPATH HDWPATH MAC export HDWEXEPATH DUSTEXEPATH DUSTPATH MAC export DUSTEXEPATH MHDEXEPATH MHDPATH MAC export MHDEXEPATH MEANEXEPATH MEANPATH MAC export MEANEXEPATH This script can be executed with HOME bin setarcdeppaths sh This line can be put e g into the bashrc file Some lines can be edited to account for individual choices and the target machine With FORTRANDISK HOME for export FORTRANDISK the master directory is specified With UIOMAC uio_mac_sun_module export UIOMAC RHDMAC rhd_mac_sun_module export RHDMAC you specify some machine dependent modules The sun modules work for most machines e g for Linux PCs With MAC 1inux you specify the name of the subdirectories with the makefiles The other lines only have to be edited if you want to organize the directories in a completely different way In this case you have to adapt the configure script too 3 5 Fortran Files Table 3 shows a list of all source files necessary to compile CO5BOLD Table 4 shows the former list 3 6 Configure Script The configure script produces a Makefile It
12. Structure lt 8274184 gt 16 tags length 78403900 refs 2 v3 TYPE STRING BOX_ID STRING DIMENSION LONG TIME FLOAT ITIME LONG XC1 FLOAT XC2 FLOAT XC3 FLOAT XB1 FLOAT XB2 FLOAT XB3 FLOAT RHO FLOAT El FLOAT V1 FLOAT V2 FLOAT V3 FLOAT uio Ig Array 2 3 10050 1 64088 Array 140 1 1 Array 1 140 1 Array 1 1 200 Array 141 1 1 1 Array 1 141 1 Array 1 1 201 Array 140 140 200 Array 140 140 200 Array 140 140 200 Array 140 140 200 Array 140 140 200 Spatial axes XC1 XC2 XC3 XB1 XB2 XB3 The indices stand for 1 x 2 y 3 z C for the grid cell centre B for the boundaries Most of the quantities are defined for the cell centres In case of doubt this can be found out by checking the array dimensions The substructure FUL EOS contains important quantities like the temperature T gas pressure P entropy S Structure lt 826a03c gt 6 tags length 109760000 refs 2 P FLOAT DPDRHO FLOAT DPDEI FLOAT T FLOAT DTDEI FLOAT S FLOAT Array 140 140 200 Array 140 140 200 Array 140 140 200 Array 140 140 200 Array 140 140 200 Array 140 140 200 The substructure FUL OPA only contains the opacity KAPPA Structure lt 826a5b4 gt 1 tags length 15680000 refs 2 KAPPA FLOAT Array 140 140 200 7 4 More IDL routines 85 7 4 More IDL routines In the directory IDL rhdpro a lot of useful routines can be found which can be used for fur
13. They were useful for the easy reading of not too complex data files By now they are replaced by the routines uio_struct_rd and uio_dataset_rd see see next Section and Sect 7 The old routines allow the opening 4 7 IDL UIO Routines 43 uio_data mode open filename model dat uio_data mode open filename model txt uio_data mode open filename model dat family mod1 uio_data mode open filename model txt family mod2 examination uio_data mode content uio_data mode files reading uio_data mode read value rho rho uio_data value temp temp uio_data value p p filename model dat uio_data value p p family mod1l plot_oi uio_d p uio_d t and closing uio_data mode close filename model dat uio_data mode close filename model txt uio_data mode close family mod2 uio_data mode allclose of UIO files 4 7 3 Reading Data with uio dataset rd pro or uio datasetlist rd pro For a detailed description of how to handle UIO files in IDL see Sect With the new IDL routines uio_struct_rd pro uio_dataset_rd pro and uio_datasetlist_rd pro files are not read entry by entry anymore but in larger blocks or data sets With uio_struct_rd all entries in a file are read and put into an IDL structure variable This is appropriate for the CO5BOLD paramete
14. Use standard method to compute the Roe states o defined Use non standard method to compute the Roe states rhd_roeid_slope_101 in rhd_slope_module F90 rhd roe 1 dimension slope loop 01 Category selection of approximation By setting this switch an additional slope reduction during the state reconstruction process within the Roe solver is activated This can improve the stability without significantly reducing the effective numerical resolution It is not fully tested yet for test purposes only do not activate unless you know exactly what you do Values o undefined default Use standard method to compute the Roe states o defined Use non standard method to compute the Roe states rhd_bound_t01 in rhd_hyd_module F90 rhd bound timing 01 Category additional output Produce timing information for inner boundary routine central potential or lower and upper boundary routines constant gravitation It can be used together with OpenMP Values 20 3 PROGRAM FILES INSTALLATION COMPILATION o undefined default no timing information o defined call subroutines to measure elapsed time e rhd_roeid_flux_t0l1 in rhd_hyd_module F90 rhd roe 1 dimension flux timing 01 Category additional output Produce timing information for the routine which computes the Roe fluxes It should not be used in conjunction with OpenMP Values o undefined default no timing information o de
15. are o lt 0 0 No output to this file o 0 0 Output at every time step o gt 0 0 Output to mean file approximately every dtime_out_mean seconds 74 5 CONTROL AND DATA FILES Because the size of one mean dataset is much smaller than one full dataset it is possible to request a higher sampling rate without using too much disk space character infile_start The filename of the initial model is specified e g with character infile_start f A80 b 80 n File name of start model rhd sta Default is rhd sta for a parameter file used within a batch system Typical filenames are st35gm04n01_01 sta or gt57g44n20dz end character outfile_end The file name for the final model can be specified with e g character outfile end f A80 b 80 n 0utput file name rhd end The default is rhd end Leaving it empty means that no final model is written This of course inhibits follow up simulations but can be useful to save time and disk space for some tests character outfile_full The name of the file for the output of additional full models at regular intervals see Sect 5 1 can be given with e g character outfile full f A80 b 80 n Output file name rhd full Leaving it empty means that no file of this type is written character outfile_mean The name of the file for the output of additional information average stratification mean fluxes surface intensities at regular intervals see Sect 5 2 can be specified wi
16. boundary is far away from the photosphere of a red supergiant the value can be even smaller On the other hand if the boundary lies somewhere within the solar chromosphere even values above 1 0 might be reasonable real c_hptopfactor In the case of a transmitting upper or outer boundary the density stratification outside the model has to be extrapolated properly Assumptions about this density affects the amount of mass flowing into the model For the extrapolation it is assumed that the density scale H scales with the pressure scale height Hp as H Hp c_hptopfactor real c_hptopfactor f E15 8 b 4 amp n Correction factor for surface pressure scale height u 1 0 8 Possible values are o C lt 0 0 No effect actually a value of 1 0 is chosen o 0 0 lt C lt 1 0 The density scale height is enlarged to account for possible effects of turbulent pressure on the scale height The density decays less rapidly with height than in an isothermal hydrostatic stratification o C 1 0 Density scale height is pressure scale height o C gt 1 0 Density scale height is smaller than pressure scale height Not really useful 5 3 Parameter File rhd par File 57 e real c_radhtautop The MSrad radiation transport module needs the specification of the scale height of the optical depth at the upper boundary e g with real c_radhtautop f E15 8 b 4 n Scale height of optical depth at top u cm 60 0E 05 e real rho_min During lo
17. controlled with e g real c_schange f E15 8 b 4 amp n Rate of entropy change for open lower boundary u 1 0 3 Guide values are o 1 0 fast adjustment 56 5 CONTROL AND DATA FILES o 0 3 typical value o 0 1 slow adjustment o lt 0 0 not allowed e real c_pchange The inoutflow boundary condition not only controls entropy and velocity but also the pressure in the bottom layers It is locally adjusted towards the global average to damp out possible instabilities The adjustment rate can be specified e g with real c_pchange f E15 8 b 4 amp n Rate of pressure change for open lower boundary u 1 1 0 real c_tchange In the case of a transmitting upper or outer boundary the temperature of the material streaming into the model is adjusted with a rate given e g by real c_tchange f E15 8 b 4 amp n Rate of temperature change for open upper boundary u 1 0 3 real c_tsurf In the case of a transmitting upper or outer boundary the temperature of the material streaming into the model is adjusted towards a temperature teff c_tsurf This temper ature can be specified as fraction of the effective temperature e g with real c_tsurf f E15 8 b 4 n Temperature factor for open upper boundary u 1 0 62 The value depends on where the outer boundary is located relative to the photosphere If the boundary lies at a point where the solar photospheric minimum temperature is located it can be fairly small If the
18. field together with non local frequency dependent radiation transport Operator splitting is applied to solve the equations of hydrodynamics including gravity the radiative energy transfer with a long characteristics or a short characteristics ray scheme and possibly additional 3D turbulent diffusion in individual sub steps The 3D hydrodynamics step is fur ther simplified with directional splitting The 1D sub steps are performed with a Roe solver accounting for an external gravity field and an arbitrary equation of state from a table The radiation transport is computed with either one of three modules e MSrad module It uses long characteristics The lateral boundaries have to be periodic Top and bottom can be closed or open solar module e LHDrad module It uses long characteristics and is restricted to an equidistant grid and open boundaries at all surfaces old supergiant module e SHORTrad module It uses short characteristics and is restricted to an equidistant grid and open boundaries at all surfaces new supergiant module There are preliminary versions of moduls for the formation and advection of dust and the transport of magnetic fields available CO5BOLD is written in Fortran90 The parallelization is done with OpenMP directives To get a brief overview you might want to look into the Quickstart Sections How to Compile CO5BOLD Sect B4 Introduction to UIO Sect 4 1 How to Ma
19. file_id f A8 b 8 n File identification character description d 1 1 f A14 p 2 b 14 n File description character history d 1 20 f A80 p 1 b 80 n File history character version f A80 b 80 n Program version label dataset n RHD model label enddataset label dataset n RHD model label enddataset Each dataset has the following structure for a supergiant simulation 5 2 File with Additional Data rhd mean File 47 label dataset n RHD model date 25 05 2001 09 41 29 405 label box date 25 05 2001 09 41 29 408 character box_id f A80 b 80 n Block identification rad label endbox label box date 25 05 2001 09 41 29 983 character box_id f A2 b 2 n Block identification z label endbox label box date 25 05 2001 09 41 30 078 character box_id f A2 b 2 n Block identification z2 label endbox label box date 25 05 2001 09 41 30 170 character box_id f A2 b 2 n Block identification z3 label endbox label box date 25 05 2001 09 41 30 260 character box id f A1 b 1 n Block identification r label endbox label box date 25 05 2001 09 41 30 359 character box_id f A80 b 80 n Block identification Zz label endbox label enddataset date 25 05 2001 09 41 30 489 There a six sub blocks delimited with box and endbox labels They contain surface intensity and flux arrays rad averages in the 23 plane z1 the 13 plane z2
20. intervals can be specified with e g character outfile_fine f A80 b 80 n 0utput file name rhd fine Leaving it empty means that no file of this type is written Specifying it means the same yet character outform_fine The format see Sect 4 3 1 of the files with frequent output can be chosen e g with character outform_fine f A80 b 80 n 0utput file format amp c0 formatted unformatted unformatted Allowed values are o unformatted default fast compact possibly machine dependent output strongly recommended o formatted slow machine independent output big files This parameter can be specified but there is no corresponding output file in CO5BOLD yet character outconv_fine The conversion type see Sect 4 3 1 of the files with frequent output can be specified e g with character outconv_fine f A80 b 80 n Dutput file conversion amp c0 ieee_4 ieee_8 crayxmp_8 native ieee_4 The allowed values depend on the machine Leaving this field empty means that the default is chosen that is build into the local UIO module If the type ieee_4 is supported which is always the case so far it should be chosen This parameter can be specified but there is no corresponding output file in CO5BOLD yet 5 4 Additional Control and Status Files rhd stop rhd cont and rhd done 79 5 4 Additional Control and Status Files rhd stop rhd cont and rhd done Before each time step CO5BOLD checks in the working dire
21. is controlled by environment variables see below It tries to use reasonable default values if they are not set properly In the script the machine type is determined with uname m According to the control variables and the machine architecture the compiler name and its compiler flags are composed These are written into the header of a Makefile which is produced in the end An existing Makefile is appended to Makefile_old Additionally the compilation command is written into the file gt compiler_flags info 3 6 Configure Script 13 File and path Abb Description hd rhd rhd F90 RHD main program hd rhd rhd_hyd_module F90 RHD hydrodynamics routines hd rhd rhd_lhdrad_module F90 RHD radiative transfer routines long characteristics supergiant case hd rhd rhd_shortrad_module F90 RHD radiative transfer routines short characteristics supergiant case hd rhd rhd_shortrad_dtauop01 f90 RHD short characteristics tau coupling hd rhd rhd_shortrad_dtauop02 f90 RHD short characteristics tau coupling hd rhd rhd shortrad operator00 f90 RHD short characteristics operator hd rhd rhd shortrad operator08 f90 RHD short characteristics operator hd rhd rhd_vis_module F90 RHD tensor viscosity routines rad hdrad rhd_rad_module f90 RAD interface for Matthias radiation routine rad hdrad MSrad3D F90 RAD Matthias radiation transport routines long characteristics periodic sides hd dust rhd_dust_module F90 DUST dust molecule form
22. memory but result in additional overhead due to frequent subroutine calls Bigger and less chunks are to be preferred for vector machines and processors with large caches Very rough guide values may be 60 5 CONTROL AND DATA FILES o 2500 Pentium III processor o 20000 RISC processor o 100000 Vector machine Note For simulations with activated OpenMP on a parallel machine the chunk size has to be made small enough to allow at least as many chunks as processors available This is particularly important for models with a small number of grid points e g 2D models e real c_visdrag This viscosity parameter controls the drag force which is if requested applied inside the hydrodynamics routines themselves It does not act on velocity gradients as usual viscosity but applies a force proportional to the velocity itself but with the opposite sign The amount can be specified e g with real c_visdrag f E15 8 b 4 amp n Drag viscosity parameter u 1 0 001 The value gives the fraction the velocity is reduced per time step Therefore reasonable values lie between 0 0 and 1 0 In almost every case the drag forces will be switched off c_visdrag 0 0 If e g strong pulsation have to be damped in the initial phase of a simulation a value around 0 001 0 01 seems appropriate e real c_visbound An additional drag force can be added locally in inflow cells in the outer layer when the transmitting boundary condition is chosen The value
23. modified slope reduction of source function o 6 default case distinction with masks weights 0 0 or 1 0 modified slope reduction of source function o 8 test version rhd_shortrad_operator_102 in rhd_shortrad_module F90 rhd short characteristics radiation operator loop 02 Category performance enhancement Select the way the short characteristics operator is accessed Values o 0 default The routine with the short characteristics operator is called within a loop and should be inlined o 1 The program fragment with the short characteristics operator is included No inlining necessary rhd_shortrad_dtauop_101 in rhd_shortrad_module F90 rhd short characteristics radiation delta tau operator loop 01 Category performance enhancement Choose type of short characteristics tau coupling operator Values o 1 case distinction with if then else construct default if rhd shortrad operator 101 1 3 5 o 2 case distinction with masks weights 0 0 or 1 0 default if rhd shortrad operator 101 2 4 6 3 7 Compiler Macros 23 e rhd_shortrad_dtauop_102 in rhd_shortrad_module F90 rhd short characteristics radiation delta tau operator loop 02 Category performance enhancement Select the way the operator for the tau coupling short characteristics module is accessed Values o 0 default The routine with the tau coupling operator is called within a loop and should be inlined o
24. module The others have reasonable default values To find the combination with the optimal performance you should look into Sect The macros are sorted into different categories Some activate a certain feature like a radiation transport module or the dust module They have to be selected by the user typically via environment variables and the configure script see Sect 3 6 each time the code is compiled for a certain purpose Other macros are meant to improve the performance by offering the choice between e g different loop structures or case distinctions These macros are set by the configure script to the best knowledge of the author s Ideally they should be checked and modified if necessary each time CO5BOLD is compiled on a new machine It should be save to modify these settings the results between runs with different settings should only differ slightly due to round off errors Some macros select between different numerical approximations A change here should be visible in a more or less drastic change of the results of a simulation Usually the default values should be accepted Other settings typically only exist to allow the comparison with older versions of CO5BOLD or because there are new developments going on which have not yet managed to become the default 3 7 Compiler Macros 17 A couple of macros only activate timing measurements and result in additional output Some of them are not thread save und should only be act
25. n side boundary conditions amp cO closed transmitting periodic transmitting Possible values are o reflective closed wall no gravity no radiation o constant open boundary with constant extrapolation of all values no gravity no radiation o closed closedtop closed wall can handle gravity open for outward radiation o closedbottom closed wall handles gravity radiation in diffusion approximation o periodic periodic boundaries for hydrodynamics and radiation o transmitting transmitting boundary for hydro and outward radiation Any of these values can be specified But in fact not all of them are recognized by all modules Therefore some parameters are for test purposes e g shock calculations only In simulations of a solar like star with the MSrad radiation transport module the side bound aries have to be periodic In simulations of a red supergiant all boundaries including the sides will typically be transmitting As an alternative closed boundaries can be chosen in this case e character top_bound The boundary condition at the top of the model is given by for instance character top_bound f A80 b 80 n top boundary conditions transmitting Possible values are o reflective closed wall no gravity no radiation o constant open boundary with constant extrapolation of all values no gravity no radiation o closed closedtop closed wall can handle gravity open for outward radiation o peri
26. of PARALLEL statement relative to outer loop in rhd_shortrad_dirX Both settings give the same results but might show a different performance on a specific machine Values o 0 default PARALLEL statement inside of outer loop o 1 PARALLEL statement outside of outer loop e rhd_shortrad_lambda_101 in rhd_shortrad_module F90 rhd short characteristics radiation lambda loop 01 Category feature activation Handling of extra arrays to allow partially implicit Lambda iteration Values o 0 default Only fully implicit Lambda iteration allowed or fully explicit treatment o 1 Also partially implicit Lambda iteration allowed e rhd_shortrad_formal_t01 in rhd_shortrad_module F90 rhd short characteristics radiation formal timing 01 Category additional output 24 3 8 3 PROGRAM FILES INSTALLATION COMPILATION Produce timing information for routine which gives the formal solution of the radiation transport equation with the help of short characteristics It can be used together with OpenMP and should cause no noticeable performance loss Values o undefined default no timing information o defined call subroutines to measure elapsed time rhd_shortrad_step_t01 in rhd_shortrad_module F90 rhd short characteristics radiation step timing 01 Category additional output Produce timing information for main short characteristics routine It can be used together with OpenMP and should cause no noticeable perfor
27. one big loop is to be preferred Values o undefined default One big loop o defined Two smaller loops rhd_rad3d_r02 in rhd_1hdrad_module F90 rhd radiation 3 dimensions radiation 02 Category test Module rhd_lhdrad_module contains a routine for the handling of periodic boundaries It is in an experimental state and is deactivated by default Values o undefined default Skip routine rhd_rad3d_dirper during compilation o defined Compile routine rhd_rad3d_dirper rhd_rad3d_solve_t01 in rhd_1hdrad_module F90 rhd radiation 3 dimensions solve timing 01 Category additional output Produce timing information for the routines which solves the 1D radiation transport equa tion along single ray This routine is called very frequently The timing measurement might slow it down somewhat It should not be used in conjunction with OpenMP Values o undefined default no timing information o defined call subroutines to measure elapsed time rhd_rad3d_dir_t01 in rhd_1hdrad_module F90 rhd radiation 3 dimensions direction timing 01 Category additional output Produce timing information for the routines which solves the radiation transport equation for one direction field The timing measurement are called very frequently and might slow down the code It should not be used in conjunction with OpenMP Values 22 3 PROGRAM FILES INSTALLATION COMPILATION o undefined default no timing informat
28. parameters the start model and the type and amount of output can be specified Parameters with the suffix _start describe the initial model these with suffix _end the corresponding final model Additional data can be written into the file described by the parameters with suffix _full full 2D 3D model dumps huge see Sect 5 1 or into the file described by the parameters with suffix _mean additional information see Sect B 2 real dtime_out_full The interval between datasets in the full file can be set e g with real dtime_out_full f E15 8 b 4 n Dutput time step u s amp c0 dtime out full lt 0 0 gt no output amp c1 dtime out full 0 0 gt output every time step 2 0E 06 Allowed values are o lt 0 0 No output to this file o 0 0 Output at every time step Attention This can produce HUGE files in no time o gt 0 0 Output to full file approximately every dtime out full seconds Some examples The classical value for this output for simulations of solar granulation is 20sec To save memory this can be increased to 30sec But in this case chromospheric shocks are very badly resolved To cover them properly a sampling rate of 10sec or below is needed real dtime_out_mean The interval between datasets in the mean file can be set e g with real dtime out mean f E15 8 b 4 n Dutput time step u s amp c0 dtime out mean 0 0 gt no output 0 5E 06 Allowed values
29. real c_vissmagorinsky and real c_visartificial But the parameter can be used to tentatively switch off the off diagonal terms completely or to change its importance compared to the other terms e real c_vistensordiv The factor in the stress tensor in front of of the divergence terms also on the diagonal can be set with e g real c_vistensordiv f E15 8 b 4 amp n Divergence factor for viscous stress tensor u 1 amp c0 typically 1 3 0 0 62 5 CONTROL AND DATA FILES This is not really parameter one would try to adjust The total amount of viscosity should be controlled with real c_vissmagorinsky and real c_visartificial But the parameter can be used to switch off the divergence terms completely or to change its importance compared to the other terms These divergence terms can be used to reduce the effect of the tensor viscosity in the case of isotropic compression But this reduction c_vistensordiv 0 333333 in 3D c_vistensordiv 0 5 in 2D is usually switched off integer n_viscellsperchunk The number of cells per box or chunk treated by the tensor viscosity scheme at one call and by one thread can be set e g with integer n_viscellsperchunk f I9 b 4 amp n Number of cells per viscosity chunk amp cO0 0 gt old chopping amp c0 12000 reasonable value 20000 It can be adjusted to improve cache efficiency and to modify the work load distribu tion onto the threads in case of p
30. rhd box module f90 RHD box handling routines hd rhd rhd dat module f90 RHD handling of additional data averages hd rhd rhd mean module f90 RHD averaging routines hd rhd rhd_io_module f90 RHD input output routines hd rhd rhd mac cray module f90 RHD machine dependent routines CRAY hd rhd rhd mac default module f90 RHD machine dependent routines default hd rhd rhd mac sun module f90 RHD machine dependent routines Sun hd rhd rhd sub module f90 RHD additional routines hd rhd rhd hyd module F90 RHD hydrodynamics routines hd rhd rhd_vis_module F90 RHD tensor viscosity routines hd rhd rhd_rad_module f90 RHD interface for Matthias radiation routine hd rhd rhd_lhdrad_module F90 RHD radiative transfer routines long characteristics supergiant case hd rhd rhd_shortrad_module F90 RHD radiative transfer routines short characteristics supergiant case hd rhd rhd F90 RHD main program Table 4 For historical reasons list of all old modules the table shows the file name with part of its path the shortcut for the directory and its description 3 6 Configure Script 15 in a form ready to be included in a Fortran program The environment variables that control the script are F90_COMPILER Fortran compiler o a machine dependent default is chosen individually for each architecture o f90 general default F90_PREFLAGS Compiler flags to be put at the beginning of the list Usually the list of compiler flags produced by the con
31. stop I control file to force controlled stop of simulation rhd cont I control file to force continuation after stop data eos I data UIO tabulated equation of state data opta I data tabulated opacities rhd sta I data UIO start model e g end model of previous run rhd done O status exit status written if run was successful rhd end O data UIO end model rhd full O data UIO sequence of 2D or 3D snapshots large rhd mean O data UIO derived data mean flux intensity rhd out O data text human readable text output Table 11 List of all control and data files 5 1 Model Files rhd sta rhd end rhd full Files If the UIO scripts Sect 4 6 are properly installed you can view the contents more precisely the headers of the data entries of an UIO file with uiolook filename e g uiolook st35gm04n05_03 end gives the output slightly edited fileform uio form unformatted convert ieee_4 version 0 1 2000 11 26 amp date 02 01 2002 16 17 26 036 system craSHi machine craSHi osrelease 10 0 0 6 amp osversion U0K 4 hardware CRAY SV1 language Fortran90 program RHD character file_id f A8 b 8 n File identification character description d 1 1 f A24 p 1 b 24 n File description character history d 1 20 f A80 p 1 b 80 n File history character version f A80 b 80 n Program version label dataset n RHD model date 02 01 2002 16 17 26 043 character dataset_id f A10 b 10 n Type of box hierar
32. the 12 plane z3 and over spherical shells r and a 2D slice through the model z 5 2 2 Contents of Individual rhd mean File Entry An individual box inside a dataset entry in a mean file can have e g the following contents describing horizontal averages in a plane parallel model With uiolook chro2D03c008_01 mean less you get this and more label box date 06 11 2002 17 58 05 533 character box_id f A2 b 2 n Block identification integer dimension d 1 2 1 3 f I7 p 6 b 4 real time f E13 6 b 4 n time amp u s integer itime f 110 b 4 n time step number amp u 1 real xc1 d 1 1 1 1 1 1 f E13 6 p 4 b 4 n xi coordinates of cell centers amp u cm amp 48 real real real real real real real real real real real real real real real real real real real real ds 0 0 1 1 0 1 xc2 d 1 1 1 1 f E13 6 p 4 b 4 ds 0 xc3 d 1 1 120 f E13 6 p 4 b 4 he po o po ds 0 xb1 d 1 0 1 f E13 6 p 4 b 4 RO ke v RO N PR ds 0 xb2 d 1 Rh pe RO N e s 0 1 1 1 f E13 6 p 4 b 4 ds 0 1 0 1 xb3 d 1 1 1 1 0 1 1 121 f E13 6 p 4 b 4 gt gt ds 0 1 0 1 0 1 rho_xmean d 1 1 1 1 1 120 f E13 6 p 4 b vi_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 v2_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 v3_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 vi_xmean2 d 1 1 1 1 1 120 f E13 6 p 4 b v2_
33. variable of general type i e it may be a scalar integer value or a 1D character array or a 3D real array together with some routines for the basic handling of 4 5 Fortran90 37 routine purpose uio_getenv Get information about environment uio mkcvls Make list with possible conversion types uiouopen Open file with special handling for conversion type uio_uclose Close file with special handling for conversion type Table 10 Contents of uio mac_module the variables I O in UIO format construction and modification of variables The module uio_varfile_module f90 contains a type definition for a file built of UIO flexible variables together with routines for the handling of these files 4 5 2 Use of UIO Modules in Fortran90 To make the UIO routines available in a Fortran program the appropriate modules have to be specified in a USE statement At maximum five modules play a role The uio_bulk_module contains the main part of the UIO routines and also uses the relevant sub modules Instead of uio_bulk_module the module uio_table_module is used if the UIO table routines are needed The modules uio_siz_module and uio_nam_module contain specifications about the size of some arrays and the length of strings and the names of types and keywords respectively The module uio_filedef_module contains some definitions in addition to the basic UIO standard as e g the label names which delimit a data set label dataset and lab
34. which can be used for first tests but does not provide all possible features Therefore it should be discarded afterwards and replaced by a version more suitable for the platform in use The 36 4 UIO DATA FORMAT File contents uio_base_module f90 Collection of basic modules uio mac module f90 Possibly machine dependent routines Standard version all machines uio mac ieee module f90 Machine dependent routines IEEE format uio_mac_sun_module f90 Machine dependent routines Sun SGI Linux PGI uio mac intel module f90 Machine dependent routines Linux Intel uio mac crayts module f90 Machine dependent routines CRAY uio mac crayxmp module f90 Machine dependent routines CRAY uio mac decalpha module f90 Machine dependent routines alpha uio bulk module f90 Main part of UIO routines uio filedef module f90 Standard file descriptors and labels uio table module f90 Table manipulation routines uio var module f90 definition and handling of UIO flexible variable uio_varfile_module f90 definition and handling of file structure of UIO flexible variables uiocop f90 Program to copy and transform UIO files uiolok f90 Program to look into UIO files uioinf f90 Program to give information about conversion types uiotst f90 Program to produce test UIO file Table 8 UIO Fortran90 files module contents uio_cst_ module channel status information uio_ cvl module convert type list of current machine uio_inf module inform
35. you have to adjust the size specification d 1 4 in the example above character history The file history has a similar purpose as the previous entry It can be used to keep infor mation about the parent parameter file as in character history d 1 2 f A80 p 1 b 80 n File history Taken from st35gm04n03_09 par Last Modification 01 01 2002 Its use is optional 5 3 3 Fundamental Model Parameters real teff The effective temperature is one of the basic model parameters and is specified e g with real teff f F13 3 b 4 n Effective Temperature u K 3500 0 for a relatively cool star Note that the actual effective temperature can only be deter mined a posteriori and that the entropy of the instreaming entropy see below is more important than teff itself In fact teff is only used to control material properties at the outer boundary Its value should be close to the expected effective temperature of the model character grav_mod Gravity is another characteristic of a stellar atmosphere The type or geometry of the external gravity field has to be specified e g with character grav_mode f A80 b 80 n Type of gravity field amp c0 constant central central Two values are possible so far 5 3 Parameter File rhd par File 53 o constant In the standard solar case the constant gravity specified with real grav is directed downward in x8 direction o central For the supergiant
36. 1 Possible values are the list is hopefully expanded in the near future o none None No handling of any dust molecule density at all o nosource Skip source term step for dust molecules entirely but do the transport o dust_simple_01 Simple and unrealistic dust formation model only for testing of the numerics o co_component01_01 Simple CO formation from Matthias Steffen with one compo nent only but realistic time scales o dust_k3mon_01 Simple C rich dust formation from Susanne Hofner with one com ponent only but realistic time scales 5 3 Parameter File rhd par File 63 o dust_k3mon_02 Simple C rich dust formation from Susanne Hofner with two com ponents for dust density and free carbon density e real c_dustOX There are five parameters real c_dust01 to real c dust05 to control each dust for mation scheme in detail A parameter can be given as in real c_dust01 f E15 8 b 4 n Dust parameter 1 0 0 The meaning and unit can vary from scheme to scheme The default value is 0 0 in each case 5 3 10 Radiation Transport Control In this part of the parameter file the radiation transport module has to be selected Depending on this selection a couple of additional parameters have to be specified Table 12 gives a list of the parameters and the modules they apply to The standard routines are now in the MSrad module for local models and the SHORTrad module for global Star in a Box models The L
37. 1 Optimization version with masks weights See Sect http www cray com craydoc 3 8 Optimization Compiler Switches 25 Drhd_hyd_upwind_p01 1 Optimization version with masks weights Drhd shortrad operator 101 2 Optimization short characteristics operator with masks weights Drhd shortrad dir 102 1 Optimization OMP PARALLEL statement outside of outer loop in rhd_shortrad_dirX 3 8 2 Compaq alpha Documentation about the Compaq Fortran compile assume byterecl Necessary for the UIO routines specify that the length of a record is measured in bytes and not in words cpp invoke the preprocessor on all source files inline speed V Force automatic inlining optimized for speed 04 General optimization Drhd_hyd_roe1d_101 0 Optimization Choose standard set of routines for Roe solver See Sect DMSrad_raytas1 Optimization choose non default version of SUBROUTINE raytas in file MSrad3D F90 3 8 3 Hewlett Packard V2500 The 12 processor machine zeipel from Hewlett Packard is a V2500 PA 2 0 system Now there is a first success to force the compiler to accept the OpenMP directives in CO5BOLD Yet CO5 when running on several processors only some routines e g rhd_shortrad_dirsimple1 in BOLD can benefit while others rhd_shortrad_dirsimple2 rhd_shortrad_dirsimple3 are significantly slower than on one processor In addition the single processor performance is not ve
38. 4 0 85 0 74558 1 00E 01 0 961 5260 4 622 0 705 1 00 0 81447 2 50E 01 0 571 5560 4 830 1 002 1 25 0 89163 4 00E 01 0 371 5850 4 926 1 251 1 40 0 99911 7 00E 01 0 133 6260 5 022 1 613 1 50 1 13453 1 00E 00 0 019 6570 5 070 1 879 1 60 1 22581 1 50E 00 0 191 6880 5 114 2 140 1 70 1 17659 2 00E 00 0 312 7160 5 140 2 363 1 80 1 13964 4 00E 00 0 597 7920 5 191 2 889 1 80 0 70033 6 00E 00 0 761 8250 5 213 3 092 1 80 0 46595 8 00E 00 0 877 8420 5 229 3 196 1 80 1 99552 1 00E 01 0 967 8500 5 242 3 245 1 80 3 76404 4 3 4 Recommendations for Standard File Structure The very first entry in an UIO file is always the fileform uio entry containing information about the file format and conversion type Afterwards entries can follow in any order But it is perhaps a good idea to start the file with three special entries file_id description history as in fileform uio form formatted convert ieee_4 4 4 Files amp Directories amp Paths 35 character file id f A80 b 80 n File identification uio demofile character description d 1 2 f A80 p 1 b 80 n File description This is a file to demonstrate the recommended start entries for all UIO files character history d 1 1 f A80 p 1 b 80 n File history UIO demo file 22 Dec 1997 14 15 15 A recommended format for sets of multi dimensional arrays e g hydrodynamics x axis y axis Z axis density velocities energy is shown in Sect 5 1 4 4 Files amp
39. 86 architecture PGI compiler version 3 3 2 pgf90 byteswapio fast Mvect sse Mcache_align Minfo inline Write compiler name and flags into file compiler_flags info Makefile already exists It is appended to Makefile_old New Makefile written ccccoooooooocooooo eens A new Makefile is produced An existing one is appended to Makefile_old Addition ally the file compiler flags info is written which contains the compiler call in Fortran format 7 Check the output of the configure script and the header of the new Makefile You get an overview over the relevant environment variables that control the configure script see Sect 3 6 with env grep F90_ Obs at the beginning there might be none 8 Look into the header and if necessary the rest of the configure script or into Sect 3 6 to find out how to change the environment variables to control the script properly For instance if you want to enable debugging options type export F90_DEBUG 1 Restart the configure script after every change in the control variables 9 Start the compilation with make to produce the executable rhd exe A simple sample installation may look like the following the sub directory for is put into the home directory Choose base directory cd HOME Put the tar file there FP Expand the tar file tar zxvf for tar gz 3 3 Directory Structure 9 Go into default master di
40. CO5BOLD User Manual Bernd Freytag Matthias Steffen Sven Wedemeyer December 11 2002 2 CONTENTS Contents 4 5 6 Gad tee a acho tan Sa NS En te ee Sede ees 6 te fe eure tie ki eerie O ana nina oh 6 poe Dena Bon an ee ee ae A ee SR aa 9 bie Since wt gh hen eee Ge hot a eas eae Be eels 9 3 50 HOrtran Files ion cc SS Ra Re RO ee he eee ER ee eee Se Sa ea hi 12 3 6 Configure Script ooa ee 12 face en nan tet an ka te a es ge es Gaye ip A 4 es eg een bates 16 Peace Bike Getta ales OPE cite SRA eee es DAN eo S 24 3 8 1 Gray OV ljea oh Sok ee oh he oP A Rae ea ae wae Ga Bee 24 E ag Gee gh Ghee eee sie ages ee aa ees ae ae 25 3 8 3 Hewlett Packard V2500 0 2 0 0000 a ee 25 3 8 4 Hewlett Packard Itanium 2 2 2 2 e 26 3 0 0 Hitachi 4 2 2 226244 Rk Rw hs ra ed rr Bae hee eh 26 Sees te ih SAG ewes deer Bh a te Aen ease ies ii mm aa 27 A ee ee ee Nan RD a 27 3 98 NECIO Glier se a ee OR a ee OO A SS An na a TOBA 28 eae poate siege henry ace Star eh ae hones eae Pa pea es ee aa 28 uae Oar ee Gs Sp Bow ete ev eh Gs eer Cee eee eg ae E Ge Geen a ee ee 29 4 UIO Data Format 30 ire ee oie eat co Gis Oe ge Pa EN a ap Geer an Gey go cena oa Pe 30 De nea ee ewe a a a es ae 30 4 3 Structure of UIO Files 2 ee 31 4 3 1 Data Representation ASCII or Binary a 31 4 3 2 Data File Structure ok 32 47323 Table ni ee eh a hw ee eee ee ee ce 33 ste eles Be Ge oe sha 34 4 4
41. Files amp Directories dz Paths 2 2 ok 35 45 Fortran9O exis egos E cea A Saha BWA aS Soe wo dow a Row 35 AE A 35 4 5 2 Use of UIO Modules im Fortran90 a 37 Sie RR ee ewe een ee es da dnd ae OS 37 A an gh epee Sg 38 fo BO A Oe ee A ee Oe cet A te i ee 39 4 6 1 Quick Examination of Files uiolook a 39 4 6 2 Transformation of Files uiocat ee 39 4 6 3 Information about Conversion Types uioinfol o 40 4 7 IDL UIO Routinesl aa 41 4 7 1 Initialization of UIO Routines under IDL 42 Ana NA i arte an oa ap weed men et A 42 4 7 3 Reading Data with uio_dataset_rd pro or ulo_datasetlist_rd pro 43 5 Control and Data Files 45 A LA A eee eee 45 5 2 File with Additional Data rhd mean Filel 46 O O O ae 46 5 2 2 Contents of Individual rhd mean File Entry 47 A A ee oe Ee a de tad dd 50 CONTENTS 6 Running a Simulation 8 5 3 1 Quickstart How to Make a Proper Parameter File 5 3 2 Header 5 3 3 Fundamental Model Parameters 00008 cee 5 3 4 Boundary Conditions 2 2 a 5 3 5 Equation of State 6 a 5 3 6 Opacities 5 3 7 Hydrodynamics Control 2 o 5 3 8 Tensor Viscosity Control o o ee tebe doe Sea yee HS bb a bee oe eee ae 5 3 10 Radiation Transport Control 0 02 02 0000 8 2 2 ee 5 3 11 Process Time Management
42. HDrad module is not maintained very much anymore Parameter Section LHDrad MSrad SHORTrad radscheme si si n radminiter 5 3 10 i si n raditer 5 3 10 si ii ii n radmaxiter 5 3 10 ji ii i radraybase 5 3 10 da T radraystar 5 3 10 li n_radtheta 5 3 10 l n_radphi 5 3 10 7 n_radsubray 5 3 10 Li n radthinpoint n_radthickpoint 5 3 10 ii si n radtaurefine 5 3 10 ki T n_radband 5 3 10 dl c_radimplicitmu 5 3 10 E c_raditereps 5 3 10 la c_raditerstep 5 3 10 c_radtvisdtau 5 3 10 si c_radtvis s c_radhtautop c_radcourant 5 3 12 il id c_radcourantmax x si c_radmaxeichange 5 3 12 js i Table 12 List of radiation transport control parameters and the modules they are relevant for e character radscheme So far there exist three different radiation transport modules The active on can be selected e g with character radscheme f A80 b 80 n Radiation transport scheme amp cO LHDrad MSrad SHORTrad amp c1 None skip radiation transport step entirely SHORTrad 5 CONTROL AND DATA FILES Possible values are o None Skip radiation transport entirely o LHDrad old supergiant module It uses long characteristics and is restricted to an equidistant grid and open boundaries at all surfaces Note that the switch Drhd r01 1 has to be set during compilation see Sect 3 7 o MSrad solar module It uses long characteristics The lateral boundaries have to be perio
43. Larger values 1 2 in the example above are only necessary for some nasty under resolved supergiant models Setting c_vissmagorinsky c_visartificial 0 0 skips the tensor viscosity step entirely e real c_visprturb The Prandtl number for turbulent mixing can be specified e g with real c_visprturb f E15 8 b 4 amp n Turbulent Prandtl number 1 8 0 Values between 1 0 and 10 0 appear reasonable Note that larger values lead to smaller amounts of turbulent mixing A value of 0 0 switches off the turbulent mixing terms but not the entire tensor viscosity e real c_vistensordiag The factor in the stress tensor in front of of the diagonal terms can be set with real c_vistensordiag f E15 8 b 4 amp n Diagonal factor for viscous stress tensor u 1 amp c0O typically 1 0 1 0 This is not really parameter one would try to adjust The total amount of viscosity should be controlled with real c_vissmagorinsky and real c_visartificial But the param eter can be used to tentatively switch off the diagonal terms completely or to change its importance compared to the other terms e real c_vistensoroff The factor in the stress tensor in front of of the off diagonal terms can be set with e g real c_vistensoroff f E15 8 b 4 amp n 0ff diagonal factor for viscous stress tensor u 1 amp cO typically 0 5 0 5 This is not really parameter one would try to adjust The total amount of viscosity should be controlled with
44. The following data block is written as sequence of lines The number of items per line is specified by the p keyword in the header 4 3 3 Tables For a table the entry header is followed by a list of headers for the individual table columns a single table header line consisting of abbreviations of the table entry identifiers and the table itself see the example in section 4 2 The dimension keyword gives the number of columns and rows in the form d 1 columns 1 rows The Holweger Miiller Atmosphere is chosen as the following real world example for a file with a table in UIO format fileform uio form formatted convert ieee_4 version 0 0 1996 10 29 amp date 20 Feb 1997 18 40 45 system Sun0S machine saturn osrelease 4 1 3 amp osversion 3 hardware sun4m language IDL 4 0 program by hand character description d 0 3 f A80 p 1 b 80 d 13 Nov 1996 18 29 48 Holweger Mueller Atmosphere Hartmut Holweger amp Edith Mueller 1974 Solar Physics 39 19 30 table II empirical solar temperature stratification to fit solar spectral lines and limb darkening character history d 0 3 f A80 p 1 b 80 d 13 Nov 1996 18 29 52 Holweger Mueller Atmosphere from 1974 34 4 UIO DATA FORMAT uio form 13 Nov 1996 18 29 52 conversion type added 20 Feb 1997 18 21 01 xi gt vmicro 20 Feb 1997 18 23 43 real teff f F6 1 b 4 n effective temperature u K texa T_ rm eff 5780 0 table atmospher
45. The recommended second order scheme o Superbee The most aggressive stable 2nd order scheme It results in the steepest shocks which works well in some test cases but might be to difficult for the radiation transport module to handle o PP Chooses the piecewise parabolic reconstruction of the PPM scheme Piecewise Parabolic Method Colella amp Woodward 1984 Results in 3rd order accuracy for the advection Usually the VanLeer reconstruction is a good choice If a more stable and diffusive scheme is needed take Minmod The PP reconstruction gives the highest accuracy e integer n_hydcellsperchunk In every directional sub step neighboring 1D columns are independent from each other They can be grouped and computed in chunks of arbitrary size The approximate number of grid cells per chunk can be specified e g with integer n_hydcellsperchunk f I9 b 4 amp n Number of cells per hydro chunk amp c0 0 gt one 2D slice at a time amp c0 1 gt minimum chunk size inefficient c0 2500 reasonable value amp cO 1000000000 maximum chunk size inefficient and memory intensive 20000 The exact number is determined at run time to get approximately equal sizes of the individual chunks The choice of this parameter does not affect the result of the computation but the memory usage and performance Smaller and more chunks may result in an optimum cache usage and need the smallest amount of
46. a list of items into its components Determine file contents list of all entries with its positions Get information about environment Initialization procedure for input output routines Merge the input term keyword value gt keyword value Merge a list of terms keywords and their values into a line table Make list with possible conversion types From column number or entry name find table entry number Open file for reading read header Open file for writing write header Print term table in pretty form Transform a string into a string with quotation marks if necessary Parse string inline and remove quotation marks if necessary Reading scalar and array data of all types Read file header Read header of variable and extract keywords Read header Read label Read table of integer real and or character data from file Skip data block Search header of variables given by list and extract keywords Parse dimension string Read uio file and put data into anonymous structure Create empty table structure Change and modify table contents rearrange lines Merge two tables in different ways Read 1d array from 2d table array all types Write 1d array into table all types Close file with special handling for conversion type Open file with special handling for conversion type Transform a string to give a correct name of a variable Produce from write format string corresponding read format string Writing scalar and a
47. ac_cray_module export RHDMAC else Default Suns MAC files UIOMAC uio_mac_sun_module export UIOMAC RHDMAC rhd_mac_sun_module export RHDMAC fi Architecture dependent sub directory names for object file and executables if uname s craSH then MAC crash elif uname s craSHi then MAC crashi elif uname s SunOS then MAC sun HP UX then ja64 then elif uname s if uname m MAC hpia64 else MAC hp fi elif uname s MAC linux elif uname n MAC vx1 else MAC sgi fi Individual libraries Timing TIMEPATH FORTRANDISK time f 90 export TIMEPATH Linux then yx1 then 3 4 Old Setup File for Paths TIMESRCPATH TIMEPATH export TIMESRCPATH Constants amp units CONPATH FORTRANDISK con f 90 export CONPATH CONSRCPATH CONPATH export CONSRCPATH 0 PES UIOPATH FORTRANDISK uio export UIOPATH UIOSRCPATH UIOPATH 90 export UIOSRCPATH String handling STRPATH FORTRANDISK mat str export STRPATH STRSRCPATH STRPATH export STRSRCPATH Math MATPATH FORTRANDISK mat export MATPATH MATSRCPATH MATPATH f 90 export MATSRCPATH gas GASPATH FORTRANDISK eos gas export GASPATH GASSRCPATH GASPATH export GASSRCPATH E09 EOSPATH FORTRANDISK eos export EOSPATH EOSSRCPATH
48. andled to improve performance Values o 0 default Temporary coefficient arrays are actually copied o 1 Temporary coefficient arrays just get a pointer link into the big arrays e rhd_box_gravo0l in rhd_box_module F90 rhd box gravitation 01 Category feature activation Switch to activate the array for the gravitational potential in the box structure If the switch is set to 1 a 3D array for the potential is created copied removed There is no module to compute the gravitational potential yet Therefore the entire thing has no practical value yet Values o 0 default no handling of array o 1 array handling activated e rhd_box_qucOl in rhd_box_module F90 and rhd F90 rhd box quantity centered 01 Category feature activation Now CO5BOLD is able to handle a number of additional quantities e g density arrays in addition to the basic hydrodynamics quantities p ei if this compiler switch is activated These additional quantities can be e g densities of dust distribution moments or densities of molecules Values o 0 default no handling of additional quantities density arrays o 1 handling of additional density arrays is activated To actually include dust formation in a simulation it is necessary to 18 3 PROGRAM FILES INSTALLATION COMPILATION 1 set the switch Drhd box guc01 1 during compilation this is done by the configure script if the environment variable F9O0_DUST is set
49. arallel runs with OpenMP Due to the special han dling of boundary cells the overhead per call increases significantly for small chunks Typically larger chunk sizes compared the the hydrodynamics chunk sizes set with integer n_hydcellsperchunk see Sect are adequate On the other hand they should not be too large to limit the usage of temporary memory and to allow parallelization the distribution of chunks to threads For simulations with activated OpenMP on a par allel machine the chunk size has to be made small enough to allow at least as many chunks as processors available This is particularly important for models with a small number of grid points e g 2D models 5 3 9 Dust Molecules CO5BOLD can now handle a number of additional density arrays They can be used to describe e g the mass density of dust distribution moments or number densities of molecules These species are properly advected with the gas density There is also already a small number of dust molecule formation models available These models have to be improved in the future and the influence on the radiation field opacities radiation pressure on dust has to be taken into account e character dustscheme A scheme for dust or molecule formation and transport can be selected e g with character dustscheme f A80 b 80 n Dust model amp c0 none default nosource dust simple Ol co_component01_01 amp ci dust_k3mon_01 dust_k3mon_02 dust_k3mon_0
50. at larger than the remotest corner of the box effectively cancels this artificial smoothing in the outer layers without changing the formula for the potential real ri_rad For a Star in a Box and particularly when only simple ray directions are allowed in the radiation tranport step the temperature in the outer corners of the box tends to become very small To artificially increase the effect of radiative heating the parameter real r1_rad can specify a radius beyond which only postive contributions of the radiative energy transport to the energy budget are taken into account This ruins the conservativity of the code in these layers and should be applied only in very remote corners which are then considered only as sort of extended boundary region but not as part of the real model The parameter can be specified e g with real ri_rad f E15 8 b 4 n Outer radiation transport radius u cm amp c0 0 0 Not used 8 00000e 13 A value of 0 0 default or below deactivates this feature 54 5 CONTROL AND DATA FILES 5 3 4 Boundary Conditions The boundary conditions at the six sides of the computational box cannot be specified indepen dently For the naming convention of the boundaries a gravitational acceleration in x3 direction is assumed Accordingly there is a bottom a top and four side boundaries e character side_bound The boundary condition at all four sides is given by e g character side_bound f A80 b 80
51. atement like use uio_bulk_module In the initial phase of the program the UIO routine package has to initialized by exactly one call of the uio_init routine with the name of the program as optional parameter call uio_init progrm uiotst The internal list of logical I O unit numbers may be changed with calls of uio_chunit and uio_chconv A file can be opened for writing with file test txt form formatted or unformatted conv ieee_4 or native crayxmp_8 call uio_openwr ncout file form form conv conv Header and data block are written together with one command as e g in call uio_wr ncout time gt time name time unit s call uio_wr ncout rho 1 10 rho name density unit g cm 3 There are two different routines to close a file after reading or writing A file opened for writing is closed by uio_closwr ncout To open a file for reading only the file name has to specified File form and conversion type are determined automatically file test txt call uio_openrd ncin file In contrast to the writing of an entry by one routine call the reading is performed in two separate sub steps for the header and the data part After the reading of the header e g with use uio_siz_module use uio_nam_module integer 1 ntt character let termt 2 nttmx call uio_rdhd ncin termt ntt the identifier type and dimension if any of the entry i
52. ation hd dust dust k3mon module f DUST 1 or 2 component dust model hd mhd rhd mhd module F90 MHD magnet fields first version eos f90 gasinter_routines f90 EOS equation of state opa opta cubit_module f OPTA cubic interpolation opa opta opta_par_module f90 OPTA parameters for opacity routines opa opta opta_routines f OPTA opacity hd rhdb rhd_action_module f90 RHDB routines for control parameter passing hd rhdb rhd_box_module f90 RHDB box handling routines hd rhdb rhd_dat_module f90 RHDB handling of additional data averages hd rhdb rhd_gl_module f90 RHDB global parameters hd rhdb rhd_io_module f90 RHDB input output routines hd rhdb rhd_mac_cray_module f90 RHDB machine dependent routines CRAY hd rhdb rhd_mac_default_module f90 RHDB machine dependent routines default hd rhdb rhd_mac_sun_module f90 RHDB machine dependent routines Sun hd rhdb rhd_mean_module f90 RHDB averaging routines hd rhdb rhd_prop_module f90 RHDB box properties hd rhdb rhd_sub_module f90 RHDB additional routines con f90 const_module f90 CON physical and mathematical constants mat str str_module f90 STR string handling time f90 timing_module f90 TIME timing routines uio f90 uio_base_module f90 UIO I O routines uio f90 uio_bulk_module f90 UIO I O routines uio f90 uio_filedef_module f90 UIO I O routines uio f90 uio_mac_crayts_module f90 UIO I O routines machine dependent part uio f90 uio_mac_crayxmp_module f90 UIO I O routines machine dependent part uio f90 uio_mac_decalpha_m
53. ation about environment uionam_module definition of names uio_siz_module string length table size uio_base_module basic set of UIO routines string processing header handling I O channel management Table 9 Contents of uio_base_module f90 file uio_mac_ieee_module f90 is appropriate for all machines with IEEE big_endian binary format Additionally there exist files containing calls of machine library routines uio mac crayts module f90 uio mac crayxmp module f90 uio_mac_sun_module f90 These make it possible to write information about the platform in use into the file header The CRAY versions allow unformatted I O in the CRAY specific format and additionally via the FFIO ASSIGN logic in IEEE format The file uio mac intel module f90 is appropriate for all machines with IEEE little endian binary format and no mechanism for automatic conversion The main set of routines is contained in uio bulk module f90 in the module uio bulk module The three files uio base module f90 uio mac module f90 and uio bulk module f90 comprise the standard set of UIO routines Additionally there exists a file uio table module f90 with the single module uio_table module which permits the I O and manipulation of a certain table format see the example in section 4 2 The latest extension comes within the modules uio_var_module f90 and uio_varfile_module f90 The module uio_var_module f90 contains a type definition for a variable uio flexible
54. be specified as in character hdscheme f A80 b 80 n Hydrodynamics scheme amp cO Roe approximate Riemann solver of Roe type amp c1 RoeMagKin Roe solver kinetic magnetic field transport amp c2 None skip hydrodynamics step entirely Roe 5 3 Parameter File rhd par File 59 Possible values are o None The hydrodynamics step is skipped entirely for test purposes Note that in this case some initializations necessary for the generation of the mean file are omitted too o Roe default The standard Riemann solver of Roe type is activated This value will in almost every case be chosen o RoeMagKin The standard Roe solver is extended to transport passively a magnetic field This is a test implementation to check if the general magnetic field handling works e character reconstruction This parameter determines the order and aggressiveness of the reconstruction scheme with e g character reconstruction f A80 b 80 n Reconstruction method amp cO Constant c1 Minmod VanLeer Superbee c2 PP Minmod Possible values are o Constant The run of the partial waves inside the cells is assumed to be constant A highly dissipative first order scheme results This values will usually only be used for test or comparison purposes o Minmod Chooses the smallest slope which still results in a second order scheme It is the most diffusive and most stable one in this class O VanLeer default
55. because one of the regular termination conditions was fulfilled e g the requested number of time steps was performed the exit status file rhd done is produced Currently it contains the date and time of its generation The existence of this file can be checked within a script to determine if the run was successful Note the existence of an rhd end file only indicates that CO5BOLD managed to exit gracefully due to an error or ina regular way 80 6 RUNNING A SIMULATION 6 Running a Simulation 6 1 Quickstart How to Run CO5BOLD The generation of a start file and the modification of the parameter file is a somewhat complex process In short the following steps have to be performed 1 2 Produce an executable rhd exe see Sect 3 1 and put it into your working directory Choose a start model e g the final model of an earlier simulation or a model produced with an IDL routine Edit the parameter file rhd par typically you will start with an existing file and edit it You should check that the paths and names of EOS opacity and start file are set correctly Watch the username For details about the parameter file see Sect 5 3 1 Start the simulation with nice nohup rhd exe gt rhd out amp You can see how the simulation proceeds with tail f rhd out The other data files usually are in a binary format this can be changed to ASCII for matted in rhd par Their contents can be read an
56. can be set e g with real c_visbound f E15 8 b 4 amp n Boundary drag viscosity parameter u 1 0 001 This extra drag force is usually not necessary and should be switched off with c_visbound 0 0 5 3 8 Tensor Viscosity Control In many test problems it is not necessary to activate the 2D 3D tensor viscosity But when strong slow shock fronts are aligned with the grid the Roe solver runs into problems and at least some additional 2D or 3D viscosity is necessary And even if the Roe solver can handle sharp shocks by its own the radiation transport algorithm might cause trouble because of the enormous opacity variations across a shock front Here the tensor viscosity is useful too e real c_vissmagorinsky A turbulent viscosity of Smagorinsky type can be activated e g with real c_vissmagorinsky f E15 8 b 4 amp n Turbulent eddy viscosity parameter Smagorinsky type u 1 1 2 In many cases values around 0 5 are sufficient to stabilize the code Larger values 1 2 in the example above are only necessary for some nasty under resolved supergiant models Setting c_vissmagorinsky c_visartificial 0 0 skips the tensor viscosity step entirely e real c_visartificial A standard artificial viscosity can be activated e g with 5 3 Parameter File rhd par File 61 real c_visartificial f E15 8 b 4 amp n Artificial viscosity tensor parameter 1 1 2 In many cases values around 0 5 are sufficient to stabilize the code
57. chpos 5 chunit closrd E closwr cpentr d data most important user routine comfortable useful Add one keyword to term table keyword value no link character Add one keyword to term table with keyword value Add one keyword to term table with keyword value or default Actualize list of conversion types for all channels Give current file position or jump to specified position Initialize store and actualize a list of free and occupied unit numbers Close file after reading Close file after writing Copy entry from one file to another Read data from uio file s in quasi direct access mode Handle uio file s in quasi direct access mode dataset_rd Read uio file and put data into anonymous structure uio_datasetlist_rd Read data from list of files and put it into an structure deform dim2st exkeyw 5 exitrm exmtrm filcon getenv 5 init meltrm memtrm mkcvls 5 nc2nt openrd openwr pptrmt qmaadd gmadel sof rds rdfifo rdhdex 5 rdhead rdlabl rdtab skipda slhdex 5 st2dim struct_rd 5 tab0 tabc tabm tabr tabw uclose uopen tt vnanrm wf2rf y wr wrfifo E wrhdme Determine the default output format for numbers Compose dimension string Extract value of keyword from table Extract one term from the input line Transform
58. chy real modeltime f E13 6 b 4 n time u s integer modelitime f 111 b 4 n time step number u 1 real dtime f E13 6 b 4 n time step u s real time_out_full_last f E13 6 b 4 n Time of last output of full model u s real time_out_mean_last f E13 6 b 4 n Time of last output of averaged data amp u s label box date 02 01 2002 16 17 26 049 character box_id f A80 b 80 n Block identification integer dimension d 1 2 1 3 f I7 p 6 b 4 real time f E13 6 b 4 n time u s integer itime f 111 b 4 n time step number u 1 real xc1 d 63 63 63 63 63 63 f E13 6 p 4 b 4 amp 46 5 CONTROL AND DATA FILES n x1 coordinates of cell centers u cm ds 0 0 0 1 0 1 real xc2 d 63 63 63 63 63 63 f E13 6 p 4 b 4 amp n x2 coordinates of cell centers u cm ds 0 1 0 0 0 1 real xc3 d 63 63 63 63 63 63 f E13 6 p 4 b 4 amp n x3 coordinates of cell centers u cm ds 0 1 0 1 0 0 real xb1 d 63 64 63 63 63 63 f E13 6 p 4 b 4 amp n x1 coordinates of cell boundaries u cm ds 0 1 0 1 0 1 real xb2 d 63 63 63 64 63 63 f E13 6 p 4 b 4 amp n x2 coordinates of cell boundaries u cm ds 0 1 0 1 0 1 real xb3 d 63 63 63 63 63 64 f E13 6 p 4 b 4 amp n x3 coordinates of cell boundaries u cm ds 0 1 0 1 0 1 real rho d 63 63 63 63 63 63 f E13 6 p 4 b 4 n Density u 8 cm 3 real ei d 63 63 63 63 63 63 f E13 6 p 4 b 4 n Internal energy u erg g real vi d
59. compiler version 4 0 on this option can be used instead of the three previous ones It contains and supersedes them e Minline Optimization Routines that should be inlined file rhd_hyd_module F90 rhd_hyd_avg rhd_hyd_upwind rhd hyd pred0 rhd hyd predm rhd_hyd_predp rhd_hyd_alpha rhd hyd constanteg rhd_hyd_minmodeg rhd_hyd_minmod rhd_hyd_vanleereg rhd_hyd_vanleer rhd hyd superbeeeg rhd_hyd_superbee rhd hyd ppeg rhd_hyd_pp rhd hyd hdflux file rhd Ihdrad module F90 rhd rad3d raylhd rhd rad3d solve rhd rad3d solveeg file rhd shortrad module F90 rhd shortrad operator rhd shortrad dtauop DMSrad raytas1 1 Optimization choose non default version of SUBROUTINE raytas in file MSrad3D F90 Drhd hyd roe1d 101 0 Optimization choose standard set of routines for Roe solver See Sect e Drhd shortrad operator 102 1 Optimization use the manually inlined version of the short characteristics operator e Drhd_shortrad_dtauop_102 1 Optimization use the manually inlined version of the optical coupling operator 3 8 7 Linux Intel Compiler With Version 7 0 of the Intel compiler CO5BOLD with the SHORTrad module only so far compiles The native format on Intel machines is little_endian With export F_UFMTENDIAN big the default can be changed to big endian The appropriate UIO modules are uio_mac_intel_module f90 in the little endian case and uio mac sun module f90 in the big endian case The c
60. created tar zxvf for tar gz cd for hd rhd mkdir YOUR_MACHINE cd YOUR_MACHINE ln s conf configure configure make The compilation process is explained in more detail in Sect The configure script is described in its header and in Sect The directory structure is shown in Tab I All Fortran files are listed in Tab 3 2 Compilation Procedure for CO5BOLD The installation procedure has changed significantly since the last release now there is a configure script see Sect 3 6 that creates the complete temporary makefile Installation procedure 1 Choose create a proper base directory This will usually be HOME Then the master directory will typically be HOME for this is the default created by the tar file Some prefer to rename it to HOME HYDRO 2 Put all source files and the configure script there This will be done typically by expanding the gzipped tar file for tar gz e g with tar zxvf for tar gz or by copying all files from an existing installation The tar file creates a sub directory for in the local directory You get sub sub directories as described in Sect 3 3 and files as listed in Tab 3 See the Readme file for README 3 Change with cd for hd rhd into the main directory 4 Look at the existing sub directories e g with 3 2 Compilation Procedure for CO5BOLD ls og grep d to see if you find one that fits your machine The directory for hd rhd conf shoul
61. ctory whether the file rhd stop exists If it has been generated e g with touch rhd stop the code exits gracefully i e it produces a proper final model which can be used to restart the code This method of stopping a simulation is to be preferred over a simple kill or qdel command because it allows to analyze the state of the model just at the end of the simulation and a smooth restart Before the restart the rhd stop file has to be deleted The simulation can be continued by just initiating a new run If the file rhd cont exists at the beginning of a simulation the code tries to resume an interrupted computation The initial model will not be taken from the start model file infile_start but from the final model outfile_end The data for the full and the mean file is not written into new files but will be appended to the existing ones In this way a simulation can be interrupted and continued in a fairly safe way It is possible to analyze the final model and to changes values in the parameter file Keep in mind that after a restart with rhd cont the specifications about the length of the job e g the number of time steps will be counted from the restart point and not from the beginning of the original simulation To interrupt a job with rhd stop can be very handy The continuation with rhd cont and the old parameter file is not to be preferred over an ordinary restart with a new parameter file If a run was successful i e it was completed
62. d analyzed with IDL routines see Sect 4 7 3 For machines with batch queue CRAYs in Kiel SUN1 in Uppsala there is the script origi nally from Hans Giinter Ludwig which can handle an entire sequence of simulations 6 2 Running CO5BOLD on a Machine with Batch System 6 2 Running CO5BOLD on a Machine with Batch System From Sven s manual Figure 1 Program scheme 81 82 7 DATA ANALYSIS WITH IDL 7 Data Analysis with IDL In this section some basic commands for handling CO5BOLD data in IDL are described See also Sect 4 7 NOTE Before using IDL the environment variables for the CO5BOLD paths should have been set Use setarcdeppaths sh or ksh csh for this purpose Im portant is UIOPATH which specifies where to find the IDL routines for the UIO handling 7 1 Preparations We recommend to create an initialisation file e g named start pro which should be called after starting IDL e g start This is necessary to define relevant paths of IDL subroutines and to provide the UIO package Thus the file should contain the following Add user IDL directory to search path addpath expand_path UIOPATH id1 addpath addpath texpand path HOME HYDRO IDL rhdpro if strtrim addpath 2 ne then path addpath path delvar addpath Initialize uio routines uio_init progrm by hand Alternatively one might want to set the IDL path variable accordingly
63. d depend particularly on gravity e real dtime_start The initial time step recommendation of a simulation is usually taken from the start model file It can be overwritten e g with real dtime_start f E15 8 b 4 n Start time step u s 1 0E 03 A value lt 0 0 means that the original value from the start model is used e real dtime_min In some rare cases it might be useful to specify explicitly the minimum time step with e g real dtime_min f E15 8 b 4 n Minimum time step u s amp cO dtime_min 0 0 gt no restriction 1 0 This value is used even if restrictions from the Courant condition try to enforce a smaller value A fixed time step can be prescribed by setting dtime_min dtime_max to some positive value A value dtime_min lt 0 0 means that this time step restriction is completely ignored which is the case that should usually be chosen e real dtime_max It is possible to explicitly specify the maximum time step too e g with real dtime_max f E15 8 b 4 n Maximum time step u s amp cO dtime_max 0 0 gt no restriction 1 0E 05 A fixed time step can be prescribed by setting dtime_min dtime_max to some positive value A value dtime_max lt 0 0 means that this time step restriction is completely ignored which is the case that should usually be chosen e real dtime_min_stop Sometimes a simulation can run into a pathological state where the time step decreases rapidly without recovering To prev
64. d not be used It contains only the configure script But any other directory will do If you don t like any of the existing directories create your own e g with mkdir YOUR_MACHINE Change into this directory with cd YOUR_MACHINE Check if there is a configure script or a link to it with ls og configure which should give something like lrwxrwxrwx 1 17 2002 12 04 17 39 configure gt If it is not there create the link with ln s conf configure conf configure Start the configure script to create the first version of the Makefile configure This gives you a screen output like Configuration script for CO5BOLD Makefile List of control environment variables F90_COMPILER F90 PREFLAGS F90_POSTFLAGS F90 PARALLEL scalar F90_DEBUG 0 F90_LHDRAD 0 F90_MSRAD 0 F90 SHORTRAD 1 No parallelization requested assume default F9O_PARALLEL scalar No debugging requested assume default F90_DEBUG 0 No LHDrad module requested assume default F90_LHDRAD 0 No MSrad module requested assume default F90 MSRAD 0 No SHORTrad module requested assume default F9O_SHORTRAD 1 No dust module requested assume default F90_DUST 0 No MHD module requested assume default F90 MHD 0 No explicit machine requested assume default F90_MACHINE local 8 3 PROGRAM FILES INSTALLATION COMPILATION F90_DUST 0 F90_MHD 0 F9O_MACHINE local gt MACHINE 1686 F90_BASEPATH home bf for Linux system with 16
65. d_solve_t01 rhd_rad3d_step_t01 rhd rad3d toray 101 21 rhd roeld flux 101 rhd roeld flux tO1 rhd roeld slope 101 rhd roeld step t01 rhd shortrad dirl 101 rhd shortrad dir 102 23 rhd shortrad dtauop 101 rhd shortrad dtauop 102 rhd shortrad formal 101 rhd shortrad formal t01 rhd shortrad operator 101 N E 87 rhd_shortrad_operator_102 rhd_shortrad_step_t01 24 rhd_vis_density_p01 rhd_vis_t01 20 timing_c_factor configure script control variables F90_BASEPATH F90_COMPILER F90_DEBUG F90_DUST F90_LHDRAD F90_MACHINE F90_MHD F90_MSRAD F90_PARALLEL F90_POSTFLAGS F90_PREFLAGS F90_SHORTRAD craSHi Cray data format dust entropy fix environment variable environment variables 9 EOS equation of state fluxes formatted Fortran Hewlett Packard Hitachi hydrodynamics hydrodynamics routines IDL UIO routines uio_data uio_dataset_rd uio_init inlining alpha Cray VX1 Intel compiler on Linux PGI compiler on Linux SGI Sun Intel 88 Itanium LHDrad Linux little_endian magnetic fields makefile configure script UIO MSrad 813 FI 20 25 27 57 63 61 NEC SX 5 opacities OpenMP activation in configure script chunk size on Cray VX1 on Hitachi on SGI on Sun output full data sets mean data rhd done radiation transport README 6 rhd cont rhd done rhd exe S
66. data ierr ierr uio_closrd listdata channel delvar listdata nxc1 n_elements ful z xc1 nxc2 n_elements ful z xc2 nxc3 n_elements ful z xc3 n timestep 1000 Some huge value to get everything Reduce for tests ierr 0 i 0 Loop over all datasets while ierr eq 0 and i lt n_timestep do begin amp Read the next dataset ful uio_datasetlist_rd modelfile listdata listdata ierr ierr amp if ierr eq 0 then begin amp print i ful z itime ful z time format A 14 16 E15 8 amp Now do the data handling demo print Mean density avg ful z rho amp i i 1 amp endif amp endwhile Note that you can specify an entire group of files with modelident _ 45 5 Control and Data Files Table 11 shows a list of all files necessary to run CO5BOLD Figure 1 gives similar information but is not quite up to date Executing the makefile produces an executable rhd exe Its name can of course be changed afterwards The names of the three control files rhd par rhd stop and rhd cont and of the status file rhd done cannot be changed without modification of the source code The names of EOS opacity and CO5BOLD data files can be chosen freely in the parameter file rhd par Table 11 only contains dummy names File Sect I O Type Description rhd exe executable main program rhd par I control data UIO central control file rhd
67. density and energy this check is usually not needed It can be switched off by setting c_maxeichange 0 0 e real c_radcourant The radiation transport routines are subject so time step restrictions too And in typical scenarios its the radiative timescale are the shortest one and poses the tightest restriction Contrary to the hydrodynamics routines the timescale relevant for the stability of the radi ation transport scheme can only be estimated using the characteristic timescale of a small sinusoidal temperature disturbance with a wavelength of the grid size in a homogeneous background and grey radiative energy exchange The radiative Courant factor can be set e g with 72 5 CONTROL AND DATA FILES real c_radcourant f E15 8 b 4 n RAD Courant factor u 1 amp cO range 0 0 lt C_radCourant typically 1 0 2 5 If the estimate of the timescale would be correct a value of 2 0 would cause the temperature fluctuation on the shortest scale to flip its sign setting the absolute stability limit A value of 1 0 would lead to a damping of theses fluctuations within one time step But in practice even higher values for example 2 5 show a reasonable behavior This might be due to the effect that the shortest radiative timescale only occurs at single points or in 2D layers but that already the immediate neighbors have longer timescales and can damp the most sensitive points Based on real c_radcourant the recommended typica
68. dic Top and bottom can be closed or open Note that the switch Drhd r02 1 has to be set during compilation see Sect 3 7 o SHORTrad new supergiant module It uses short characteristics and is restricted to an eguidistant grid and open boundaries at all surfaces Note that the switch Drhd_r03 1 has to be set during compilation see Sect 3 7 e integer n radminiter Usually the stability considerations dictate a radiative time step smaller than the hydrody namics or tensor viscosity time step To remedy this situation it is possible to allow several radiation transport steps per global time step Hitherto all three radiation transport mod ules support this iteration The minimum number of iterations radiative sub steps can be specified e g with integer n radminiter f 14 b 4 amp n Minimum number of radiation transport iterations c0 8 1 If less iterations are needed the time step limit for the next step is increased This value will in almost any case for explicit radiation transport be set to 1 In the implicit case it is set to a higher value typically 5 e integer n_raditer After each complete radiative time step the recommendation for the next time step will be chosen so that n_raditer iterations will probably needed The parameter can be set e g with integer n_raditer f 14 b 4 amp n Number of radiation transport iterations c0 10 8 For a simulation of a solar type star with comparatively lo
69. e d 1 7 1 29 f X b 1 n Holweger Mueller Atmosphere amp cO Hartmut Holweger Edith Mueller 1974 Solar Physics 39 19 30 table II c1 Teff Sun 5780K real tauross f E9 2 b 4 n optical depth Rosseland u 1 real tau5000 f F7 3 b 4 n optical depth lambda5000 u 1 t logi0 3 real t f F7 0 b 4 n temperature u K real pgas f F6 3 b 4 n gas pressure u dyn cm 2 real pel f F6 3 b 4 n electron pressure u dyn cm 2 real vmicro f F4 2 b 4 n microturbulence u km s real q f F8 5 b 4 n Hopf function u 1 c0 g T tau Teff 4 0 75 tau tauross tau5000 t pgas pel vmic q 2 00E 07 6 539 3900 0 769 3 140 0 00 0 27637 2 50E 07 6 279 3920 1 171 2 752 0 00 0 28208 5 00E 07 5 868 3970 1 598 2 342 0 00 0 29675 1 00E 06 5 588 4030 1 842 2 105 0 00 0 31510 2 00E 06 5 334 4080 2 042 1 910 0 00 0 33103 5 00E 06 5 001 4160 2 279 1 674 0 00 0 35776 1 00E 05 4 747 4210 2 450 1 508 0 00 0 37527 2 00E 05 4 486 4270 2 618 1 341 0 00 0 39712 5 00E 05 4 131 4340 2 835 1 128 0 00 0 42377 1 00E 04 3 856 4400 2 999 0 967 0 50 0 44765 2 00E 04 3 577 4460 3 162 0 804 0 50 0 47248 5 00E 04 3 200 4530 3 377 0 596 0 50 0 50256 1 00E 03 2 912 4590 3 541 0 437 0 50 0 52925 2 00E 03 2 621 4640 3 704 0 279 0 50 0 55173 5 00E 03 2 233 4720 3 919 0 070 0 50 0 58792 1 00E 02 1 939 4800 4 083 0 094 0 50 0 62415 2 00E 02 1 645 4900 4 245 0 266 0 65 0 66867 5 00E 02 1 256 5080 4 460 0 50
70. e opening a file for writing the file format formatted or unformatted and the conversion type native e g ieee_4 have to be specified The formatted ASCII data representation allows I O independent of platform or compiler It is useful for parameter files which can be read and edited by hand for the direct inspection of data the transfer between very different systems or for the import of data which exist e g in a table format From the specified conversion type only the default output format for numbers e g E13 6 for 4 byte reals is determined The unformatted binary I O is much faster and gives usually more compact files with higher accuracy ideally exact in the numerical data representation But in principle the file format is machine dependent Fortunately the IEEE format turns out to become a quasi standard among a variety of machines Most workstations work internally with this format Some CRAYS which have a different internal data representation allow the hidden transformation between the internal and IEEE format during the I O process The UIO routines support this feature of CRAY FORTRAN compilers by means of a module uio_mac_module individually designed for two types of CRAY machines using certain CRAY specific system calls CRAY FFIO assign logic Nevertheless there is also a machine independent version of this module written completely in standard Fortran90 but providing less fea
71. el enddataset A typical case for the use of UIO modules is use uio_bulk_module use uio_siz_module use uio_nam_module 4 5 3 Compiling and Makefiles There is a Makefile for the UIO routines For a certain platform it is necessary to change the name of the module file with the machine dependent routines uio_mac _module f90 For this purpose the environment variable UIOMAC has to set to name of the appropriate routine see Sect 3 3 Many compilers generate module information files with suffixes like M mod or kmo To clean up information files with other suffixes they have to be included in the cleaning step Calling examples make make UIO make UIO FO9OFLAGS g make clean make cleanall make remove make removeall A section of a typical makefile using the UIO routines may be Compiler options F90C f90 F9OFLAGS Libraries UIOMAC uio mac sun module Dependencies of exe files on object files and libraries test exe test o F90C F9OFLAGS o 38 4 UIO DATA FORMAT UIOPATH 90 uio_base_module o UIOPATH f90 UIOMAC o UIOPATH 90 uio_bulk_module o test o UIOPATH f90 UIO test f90 F90C c F9OFLAGS M UIOPATH 90 test 90 Dependencies on used modules UIOPATH f90 UIO cd UIOPATH 90 make UIO F9OFLAGS 4F90FLAGS 4 5 4 Sample Calls of Fortran UIO Routines The needed modules have to be declared by a use st
72. ent a simulation in such a case from running forever or until some other process time restriction applies without actually advancing significantly in time it is possible to specify an absolute minimum time step e g with real dtime_min_stop f E15 8 b 4 n Minimum time step u s amp cO dtime_min_stop 0 0 gt no restriction amp c1 dtime lt dtime_min_stop gt program stop 1 0 If the actual time step falls below this value the simulation finishes gracefully This val ues has to specified as absolute time and has to be chosen carefully for each individual model or each group of models This time step restriction can be switched off by setting real dtime_min_stop 0 0 But in general one should keep it activated and try to find a proper positive value 5 3 Parameter File rhd par File 71 e real dtime incmax Sometimes a time step restriction can lead to a sudden drastic drop in the time step To prevent unwanted oscillations in the size of the time step its increase can be restricted e g with real dtime incmax f E15 8 b 4 n Maximum time step increment factor u 1 amp cO dtime_max lt 1 0 gt no restriction cl typically 1 1 1 2 This value specifies the maximum factor by which the time step can be increased from step to step even if the new Courant condition etc would allow more A value value lt 0 0 deactivates this restriction e real c_courant A typical Courant factor for each 1D hydrodynamic
73. er file will fail with an error message Additional entries can be added if the names differ from the standard ones described below Theses entries will be ignored by CO5BOLD but read by the IDL input routine They can be used to provide comments additional information about the model or control parameters for further processing 5 3 1 Quickstart How to Make a Proper Parameter File You will never write a new parameter file from scratch Typically you take an old file e g the one controlling the simulation which produced the model which is used to start the new run and edit it 5 3 Parameter File rhd par File 51 1 Take the parameter file corresponding to the model you want the new simulation to start with 2 Most of the parameters should be already OK E g most of the parameters controlling the boundaries do not have to be changed 3 Write a brief description of the purpose of the planned simulation into the character description array You might but a remark about the parent file of the pa rameter file under construction and the current date into the character history array see Sect 5 3 2 4 Check modify the name of start model and output files infile_start outfile_end outfile_full outfile_mean On a system with batch queue this has not to be done in the parameter file itself but in the external command file see Sect 5 3 13 5 Check modify the fundamental parameters including boundary condition specifiers see
74. er line is an individual record containing a string with exactly 80 characters The following data block scalar or array is one single record 4 3 Structure of UIO Files 33 keyword description example descriptor info necessary b byte number 4 format yes d dimension 0 9 format yes arrays ds dimension shift 1 1 yes f Fortran format E13 6 format yes p values per line 4 format yes arrays t transformation log10 format n name density yes u unit g cm 3 yes date date 1 1 98 yes c0 9 comment Dichte yes form file format formatted file yes file header convert conversion ieee_4 file yes file header version version 0 1 1997 11 29 yes system system IRIX yes machine machine name atlas yes osrelease OS release 6 3 yes osversion OS version 12161207 yes hardware machine hardware IP32 yes language program language Fortran90 yes program program uiotst yes XYZ user defined source yes Table 7 Standard entry header keywords The keyword is given with a short description and an example The fourth fifth and sixth column indicate if the keyword is a mandatory descriptor in the file header or for the format of an entry or if it gives only additional information and is optional and therefore not necessary to specify In a formatted file each header line is a string of at most 80 characters delimited by a LINEFEED of whatever the operating system decided to be appropriate as EOL character sequence
75. es and stops execution For example on a CRAY one typically wants to use most of the CPU time given for an individual batch job In this case one can set e g real cputime_remainlimit 2000 0 and the values for the other halt conditions to 1 0 or 1 e real starttime The start time of a simulation is usually taken from the start model file But sometimes is simulation is to be started with the final model of a previous run but should start at time 0 0 This can be achieved by setting the start time with real starttime f E15 8 b 4 n Start time u s 0 0 Allowed values are o gt 0 0 Set the initial time of the simulation to this value and override value from start model o lt 0 0 default Take the initial time from start model integer starttimestep The start time step count of a simulation is usually taken from the start model file But sometimes is simulation is to be started with the final model of a previous run but should start at time step 0 This can be achieved by setting the start time step count with integer starttimestep f I11 b 4 n Start time step number u 1 0 Allowed values are o 5 0 Set the initial time step of the simulation to this value and override value from start model o lt 0 default Take the initial time step count from start model real cputime Because of the long simulation time usually COSBOLD will run in some sort of batch mode which might impose limits on the execution
76. evious or standard model The history array may contain the predecessor of the parameter file to simplify a tracing of parameter changes e fileform uio The header of the parameter file e g fileform uio form formatted convert ieee_4 date 01 01 2002 amp program by hand can be abbreviated to fileform uio form formatted convert ieee_4 which indicates that the file is in UIO form and Fortran formatted ASCII The speci fication of the conversion type convert ieee_4 is more relevant for unformatted files These terms should not be changed But it can be of interest to append e g the date of the last modification e g date 01 01 2002 52 5 CONTROL AND DATA FILES character file_id The file identification string character file_id f A80 b 80 n File identification rhd parameter indicates the intended use of the file as parameter file for the RHD code CO5BOLD Do not edit character description The header of the file can should contain a short description of the simulation as in e g character description d 1 4 f A80 p 1 b 80 n File description Parameter file for RHD code Full size 3D Betelgeuse model 5 M_Sun 650 R_Sun Start with st35gm04n03_09 end 12773 gt 17173 Run with SHORTrad This entry is optional it can be omitted completely but it is recommended to put at least some relevant keywords into this array If you change the number of lines between 1 and 20
77. figure script should be pretty complete But you might want to add special switches like Bstatic to enforce static linking of libraries o No extra flags F90_POSTFLAGS Compiler flags to be put at the end of the list Usually the list of compiler flags produced by the configure script should be pretty complete However you might want to overwrite some settings This can be done by setting this variable to a none empty value because typically a compiler should interpret the flags from left to right o No extra flags F90_PARALLEL Parallelization scheme o scalar no parallelization default o openmp OpenMP appropriate for CO5BOLD o auto auto parallelization not implemented for all machines F90_DEBUG Debugging level o 0 No extra debugging information produced full optimization is chosen default o 1 standard debugging mode typically switch g instead of fast o 2 other debbuging or array checking modes possible if implemented for the requested machine F90_LHDRAD LHDrad radiation transport o 0 do not activate compile and link this module default o 1 activate this radiation transport module F90_MSRAD MSrad radiation transport o 0 do not activate compile and link this module default o 1 activate this radiation transport module F90_SHORTRAD SHORTrad radiation transport o 0 do not activate compile and link this module default o 1 activate this radiat
78. fined call subroutines to measure elapsed time rhd_roeid_step_t01 in rhd_hyd_module F90 rhd roe 1 dimension step timing 01 Category additional output Produce timing information for the routine which performs the Roe step It should not be used in conjunction with OpenMP Values o undefined default no timing information o defined call subroutines to measure elapsed time Hydrodynamics tensor viscosity e rhd_vis_density_p01 in rhd_vis_module F90 rhd viscosity density parameter 01 Category selection of approximation Choose formula for density average at cell boundary in tensor viscosity routines Values o 0 rhomean min rholeft rhoright o 1 default rhomean 0 5 rholeft rhoright rhd_vis_t01 in rhd_vis_module F90 rhd viscosity timing 01 Category additional output Produce timing information for 2D 3D tensor viscosity routines It should not be used in conjunction with OpenMP Values o undefined default no timing information o defined call subroutines to measure elapsed time Radiation transport e rhd_rO0l1 in rhd F90 rhd radiation 01 Category feature activation Switch to include LHDrad radiation transport module It uses long characteristics and is restricted to an equidistant grid and open boundaries at all surfaces old supergiant module Values o undefined default LHDrad routines are deactivated o 1 LHDrad routines are recogn
79. g in IDL real abux real abuy 76 real c_radkappasmooth 77 real c_courant 71 real c_courantmax 71 real c_dust0X 63 real c_hptopfactor 56 real c_maxeichange 71 real c_pchange 56 real cputime 68 real cputime remainlimit real c_radcourant 71 real c_radcourantmax 72 real c_radhtautop 57 real c_radimplicitmu 67 real c_raditereps 67 real c_raditerstep 67 INDEX real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real c_radmaxeichange c_radthintimefac c_radtintminfac 77 c_radtsmooth 77 c_radtvis c_radtvisdtau 67 c_schange c_tchange c_tsurf c_visartificial c_visbound c_viscourant c_viscourantmax c_visdrag c_visneul 76 c_visneu2 77 c_visprturb c_vissmagorinsky c_vistensordiag 61 c_vistensordiv c_vistensoroff 61 dtime_incmax dtime_max 70 dtime_min 70 dtime_min_stop 70 dtime_out_full dtime_out_mean dtime_start 70 endtime gamma 76 grav luminositypervolume mass_star plustime qmo1 76 r0_grav 53 ri_grav ri_rad 53 rho_min s_inflow starttime teff tensor viscosity time step rhd stop Roe solver SGI short characteristics SHORTrad Sun tensor viscosity tensor viscosity routine
80. hannel nc ierr ierr outstr err_msg IDL gt endfor amp IDL gt uio_closrd nc Again this operation would cause an error if the wanted time step is not contained in the file Via checking the error flag ierr of the routine uio_dataset_rd such errors can be avoided This way it is unnecessary to know exactly of how many time steps the model file consists IDL gt uio_openrd nc modelfile outstr ierr IDL gt i 0 IDL gt repeat begin amp IDL gt ful uio dataset _rd modelfile channel nc ierr ierr outstr err msg amp IDL gt if ierr eq 0 then begin amp IDL gt hier Daten bearbeiten oder in anderer Variable speichern IDL gt i i 1 amp IDL gt endif else begin amp IDL gt print IDL gt Reached EOF amp IDL gt endelse amp IDL gt endrep until ierr ne 0 or EOF nc IDL gt uio_closrd nc To read a number of entries from a list of files in sequence the routine uio_datasetlist_rd pro see Sect is appropriate 7 2 3 Loading the Equation of State IDL gt eosfile eos dat par eosfile IDL gt tabinter_rdcoeff eosfile eos The table for the equation of state is provided in the structure EOS NOTE Always check file name and path 7 2 4 Loading the Opacity Table IDL gt opafile opa dat par opafile IDL gt dfopta opafile The opacity table will be stored as common block OPTA_COMMON NOTE Always check file name and path 7 2 5 Computation of Deduced Quantities Afte
81. in the optically thin by specifying e g real c_radthintimefac f E15 8 b 4 amp n time scale reduction in optically thin u 1 amp cO range 0 1 1 0 typically 0 5 0 60 A value lt 0 0 or real c_radtvisdtau lt 0 0 switches off this relaxation real c_viscourant The tensor viscosity routines have their own time step restriction The recommended typical viscous time step can be set e g with real c_viscourant f E15 8 b 4 n viscous Courant factor u 1 amp cO range 0 0 lt C_visCourant typically 0 5 1 0 better 0 25 0 5 5 3 Parameter File rhd par File 73 As the corresponding viscous timescale is typically longer than the radiative one and even the Courant timescale from the Roe hydrodynamics routines this factor is often irrelevant The absolute upper stability limit is located at c_viscourant 2 0 Values around 0 5 to 1 0 are more typical In some extreme cases in simulations of the solar chromosphere it has turned out that an even lower value 0 2 is necessary to prevent some spikes in the neighborhood of strong colliding shocks real c_viscourantmax The absolute upper limit for the viscous time scale can be set with real c_viscourantmax f E15 8 b 4 n maximum viscous Courant factor u 1 amp cO range C_visCourant lt C_visCourantmax typically smaller than 2 0 1 0 Its value should be slightly above c_viscourant and below 2 0 5 3 13 Input Output Control With this group of
82. ion o defined call subroutines to measure elapsed time e rhd_rad3d_step_t01 in rhd_1hdrad_module F90 rhd radiation 3 dimensions step timing 01 Category additional output Produce timing information with main 3D radiation transport routine It can be used together with OpenMP and should cause no noticeable performance loss Values o undefined default no timing information o defined call subroutines to measure elapsed time rhd_shortrad_operator_101 in rhd_shortrad_module F90 rhd short characteristics radiation operator loop 01 Category performance enhancement selection of approximation Choose type of short characteristics operator The operators usually come in pairs 1 2 3 4 5 6 There is a development from 1 2 over 3 4 to 5 6 towards higher stability Both members of each pair should do the same operation but use different ways to do a case distinction The even operator has in most case the better performance But the odd operator might be saver to use Values o 0 simple test operator fast but results are utterly useless o 1 case distinction with if then else construct case distinction with masks weights 0 0 or 1 0 0 1 2 o 3 case distinction with if then else construct slope reduction of source function 4 case distinction with masks weights 0 0 or 1 0 slope reduction of source function 5 case distinction with if then else construct
83. ion 3 8 3 U77 Link proper library to make the machine understand e g call flush 6 cpp yes Switch on the C preprocessor Note that all Fortran90 files have to end with 90 The F90 suffix does not seem to work tOfast High optimization level and Ofaster is even higher Dopenmp Onoautopar Try to enable parallelization with OpenMP directives disable auto parallelization The code compiles and runs fast but crashes after a few time steps 3 8 5 Hitachi conti199 Up to 199 continuation lines can be interpreted otherwise not more than 39 continuation lines are accepted limit Limits the amount of time and memory for compilation opt ss use highest possible optimization level nopredicate this option switches off a sub option activated by opt ss It is necessary to disable the predicate option because the code crashes otherwise segmentation violation The switch must appear after setting opt ss pvfunc 2 References the pseudo vectorizing mathematical function and applies the tem porary array to reference the pseudo vectorizing mathematical function omp parallel 1 parallelize based on OpenMP directives only procnum 8 generated code for 8 processors on one node orphaned 1 Checks if the regions sequentially executed contain orphaned directives dur ing run time when PROCNUM 3 is specified If a sequentially executed region contains an orphaned directive the system outputs a message and ter
84. ion transport module 16 3 PROGRAM FILES INSTALLATION COMPILATION e F90_DUST DUST module o 0 do not activate compile and link this module default o 1 activate this radiation transport module If this variable is set to 1 the compiler is called with Drhd box guc01 1 see Sect e F90 MHD MHD module o 0 do not activate compile and link this module default o 1 activate this radiation transport module F90_MACHINE Explicit machine specification This isusually not necessary use local or y instead o local machine o sun4u Sun o See the header of the configure script for an up to date list o local local machine default o dummy Do not use any machine dpedendent flags but use module selections o empty Compiler flags are composed from F90_PREFLAGS and F90_POSTFLAGS only e F90_BASEPATH Path for COSBOLD base directory o gt The configure script tries to determine the base directory name automatically de fault This should work if the local directory is located somewhere below hd rhd o otherwise This string is used as base directory name e g home user for Some examples can be found in Sect 3 7 Compiler Macros Some of the modules of the CO5BOLD code with suffix F90 employ compiler macros to switch between code versions during compile time Typically you define at least one of the three switches rhd_r01 rhd_r02 or rhd_r03 to choose a radiation transport
85. ist of old source directories with path and file name abbreviation and a short description The executables and makefiles object files module information files are usually located in subdirectories of the source code directories These subdirectories typically have the name of the machine architecture or operating system the executable is compiled for 3 4 Old Setup File for Paths For the previous version of COSBOLD all paths were stored in environment variables and could be set with the scripts 10 3 PROGRAM FILES INSTALLATION COMPILATION setarcdeppaths sh or setarcdeppaths csh These variables are now ignored by the configure script that produces the Makefile to generate the CO5BOLD executable rhd exe However they are still used e g by the makefile that produces the executables that are called by the UIO scripts The environment variables for the UIO routines can be e g UIOSRCPATH home user for uio f90 UIOEXEPATH home user for uio f90 sun A script to set all necessary variables and paths can be here for the Bourne shell bin sh Disk where all Fortran programs are located FORTRANDISK HOME for export FORTRANDISK if uname s craSH then Kiel craSHi UIOMAC uio_mac_crayxmp_module export UIOMAC RHDMAC rhd_mac_cray_module export RHDMAC elif uname s craSH then Kiel craSH UIOMAC uio_mac_crayts_module export UIOMAC RHDMAC rhd_m
86. ivated for runs on one thread as done by the configure script It is always save to switch any of them off by removing or undefining them The macros in the category test mark parts of code under development The default values should only be changed with great care typically by the author of that code segment The configure script does not touch these settings General e timing_c_factor in timing_module F90 timing count factor Category account for property of machine To produce the timing statistics printed at the end of a simulation run the standard Fortran routine SYSTEM_CLOCK is used The macro timing_c_factor specifies by how much the count rate of this routine is reduced when storing its count value This does not prevent all overflows but can make the output much more useful Values o 1 default count rate of SYSTEM_CLOCK is used directly o otherwise e g 1000 count rate of SYSTEM_CLOCK is reduced by this factor By a proper choice of this factor the timing measurements of individual routines can be made meaningful the reduction of the count rate prevents overflows due to the addition of several measurements An overflow during an individual measurement can not be prevented Therefore the count rate for the entire program still tends to produce overflows e gasinter_101 in gasinter_routines F90 gas interpolation 101 Category performance enhancement This switch determines how temporary arrays are h
87. ix parameter 01 Category performance enhancement The entropy fix can be done in one of two ways to get optimum performance with essentially the same results Values o 0 default if then else construction o 1 use a mask and the signum function rhd hyd upwind p01 in rhd hyd module F90 hd hydrodynamics upwind parameter 01 Category performance enhancement The determination of the upwind direction can be done in one of two ways to get optimum performance with essentially the same results Values o 0 default if then else construction o 1 use a mask and the signum function rhd hyd roeld 101 inrhd hyd module F90 rhd hydrodynamics roe 1 dimension loop 01 Category performance enhancement The computation of the Roe fluxes can be done by either of two sets of routines to find the set which gives optimum performance with essentially the same results Values o 0 default lots of small routines acting on scalars inlining needed cache reuse is optimized o 1 routines acting on arrays more temporary arrays necessary vectorization is easier rhd_roeid_flux_101 in rhd_hyd_module F90 rhd roe 1 dimension flux loop 01 Category test By setting this switch an alternative way of computing the upwind centered Roe states is activated only for constant reconstruction for performance test purposes only do not activate Values o undefined default
88. ized by the compiler rhd_r02 in rhd F90 rhd radiation 02 Category feature activation Switch to include MSrad radiation transport module It uses long characteristics The lateral boundaries have to be periodic Top and bottom can be closed or open solar module Values 3 7 Compiler Macros 21 o undefined default MSrad routines are deactivated o 1 MSrad routines are recognized by the compiler rhd_r03 in rhd F90 rhd radiation 03 Category feature activation Switch to include SHORTrad radiation transport module It uses short characteristics and is restricted to an equidistant grid and open boundaries at all surfaces new supergiant module Values o undefined default SHORTrad routines are deactivated o 1 SHORTrad routines are recognized by the compiler rhd_rad3d_toray_101 in rhd_lhdrad_module F90 rhd radiation 3 dimensions to ray loop 01 Category performance enhancement There might be a performance gain by splitting the main loop in routine rhd_rad3d_toray into three separate loops Typically one big loop is to be preferred Values o undefined default One big loop o defined Three smaller loops rhd_rad3d_fromray_101 in rhd_lhdrad_module F90 rhd radiation 3 dimensions from ray loop 01 Category performance enhancement There might be a performance gain by splitting a big loop in routine rhd_rad3d_fromray into two separate loops Typically
89. ke a Proper Parameter File Sect 5 3 1 How to Run CO5BOLD Sect 6 1 2 Basic Equations The 3D hydrodynamics equations including source terms due to gravity are the mass conservation equation Op Opvl Opv2 pv H 0 1 a sl r2 0x3 1 the momentum eguation pul pul v1 P pul v2 pul v3 p gl pv2 pv2v1 pv2v2 P pv2v3 p92 2 2 pu3 on pu3 v1 ae pu3 v2 0x8 pv3 v3 P p 93 and the energy equation Opeik O peik P vl peik P v2 p O peik P v3 at dx1 912 Ing p gl v1 g2 v2 g3 v3 3 In addition there are equations for the 3D tensor viscosity and the non local radiation transport 6 3 PROGRAM FILES INSTALLATION COMPILATION 3 Program Files Installation Compilation In this section all the files and modules CO5BOLD contains are listed The installation procedure is outlined and compiler switches necessary to compile CO5BOLD and to optimize its performance are described 3 1 Quickstart How to Compile CO5BOLD If you are going to install CO5BOLD on a machine with a known to setup script and makefile operating system and compiler see Sections and then the procedure should be fairly easy The general compilation procedure is now If a directory for the current machine exists in the tar ball and the configure script is there tar zxvf for tar gz cd for hd rhd YOUR_MACHINE configure make If the directory for the current machine has to be
90. l radiative time step is computed real c_radcourantmax With this parameter the maximum allowed radiative time step is prescribed as e g in real c_radcourantmax f E15 8 b 4 n maximum RAD Courant factor u 1 amp cO range C_radCourant lt C_radCourantmax typically 2 0 3 0 This value will typically be somewhat larger than real c_radcourant real c_radmaxeichange The relative energy change per radiative sub step can be restricted e g with real c_radmaxeichange f E15 8 b 4 n maximum radiative energy change amp u 1 cO range 0 01 1 0 0 25 The default is 0 5 Values between 0 1 and 0 5 seem reasonable A value lt 0 0 deactivates this time step check However the check of the radiative energy change should usually be performed A way to maximize the radiative time step and therefore the performance of the entire code can be to first set real c radmaxeichange to a proper value say 0 25 Then real c_radcourant and real c_radcourantmax are adjusted by trial and error in a way that the radiative time step is almost always restricted by the Courant condition and only sometimes in extreme cases by the maximum energy change restriction The computed output intensity should be checked for the size of its fluctuations due to a possibly too large value of c_radmaxeichange real c_radthintimefac In the LHDrad module only the radiative time step restriction due to energy changes can be relaxed further
91. like Try to determine language if n_elements X TICKV eq 150 then langua WAVE else langua IDL Add user IDL directory to search path if langua eq IDL then begin amp addpath expand path UIOPATH id1 amp endif else begin amp addpath home supas024 uio idl home supas024 wave endelse if strtrim addpath 2 ne then path addpatht path delvar addpath Alternatively one might want to set the IDL path variable accordingly like export IDL_PATH UIOPATH id1 for example in the bashrc file It is reasonable to include the UIO initialization in the startup procedure as e g 3 Initialize uio routines uio_init progrm by hand IDL can handle the conversion types native ieee_4 ieeele_4 ieee idl xdr Here ieee_4 is the default and should be used as a standard Attention The IDL type long corresponds to the standard Fortran type integer The IDL types byte and integer are not known in standard Fortran and are therefore transformed to the IDL type long before writing in the IDL routine uio wr Be aware of The parsing and interpretation of the entry headers can only be done by scalar operations which are comparatively slow in IDL 4 7 2 Reading Data with uio_data pro The IDL routine uio_data and the IDL function uio_d were the first set of high level routines to read UIO data in IDL
92. like export IDL_PATH UIOPATH id1 for example in the bashrc file 7 2 CO5BOLD Data in IDL Important to know is that all operations can be performed in the command line of IDL This allows an interactive processing of COSBOLD data Moreover there are already prepared IDL scripts for this purpose but most of them are rather complex and still have to be edited e g changing file names For the beginning it is more clear to use single commands We give a short overview of some essential commands 7 2 1 Loading the Parameter File IDL gt parfile mymodel par IDL gt par uio_struct_rd parfile All control parameters are provided in the structure PAR 7 2 2 Loading CO5BOLD Data full sta end IDL gt modelfile home user mymodel full amp n 0 IDL gt ful uio_dataset_rd modelfile n n First the name and full path if not in the actual directory of the model file and the wanted time step should be defined Here time step means the consecutive number of the model snapshot in the file Declaring a time step number greater than the number of snapshots contained in the file will cause an error Otherwise all data of the particular time step n will be provided in the structure FUL Loading more than one timestep from the same file could be achieved as follows IDL gt uio_openrd nc modelfile outstr ierr 7 3 IDL Data Structure 83 IDL gt for i 0 ntime 1 do begin amp IDL gt ful uio_dataset_rd modelfile c
93. lity The identifier of an entry together with the name n and the unit u should give a first hint about the meaning of the quantity The suffix _xmean indicates a simple average The suffix _xmean2 indicates the root mean square average note the simple average is not subtracted Some entries e g ferb_xmean have a hidden b in their name have one element more e g 121 instead of 120 than most of the others and are characterized by the ds keyword see Table 7 These quantities are located at the cell boundaries in contrast to the usual cell centered quantities Clearly there are also two sets of axes e g xc3 and xb3 corresponding to the cell or boundary centered quantities Note The total energy flux can be written as sum feb total feipkgvrb feipb fekb fegb fevb ferb The flux fepb is already part of feipb 5 3 Parameter File rhd par File The parameter file rhd par also has the UIO format But it will be usually Fortran formatted ASCII It contains a list of parameter entries which are collected in groups to make it easier to find an entry Otherwise the order is arbitrary except for the very first fileform uio entry If there are more than one entry with the same name the first occurence will be used by COSBOLD But the doubling of entries is strongly discouraged because it will almost certainly lead to confusion at some time In addition the IDL routine to read the paramet
94. lls the Fortran program uiolok f90 The man page UIOLOOK 1V Misc Reference Manual Pages UIOLOOK 1V NAME uiolook print entry headers of file in uio form SYNOPSIS uiolook h p 1 filename AVAILABILITY DESCRIPTION The routine uiolook reads each filename file in uio form in sequence and displays the headers of the entries in pretty form OPTIONS h Print usage of uiolook p Entry header keywords in long pretty form SunOS 5 5 1 Last change 27 November 1996 1 4 6 2 Transformation of Files uiocat The shell script uiocat calls the Fortran program uiocat f90 The man page 40 4 UIO DATA FORMAT UIOCAT 1V Misc Reference Manual Pages UIOCAT 1V NAME uiocat concatenate file s in uio form SYNOPSIS uiocat c conversion f format h 1 1 copylist o outputfilename filename DESCRIPTION The routine uiocat reads each filename file in uio form in seguence and displays its contents formatted on standard output or writes it into a file In the latter case the format change from formatted to unformatted or vice versa is possible OPTIONS c Conversion type native ieee_4 machine dependent its specification is only relevant if an output file is specified with the o option and output format unformatted f Output format formatted or unformatted Its specification is only relevant if an output file is specified with the o o
95. ly on a CRAY machine The gain is marginal if present at all The parameter is usually set to zero or left undefined Values o 0 default no padding cells o 1 2 3 extra padding cells e rhd_hyd_gravcorr_p01 in rhd_hyd_module F90 rhd hydrodynamics gravitation correction parameter 01 Category selection of approximation This parameter controls the way the Roe solver handles the source terms due to gravity A different choice results in different simulation results and not just in slightly faster or slower code The problem is that the original Roe solver interpretes the pressure gradient in a hydrostatic stratification a fluctuation due to shock waves In case of strong stratification this can lead to weird effects With activated correction the Roe solver treats only the deviations from a hydrostatic stratification as due to waves or shocks Several correction formulas have been tried The latest is the recommended default Values No pressure correction terms in Roe solver Simple correction with rhomean no new average pressure Simple correction with rhomean new average pressure Correction with local rho limited new average pressure O PB W N FP O Correction with local rho new different formula average pressure 3 7 Compiler Macros 19 o 5 default Correction with local rho new limit new average pressure rhd_hyd_entropyfix_p01 in rhd_hyd_module F90 rhd hydrodynamics entropy f
96. mance loss Values o undefined default no timing information o defined call subroutines to measure elapsed time Optimization Compiler Switches In this section some mandatory or useful compiler flags are described These have different functions Enable necessary macro processing expansion for the F90 files Force proper handling of binary I O Choose module for radiative transfer Activate module for dust formation and or magnetic field transport Enable parallelization with OpenMP directives Choose a version of a subroutine or loop which is optimized for a specific architecture Tell the compiler if and what to inline Improve the general performance 3 8 1 Cray SV1 On craSHi in Kiel a CRAY SV1 20 32768 SN9542 now out of service CO5BOLD could use all 4 processors per board Documentation about the system and the compiler can be found with the CRAYdod system The new configure script still includes a branch for this system even if has never been tested on that machine In some cases the non default versions of loops in the CO5BOLD code vectorize better and are preferred over the standard ones F Enable macro expansion Otask1 Parallelization Enable tasking in this case OpenMP Oinline3 Optimization enable high level of inlining Ovector3 Oscalar3 General optimization Drhd hyd roe1d 101 1 Optimization Choose non standard set of routines for Roe solver See Sect Drhd_hyd_entropyfix_p01
97. minates the program nestcheck 1 Checks for nesting errors in parallel regions If a parallel region is nested the system returns an error and terminates the program Without this option the code aborts with an error message indicating illegal nesting Compiler bug pmpar Collects the performance monitor information for each parallelization unit pmfunc Collects the performance monitor information for each procedure Drhd hyd roe1d 101 1 Optimization Choose non standard set of routines for Roe solver See Sect DMSrad raytasl Optimization choose non default version of SUBROUTINE raytas in file MSrad3D F90 Important note The UIO routines need in addition the compiler option subchk Array bound checking Without this checking option some UIO routines are not working properly compiler bug 3 8 Optimization Compiler Switches 27 3 8 6 Linux PGI Compiler So far under Linux the compiler of the Portland Group has been used mostly to compile CO5BOLD It is called with pgf90 Important switches are e byteswapio With this flag set binary files in big_endian format the standard for UIO files are automatically transformed to little_endian and vice versa e fast General optimization flag to choose close to optimum optimization for local ma chine e Mvect sse Optimization Allow Pentium III vector commands e Mcache_align Optimization Align some data object on cache line boundaries e fastsse From
98. n character tables with columns of type integer real single precision or character or structuring information labels Each entry consists of the header and the possibly empty data block Each header is a list of at most 20 terms separated by blanks The first term is the entry type see table 6 followed by an identifier This identifier should follow the standard rules for variables small capital letters numbers underline starting with letter a name as e g rho v_1 The rest of the terms come in the form keyword value See Tab entry type entry contents fileform file description first entry integer scalars 1D 4D arrays real scalars 1D 4D arrays single amp double precision complex scalars 1D 4D arrays single precision character scalars 1D 4D arrays table table with integer real character columns label label entry for file structuring Table 6 Entry types A header line has a maximum length of 80 characters A continuation line is indicated by 1 amp at the end of the line A header consists of 20 lines at maximum It can be preceded by empty lines except for the file header entry Example real time f F9 2 b 4 n Time u s c0 Simulation time in seconds amp ci Time count starts at 0 0 12 34 The entry header is followed by the entry data block This block is empty for labels and the fileform entry but non empty otherwise In an unformatted file each head
99. n Negative temperature spikes may result This smoothing should not be used anymore character radpressure In the LHDrad module there exists a simple prescription for the radiative pressure reason able in the optically thin which can be activated with character radpressure f A80 b 80 n Radiation pressure mode amp c0 on off on Allowed values are o on Radiation pressure on o off Radiation pressure off The scheme is pretty slow and wrong in the optically thick Do not use real c_radtintminfac In the LHDrad module The fraction the interpolated temperature at a point on the ray may exceed the minimum temperature at its four neighbors on the HD grid can be set e g with 78 5 CONTROL AND DATA FILES real c_radtintminfac f E15 8 b 4 amp n Temperature interpolation parameter u 1 amp c0 lt 1 0 only bilinear 1 1 reasonable weighting between min und bil 0 0 The introduction of this parameter was an attempt to reduce the negative cooling effect of a single hot cell on its cool neighbors It should be switched off e g by setting it to 0 0 integer dtimestep_out_fine This parameter can be specified but there is no corresponding output file in CO5BOLD yet integer dtimestep_out_fine f I4 b 4 n Dutput time step number u 1 cO dtimestep_out_fine lt 0 gt no output 1 character outfile_fine The name of the file for the output of additional information at regular small
100. n Roe solver amp cO 0ff0 default0 default default2 default3 default5 In recent versions this coupling has to be specified at compile time with the switch rhd hyd gravcorr p01 see Sect e real c visneul 5 3 Parameter File rhd par File 77 real c_visneul f E15 8 b 4 amp n Linear viscosity parameter von Neumann Richtmyer type u 1 0 0 real c visneu2 real c_visneu2 f E15 8 b 4 amp n Quadratic viscosity parameter von Neumann Richtmyer type u 1 0 0 real c_radkappasmooth In the LHDrad module the opacity along each ray can be smoothed The amount of smooth ing can be set e g with real c_radkappasmooth f E15 8 b 4 n Opacity smoothing parameter u 1 amp c0 0 0 no smoothing 0 25 light smoothing 0 666 strong smoothing 0 0 The smoothing can perhaps reduce the noise in the intensity images somewhat but has no general beneficial effect and should usually not be used real c_radtsmooth In the LHDrad module the 3D temperature array can be smoothed The amount of smooth ing can be set e g with real c_radtsmooth f E15 8 b 4 n Temperature smoothing parameter u 1 amp c0 0 0 no smoothing 0 5 reasonable smoothing 1 0 max smoothing 0 0 The smoothing can sometimes reduce the noise in the intensity images but causes amplifies some anomalies of the radiative Greens function Some cool cell just above the sharp sub photospheric temperature drop are not heated but cool further dow
101. ng periods of matter infall the density at an open outer boundary can become very low To limit the decrease of the density a lower limit in the extrapolated ghost cells can be set e g with real rho_min f E15 8 b 4 n Minimum boundary density u g cm 3 1 0E 25 The density within the model will typically not fall much below this value A value of 0 0 default or below deactivates this feature 5 3 5 Equation of State e character eosfile The equation of state file together with the opacity file implicitly determine the chemical composition The EOS file can be specified for instance with character eosfile f A80 b 80 n EOS file name amp cO eos_gamma140 eos eos_mm20_1 eos eos_mm00_13 eos So far there exists only a relatively small number of files o eos_mm00_13 eos Standard EOS file for solar composition with extra large density range towards low densities There exist two other files for the same composition but smaller density range eos_mm00 eos eos_mm00_1 eos o eos_mm20_l eos Standard EOS file for metal poor star M H 2 0 with ex tended range in internal energy and density towards lower values The older file eos_mm20 eos did not reach far enough o eos gamma140 eos EOS table for simple gas with constant 1 4 In this case all quantities could be faster computed than by interpolation in a table Nevertheless for compatibility reasons to be able to use the existing EOS Fortran routines the table is
102. ng radiative time scales it will typically be set to 1 For starts with shorter radiative time scales values around 10 may be considered All three radiation transport modules understand this parameter e integer n_radmaxiter The absolute maximum number of iterations can be specified e g with integer n_radmaxiter f 14 b 4 amp n Maximum number of rad transport iterations c0 30 0 If more iterations are needed the computation for the current time step is stopped and resumed with a smaller one which means that the hydrodynamics and the tensor viscosity step have to be done again Usually n_radmaxiter will either be set to a values somewhat larger than the recommended number of iterations n_raditer or to 0 which disable the check for too many iterations completely This can be safely allowed in many cases and has the advantage that there is no need to save the initial model before calling the radiation transport module which saves some memory To disable the iteration of the radiation transport sub step set n_radminiter n_raditer n_radmaxiter 1 All three radiation transport modules understand this parameter 5 3 Parameter File rhd par File 65 e character radraybase Using the modules LHDrad or SHORTrad the orientation of the base axis system can be selected e g with character radraybase f A80 b 80 n Base axis system amp cO unity random randomgroup random Allowed values are o unity default During all time
103. odic periodic boundaries for hydrodynamics and radiation o transmitting transmitting boundary for hydro and outward radiation In almost every simulation of stellar convection a transmitting top boundary will be selected the closed one is an alternative The periodic condition is only recognized by the hydrodynamics routines and not by any radiation transport routine e character bottom_bound The boundary condition at the bottom of the model is given for instance by character bottom_bound f A80 b 80 n bottom boundary conditions amp cO closedbottom transmitting 5 3 Parameter File rhd par File 55 Possible values are o reflective closed wall no gravity no radiation o constant open boundary with constant extrapolation of all values no gravity no radiation o closed closedtop closed wall can handle gravity open for outward radiation o closedbottom closed wall handles gravity radiation in diffusion approximation o periodic periodic boundaries for hydrodynamics and radiation o transmitting transmitting boundary for hydro and outward radiation The parame ters real c_tchange real c_tsurf and real c_hptopfactor have to be specified o inoutflow classical open lower boundary for deep convection gravity and radiation possible The parameters real s_inflow real c_schange and real c_pchange have to be specified In simulations of a solar like star with the MSrad radiation transport module the bot tom bo
104. odule f90 UIO I O routines machine dependent part uio f90 uio_mac_ieee_module f90 UIO I O routines machine dependent part uio f90 uio_mac_intel_module f90 UIO I O routines machine dependent part uio f90 uio_mac_module f90 UIO I O routines m d minimal version uio f90 uio_mac_nec_module f90 UIO I O routines machine dependent part uio f90 uio_mac_sun_module f90 UIO I O m d works in most cases Table 3 List of all modules the table shows the file name with part of its path the shortcut for the directory and its description 14 3 PROGRAM FILES INSTALLATION COMPILATION File and path Abb Description mat str str module f90 STR string handling uio f90 uio base module f90 UIO I O routines uio f90 uio bulk module f90 UIO I O routines uio f90 uio filedef module f90 UIO I O routines uio 90 uio mac crayxmp module f90 UIO I O routines machine dependent part eos f90 gasinter_routines f90 EOS equation of state rad hdrad cubit_module f RAD cubic interpolation rad hdrad opta par module f90 RAD parameters for opacity routines rad hdrad opta routines f RAD opacity rad hdrad MSrad3D F90 RAD Matthias radiation transport routines long characteristics periodic sides hd rhd timing_module 90 RHD timing routines hd rhd rhd_const_module f90 RHD physical and mathematical constants hd rhd rhd gl module f90 RHD global parameters hd rhd rhd action module f90 RHD routines for control parameter passing hd rhd
105. ollowing data block This data block usually consists of a scalar or an array In some cases it is empty e g for labels or it contains more complex information for tables The first version of UIO routines was written in FORTRAN77 They still exist But further development was done with the Fortran90 versions Therefore the use of the FORTRANT7 routines is not recommended anymore The current Fortran version of the UIO routines is a set of Fortran90 modules To allow a communication between Fortran and IDL programs an IDL version of the UIO routines has been written The correspondence between Fortran and IDL routines is rather close But in detail there are differences Currently IDL Version 5 4 sunos sparc is used Amazingly the UIO routines also used to work under PV WAVE Version 6 01 sun4 solaris sparc The UIO routines have been successfully compiled and used on Cray alpha HP V2500 HP Itanium2 Hitachi Linux with PGI and Intel compiler SGI and Sun machines So far there exist three UNIX shell scripts calling Fortran routines useful to quickly examine data sets or to change the format or conversion type of files 4 2 Example of UIO Data File To give a first impression about the data structure here follows a simple test file which contains the header a label a couple of scalars an array and a short table fileform uio form formatted convert native version 0 1 1997 11 29 amp date 29 11 1997 21 23 39 835 sy
106. ompiler is called with ifc Important switches are e Vaxlib Link proper library to make the machine understand e g call flush 6 e fpp Activate the preprocessor silently e 03 General optimization flag e tpp6 xK Optimization especially for Pentium III includes SSE vector commands 28 3 PROGRAM FILES INSTALLATION COMPILATION e ip Optimization activate interprocedural optimization within each source file This enables inlining e Drhd_shortrad_dir1_101 1 Optimization Transpose arrays and use routine rhd_shortrad_dir3 for rays in xl direction See Sect e openmp Parallelization OpenMP directive are activated Note that the UIO routines should be compiled without OpenMP support even if they do not contain any OpenMP directives themselfes 3 8 8 NEC SX 5 First attempts to compile COSBOLD on neSH An environment variable has to be set to F_RECLUNIT BYTE before execution of a program to enable UIO to compute proper record lengths The cross compiler on kueste is called with sxf90 No optimized version of CO5BOLD has been achieved yet Some maybe useful switches are e sx5 generate instructions for SX 5 e C vopt normal optimization in vector mode e Wf M noflunf M noinv M noinexact M setall suppress some exceptions e P openmp parallelization with OpenMP e Ep call cpp preprocessor e pi exp inlining e dw float0 no special environment variable use internally and in file
107. onvergence is safe but too slow A too large step size inhibits convergence and leads to a decrease in the time step which results in a bad performance too e real c_radtvisdtau Using the LHDrad module the limit in delta optical depth rho kappa dx below which the radiative temperature viscosity temperature smoothing is to be applied can be set with e g real c_radtvisdtau f E15 8 b 4 amp n Optical depth limit for temperature viscosity u 1 0 1 68 5 CONTROL AND DATA FILES The introduction of this temperature diffusion is a somewhat desperate and inelegant attempt to improve the behavior of the Greens function hot cells should be cooled cool cells should be heated This diffusion is necessary for not well resolved models It is switched off with c_radtvisdtau lt 0 0 real c_radtvis Using the LHDrad module the amount of the radiative temperature viscosity tempera ture smoothing can be specified e g with real c_radtvis f E15 8 b 4 n Temperature viscosity u 1 1 6 For well resolved models it should be switched off with c_radtvis lt 0 0 But often its use is necessary 5 3 11 Process Time Management In this group several parameters can be set which control the start of the time counting during a simulation and the total length of a job If either one of the halt conditions below is met CO5BOLD finishes the current step writes a final model plus some final information to other fil
108. onversion type are determined automatically from the file if the conversion type of the data in the file is among the conversion types supported by the compiler If the file has a conversion type native but is created on a 32 4 UIO DATA FORMAT conversion type I R D description native internal data format on all machines sometimes useful but not recommended ieee_4 4 4 8 standard IEEE big_endian format recommended ieeele_4 4 4 8 IEEE little endian format ieee_8 8 8 16 double precision IEEE big_endian format on some machines possible crayxmp_8 8 8 16 CRAY internal data format idl 4 4 8 IDL format but IDL also supports ieee_4 xdr 4 4 8 format possible with IDL ieee 4 limit 4 8 8 standard IEEE format ieee_4 ieee 2 IEEE format unknown length not recommended Table 5 Conversion types with length of integers single precision reals and double precision reals in bytes and an explanation machine with different internal data representation the file header might be readable but an error will probably occur during the reading of a real variable 4 3 2 Data File Structure The UIO routines only handle sequential files Each file consists of a list of entries The first entry describes the file format conversion type and the machine who is responsible for it The following entries contain data scalars and 1D 4D arrays of type integer real single amp double precision complex single precisio
109. provided o eos_gamma166 eos EOS table for simple gas with constant 5 3 e character eospath The equation of state file does not have to be in the working directory Instead its path can be specified e g with character eospath f A80 b 80 n path of EOS file amp cO astro b bf for eos dat home a_bf for eos dat 5 3 6 Opacities e character opafile The opacity file can be specified with e g 58 5 CONTROL AND DATA FILES character opafile f A80 b 80 n opacity file name amp c0 g2va opta big_grey opta c1 empty gt no radiation transport phoenix_opal_grey opta So far there exist already a couple of files O O O davmf opta f5v opta g2va opta g2v_lowhe opta g2v_m20 opta g2v opta hmin_p00 opta opal_lowhe opta opal_m05 opta opal_m10 opta opal_m20 opta phoenix_dust_grey opta phoenix_dust_ob4 opta phoenix_opal_grey opta ross_m05 opta ross_m10 opta ross_m20 opta sunurl opta sunur2 opta t5000844mm20 opta t5000847mm20 opta t6300g40mm20 opta t6500 44mm20 opta zzcetilg opta zzcetil opta e character opapath The opacity file does not have to be in the working directory specified e g with Instead its path can be character opapath f A80 b 80 n path of opacity file amp c0 astro b bf for opa dat home a bf for opa dat 5 3 7 Hydrodynamics Control e character hdscheme With this parameter the type of the hydrodynamics scheme can
110. ption h Help print usage of uiocat zL List of entries to be copied E g uiocat l real rho uiocat 1 real rho integer i uiocat 1 label real rho integer i uiocat l label real rho i Here copylist is a list separated by Each item consists of exactly two items separated by a blank No additional blanks are allowed Use copylist with as above 0 Output file name If omitted standard output is used and c and f are meaningless SunOS 5 5 1 Last change 12 January 1998 1 4 6 3 Information about Conversion Types uioinfo The shell script uioinfo calls the Fortran program uioinf f90 The man page uioinfo 1V Misc Reference Manual Pages uioinfo 1V NAME uioinfo print machine dependent information SYNOPSIS uioinfo DESCRIPTION The routine uioinfo prints information about its environment and a list of possible conversion types OPTIONS SunOS 5 5 1 Last change 12 January 1998 1 4 7 IDL UIO Routines 41 4 7 IDL UIO Routines The UIO package in IDL comes as a list of routines with names quite similar to the Fortran90 version Instead of using global variables as in Fortran90 there are now common blocks in Include files 5 FR ak ak ee dale ad al led le dd od ale dad le ad ad led k ak kakak dd ale ad al kakak ak kakak k 3K K k 2K K k led al le kakak ad K ak ok ak K Routines functions uio_ pro adkeyl adkey2 adkey3 5 chconv
111. r file or for the UIO table file in Sect e g par uio_struct_rd st35gm04n05_03 par atm uio_struct_rd holmu atm When groups of entries in an UIO file are properly marked with label dataset and label enddataset delimiters confer the example in Sect 5 1 each group can be accessed with uio_dataset_rd The first block can be read with ful uio_dataset_rd st35gm04n05_03 full or ful uio_dataset_rd st35gm04n05_03 full ndataset 0 Dataset number i 1 counting starts at zero can be read with ful uio_dataset_rd st35gm04n05_03 full ndataset i If a dataset with that number does not exist an empty structure is returned In this case when called with additional keywords like ful uio_dataset_rd st35gm04n05_03 full ndataset i outstr outstr ierr ierr an error message is returned in outstr and ierr is set to a value larger than 0 To read all entries in a list of files in sequence the routine uio_datasetlist_rd pro is con venient as in 44 4 UIO DATA FORMAT model st33gm06n03 amp modelident _ amp parmodelident _01 modeldisk getenv HOME dat rhd d model modelfile modeldisk model modelident full parfile modeldisk model parmodelident par Read parameter file par uio_struct_rd parfile Open first dataset to get some information about array sizes delvar listdata ful uio_datasetlist_rd modelfile listdata list
112. r having read the model data FUL and the tables for the equation of state EOS and opacity OPTA COMMON see 7 2 3 7 2 4 more quantities can be calculated IDL gt eosbox ful eos eos opa ierror ierror This operation adds the tags EOS and OPA to the data structure FUL which contain more quantities like e g the temperature see Sect 7 3 7 3 IDL Data Structure The data structure FUL contains the following variables and substructures Use help str ful to get this information See also the short description of the contents of a model file in Sect and particularly the man page of the script uiolook in Sect which gives you even more detailed information directly from the file Structure lt 828 a0c gt 9 tags length 78404128 refs 1 84 TYPE STRING HEAD STRUCT DATASET_ID STRING MODELTIME FLOAT MODELITIME LONG DTIME FLOAT TIME_OUT_FULL_LAST FLOAT TIME_OUT_MEAN_LAST FLOAT Z STRUCT 7 DATA ANALYSIS WITH IDL uio gt lt Anonymous gt Array 1 gt single _box 10050 1 64088 0 176381 10050 1 10040 0 gt lt Anonymous gt Array 1 If the command in Sect has been performed the following substructures are present EOS STRUCT OPA STRUCT gt lt Anonymous gt Array 1 gt lt Anonymous gt Array 1 The substructure FUL Z contains the original data arrays from the model file like the spatial axes density rho internal energy ei and the three spatial components of the velocity v1 v2
113. real abux f E15 8 b 4 n hydrogen abundance number fraction u 1 amp c0 standard solar mixture 0 90851003E 00 It has no practical consequences because the actually used chemical composition is deter mined by the files for equation of state and opacity e real abuy This optional information parameter can be specified with real abuy f E15 8 b 4 n helium abundance number fraction u 1 amp cO standard solar mixture 0 90850003E 01 It has no practical consequences because the actually used chemical composition is deter mined by the files for equation of state and opacity e real qmol This optional information parameter can be specified with real qmol f E15 8 b 4 n mean molecular weight u u amp cO standard solar mixture 0 13018000E 01 It has no practical consequences because the actually used chemical composition is deter mined by the files for equation of state and opacity e real gamma This optional information parameter can be specified with real gamma f E15 8 b 4 n Adiabatic coefficient u 1 amp c0 0 0 1 6666666666666 1 4 0 0 It has no practical conseguences because the actually used chemical composition is deter mined by the files for eguation of state and opacity e gravcorr_terms In former versions of CO5BOLD the type of the coupling of gravity into the Roe solver could be specified with character gravcorr terms f A80 b 80 amp n Type of gravity correction i
114. rectory cd for hd rhd YOUR_MACHINE Activate OpenMP und MSrad radiation transport export F90_PARALLEL openmp export F90_MSRAD 1 Start the configure script configure Compile make echo Voila 3 3 Directory Structure The files necessary to compile CO5BOLD are distributed over a few directories A typical setup would be to put everything into the main directory for Then the source files would be located as in Tab Paths Abb Description HOME for con f90 CON constants and units HOME for dust f 90 DUST source terms due to dust or molecules HOME for eos f90 EOS equation of state HOME for hd mhd MHD MHD routines HOME for hd rhd RHD main rhd routines hydro Bernd s radiation transport HOME for hd rhdb RHDB basic rhd routines HOME for mat str STR string handling HOME for opa opta OPTA opacities HOME for rad hdrad RAD Matthias radiation transport HOME for uio 90 UIO I O routines HOME for time f90 TIME timing routines Table 1 List of source directories with path and file name abbreviation and a short description Paths Abb Description HOME for mat str STR string handling HOME for uio f 90 UIO I O routines HOME for eos 90 EOS equation of state HOME for rad hdrad RAD opacities Matthias radiation transport HOME for hd rhd RHD main rhd routines Table 2 For historical reasons l
115. rhd par 45 50478 boundary conditions character bottom_bound 54 character description character dustschene 62 character eosfile 57 character eospath 57 character file_id 52 character gravcorr_terms 76 character grav_mode 52 character hdschene 58 character history character infile_start 74 character opafile 57 character opapath 58 character outconv_end 74 character outconv_fine character outconv_full character outconv_mean character outfile_ena 74 character outfile_fine character outfile_full 74 character outfile_mean 74 character outform_end 74 character character character character character character character character character character dust INDEX outform_fine outform_full outform_mean radpressure 77 radraybase radraystar radschene reconstruction 59 side_bound 54 top_bound effective temperature equation of state fileform uio gravity header hydrodynamics input output integer dtimestep_out_fine integer endtimestep integer n_ integer n_ integer n_ integer n_ integer n_ integer n_ integer n_ integer n_ integer n_ integer n_ hydcellsperchunk 59 radband 66 raditer radmaxiter 64 radminiter 64 radphi radsubray radtheta radthickpoint viscellsperchunk integer plustimestep integer starttimestep luminosity opacities process management radiation transport readin
116. rray data of all types Write file header Write header of variable input term table 42 4 UIO DATA FORMAT wrhead Write header of variable input line table wrlabl Write label wrtab Write table of integer real and or character data to file J AEk k k CI k ak ak ak IRI RK aK aK ak a K K A A A ak I kk 3K 21 1 3K K K K AC 3K 3K 3K 3K 3K 2 CACC ACR A K K K K OO KK Include Files uio_ pro filedefinc uiocstinc channel status information common uio chainf uiocvlinc convert type list of current machine common uio_cvlist uionaminc names of types keywords identifiers default formats H common uio_defnam uiosizinc length of strings size of tables trmtab lintab uiotabinc empty table structure common uio_taborg JAAR I I 3k k ak I I IKI 1 1 1 3K ok ok K aK AC aK ak 2A 3K 3K 3K 3K 12 CACC 3K 3K 3K K K K EEE ok okokokokokakakakakakokokokokokokok Most of the routines are low level ones and do not have to be worried about because they rarely will be used directly For accessing data in UIO format within IDL the initialization routine uio_init see Sect 4 7 1 and the high level reading routines uio_struct_rd pro uio_dataset_rd pro and uio_datasetlist_rd pro see Sect 4 7 3 might suffice 4 7 1 Initialization of UIO Routines under IDL The directory containing the IDL UIO routines should be added to the IDL variable PATH This could be done by a program segment in the startup procedure
117. ry good partly because the achievable optimization level is not very high Some macros which seem to be necessary U77 Link proper library to make the machine understand e g call flush 6 cpp yes Switch on the C preprocessor Note that all Fortran90 files have to end with 90 The F90 suffix does not seem to work Oparallel tOopenmp Onoautopar Try to enable parallelization with OpenMP direc tives disable auto parallelization Onoinline Disables inlining This can simplify things With a proper choice of routine versions inlining is not really necessary anymore 03 Olimit General optimization with limited resource usage during compilation Some modules should only be compiled with 02 others compile even with 03 Onolimit http www compaq com fortran docs index html ttp devresource hp com devresource Tools lang html 26 3 PROGRAM FILES INSTALLATION COMPILATION 3 8 4 Hewlett Packard Itanium 2 The 2 processor system gunnar from Hewlett Packard is a dual Itanium 2 machine with two 900MHz ia64 CPU modules 4GB of RAM and 70GB user diskspace The single processor performance of COS5BOLD is very good On two processor the code runs even faster but just stops after a few time steps The number of time steps varies even for simulations with the very same start model and parameter file The compiler settings are somewhat similar to the settings of the HP V2500 system in Sec t
118. s and use routine rhd shortrad dir3 for rays in xl direction See Sect e Drhd hyd entropyfix p01 1 Optimization version with masks weights See Sect 3 7 http www sun com forte fortran 30 4 UIO DATA FORMAT 4 UIO Data Format 4 1 Quickstart Introduction to UIO The UIO Universal Input Output routines are a set of routines in Fortran90 and IDL to manage I O of scalars arrays and a certain table type Files can be formatted or unformatted The formatted ASCII text data representation is machine independent and appropriate for human reading The unformatted binary representation provides much faster I O gives smaller files and the IEEE format is a quasi standard among many platforms compilers On all platforms the native binary representation can be chosen On some machines additional conversion types are offered IEEE on most machines CRAY format an CRAYs Files produced with UIO are not automatically readable on all machines But it is always possible to produce formatted UIO files on a machine which are readable on all others And with some fiddling with compile options or the call of machine specific subroutines provided by the compiler vendor it was up to now always possible to enable the access to binary UIO files on all machine tested Each file entry is a header data unit The header contains information on the one hand to identify the entry and on the other hand to specify the format and size of the f
119. s contained in the character array termt with ntt entries and special actions may be taken The data part may be skipped with uio Skipda ncin termt ntt or it can be read with 4 6 UNIX Scripts 39 call uio_rd ncin termt ntt time ident If the entry is an array it may be necessary to allocate memory call uio_exkeyw termt ntt dimna dimstr call uio_st2dim dimstr ilow iup ndim ndim allocate rho ilow 1 iup 1 call uio_rd ncin termt ntt rho ident ilb ilow 1 1 Alternatively it is possible to search in the file for a special entry or to search in an specially generated entry list with call uio srhd ncin termt ntt type real ident rho outstr outstr ierr ierr Additionally the module uio_var_module makes it possible to read any entry into an UIO flexible variable and the module uio_varfile_module allows the reading of a complete file into a special file structure of UIO flexible variables To close file after reading use uio_closrd ncin There are several examples of programs with UIO routines like uio var test f90 uio_varfile_test f90 uiotst f90 uio_demo f90 4 6 UNIX Scripts So far there exist three UNIX shell scripts useful to quickly examine data sets uiolook to change the format or conversion type of files uiocat or to print some information about the conversion types possible on the local machine uioinfo 4 6 1 Quick Examination of Files uiolook The shell script uiolook ca
120. s step can be specified with e g real c_courant f E15 8 b 4 n HD Courant factor u 1 amp cO range 0 0 lt C_Courant lt 1 0 typically 0 5 0 5 From the minimum cell crossing time of a partial wave and this factor a recommendation for the next time step is computed A value of 1 0 is the upper limit which guarantees stability for some simple linear test problems Values around 0 5 are recommended for fully non linear simulations e real c_courantmax A typical Courant factor for each 1D hydrodynamics step can be specified with e g real c_courantmax f E15 8 b 4 n maximum HD Courant factor u 1 amp cO range C Courant lt C_Courantmax lt 1 0 typically 0 9 0 8 From the minimum cell crossing time of a partial wave and this factor an upper limit for the current time step is computed If this limit is exceeded the computation is interrupted and resumed with a smaller time step based on c_courant Usually this parameter should be restricted by c_courant lt c_courantmax lt 1 0 A value around 0 8 appears to be a good choice e real c_maxeichange The relative change in internal during a single 1D hydrodynamics step can be used to restrict the time step by specifying real c_maxeichange f E15 8 b 4 n maximum hydro energy change u 1 amp cO range 0 1 1 0 typically 0 5 off 0 0 0 5 The default is 0 9 Nevertheless since the Roe solver is constructed to handle shocks and rapid changes in
121. s the 4 Byte big_endian format The compiler flags in the configure script are F9OFLAGS C hopt sx5 dw float0 Wf L nostdout L fmtlist L inclist L mrgmsg L transform M noflunf M noinv Mnoinexact M setall pi exp rhd shortrad operator exp rhd_shortrad_dtauop F90MODULES F9OTIME DMSrad raytas1 3 8 9 SGI Origin CO5BOLD has been compiled and tested on up to 8 processors on the SGI 2000 machine at TAC in Copenhagen and the SGI 3800 machine at the NSC in Linkoping See e g the excellent SGI Fortran90 manuaf Note that recent versions of the code or the configure script have not been tested on any SGI machine Important switches are e macro_expand Enable macro expansion e mp Enable parallelization with OpenMP directives e INLINE aggressive 0N INLINE list INLINE preempt 0N General keywords for in lining http www nsc liu se systems sgi3k 3 8 Optimization Compiler Switches 29 e INLINE must Optimization Routines that should be inlined file rhd_hyd_module F90 rhd_hyd_avg rhd_hyd_upwind rhd hyd pred0 rhd hyd predm rhd hyd predp rhd hyd alpha rhd hyd constanteg rhd_hyd_minmodeg rhd_hyd_minmod rhd_hyd_vanleereg rhd_hyd_vanleer rhd hyd superbeeeg rhd_hyd_superbee rhd hyd ppeg rhd_hyd_pp rhd hyd hdflux file rhd Ihdrad module F90 rhd rad3d raylhd rhd rad3d solve rhd rad3d solveeg file rhd shortrad module F90 rhd shortrad operator rhd shortrad dtauop e 03
122. set e g with real plustime f E15 8 b 4 n simulation advance time u s 5 0E 07 A value lt 0 0 cancels this halt condition it is not checked at all This condition assures if it is the only one that all individual simulation runs cover approximately the same stellar time e integer endtimestep If the simulation should run up to a certain time step its values can be specified e g with integer endtimestep f 111 b 4 n total simulation time step number u 1 1234 This might be useful to advance the simulation up to a point shortly before a previous simulation crashed A value lt 0 cancels this halt condition it is not checked at all e integer plustimestep If the initial model should be advanced by a certain number of time steps their number can be set e g with integer plustimestep f I11 b 4 n simulation advance time step number u 1 2000 A value lt 0 deactivates this halt condition it is not checked at all 70 5 CONTROL AND DATA FILES 5 3 12 Time Step Control In this group parameters to control the time step restrictions can be set They are important because decide about performance and stability of CO5BOLD They should be tested and adjusted for a simulation of a new type of object But all the dimensionless parameters can stay unchanged for a group of similar simulations Only the parameters with an explicit time dimension should be checked in all cases they scale with characteristic timescales an
123. stem IRIX machine atlas osrelease 6 3 amp osversion 12161207 hardware IP32 language Fortran90 program uiotst label testdata n sample test data field date 29 11 1997 21 23 39 835 integer ia f 13 b 4 n This is the answer 42 complex ca f F13 6 E13 6 b 8 n This is a complex answer 0 400000E 01 0 200000E 01 real da f E23 15 b 8 n precise answer 0 420000000000000E 02 real answer f F4 0 b 4 n answer u 1 42 real real2d d 100 103 200 204 f E13 6 p 4 b 4 0 100000E 01 0 200000E 01 0 300000E 01 0 400000E 01 0 500000E 01 0 600000E 01 0 700000E 01 0 800000E 01 0 900000E 01 0 100000E 02 0 110000E 02 0 120000E 02 4 3 Structure of UIO Files 31 0 130000E 02 0 140000E 02 0 150000E 02 0 160000E 02 0 170000E 02 0 180000E 02 0 190000E 02 0 200000E 02 table f77table d 1 5 1 7 f 1X b 1 n test table to test the table routines integer inti f 15 b 4 n Integer 1 Spalte real reall f F5 1 b 4 n Real 2 Spalte character chari f A16 b 16 n Char 3 Spalte real real2 f E13 6 b 4 n Real 4 Spalte integer int2 f 15 b 4 n Integer 5 Spalte inti reali chart real2 int2 1 2 0a 0 100000E 02 1 2 4 0 ab 0 200000E 02 2 3 6 0 abc 0 300000E 02 3 4 8 0 abcd 0 400000E 02 4 5 10 0 abcde 0 500000E 02 5 6 12 0 abcdef 0 600000E 02 6 7 14 0 abcdefg 0 700000E 02 7 4 3 Structure of UIO Files 4 3 1 Data Representation ASCII or Binary Whil
124. steps and radiative sub steps the direction of the rays stays the same o random At each time step and radiative sub step a new base axis system is chosen at random o randomgroup At each new time step a new base axis system is chosen at random It is kept for all radiative sub steps Because typically only a relatively small number of rays is chosen per time step with radraystar it is advisable to vary the directions of the rays by choosing radraybase random or randomgroup to cover the entire sphere at least over a longer time e character radraystar Using the modules LHDrad or SHORTrad the list of ray directions i e the number of rays and their coordinates relative to the base axis system can be specified with e g character radraystar f A80 b 80 n List of relative ray directions amp cO x1 1 x2 1 x3 1 oktaeder 3 tetraeder 4 cube 4 amp c1 ikosaeder 6 dodekaeder 10 oktaeder Examples for allowed values are o x1 N 1 one single ray along xl axis not enough to specify fluxes in all directions o x2 N 1 one single ray along x2 axis not enough to specify fluxes in all directions o x3 N 1 one single ray along x3 axis not enough to specify fluxes in all directions oktaeder N 3 default octahedron tetraeder N 4 tetrahedron o cube N 4 o ikosaeder N 6 icosahedron dodekaeder N 10 dodecahedron ke O O o list 01 list 01 3 Choose ray systems from a lis
125. t oktahedrons tetrahedrons If character radraybase is set to unity the rays will only be aligned to the axes or diag onals and thus avoid the time consuming interpolation step of the short characteristics method Several other choices are possible which are meant for test purposes only Choosing one of the five Platonic solids Ops German Greek names only so far means that the 3 to 10 rays are equally distributed over the solid angle from the center to each corner of the respective solid e integer n_radtheta Using the MSrad module the ray directions have to specified in a different way The number of ray sets in theta direction can be chosen with e g 66 5 CONTROL AND DATA FILES integer n_radtheta f 14 b 4 amp n NTHETA Number of ray sets in theta direction c0 2 2 integer n_radphi Using the MSrad module the number of ray sets in phi direction can be set e g with integer n_radphi f 14 b 4 amp n NPHI Number of ray sets in phi direction c0 2 2 integer n_radsubray Using the MSrad module the number of rays per cell with the same direction can be specified e g with integer n_radsubray f 14 b 4 n KPHI Number of rays per cell c0 2 2 integer n_radthickpoint With the MSrad module the lower part of the model can be computed in diffusion approxi mation The number of points in diffusion approximation can be set with e g integer n_radthickpoint f 14 b 4 amp n Number of grid points wi
126. th e g character outfile_mean f A80 b 80 n Qutput file name rhd mean Leaving it empty means that no file of this type is written character outform_end The format see Sect 4 3 1 of the final model files can be chosen e g with character outform_end f A80 b 80 n QOutput file format amp c0O formatted unformatted unformatted Allowed values are o unformatted default fast compact possibly machine dependent output strongly recommended o formatted slow machine independent output big files character outconv_end The conversion type see Sect 4 3 1 of the final model files can be specified e g with 5 3 Parameter File rhd par File 75 character outconv_end f A80 b 80 n Output file conversion amp c0 ieee_4 ieee_8 crayxmp_8 native ieee_4 The allowed values depend on the machine Leaving this field empty means that the default is chosen that is build into the local UIO module If the type ieee_4 is supported which is always the case so far it should be chosen e character outform_full The format see Sect 4 3 1 of the full model files can be chosen e g with character outform full f A80 b 80 n 0utput file format amp c0O formatted unformatted unformatted Allowed values are o unformatted default fast compact possibly machine dependent output strongly recommended o formatted slow machine independent output big files e character outconv_full The con
127. th optically thick diff approximation amp cO 0 no diffusion approximation 0 Setting this value to O means that the diffusion approximation is not used in any part of the model integer n_radtaurefine With the LHDrad and the MSrad module the number of points on the rays can be finer than the number of points in the basic numerical grid The refinement can be set e g with integer n_radtaurefine f 14 b 4 amp n Refinement factor 0 integer n_radband It can be specified whether the grey opacity table or the binned frequency dependent part of the opacity table is used during the computation The grey part contains only one bin The other possibly non grey contains one or more bins depending on the table chosen The parameter is specified with e g integer n_radband f 14 b 4 n Number of frequency bins amp c0O 1 grey opacities amp c1 2 non grey opacities if available from table 1 Allowed values are o 1 Use the grey part of the table o 2 Use the other possibly non grey frequency dependent part of the table Only the MSrad module so far can handle non grey tables 5 3 Parameter File rhd par File 67 e real c_radimplicitmu So far only the LHDrad and the SHORTrad module tentatively support implicit radiation transport It can be activated with the parameter real c_radimplicitmu f E15 8 b 4 amp n Implicitness parameter for radiation transport u 1 amp c0 0 0 explicit
128. ther processing and visualisation of COSBOLD data For the visualisation of 2 D models or 2 D data slices in general we recommend plotfield pro With combox pro unfortunately not commented yet further quantities can be calculated Furthermore we currently develop a widget based analysis tool called COBOLD AT abbrev CAT which will help to work with CO5BOLD data without having to write and edit own IDL code The routines are stored if available in the directory IDL COBOLDAT and have to be started with cat A more detailed documentation is planned 86 8 GLOSSARY 8 Glossary e CO5BOLD or COBOLD is the short form of COnservative COde for the COmputation of COmpressible COnvection in a BOx of L Dimensions with 1 2 3 e EOS Equation Of State e RHD Radiation HydroDynamics e UIO the Universal Input Output format It is used in CO5BOLD for parameter model and EOS files Index alpha batch queue big_endian boundary conditions chemical composition CO5BOLD compilation compiler alpha Cray Hewlett Packard Hitachi Intel NEC SX 5 PGI SGI Sun compiler macro category gasinter_101 IDF I8 rhd_shortrad_lambda_101 rhd_bound_t01 rhd_box_bmag01 rhd box grav01 rhd box guc01 rhd hyd entropyfix p01 rhd hyd gravcorr p01 I8 rhd hyd roeld 101 rhd hyd upwind p01 rhd_r01 rhd_r02 rhd_r03 rhd_rad3d_dir_t01 rhd_rad3d_fromray_101 21 rhd_rad3d_r02 rhd_rad3
129. time per run On a CRAY the CPU time that is left can be accessed with a special subroutine in call tremain in rhd_mac_cray_module f90 On other machines it is possible to specify the allowed total time for the job e g with 5 3 Parameter File rhd par File 69 real cputime f E15 8 b 4 n CPU time u s 1000000 0 During the run of COS5BOLD the leftover CPU time is computed by subtracting the used CPU time which is given by e_time etime tarray in rhd_mac_sun_module f90 from the specified total CPU time for the job e real cputime_remainlimit Because CO5BOLD needs some time to finish the last time step it should start exiting well before all CPU time is used up This amount of buffer CPU time can be specified e g with real cputime_remainlimit f E15 8 b 4 n maximum remaining CPU time u s 2000 0 Its value depends on the size of the model and the speed of the machine more precisely the maximum CPU time per time step e real endtime If the simulation should run up to a certain stellar time its values can be specified e g with real endtime f E15 8 b 4 n total simulation time limit u s 10000 0 A value lt 0 0 deactivates this halt condition it is not checked at all If this parameter is set to a non negative value a follow up simulation should not use the same parameter file it would stop immediately e real plustime If the initial model should be advanced by a certain stellar time span this value can be
130. time step 89 timing statistics total energy flux vio example Fortran IDL makefile Unix scripts uiocat uio datasetlist rd 43 uio dataset rd uioinfo 40 uiolook uio struct rd unformatted
131. to 1 see the description of the variable in Sect 3 6 2 put arrays specifying the initial conditions of the additional density into the start model as real guc001 real quc002 3 select a proper model describing dust or molecule formation in the parameter file with character dustscheme e rhd_box_bmag01 in rhd_box_module F90 and rhd F90 rhd box b magnetic 01 Category feature activation CO5BOLD can handle magnetic field arrays if this compiler switch is set Values o default no handling of magnetic field arrays o handling of magnetic field arrays is activated To actually account for magnetic fiels in a simulation it is necessary to 1 set the switch Drhd box bmag01 1 during compilation this is done by the configure script if the environment variable F90_MHD is set to 1 see Sect 3 6 2 put arrays specifying the initial conditions of the boundary centered magnetic field arrays into the start model as real bb1 real bb2 real bb3 3 select an hydrodynamics scheme that is able to handle magnetic fields in the parameter file with character hdscheme Hydrodynamics Roe solver e IDF in rhd_hyd_module F90 Integer Delta Flux Category performance enhancement Number of padding cells for flux like variables This number was introduced to check whether the increase of the size of vectors for flux like quantities defined at cell boundaries can improve the performance especial
132. tures than the machine dependent versions Besides the format the conversion type see table 5 has to be specified The native con version type is the internal binary data representation which is also standard for unformatted Fortran output If this representation happens to be conformal with the IEEE standard the conversion type ieee_4 should be used It gives the same data format but in the header of the file the term convert ieee_4 instead of convert native describes the data format precisely in a way also understandable by other machines On CRAY machines the native format is equal to the conversion type crayxmp_8 but also the conversion types ieee_4 ieee_4_limit and ieee 8 can be chosen The last three conversion types correspond to the CRAY internal types leee_32 ieee_dp and ieee_64 respectively On a machine with an internal data representation not within the list in the existing uio_mac _module f90 files one could use the standard file uio mac module f90 and is restricted to the native conversion type But it is better to invent an appropriate name for the new data format and to build a proper machine dependent UIO file e g from uio mac ieee module f90 Some attention has to be paid if weird compiler switches as e g r16 i2 are used to modify the accuracy and standard memory size of variables If an existing file is opened for reading the file format and c
133. undary is typically of type inoutflow A supergiant simulation will have a transmitting lower boundary e real luminositypervolume The luminosity of a Star in a Box can be set with this parameter To avoid numbers that do not fit into a 4 Byte real the luminosity per volume has to be specified as e g in real luminositypervolume f E15 8 b 4 n Luminosity per core volume amp u erg cm 3 s 4 5E 02 Reference volume is 4 307 OS ray If this parameter is set to a value of 0 0 or below the entropy of the material within the core defined by as all cells within radius r0_grav is adjusted instead e real s_inflow The entropy of the material streaming through an open boundary of type inoutflow into the model can be specified e g with real s_inflow f E15 8 b 4 n Entropy of core material amp u erg K g 3 25E 09 In the case of a central potential the entropy in a sphere with radius r0_grav is adjusted towards this entropy value In both geometry supergiant as well as solar this value is very important as it finally but indirectly determines the luminosity and effective temperature of the star A value of 0 0 default or below disables this energy input e real c_schange The entropy s_inflow of the material in the bottom layer solar case inoutflow boundary condition or the central region of the model supergiant case is not just set to the specified but adjusted towards it The adjustment rate can be
134. version type see Sect 4 3 1 of the full model files can be specified e g with character outconv_full f A80 b 80 n Output file conversion amp c0 ieee_4 ieee_8 crayxmp_8 native ieee_4 The allowed values depend on the machine Leaving this field empty means that the default is chosen that is build into the local UIO module If the type ieee_4 is supported which is always the case so far it should be chosen e character outform_mean The format see Sect 4 3 1 of the additional data files can be chosen e g with character outform mean f A80 b 80 n Output file format amp cO formatted unformatted unformatted Allowed values are o unformatted default fast compact possibly machine dependent output strongly recommended o formatted slow machine independent output big files e character outconv_mean The conversion type see Sect 4 3 1 of the additional data files can be specified e g with character outconv_mean f A80 b 80 n Output file conversion amp c0 ieee_4 ieee_8 crayxmp_8 native ieee_4 The allowed values depend on the machine Leaving this field empty means that the default is chosen that is build into the local UIO module If the type ieee_4 is supported which is always the case so far it should be chosen 76 5 CONTROL AND DATA FILES 5 3 14 Additional Information Obsolete and Test Parameters e real abux This optional information parameter can be specified with
135. with Additional Data rhd mean File real bc3_xmean2 d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Magnetic field 3 amp u G real ei_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 n Internal energy amp u erg g real rhoei_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Internal energy amp u erg cm 3 real rhoek_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Kinetic energy u erg cm 3 real rhoeg_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Gravitational energy amp u erg cm 3 real t_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 n Temperature amp u K real t_xmean4 d 1 1 1 1 1 120 f E13 6 p 4 b 4 n Temperature amp u K real t_xmeankapparho d 1 1 1 1 1 120 f E13 6 p 4 b 4 n Temperature amp u K real p_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 n Pressure amp u dyn cm 2 real s_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 n Entropy amp u erg K g real rhos_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Entropy amp u erg K cm 3 real gammal xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n ist Adiabatic Coefficient amp u 1 real gamma3_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n 3rd Adiabatic Coefficient amp u 1 real delta_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Expansion coefficient amp u 1 real kapparho_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 n Absorption Coefficient amp u 1 cm real guc001 xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n
136. xmean2 d 1 1 1 1 1 120 f E13 6 p 4 b v3_xmean2 d 1 1 1 1 1 120 f E13 6 p 4 b rhovi_xmean d 1 1 1 1 1 120 f E13 6 p 4 rhov2_xmean d 1 1 1 1 1 120 f E13 6 p 4 rhov3_xmean d 1 1 1 1 1 120 f E13 6 p 4 bc1_xmean d 1 1 1 1 1 120 f E13 6 p 4 b bc2_xmean d 1 1 1 1 1 120 f E13 6 p 4 b bc3_xmean d 1 1 1 1 1 120 f E13 6 p 4 b bc1_xmean2 d 1 1 1 1 1 120 f E13 6 p 4 b bc2_xmean2 d 1 1 1 1 1 120 f E13 6 p 4 b 5 CONTROL AND DATA FILES n x2 coordinates u cm amp n x3 coordinates u cm amp n x1 coordinates u cm amp n x2 coordinates u cm amp n x3 coordinates u cm amp 4 amp n Density amp u g cm 3 amp n Velocity x1 amp u cm s amp n Velocity x2 amp u cm s amp n Velocity x3 amp u cm s 4 n Velocity x1 u cm s 4 n Velocity x2 u cm s 4 n Velocity x3 amp u cm s b 4 amp n Mass Flux x1 u g cm 2 s b 4 amp n Mass Flux x2 u g cm 2 s b 4 amp n Mass Flux x3 u g cm 2 s 4 amp amp amp amp of of of of of n Magnetic field 1 u G 4 n Magnetic field 2 u G 4 n Magnetic field 3 u G 4 amp n Magnetic field 1 u G 4 amp n Magnetic field 2 u G cell cell cell cell cell centers amp centers amp boundaries amp boundaries amp boundaries amp 5 2 File

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