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CO5BOLD User Manual

1. error may have occurred during execution of rhd exe if RHD_EXIT 0 then echo Non zero exit status RHD_EXIT occurred during execution of RHD else echo No rhd done file found assume error during execution of RHD fi echo Execution of job chain terminated Modify nrhd cmd set termination character awk X print next print next print next DONE T printf 7 77s n 0 DONE T next print rhdi cmd cat gt nrhd cmd Terminate chain by simulating ACT eoc ACT eoc else Modify command file add in appropriate column to indicate proper execution awk j X print next print next print next DONE T print gt cmdline printf 77s n 0 DONE T next print rhdi cmd cat gt nrhd cmd fi Ils L Move data into backup directory cp p rhd par BAKDIR PARFILE mv rhd out BAKDIR OUTFILE out mv rhd par BAKDIR OUTFILE par mv rhd sta BAKDIR 0UTFILE sta mv rhd end BAKDIR 0UTFILE end mv rhd full BAKDIR 0UTFILE full mv rhd mean BAKDIR 0UTFILE mean mv rhd chu1 BAKDIR 0UTFILE chu1 chmod go r BAKDIR PARFILE BAKDIR OUTFILE chmod go w BAKDIR PARFILE BAKDIR OUTFILE AREH AR RE E EE HEEE EA E E RE EH E SEE EE EE E EHE E BEHE RE EEEE TEHE E EEE R EE E H HE TEHE EHE E EE EEE E E
2. o bottom_entropy1 The entropy in the bottom layers defined as being less than r0_grav above the bottom of the model is adjusted towards s_inflow on a rate given by c_schange o bottom_energyl Energy in the bottom layers is added according to luminositypervolume o core_entropy1 The entropy in the core is adjusted towards s_inflow on a rate given by c_schange o core_energy1 Energy in the core is added according to luminositypervolume o core_energy2 Energy in the core is added according to luminositypervolume with a Gaussian distribution of the energy source e real luminositypervolume The luminosity of a Star in a Box or a local model with the appropriate heat __mode 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 3 T rOZrav 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 5 4 Parameter File rhd par 81 In the case of a central potential the entropy
3. 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 e integer istep_in_start The index number of the dataset in the start model file to be used can be specified e g with integer istep_in_start f I4 b 4 n Number of dataset to read as start model amp u 1 c0 1 first dataset default 2 second dataset 1 e character outfile_end The file name for the final model can be specified with e g character outfile_end f A80 b 80 n Output 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 e 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 124 5 CONTROL AND DATA FILES 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 3 can be specified with e g character outfile_mean f A80 b 80 n Output file name rhd mean Leaving it empty means that no file of this type is written characte
4. character hion_abufile 105 character hion_atomfile 105 character hion_datapath character hion_edensfile 105 character hion_pffile 105 character history 75 character infile_start 123 character opafile 86 character opapath 86 character outconv_end character outconv_fine 127 character outconv_full character outconv_mean 125 character outfile_chul character outfile_end 123 character outfile_fine 127 character outfile_full 123 character outfile_mean character outform_end character outform_fine 127 character outform_ful1 124 character outform_mean 125 character radpressure 126 character radraybase 111 character radraystar character radscheme 110 character reconstruction character side_bound 78 character side_bound_mag_x1 character side_bound_mag_x2 character top_bound 79 character top_bound_mag chemical reaction network dust effective temperature equation of state fileform uio 75 gravity header 75 hydrodynamics hydrogen ionization input output integer dtimestep_out_fine 127 integer endtimestep 117 integer hion_chunks 106 integer istep_in_start 123 integer n_outslicedim_mean integer n_dustgrainradius integer n_hydcellsperchunk integer n_hyditer 96 integer n_hydmaxiter 96 integer n_magdiffbottom integer n_magdiffside integer n_magdifftop 99 152 integer n_orderconstrainedtransport integer in
5. first order reconstruction method It results in the steepest shocks which works well in some test cases but tends to turn smooth gradients into steps and might be to difficult for the radiation transport module to handle PPmimo MinMod reconstruction based on boundary values from PP PP Chooses the piecewise parabolic reconstruction of the PPM scheme Piecewise Parabolic Method Colella and Woodward 1984 Results in 3rd order accuracy for the advection FRmimo MinMod reconstruction based on boundary values from FRmono FRmono 2nd order monotonic reconstruction derived from PP WENO and MinMod Frankenstein s Method FRmono2 2nd order monotonic reconstruction derived from PP WENO and Min Mod It is identical to FRmono if real c_slopered 0 0 the usually adopted default choice see Section 5 4 7 However for real c_slopered gt 0 0 it uses Constant reconstruction as fallback instead of 90 5 CONTROL AND DATA FILES o Minmod as o FRmono does This is the recommended version for low resolution red supergiant mod els o FRweno 2nd order non monotonic version of FR o FRweno2 2nd order non monotonic version of FR It is identical to FRweno if real c_slopered 0 0 the usually adopted default choice see Section 5 4 7 How ever for real c_slopered gt 0 0 it uses Constant reconstruction as fallback instead of o Minmod as o FRweno does This is the recommended version for low resolution
6. since or ds dlnp c dinp 50 Entropy change at constant density This relation is obtained from the equality of the mixed derivatives in Eq 20 together with Eq 44 Entropy change at constant pressure This relation is obtained from the equality of the mixed derivatives in Eq 21 together with Eq 46 14 2 EQUATIONS Specific heat at constant density 53 To derive the specific heat at constant pressure we start from the relation OlnT OlnT InT dinT SET dino Ds as 54 from which we get Os OlnT OlnT 55 Ge ao as 55 Using Eqs 44 and 53 we obtain 56 Now 57 e o o Ol ol s s np np ds dl dnT j step n 27 dur j Os ast pa hence Os Olnp Os Os Olnp 1 dInp InT ad Ga E Go Ge mr ur 60 and finally ee Using Eqs 27 44 52 56 we finally obtain the relation for the specific heat at constant pressure Alternatively c can be obtained from Eq 32 or 63 or from 64 2 3 A collection of thermodynamic relations M Steffen AIP 15 once and xr are known see below We can now express the thermodynamic coefficients provided by CO5BOLD in terms of cy T T3 and Vad 65 66 67 70 We consider again Eq 39 replacing de by de de de 7 dT 5 dp 71 or Op y _ 1 de st e p z ko rahe The requirement that the
7. 99911 13453 22581 17659 13964 70033 46595 80 i 80 3 99552 76404 4 4 Files amp Directories amp Paths 57 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 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 4 4 Files amp Directories amp Paths All UIO routines are located in sub directories of a common directory called e g uio which also contains a old 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 AT X the mos
8. 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 array data of all types Write file header Write header of variable input term table Write header of variable input line table Write label Write table of integer real and or character data to file ES y 9 3 Include Files uio_ pro filedefinc ulocstinc uiocvlinc uionaminc uiosizinc uiotabinc channel status infor
9. _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 6 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 74 5 CONTROL AND DATA FILES The flux fepb is already part of feipb 5 4 Parameter File rhd par 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 occurrence will be used by CO5BOLD 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 parameter 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 COSBOLD but read by the IDL
10. 200 T FLOAT Array 140 140 200 DTDEI FLOAT Array 140 140 200 S FLOAT 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 In the directory IDL bflib a lot of useful routines can be found which can be used for further processing and visualisation of CO5SBOLD data For the visualisation of 2 D models or 2 D data slices in general we recommend plotfield pro With combox pro further quantities can be calculated Furthermore we currently develop a widget based analysis tool called COBBOLD 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 144 8 DOCUMENT HISTORY 8 Document history 2002 02 16 First version on the web lots of extensions and changes in between 2004 02 23 SGI Origin compiler settings section modified for CINES machines 3 7 16 2004 02 23 2004 03 02 2004 03 02 2004 03 03 2004 03 04 2004 03 04 2004 03 04 2004 03 04 2004 03 04 2004 03 04 2004 03 04 2004 03 04 2004 05 03 2004 05 14 2004 07 26 2004 08 18 short example for uio_datasetlist_rd pro usage 4 7 3 Intel compiler settings section modified LD_ASSUME_KERNEL 2 4 19 S
11. 63 63 63 63 f E13 6 p 4 b 4 Y 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 g cm73 real real real real ei d 63 63 63 63 63 63 vi d 63 63 63 63 63 63 v2 d 63 63 63 63 63 63 v3 d 63 63 63 63 63 63 f E13 6 p 4 b 4 n Internal energy u erg g f E13 6 p 4 b 4 n Velocity 1 u cm s f E13 6 p 4 b 4 n Velocity 2 u cm s 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 p
12. 88 5 CONTROL AND DATA FILES real c_hydlowmachcsfactor f E15 8 b 4 amp 2 0 n Low Mach Number sound speed reduction parameter amp c0 lt 0 0 off old settings recommended default amp ci 1 0 small value 2 0 reasonable value 5 0 large value Typical choices are o o o o 0 0 The extra reduction factor is not applied This is the standard Roe scheme It is still the recommended default excepd for very low Mach number flows 1 0 Smallest meaningful value to switch on the reduction 2 0 Reasonable value 5 0 Rather large value The recommeded default is not to use this reduction and leave the parameter at 0 0 This parameter is not recognized by the MHD module e character hdtimeintegrationschene With this parameter the type of the time integration scheme can be specified as in character hdtimeintegrationscheme f A80 b 80 n Time integration scheme amp c0 Single Hancock Euler1 RungeKutta2 RungeKutta3 Single Possible values are o o o Single default for HD Roe Compute all updates in one single step Terms higher or der in time are provided by the Roe solver depending on the order of the reconstruction scheme Hancock default for MHD HLLE Terms of second order in time are approximated by a Hancock predictor step Euler1 only for MHD A single Euler step is used which is only first order in time RungeKutta2 A two step predictor corrector Runge
13. a positive feature when it comes e g to convection with smaller Mach numbers in the deeper layers of a solar model or the absence of vertical net mass fluxes in a hydrostatic atmosphere However it can be a drawback e g in the case of a transsonic rarefaction wave where an entropy fix is applied since the beginning see Leveque Numerical Methods for Conservation Laws or in the rather quiet center of a Sedov blast wave where a cross like structure with comparably low temperature is visible This artefact can be removed by applying the standard tensor viscosity including the energy dissipation down an entropy gradient controlled with C_visPrturb of by the new rather simple option to the Roe solver to apply additional energy dissipation down a temperature gradient but only in cells adjacent to a local temperature minimum in 1D It works nicely for the Sedov blast wave and does not have any visible adverse impact in any other cases so far I don t expect it to do any harm for convection simulations and recommend to activate it per default Cautious people might not like it and see how well it works without though Still unlike the tensor viscosity with turbulent Prandtl number there is no viscous flux down the subphotospheric temperature or entropy gradient unless there is a local minimum at the bottom The linear diffusion can be set e g with real c_hydtdifflin f E15 8 b 4 amp n Parameter 1 for energy diffusion near local
14. after reconstructing them can be activated For the diffusion velocity all three velocity components are used i e there is a diffusion even transversal to the flow speed This makes the diffusion more isotropic and lets numerical solutions to the Sedov blast wave problem look smoother The value can be set e g with real c_hydvdiffvelo f E15 8 b 4 amp n Parameter for transversal momentum diffusion down a velocity step u 1 amp c0O typically 1 0 10 Possible choices are for example o 0 0 No extra energy diffusion down an entropy gradient default o 0 2 Small value o 0 5 Reasonable value o 1 0 Reasonable value o 3 0 Large value The type of dissipation that can be added with this option is similar to that provided by the tensor viscosity Sect B 4 8 Therefore 1 recommend to use only small values 0 5 to 1 0 to reduce the directional dependence of the dissipation applied by the Roe solver and to use an explicite tensor viscosity Sect 5 4 8 in case of emergencies This parameter is not recognized by the MHD module but in fact the HLLE solver applies a somewhat similar but stronger dissipation by construction e real c_hydtdifflin The Roe solver correction does not have any dissipation for standing waves and very little for slowly moving ones unlike the MHD HLLE solver that always has quite some minimum dissipation depending on the reconstruction though The small amount of dissipation is
15. 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 r1_grav specified with real ri_grav f E15 8 b 4 n Duter 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 somewhat larger than the remotest corner of the box effectively cancels this artificial smoothing in the outer layers without changing the formula for the potential e real r2_grav Using real r2_grav instead of real r1_grav means that a potential function more ap propriate for a polytropic stellar interior model is used It can be set e g with real r2_grav f E15 8 b 4 n Duter Smoothing Radius u cm amp c0 0 0 Not used 11 35000e 13 Setting this parameter to zero means the potential parametrized with real r1_grav is used This parameter is similar to real ri_grav i e it enlarges the pressure scale hight in the outer layers but does not change the smoothing formula in the center This parameter is only effective if real r1_grav is set to zero e real ri_rad For a Star in a Box and particularly when only simple ray directions are allowed in the radiation transport step the temperature in the outer corners of the box tends to bec
16. components of the boundary centered field being zero at the boundary o vertical2 constant extrapolation for the vertical component The transversal cell centered field is set to zero o reflective The magnetic field is mirrored at the boundary This boundary condition is unphysical because the magnetic field is an axial vector and because it violates the divergence free property of the magnetic field Therefore this boundary condition should be used with caution The fixed conditions are realized by setting the electric field at those cell edges that coincide with the physical boundary zero This is done in the constrained transport module 84 5 CONTROL AND DATA FILES e character top_bound_mag The boundary condition at the top of the model is given by for instance character top_bound_mag f A80 b 80 n bottom boundary conditions magnetic vertical Possible values are o constant constant extrapolation of all magnetic field components into the ghost cells o periodic periodic continuation of all magnetic field components into the ghost cells o fixed the component normal to the boundary is kept fixed at its inital value Con stant extrapolation applies for the transversal components o vertical constant extrapolation for the vertical component The transversal cell centered field is mirrored with the opposite sign That should result in transversal components of the boundary centered field being zero at the bound
17. hm e character dustreconstruction While usually i e when this parameter is not set the reconstruction scheme for the addi tional density fields is the same as for the normal hydrodynamics quantities see 5 4 7 it can make sense to chose a more aggressive but strictly monotonic scheme for these additional fields It can be chosen e g with character dustreconstruction f A80 b 80 n Reconstruction method for qucs amp cO Constant c1 Minmod VanLeer Superbee c2 PP PPmimo amp c3 FRmimo FRmono FRmono Usuful combinations are o reconstruction vanLeer dustreconstruction Superbee o reconstruction FRweno dustreconstruction FRmono o reconstruction FRweno dustreconstruction PP real c_dustOx There are ten parameters real c_dust01 to real c_dust10 to control each dust forma tion scheme in detail A parameter can be given as in real c_dust01 f E15 3 b 4 n Dust parameter 1 0 0 5 4 Parameter File rhd par 105 The meaning and unit can vary from scheme to scheme The default value is 0 0 in each case Important The parameter real c_dust01 must be set to 1 0 in order to activate advec tion of particle densities for the CHEM chemreacnet and the HION hiontd module The default value is 0 0 i e advection is switched off e character chem_reacfile The name of the input file containing the chemical reaction network character chem_reacfile f A80 b 80 n file name of reaction table chem dat
18. integer n_hyditer f 14 b 4 amp n Number of hydrodynamics iterations c0 10 8 For a simulation of a solar type star it will typically be set to 1 E g for brown dwarfs with shorter hydrodynamical time scales values around 10 may be considered Note that the hydrodynamics iteration works somewhat differently than the radiation transport iteration in the latter case the size of the actual time step can be determined after computing the fluxes whereas the hydrodynamics step is possibly of at least second order in time and the time step has to be known in advance In case of the MHD module this can reduce the computation time significantly because the MHD time step is often much smaller than the other timestep limits However this pa rameter does not determine the nuber of substeps directly Instead the number of substeps is determined by the requested timestep and the timestep of each MHD substep which is determined by the standart Courant condition So the number of MHD substeps varies during the simulation So the exact value of this parameter has no direct influence on the number of substeps If this parameter is set to zero this features is turned of See also parameter va_max for speeding up MHD simulations integer n_hydmaxiter The absolute maximum number of hydro iterations can be specified e g with integer n_hydmaxiter f I4 b 4 amp n Maximum number of hydro iterations c0 14 0 If more iterations are needed t
19. 0 5 are recommended for fully non linear simulations e real c_courantmax A typical maximum 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_hydsoundcourant In addition to the normal Courant factor c_courant that gives a time step restriction based on c abs v1 another factor can be specified that is based only on the sound speed c e g with real c_hydsoundcourant f E15 8 b 4 n HD sound speed Courant factor u 1 amp c0O range 0 0 lt c_hydsoundcourant lt 0 5 typically 0 45 0 48 The check for this condition should be activated by giving c_hydsoundcourant a positive value for 3D simulations with hdsplit CTU see Sect and Table In this case a value slightly smaller than 0 5 is a reasonable choice e real c_hydsoundcourantmax In addition to the normal maximum Courant factor c_courantmax that gives a time step restriction based on c abs vl another factor can be s
20. 140 200 V3 FLOAT Array 140 140 200 Spatial axes XC1 XC2 XC3 XB1 XB2 XB3 The indices stand for 1 2 2 y 3 z or h 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 Z can contain additional arrays in case of dust formation chemical reaction networks or time dependent hydrogen ionization QUCOO1 FLOAT Array 140 140 200 QUCOO2 FLOAT Array 140 140 200 QUC003 FLOAT Array 140 140 200 QUCOOA FLOAT Array 140 140 200 The magnetic field components are also stored in this substructure BB1 FLOAT Array 141 140 200 BB2 FLOAT Array 140 141 200 BB3 FLOAT Array 140 140 201 7 4 More IDL routines 143 The magnetic field is defined on the cell boundaries in the direction of the spatial components e g BB1 in direction 1 and in the cell centres for the other directions The resulting array dimensions differ from the cell centred quanties like e g rho The array values must be multiplied with a factor Y4r in order to obtain the field strength in Gauss The substructure FUL EOS which is present only after a call of e g eosbox pro contains important quantities like the temperature T gas pressure P entropy S Structure lt 826a03c gt 6 tags length 109760000 refs 2 P FLOAT Array 140 140 200 DPDRHO FLOAT Array 140 140 200 DPDEI FLOAT Array 140 140
21. 3 b 4 n Number fraction of rarest component u 1 amp cO For Mg2Si04 Mg is the rarest its fraction is 3 1187E 05 amp c1 Mg2Si04 contains 2 Mg gt 1 2 gt 1 55935e 05 1 55935e 05 5 4 Parameter File rhd par 109 For Mg2SiO the rarest component is usually Mga So half the magnesium abundance is required as value The default value is 0 0 e real c_dust04 The lower dust limit fraction is specified with e g real c_dust04 f E15 8 b 4 n Lower dust limit fraction u 1 1 0E 10 If the density in a bin relative to the gas density falls below this value the bin is completely emptied and the material is added to the bin with the largest dust or monomer density Typical values are 1 0E 09 or so The default value is 0 0 e real c_dust06 The sticking coefficient for the condensation rate is specified with e g real c_dust06 f E15 8 b 4 n Sticking coefficient u 1 amp c0 For C rich dust 0 37 can be between O and 1 1 0 Typical values are between 0 0 deactivating this process and 1 0 The default value is 0 0 The standard choice is 1 0 e real c_dust07 The sticking coefficient for the coagulation rate is specified with e g real c_dust07 f E15 8 b 4 n Sticking coefficient for coagulation u 1 amp c0 Typically between O and 1 1 0 Typical values are between 0 0 deactivating this process and 1 0 The default value is 0 0 e real c_dust08 The sticking coefficient for t
22. 459961 8 026230 HYD 3 2000 16520 798828 8 260400 Viscosity routines 3D 2000 25446 400391 12 723200 VIS make_box modelvis 2000 0 010000 0 000005 VIS copy_box modelvis 2000 1750 960083 0 875480 VIS delete_box modelvis 2000 0 000000 0 000000 Radiation transport routines 2000 243729 000000 121 864502 SHC step 2020 244064 515625 120 824020 SHC step dtime init EOS 16024 49312 738281 3 077430 SHC step dtime explicit 16024 174542 343750 10 892558 SHC formal 16024 170085 437500 10 614418 SHC formal init 16024 35591 378906 2 221129 SHC formal dirloop 16024 133010 687500 8 300717 SHC formal exp 28014 9014 280273 0 321778 SHC formal exp expl2t 28014 3950 409912 0 141016 SHC formal dir3 36083 63222 242188 1 752134 SHC time dir3 36083 19676 009766 0 545299 SHC formal limitei 16024 1306 419922 0 081529 SHC step dtime final 16024 12730 129883 0 794441 SHC formal dir2 11959 22205 000000 1 856761 SHC time dir2 11959 5731 149902 0 479233 SHC formal diri 4044 10674 429688 2 639572 SHC time dirl 4044 1893 760010 0 468289 SHC step dtime final output 181 8620 870117 47 629116 Radiation trans output only 20 335 929993 16 796499 In this example the value for the overall time rhd code 410 830017 sec is not useful because of an overflow in the counter However it is evident that the radiation transport consumes most of the time 243729 000000 sec followd by the hydrodynamics routines 48944 660156 sec and
23. C_hydExpCourant C_hydExpCourantmax 5 4 15 2008 03 17 Hydrostatic pressure correction in waves 3 and 6 switch on and offable with C_hydPredfactor 5 4 7 145 2008 04 27 Expansion viscosity C_visExpansion 5 4 8 2008 07 03 Linear viscosity C_visLinear 5 4 8 2008 08 13 Parameters N_radrsyslevel N_radoutput C_radTcool C_radDcool C_radscool in MSrad 5 4 13 parameters C_radTinci and C_radDinci to control inci dent radiation in MSrad 5 4 13 2008 08 14 Compiling double precision code 8 7 3 2008 08 19 Some parameters possibly valid for MHD module 2008 08 28 Rather old parameters for additional I O control integer n_outslicedim_mean 5 4 16 integer istep_in_start 5 4 16 2009 01 12 README_MHD 2010 03 17 Performance enhancement for EOS gasinter_102 2010 03 19 Performance enhancement during box handling rhd_box_arrays01 2010 04 09 Transmitting upper boundary condition c_rhochangetop Better counters for timing statisctis timing_c_range 2010 04 11 Merging of previous introductory text to Sect 2 2 by BF with README_MHD by WS Update of various text passages Shift of parameter description to Sect Removal of remarks relating to the magnetic field in descriptions of parameters side_bound top_bound and bottom_bound Description of boundary parameters for the magnetic field side_bound_mag_x1 side_bound_mag_x2 top_bound_mag bottom_bound_mag b1_inflow C_magthetaB and C_magphiB
24. E 5 o 1100 b a 2068 G e HE a F F bast Seal 4 Fi 14 h Pree t P e FER de tl Fi he h ER o de Fi L FF s 900F A Ef er ae n PE AD y a KODU E L ra PE E ar ad 3 04 105 106 103 10 cA 194 chunk size chunk size 7 r 1 0 A oe Y n J pags 4 J L tA 4 aml ns WO r re z 4 L J d E T 7 1 a 6 f i 5 5 1 ii E ld E PA Pi 5 7 Y k E Y 04 ete 4 4 L i J a J 1 1 30 ea 0 e 0 2 i j mn 2 2 A i I ws 4 bs a 0 0 f a 0 0 A 104 por 107 106 109 1g 10 10 chunk size chunk size Figure 2 Performance tests on Hitachi SR8000 at HLR Stuttgart For models with 128x128x192 and 252x252x188 grid cells different values for the hydrodynamics and viscosity chunk size pa rameters were used See text for more details 3 7 Optimization Compiler Switches 43 chunk sizes whereas the required memory increases in particular for very large chunk size values Moreover performance and CPU time can be optimized by choosing the right parameter values Interestingly the optimum chunk size is different for hydrodynamics and viscosity Based on these tests a larger value seems to be preferable for the viscosity n_viscellsperchunk In the case of the smaller model 50000 seems to be fine for the hydrodynamics whereas the optimum viscosity chunk size is 200000 This difference explains the double peaked structure of performance and CPU
25. F90_PREFLAGS subchk configure make UIO export F90_PREFLAGS configure make Performance tests on hwwsr8k Some tests have been performed on the machine hwwsr8k at HLR Stuttgart in order to de termine the optimum chunk sizes which are set by the parameters n_hydcellsperchunk and n_viscellsperchunk see Sect 5 4 7 and Sect 5 4 8 Two different models have been used one consisting of 128x128x192 grid cells the other of 252x252x188 respectively Grey radiative trans fer has been performed with the MSrad module Different values for the chunk size s have been assumed where the hydrodynamics and the viscosity parameter were set equal In all cases three time steps have been computed The results are shown in Fig 2 The number of resulting chunks for step HYD1 the values for HYD2 HYD3 and VIS are very similar total memory perfor mance and the wall clock duration of the hydrodynamics and the viscosity routines are shown as functions of the chunk size parameter s Clearly the number of chunks decreases towards larger 42 3 PROGRAM FILES INSTALLATION COMPILATION Performance test on Hitachi SR8000 at HLRS 4 178212842192 3 time steps ua 252x252x108 3 time steps ya an ye wT J norm 0 8 0 6 n aa FA 3 L a co en AR pr Alert a 1 0 0 fe on dad IL 212 Lal aa 4 1 l E qa nt ge 158 G pr m 16 chunk size chunk size J A la 7 ann a de J300
26. Heating modes for core heating 5 4 4 2011 12 09 New parameter r2_grav New option for old parameter c_radhtautop 2012 01 10 A few new references including links Removal of old uio_mac_modules mention of rhd_rec_module f90 New reconstruction methods PPmimo FRmimo FRmono FRweno FRcont 5 4 7 New parameters r2_grav r0_core ar_RotationAxis centrifugal_force hdTransVeloMode 2012 01 11 Parameter real C_visDrag is obsolete Compiler switches rhd_roe1d_slope_101 IDF rhd_hyd_roe1d_101 are obsolete Updates for c_slopered New options for parameters hdsplit CTU for HD Roe solver hdtimeintegrationscheme Single RungeKutta2 RungeKutta3 New parameters C_hydTdiffLin C_hydTdiffMach C_RecContShift C_RecContSteep dustReconstruction 5 4 9 2012 01 12 New parameters C_hydSoundCourant C_hydSoundCourantmax C_v3ChangeLinBottom C_v3ChangeSqrBottom 2012 02 16 New parameter C_TminLimit 5 4 13 2012 04 06 Added some lines in the Intel compiler section 3 7 11 2012 09 04 New options for hdTransVeloMode 5 4 7 New parameters C_hydLowMachcsFactor hdEntropyWaveMode hdEnthalpyAvgMode 5 4 7 C_hydsDiffVelo C_hydvDiffVelo C_visP2PhypSmagorinsky C_visP2PhypArtificial C_visP2PhypExpansion C_visP2Phypdivrhov 2012 11 07 New options for hdEntropyWaveMode hdEnthalpyAvgMode character reconstruction 147 9 Glossary 10 CAT CO5BOLD Analysis Tool CO5BOLD or COBOLD
27. UIO modules is use uio_bulk_module use uio_siz_module use uio_nam_module 4 5 3 Compiling and Makefiles For a certain platform it was necessary to change the name of the module file with the machine dependent routines uio_mac _module f90 in a Makefile for the UIO routines For this purpose the environment variable UIOMAC had to be set to the name of the appropriate routine see Sect 3 3 In the current version of COSBOLD there is only one file uio_mac_module F90 with a capital F90 that can be changed during the compilation by preprocessor switches see 3 6 For CO5BOLD or the UIO Unix scripts the respective configure script takes care of either of these steps 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 FYOFLAGS g make clean make cleanall make remove make removeall A section of a typical makefile using the UIO routines may be Compiler options F90C 90 F9OFLAGS Libraries UIOMAC uio_mac_module 60 4 UIO DATA FORMAT Dependencies of exe files on object files and libraries test exe test o F90C F9OFLAGS o 0 UIOPATH 90 uio_base_module o UIOPATH 90 UIOMAC o ULOPATH 90 uio_bulk_module o test o UIOPATH f90 UIO test f 90 F90C c F9OFLAGS M UIOPAT
28. Updates for reconstruction PP c_slopered n_hyditer n_hydmaxiter 5 4 7 Updates and introduction of parameters for the MHD module c_resb c_resbconst c_resepsilon beta_inv va_max N_magDiffSide N_magDiffTop and n_magbiffbottom F90_MHD comment about zero magnetic fields Removal of first version for MHD entry in table of high level modules References Balsara 1999 Janhunen 2000 Stone amp Pringle 2001 2010 04 14 Some parameters in MHD module were renamed B_theta B_phi N_side N_top N_bottom C_magthetaB C_magphiB N_magDiffSide N_magDiffTop N_magDiffBottom 2010 04 29 The files rhd_mac_ module f90 were removed The single routine from it was put into timing_module F90 2010 05 06 Compiler switch timing_r_type explained Input output UIO compiler switches explained accompanied by some changes con cerning the files uio_mac _module F 90 2010 06 14 Output of additional chunks described in 5 4 16 and 5 4 16 New versions of bottom boundary conditions better suited for HLLMHD solver 5 4 4 The HLLMHD solver can do different time integration schemes 5 4 7 In the HLLMHD step the CheckFlux step can be des activated MHD module allows unsplit update 5 4 7 2011 02 10 New parameters for MHD module 2011 03 28 New option vertical2 for magnetic boundary conditions 5 4 4 146 8 DOCUMENT HISTORY 2011 07 04 MHD equations New parameters r0_core centrifugal_force 5 4 3
29. With version 9 1 and up everything compiles smoothly The native format on Intel machines is little_endian With export F_UFMTENDIAN big to be set at runtime after compilation before running CO5BOLD the default can be changed to big_endian In 3 6 the preprocessor switches are listed that control the modern single version uio_mac_module F90 The compiler is called with ifort ifc on older compiler versions Important switches are e Vaxlib Link proper library to make the machine understand e g call flush 6 e fpp Activate the preprocessor silently http www pgroup com 3 7 Optimization Compiler Switches 45 e 03 General optimization flag e tpp6 xK Optimization especially for Pentium III and Athlon includes SSE vector com mands e tpp7 xW Optimization especially for Pentium IV includes SSE2 vector commands e xP Optimization especially for Core 2 Duo and simular architectures e ip Optimization activate interprocedural optimization within each source file This enables inlining e DMSrad_raytas 2 Optimization choose non default version of loop in SUBROUTINE raytas in file MSrad3D F90 See Sect e Drhd_shortrad_dir1_101 1 Optimization Transpose arrays and use routine rhd_shortrad_dir3 for rays in x1 direction See Sect e openmp Parallelization OpenMP directives are activated Note that the for compiler versions before 9 0 the UIO routines should be compiled without Ope
30. and PGI compiler a dynamic scheduling activated with export OMP_SCHEDULE DYNAMIC 1 is advantageous The size of the individual chunks might be set to larger values than 1 in the examples above The optimal value has to be found empirically A good starting point is number_of_grid_points_in_1D Number_of_treads which gives for a model with 171 grid points on a 4 processor machine export OMP_NUM_THREADS 4 export OMP_SCHEDULE STATIC 43 The behavior of the other modules is not affected The number of threads should equal the number of available processors and has to be set at run time with the environment variable OMP_NUM_THREADS e g with export OMP_NUM_THREADS 16 3 7 2 General Inlining Candidate routines for inlining are i e they should be inlined if anyhow possible e 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_ppeq rhd_hyd_pp rhd_hyd_hdflux e file rhd_lhdrad_module F90 rhd_rad3d_raylhd rhd_rad3d_solve rhd_rad3d_solveeq 38 3 PROGRAM FILES INSTALLATION COMPILATION e file rhd_shortrad_module F90 rhd_shortrad_operator rhd_shortrad_dtauop On some machines the makefile generated by the configure script contains this list explicitely On others one has to rely on automatic inlining see the following sect
31. arrays that is potentially faster Values o 0 classical pointer arrays default o 1 new allocatable arrays probably faster rhd_box_grav01 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 3 6 Compiler Macros 29 o 0 default no handling of array o 1 array handling activated e rhd_box_quc01 in rhd_box_module F90 and rhd F90 rhd box quantity centered 01 Category feature activation CO5BOLD is able to handle a number of further quantities quc quantity centered 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 They are required for the treatment of chemical reaction networks and time dependent hydrogen ionization For the latter the quc arrays contain the number densities of the atomic level populations For the chemical reaction network the arrays contain the species number densities in cm and with headers following this example Number density of H2 Values o 0 default no handling of additional quan
32. band with CO opacity calculated with CO density resulting from time dependent chemistry Only the MSrad module so far can handle non grey tables e integer n_radrsyslevel This parameter specifies the zero point of the ray system default 0 MSrad only The parameter is specified with e g 114 5 CONTROL AND DATA FILES integer n_radrsyslevel f I4 b 4 n Zero index of ray system amp c0 0 default amp 0 integer n_radoutput This parameter controls additional output into the file rhd qrad default 0 MSrad only The parameter is specified with e g integer n_radoutput f 14 b 4 n Output level of MSrad amp c0 0 default amp 1 real c_radtcool Parameter for surface cooling option N_radband lt 0 of MSrad It can be activated with the parameter real c_radtcool f E15 8 b 4 amp n Surface cooling u 1 amp c0 0 0 default 0 0 real c_raddcool Parameter for surface cooling option N_radband lt 0 of MSrad It can be activated with the parameter real c_raddcool f E15 8 b 4 amp n Surface cooling u 1 amp c0 0 0 default 0 0 real c_radscool Parameter for surface cooling option N_radband lt 0 of MSrad It can be activated with the parameter real c_radscool f E15 8 b 4 amp n Surface cooling u 1 amp c0 0 0 default 0 0 real c_radtinci Temperature of black body that emits incident radiation default 0 0 MSrad only It
33. boundary centered enthalphy flux To this flux the Roe corrections are added It can be set e g with character hdenthalpyavgmode f A80 b 80 amp n Mode for enthalpy averaging amp c0 Normal old default CA1 CA1lg CA1gMps recommeded CA1M CA1Ms CA1p CA1s amp c1 CA2 CA2g CA2M CA2p CA2s CA3 CA4 CAigMps The choices are o Normal Use the standard Roe averaging of the enthalpy kinetic energy fluxes old default o CA1 Average the enthalpy and multiply with the average mass flux Average the kinetic energy fluxes as in the standard Roe case o CAlg Use the consistent advection centering for the average enthalpy flux as in CA1 for small fluctuations Switch smoothly to the Normal Roe averaging for large non hydrostatic pressure fluctuations o CAlgMps Use the consistent advection centering for the average enthalpy flux as in CA1 for small Mach numbers Switch smoothly to the Normal Roe averaging for large Mach numbers or large fluctuations fluctuations in pressure directly and after subtracting the hydrostatic pressure correction and entropy This case is recommended o CA1M Use the consistent advection centering for the average enthalpy flux as in CA1 for small Mach numbers Switch smoothly to the Normal Roe averaging for large Mach numbers o CAiMs Use the consistent advection centering for the average enthalpy flux as in CA1 for small Mach numbers Switch smoothly to the Normal Roe averaging
34. can be used e g with real c_radtinci f E15 3 b 4 amp n Temperature of black body that sends incident radiation u K amp c0 0 0 default 0 0 real c_raddinci Dilution factor R d of black body that emits incident radiation default 0 0 MSrad only It can be used e g with real c_raddinci f E15 8 b 4 amp n Dilution factor of black body that sends incident radiation u 1 amp c0 0 0 default 0 0 5 4 Parameter File rhd par 115 e real c_radimplicitmu So far only the LHDrad and the SHORTrad module 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 c0 0 0 explicit 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 tr
35. f90 uio_filedef_module f90 UIO I O routines uio f90 uio_mac_module F90 UIO I O routines machine dependent part 25 Table 3 List of all low level modules the table shows the file name with part of its path the shortcut for the directory and its description o scalar no parallelization default o openmp OpenMP appropriate for CO5BOLD o auto auto parallelization not implemented for all machines e 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 debugging or array checking modes possible if implemented for the requested machine e F9O_LHDRAD LHDrad radiation transport o 0 do not activate compile and link this module default o 1 activate this radiation transport module e F9O_MSRAD MSrad radiation transport o 0 do not activate compile and link this module default o 1 activate this radiation transport module e F9O_SHORTRAD SHORTrad radiation transport o 0 do not activate compile and link this module default o 1 activate this radiation transport module e F90_CHEM CHEM module chemical reaction networks o 0 do not activate compile and link this module default 26 3 PROGRAM FILES INSTALLATION COMPILATION o 1 activate this source step module Setting this variable to 1 will set F90_DUST 1 The compile
36. for large Mach numbers or large entropy fluctuations o CAlp Use the consistent advection centering for the average enthalpy flux as in CA1 for small pressure fluctuations Switch smoothly to the Normal Roe averaging for large pressure fluctuations o CAls Use the consistent advection centering for the average enthalpy flux as in CA1 for small entropy fluctuations Switch smoothly to the Normal Roe averaging for large entropy fluctuations o CA2 Average the enthalpy plus kinetic energy and multiply with the average mass flux o CA2g Use the consistent advection centering for the average enthalpy plus kinetic energy flux as in CA2 for small fluctuations Switch smoothly to the Normal Roe averaging for large non hydrostatic pressure fluctuations o CA2M Use the consistent advection centering for the average enthalpy plus kinetic energy flux as in CA2 for Mach numbers Switch smoothly to the Normal Roe averaging for large Mach numbers 94 5 CONTROL AND DATA FILES o CA2p Use the consistent advection centering for the average enthalpy plus kinetic energy flux as in CA2 for small pressure fluctuations Switch smoothly to the Normal Roe averaging for large pressure fluctuations o CA2s Use the consistent advection centering for the average enthalpy plus kinetic energy flux as in CA2 for small entropy fluctuations Switch smoothly to the Normal Roe averaging for large entropy fluctuations o CA3 Take the Roe tilde average enthalpy
37. 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 4 15 and 5 4 16 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 4 Parameter File rhd par 75 5 4 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 previous 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 filef
38. 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 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 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 n Rate of pressure change for open lower boundary u 1 1 0 e real c_v3changelinbottom For the open lower boundary condition inoutflow and inoutflow2 a damping of the vertical velocity at the open boundary can be specified e g with real c_v3changelinbottom f E15 8 b 4 amp n Linear velocity reduction rate at bottom u 1 0 0025 The open lower bou
39. 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 3 6 Compiler Macros 33 o 1 LHDrad routines are recognized by the compiler e 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 o undefined default MSrad routines are deactivated o 1 MSrad routines are recognized by the compiler e 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 dea
40. is the short form of COnservative COde for the COmputation of COmpressible COnvection in a BOx of L Dimensions with 1 2 3 EOS Equation Of State HION Hydrogen IONization MHD Magneto HydroDynamics RHD Radiation HydroDynamics UIO the Universal Input Output format It is used in CO5BOLD for parameter model mean and EOS files Trademarks AMD is a trademark of Advanced Micro Devices Inc Compaq is a US trademark of Compaq and or Hewlett Packard Company Cray is a trademark of Cray Research HP is a US trademark of Hewlett Packard Company IBM is a US trademark of International Business Machines IDL is a registered trademark of Research Systems Inc Intel Itanium and Pentium are US trademarks of Intel Corporation Linux is a trademark of Linus Torvalds NEC is a registered trademark of Nippon Electric Company PGI is a trademark of The Portland Group Compiler Technology SGI is a trademark of Silicon Graphics Solaris Sun SunOS and SunFire are US trademarks of Sun Microsystems Inc Sparc is a US trademark of SPARC International Inc UNIX is a registered trademark of The Open Group All other product names mentioned in this manual are trademarks or registered trademarks of their respective owners References Balsara 1999 Balsara D S 1999 J Comput Phys 149 270 Colella and Woodward 1984 Colella P and Woodward P R 1984 The Piecewise Parabolic Method P
41. mixed derivatives must be equal then yields GE _ a G 9 A 73 cl le 2 p T NOTES a OT T N0p r Tp 1 de 1 1 Op p 4 u EN p E 2 74 CE gt Comparison with Eq 69 implies so or Finally 16 Similarly replacing de by a a II e e ae d 5 Lap j in Eq 39 we get ds 1 DEN 45 1 e p SET ap T e TP and the requirement that the mixed derivatives must be equal then yields or 0 3 P oJ Op T X0p Tp ee or 1 T o 0 o o Op o oT Op InT Inp a Ges EG Since OlnT J OmT _ Olnp Olnp p Olnp Olnp UN we finally obtain using Eqs 29 and 70 The isothermal sound speed is then obtained as and 2 3 5 Ideal gas with constant specific heats polytropic gas In this case we obtain much simpler relations 1 ST pal h oT Y pal s Cy ln p y In p const y Ty I2 T3 const p _ GG t aR e v v 2 EQUATIONS 2 3 A collection of thermodynamic relations M Steffen AIP e 2 ae Op p ee 2 gi Op r p 18 3 PROGRAM FILES INSTALLATION COMPILATION 3 Program Files Installation Compilation In this section all the files and modules COSBOLD contains are listed The installation procedure is outlined and compiler switches necessary to compile COSBOLD and to optimize its performance are described 3 1 Quickstar
42. not specified this parameter is set 1 0 Values lt 0 disactivate this feature See also Eq e integer N_magDiffSide Increases the diffusivity of the scheme near the side boundaries within a thickness of the diffusion layer of N_magDiffSide computational cells Example integer n_magdiffside f 19 b 4 amp n Number of cells of diffusive side boundary layer 8 c0 0 gt deactivates this feature amp c1 10 reasonable value e integer N_magDiffTop Increases the diffusivity of the scheme near the top boundary within a thickness of the diffusion layer of N_magDiffTop computational cells Example integer n_magdifftop f 19 b 4 amp n Number of cells of diffusive top boundary layer amp co 0 gt deactivates this feature c1 10 reasonable value 100 5 CONTROL AND DATA FILES e integer N_magDiffBottom Increases the diffusivity of the scheme near the bottom boundary within a thickness of the diffusion layer of N_magDiffBottom computational cells Example integer n_magdiffbottom f 19 b 4 amp n Number of cells of diffusive bottom boundary layer amp c0 0 gt deactivates this feature amp ci 10 reasonable value 5 4 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 necessar
43. or links the UIO IDL routines to a location in the standard IDL search path It is reasonable to include the UIO initialization in the startup procedure as e g Initialize uio routines uio_init progrm by hand IDL can handle the conversion types native ieee_4 ieeele_4 ieee idl xdr compare Tab 4 in Sect 4 3 1 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 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 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 m
44. output sxf90 EP P openmp Chopt sx8 W1 Z 8G m dw floatO Wf L nostdout L fmtlist map summary transform L inclist L mrgmsg M noflunf M noinv Drhd_r03 Drhd_shortrad_step_t01 Drhd_shortrad_formal_t01 DMSrad_raytas 1 Drhd_hyd_entropyfix_p01 1 Drhd_hyd_upwind_p01 1 Drhd_hyd_roeid_101 1 Dgasinter_101 2 gcc gnu org fortran i ttp www gnu org 48 3 PROGRAM FILES INSTALLATION COMPILATION 3 7 16 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 Jin Link ping The code was used on the UKAFF machines see Sect 3 7 17 and the computers at CINES See e g the excellent SGI Fortran90 manual Information about the CINES machines can be found under CINES or CINES Introduction 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 e INLINE must Optimization routines that should be inlined see Sect 13 7 2 e Ofast OPT Olimit 0 General optimization On older compiler versions 03 was the achievable optimum e IPA plimit 5500 Even more optimization This option requires lots of memory 1 GByte To get it it might be necessary to ask for more than one processor for the compi lation especially on the CINES machines e CG l
45. path addpath expand_path UIOPATH id1 addpath addpath expand_path HOME HYDRO IDL rhdpro if strtrim addpath 2 ne then path addpath path delvar addpath Initialize uio routines uio_init progrm by hand Note Before using IDL the environment variables for the CO5BOLD paths should have been set Use setarcdeppaths sh or ksh csh for this purpose Important is UIOPATH which specifies where to find the IDL routines for the UIO handling in the script above Alternatively one might set the IDL path variable accordingly like export IDL_PATH UIOPATH id1 for example in the bashrc file before starting IDL Or you just make a symbolic link from the UIO IDL routines at their original location to a sub directory of the main IDL directory which should be in the IDL path anyway The initial single call of uio_init is necessary in any case 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 Huuhh 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_struc
46. problems occur close to strong density jumps one can try to cure them by setting it e g to 0 02 or so One could even think off other criteria e g low temperatures very high Mach numbers to activate this slope reduction That could be implemented if if would deem beneficial e real c_reccontshift The second order reconstruction schemes except FRcont have the option to make the re construction even more continuous in the case of very low Mach numbers controlled with C_RecContShift and C_RecContSteep The value can be set e g with real c_reccontshift f E15 3 b 4 amp n Enhanced reconstruction continuation parameter 1 for shifting amp c0 0 0 off 1 0 reasonable value 0 2 Typical choices are o 0 0 No attempt is made to make the reconstruction more continuous The original reconstruction is used o 0 1 Make the transition to a smoother reconstruction at lower Mach numbers o 1 0 Reasonable value o 10 0 Make the transition to a smoother reconstruction at higher Mach numbers While the resulting scheme works for solar simulations the parameters are really of benefit only in the case of brown dwarfs or exoplanets or the deep layers of M dwarfs e real c_reccontsteep The second order reconstruction schemes except FRcont have the option to make the re construction even more continuous in the case of very low Mach numbers controlled with C_RecContShift and C_RecContSteep The value can be set e g with real c
47. read with the IDL uio_dataset_rd filename function The result ing data structure contains mass density gas temperature electron density of the atmosphere as well as the axes in the atmos substructure The atom substructure contains the time dependent populations ntd the LTE populations nstar the total population ntot a number of atomic pa rameters and 1_ntr and c_ntr arrays of the z index per column where the radiation temperature in a transition starts to deviate from the gas temperature Refer to Leenaarts amp Wedemeyer Bohm 2005 for more details 135 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 4 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 bina
48. 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 o 2500 Pentium III Core 2 Duo 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 An example is given for the Hitachi SR8000 in Sect 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 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 The following parameters apply only to the MHD module see also Sect 2 2 for details e integer n_orderconstrainedtransport Order of reconstruction of the electric field in the constrained transport step The parameter can be set e g with integer n_orderconstrainedtransport f 14 b 4 amp n Number of hydrodynamics iterations amp c0 order of reconstruction of electric field in constrained transport step amp c1 1 Simple arithmetic average default 2 Quadratic in
49. rhd fulll o o 68 5 2 Files with additional chunks of data rhd chull o 69 ee A ad 69 acd yet A Boe ee Bale ot Sok 70 5 3 2 Contents of Individual rhd mean File Entry 71 Gea ae ee ae De O eee 74 HRB e A 74 5 4 2 Header 2 4 03 a2 a 25 son a a A a 75 5 4 3 Fundamental Model Parameters 2 2 2 2 22 nn nn 76 A Ql a ee ak a een eS 78 binds hh ee Ne ee ws ot EE hs ae coe 85 0 4 6 Opacities s lt s ssa etapa adawa ce eukw a a a kpaa eE 86 5 4 7 Hydrodynamics Control HD and MHD 87 5 4 8 Tensor Viscosity Control ooa a 100 5 4 9 Dust Molecules Hydrogen Ionization General ooa aaa 103 5 4 10 Dust dustscheme dust_moment04_c2l 2 22 2 2 a 106 5 4 11 Dust dustscheme dust_k3mon 03 2 2 2 rn nn nn nn 106 5 4 12 Dust dustscheme dust_ bins Dll 2 2 22 2 on nn 108 5 4 13 Radiation Transport Control Coon 109 5 4 14 Process Time Management 2 2 Cm on ee 116 5 4 15 Time Step Controll a 118 5 4 16 Input Output Control u oe 42 ge Be kee ee ere RSS HS eS 121 cee endo 125 129 5 6 Text Output rhd out a 129 5 7 Chemistry Input 132 59 HION Input cca x g wit oo a um Sow ae Gk es ee Bo ek ee 133 5 9 HION Output oa ae ew ee eRe a te be ok A 134 135 at te ee ee ard Beats le St ee es as ee sey 135 ia ae ee ne Gens 136 140 san bo hae Hoe weed SA A eee ee hoe aR ea oS Se aS 140 142 COD
50. this check is usually not needed It can be switched off by setting c_maxeichange 0 0 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 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 typical radiative time step is computed real c_radcouran
51. time Note that the optimum values do not only depend on the architecture used but also on the dimensions of the model We recommend to test some chunk size values since it might lead to a higher performance 3 7 9 IBM Useful links IBM compiler documentation IBM XL Fortran especially IBM AIX compiler information center P Another source of the compiler documentation Documentation for AIX Systems P especially IBM XL Fortran for AIX Version 8 1 1 Library Particularly useful hints Porting Programs from the Crays to the sE The compiler to be used for OpenMP runs is called with x1f90_r which binds the object files to the thread safe components IBM documentation For scalar code x1f90 might be sufficient Important switches are e qsuffix f f90 qsuffix cpp F90 To tell the compiler about the existence of Fortran90 and to enable the preprocessing for files with suffix F90 e qextname flush etime Append underscore to both routine names In the prepro cessor switches are listed that control the modern single version uio_mac_module F90 e WF Drhd_r03 The compiler does not send switches starting with D to the preprocessor but tries to interpret it itself unlike all other compilers Therefore each switch e g Drhd_r03 has to escaped with WF as e g WF Drhd_r03 e q64 Activate the 64 bit mode In the default 32 bit mode a very small model with total memory requirement
52. time that is used in a scalar i e single processor setup Ideally one would like a constant behavior which stays close to one 2 0 Machine grand 1 8 125x125x81 grid points 4 OBM band 10 time steps 1 6 1 4 0 5 10 15 20 25 Number of processors Per processor execution time increase Figure 3 UKAFF machine grand small model The perhaps most interesting result is that the speedup on ukaff is about 11 for the large model on 16 processors Perhaps not ideal but within the range of practical interest In general the hydrodynamics routines scale more favorably than the radiation routines This is perhaps sim ply related to the fact that in explicit hydrodynamics communication is restricted to neighboring grid cells For those wondering the black curves do not lie between the red and green curve since more components than just radiation and hydrodynamics add up to the total time Furthermore the normalization of the execution times given by CO5BOLD is not exact 3 7 18 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 and later An older version was not able to compile COSBOLD properly Information about Fortran and the Sun 50 Per processor execution time increase Per processor execution time increase 3 PROGRAM FILES INSTALLATION COMPILATION Machine grand 315x
53. 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 timing_c_range in timing_module F90 timing counter range 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_range specifies the number of digits the range used for the integers storing the counters The value appears in the code e g in integer kind selected_int_kind timing_c_range count_total Fortran standard is the use of 4 byte integers However that is often not sufficient and can lead to overflows Many compilers can use longer integers though That can be tried by setting the timing_c_range not to 9 the default but e g to 15 If it works overflows 28 3 PROGRAM FILES INSTALLATION COMPILATION are essentially ruled out If it does not work the compilation stops with an error message Values o 9 default use standard 4 byte integers for timing counters o 15 or otherwise use this number for the range of Fortran integers By a proper choice of this number all the timing measurements can be made meaningful even for long runs on machines with fast counters timi
54. 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 features than the machine dependent versions Besides the format the conversion type see table has to be specified The native conversion 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 and ieee_8 can 54 4 UIO DATA FORMAT be chosen The last two conversion types correspond to the CRAY internal types ieee_32 and jeee_64 respectively On a machine
55. with an internal data representation not within the list in the existing uio_mac_module F90 file one could use the native conversion type only But it is better to invent an appropriate name for the new data format and to build a proper machine dependent branch with its own compiler switch However it was possible in all cases so far to activate some internal conversion process which allowed the handling of UIO files in the standard Big Endian IEEE format conversion type I R D description native 2 7 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 gt ieee_4 ieee 7 IEEE format unknown length not recommended Table 4 UIO conversion types with length of integers single precision reals and double precision reals in bytes and an explanation 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 conversion type are determined automatically from the file if the conversion type of the d
56. 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 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 5 4 Parameter File rhd par 119 real dtime_incmax f E15 3 b 4 n Maximum time step increment factor u 1 amp c0 dtime_max lt 1 0 gt no restriction ci 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 hydrodynamics 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
57. 13 6 p 4 b 4 n Internal energy amp u erg g 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 rhoek_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Kinetic energy amp u erg cm 3 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 t_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 n Temperature amp u K t_xmean4 d 1 1 1 1 1 120 f E13 6 p 4 b 4 n Temperature amp u K t_xmeankapparho d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Temperature amp u K p_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 n Pressure amp u dyn cm 2 s_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 n Entropy amp u erg K g 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 gammai_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n 1st Adiabatic Coefficient amp u 1 gamma3_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n 3rd Adiabatic Coefficient amp u 1 delta_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Expansion coefficient 8 u 1 5 3 File with Additional Data rhd mean 73 real kapparho_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Absorption Coefficient amp u 1 cm real quc001_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n 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
58. 31 5x81 grid points 1 OBM band 3 time steps 5 10 15 20 25 Number of processors Figure 4 UKAFF machine grand large model Machine ukaff 315x315x81 grid points 1 OBM band 3 time steps 5 10 15 20 25 Number of processors Figure 5 UKAFF machine ukaff large model 3 7 Optimization Compiler Switches 51 compiler can be found on the Sun Fortran data sheet pag under Documentation ngstr m Sun cluste Important switches are openmp Enable OpenMP 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 required This is done automatically in the Makefile inline Optimization routines that should be inlined see Sect DMSrad_raytas 2 Optimization choose non default version of loop in SUBROUTINE raytas in file MSrad3D F90 See Sect Drhd_shortrad_formal_101 1 Optimization split loop for exp dtau computation into two loops See Sect Drhd_shortrad_dir1_101 1 Optimization Transpose arrays and use routine rhd_shortrad_dir3 for rays in x1 direction See Sect Drhd_hyd_entropyfix_p01 1 Optimization version with masks weights See Sect 3 6 xarch native64 Produces 64 bit code optimized for local machine 20 http developers sun com sunstudio products previ
59. 4 9474 l gt gt gt Ok gt o R gt gt l l l 47 49 4944 74 l l l gt gt gt Ok gt R gt gt l l l 4 7 4 9 4 4 9474 l l l gt gt gt gt gt gt D gt l l l l 4 7 49 4 4 9474 l l l gt gt gt gt gt gt gt 47 494 949474 hydrodynamic variables gt x1 component of the magnetic field x2 component of the magnetic field 10 2 EQUATIONS The extension to 3 dimensions should be clear Variables at the left or the bottom boundary have the same indices as the cell For a box with 120 120x120 cells the header for the magnetic field arrays in the start model may look like real bbi d 1 121 1 120 1 120 f E13 6 p 4 b 4 Y n cell boundary magnetic field 1 u G sqrt 4pi real bb2 d 1 120 1 121 1 120 f E13 6 p 4 b 4 Y n cell boundary magnetic field 2 u G sqrt 4pi real bb3 d 1 120 1 120 1 121 f E13 6 p 4 b 4 Y n cell boundary magnetic field 3 u G sqrt 4pi For simplicity the MHD module uses units such that the 4 pi factors do not appear in the MHD equations Therefore one has to multiply the original magnetic fields in gauss with the factor 1 V 4m in order to get the correct magnetic field strength for COSBOLD After the computation one has to multiply the magnetic fields from the COSBOLD output with the factor VAr in orde
60. 6 p DOE 06 00E 06 5 OOE 05 4 OOE 05 4 OOE 05 4 OOE 04 3 OOE 04 3 OOE 04 3 OOE 03 2 00E 03 2 00E 03 2 00E 02 1 00E 02 f 00E 02 1 00E 01 0 SOE 01 0 00E 01 0 O0E 01 0 00E 00 O 50E 00 0 00E 00 00E 00 O0 00E 00 0 00E 00 O O0E 01 0 2179 868 588 334 001 TAT 486 131 856 577 200 912 621 233 939 645 256 961 571 371 133 019 191 312 597 COL 8TT 967 3920 3970 4030 4080 4160 4210 4270 4340 4400 4460 4530 4590 4640 4720 4800 4900 5080 5260 5560 5850 6260 6570 6880 7160 7920 8250 8420 8500 naaa aaa aa PP SP BP WWBWWWNHNNNNNRFP KR BS ELL 598 842 042 219 450 618 835 999 162 ort 541 704 2919 083 245 460 622 830 926 022 070 114 140 191 213 229 242 WWWNHNONRFPRFPRFPRF OOO 8 752 342 105 910 674 508 341 128 967 804 596 437 279 070 094 266 504 705 002 201 613 879 140 363 889 092 196 245 00 00 00 00 00 00 00 00 50 50 50 50 50 50 50 65 85 00 25 40 50 60 FO 80 80 RRRRRRPRRAR RR RPRP OOOOOOOOOOOOOOOoOo oO oOo Ff rr FE Oo Oo COO CO CG COO CO Oo CG 5 999098 00 l 28208 29675 31510 33103 35776 37527 39712 42377 44765 47248 50256 52925 55173 58792 62415 66867 74558 81447 89163
61. 80 n Dust model amp cO none default nosource dust_simple_01 co_component01_01 Y c1 dust_k3mon_01 dust_k3mon_02 dust_k3mon_01 The following values are currently possible 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 routines from Susanne H fner with one component only but realistic time scales o dust_k3mon_02 Simple C rich dust formation routines from Susanne H fner with two components for dust density and free carbon density o dust_k3mon_03 Simple Forsterite dust formation based on routines from Susanne H fner with two components for dust density and free Forsterite monomer density o dust_bins_01 Multi size bin Forsterite dust formation based on Rossow s equations with one bin for the monomers and several bins for the different grain sizes o dust_moment04_c2 C rich dust chemistry 4 moments routines from Susanne H fner chemreacnet chemical reaction networks routines from Sven Wedemeyer B hm and Inga Kamp O o hiontd time dependent hydrogen ionization routines from Jorrit Leenaarts and Sven Wedemeyer B
62. 90 CHEM chemical reaction network solver hion_main_module f90 HION hydrogen ionization hion_io_module f90 HION hydrogen ionization I O hion_def_module f90 HION hydrogen ionization definitions hion_dvode_module f90 HION hydrogen ionization solver hion_lineq_module f90 HION hydrogen ionization linear algebra hion_util_module f90 HION hydrogen ionization utility package hion_devel_module f90 HION hydrogen ionization developer kit edens_module f90 HION electron densities Table 2 List of all high level modules the table shows the file name with part of its path the shortcut for the directory and its description 3 5 Configure Script File and path Abb Description 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_gl1_module f90 RHDB global parameters hd rhdb rhd_io_module F90 RHDB input output routines hd rhdb rhd_mean_module f90 RHDB averaging routines hd rhdb rhd_prop_module f90 RHDB box properties hd rhdb rhd_rec_module f90 RHDB reconstruction routines 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
63. A 414 1121 link to ADS Wedemeyer B hm et al 2005 Wedemeyer B hm S Kamp I Bruls J amp Freytag B 2005 A amp A 438 1043 link to ADS Index alpha AMD batch queue 136 big_endian 39 44 46 47 boundary conditions centrifugal force chem dat chemical composition chemical reaction network 6 CINES CO5BOLD 6 Compaq 147 compilation compiler alpha Cray 895 46 gfortran Hewlett Packard Hitachi SR8000 IBM Intel NEC SX 5 SX 6 SX 8 PathScale PGI SGI UKAFF Sun compiler macro category gasinter_101 gasinter_102 28 IDF MSrad_raytas rhd_shortrad_lambda_101 rhd_bound_t01 rhd_box_arrays01 rhd_box_bmag01 rhd_box_grav01 rhd_box_quc01 rhd_hyd_entropyfix_p01 rhd_hyd_gravcorr_p01 31 rhd_hyd_roeid_101 rhd_hyd_upwind_p01 rhd_r01 rhd_r02 rhd_r03 149 rhd_rad3d_dir_t01 rhd_rad3d_fromray_101 rhd_rad3d_r02 rhd_rad3d_solve_t01 rhd_rad3d_step_t01 84 rhd_rad3d_toray_101 rhd_roeid_flux_101 rhd_roeld_flux_t01 rhd_roeld_slope_101 rhd_roeid_step_t01 32 rhd_shortrad_dir1_101 rhd_shortrad_dir_102 rhd_shortrad_dtauop_101 rhd_shortrad_dtauop_102 3 rhd_shortrad_formal_101 rhd_shortrad_formal_t01 rhd_shortrad_operator_101 rhd_shortrad_operator_102 rhd_shortrad_step_t01 rhd_vis_density_p01 rhd_vis_t01 timing_c_factor timing_c_range timing_r_type uio_switch_crayxmp_101 uio_switch_ieeebe_101 uio_switch_ieee
64. BOED Data im UU 4 4 2 aa A esa FR ee eee ee ea a 140 West baw ky Si a ER Ge at ws Se ee hc 140 7 2 2 Loading CO5BOLD Data full sta end 140 A oe Soe 141 A pe a Goes 141 lat BAe date ee A tee ay 141 3 IDL Data Structurel 2 2 4 65 Sea eR wR ee ee ee ee es 142 TA More IDL routines oaoa aa a 143 CONTENTS ES 8 Document history 144 10 Trademarks 147 147 LIST OF FIGURES 5 List of Figures peste te eae es teas Bien Tacs Ge pate ote hen A eee 22 2 Performance tests on Hitachi SR amp 8000 20 0202 0000 42 3 UKAFF machine grand small model 0 022000005 49 4 UKAFF machine grand large model 2 2 2 2 nn nn nn 50 5 UKAFF machine ukaff large model ooo aaa a 50 guy e aa Guess ape Gs Ge ese e R 136 List of Tables 1 List of source directores 23 se tex cata ee te eave Oe Bu ee ee 24 3 List of all low level modules En 25 a Sea aea A he es oe A 54 Scie nats Bat ats A ASS oh eth Ae ed de ee eve aes 55 O a xaos he eth ne a aed ee Gates cere ee 56 7 UIO Fortran90 t s escra e 2232 a SOE ee wre Da 58 8 Contents of uio_base_module f90 2 22 22 22mm nn 58 9 Contents of uio mac Module 58 10 CO5BOLD control and data files 2 22 22 Co LEE nn 68 11 Combinations of HD options 2 2 2 En nn nn nn 87 12 Radiation transport parameters 22 22 oo mon nn 110 6 1 INTRODUCTION 1 Introduction CO5BOLD nickna
65. CO5BOLD User Manual Bernd Freytag Matthias Steffen Sven Wedemeyer B hm Hans G nter Ludwig Jorrit Leenaarts Werner Schaffenberger April 2 2015 2 CONTENTS Contents 6 7 De A a ee oe ee a re 7 2 2 Magnetohydrodynamics W Schaffenberger 2 22 22 8 2 3 A collection of thermodynamic relations M Steffen AIP 2 2 2 2 11 2 3 1 Basic thermodynamic equationsl o nn 11 PR cebd aoe u ee A 12 eneus pop a en ee 12 2 3 5 Ideal gas with constant specific heats polytropic gas 16 18 a a ee 18 Sie Nee ae ee ee a eee gue meee ae 18 BA cue See A ee et shor Hees ee de 21 34 Fortram Files ss e s sw 2 2a ea ee ee Bea ann ne nn 21 3 5 Configure Script gt s sat sad edda adda a ea ner eS 23 La A ie eS ee a Baek ne ed 27 o o See rede Se ee ee a 36 3 7 1 General OpenMP settings 2 2 2 non ee 37 3 7 2 General Inlining 2 22 22 cu on nn 37 E SEE ogee 38 DA Oray llo e str Sara Bod Gf oe aha Goce Gone Bw care A ae a 38 koe een Gad ee se ee ee es See ee See 39 3 7 6 Hewlett Packard V2500 2 2 2 CE nn 39 3 7 7 Hewlett Packard Itanium 2 e e 40 3 7 8 Hitachi SR8000 2 a 40 ears var ee we ne es Ge Gs ae Ge Ge es Gi are 43 Spe ft WhO BY are ae Gees sat ee Bd Geos Gd Oe we 44 nd ie HE re ds er ai 44 En ol ee ee He eee eS 46 La RBS ed eG A co a had a SS 46 So eens i ns Ge ee ee eee 47 3 7 15 NEC SX 5 SX 6 SX 8
66. E 03 8 884E 02 4 814E 03 End of rhd_shortrad_step A simulation ends with e g Time step number itime 49050 time 2 6823742E 08 t_job 1 273407E 06 End Computation 22 2222 gt SS SS SS SS Exit information Requested number of time steps done Exit status 0 In this case a file rhd done see Sect 5 5 is produced A messages like BR 3 3 3 3 ak af ak ak ak ak ak ak ak a af af af af ak aka af ak ak ak ak ak ak ak ak a A a I a aa aa 21 25 ak ak ak ak ak a a A a ak ak ak ak ak ak 21 1 ak ak 2 2 kkk kkk kkk k Severe error SHORTRAD Time step below absolute limit Error index 100 Interrupt computation BR 3 3 3 3 3 ak ak ak ak ak ak ak ak a af a a af ak aka ak ak ak ak ak ak ak ak ak a A A A a aka aa a ak ak ak ak ak ak ka a A ak ak ak ak ak ak ak KK 2 k kkk kkk kk kkk k k k k 132 5 CONTROL AND DATA FILES marks an exit with an error and without rhd done file A message about the final model like ACTION Write final model lt lt lt lt lt lt lt lt Model file rhd end opened on channel 12 is followed by some timing information like e g Timing statistics rate x factor 1000000 x 10000 Process Samples Total time Mean time sec sec RHD code 1 410 830017 410 830017 uio output routines 27 37 469997 1 387778 HYD bound_3Dcenter 2000 3 540000 0 001770 Hydrodynamics routines 2000 48944 660156 24 472330 HYD 1 2000 16350 610352 8 175305 HYD 2 2000 16052
67. E E fi ale E E 2027878 A E EE A E A E E 0027878020278 72 02020802027 278 202087800020 A ARAA AEREA REAREA Dispose modified command file for next job cp p nrhd cmd STADIR rhd1 cmd Exit loop if end of chain reached if test ACT eoc then break fi 6 2 Running CO5BOLD on a Machine with Batch System f End of Loop gt done Submit next job if not end of chain reached if test ACT eoc then cd STADIR echo Resubmit job tt usr local bin qsub rhdi job qsub rhdi job nice nohup rhdi1 job amp nohup rhdi job amp else echo End of job chain fi FEREIEEETETEIETE TE BETA HEHE EGE EE EEE E EE E AEH EE PETE AE HEED HE HH EEE PE E HEHE EEE PE EEE HEHEHE HEHEHE 139 A more detailed description of the script will come sometime in the future e g from Sven s manual 140 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 7 1 Preparations Make the UIO IDL routines visible to IDL somehow There are several ways to do that Three are described below We recommend to create an initialization 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
68. ES INSTALLATION COMPILATION e 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 o undefined default no timing information o defined call subroutines to measure elapsed time rhd_roeid_flux_t01 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 defined 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_p0l1 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
69. Example real c_magphib f E15 8 b 4 n angle magnetic field w r to the x axis amp u rad cO used in combination with oblique conditions 0 0 5 4 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 E0S file name amp cO eos_gamma140 eos eos_mm20_1 eos eos_mm00_13 eos eos_mm00_15 eos There exists an increasing 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_XXXX_14 eos Several EOS tables for various compositions o eos_mm00_15 eos EOS file for solar composition with temperature range extended to very low values by keeping u fixed below 500 K The number of points for the density sampling has been reduced The number of points for the energy sampling has been increased 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_gammal40 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 r
70. 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 q 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 56 4 UIO DATA FORMAT 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 6 Standard UIO 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 FOOoORNFRFREFN eNe ONFPONFPONF OO NF ON FS OND BOE 07 6 Q0E 07 5 OOE 0
71. GI Origin compiler settings section modified IBM compiler settings section added 3 7 9 Document history started pretty late Dedicated OpenMP section 8 7 1 Dedicated inlining section 8 7 2 Parameter for core drag force New EOS table for solar composition B 4 5 Trademarks List of new dust files the table was split into two 3 4 Installation of UIO UNIX scripts with configure 1 6 1 Thermodynamic relations Point to point tensor viscosity 5 4 8 New gravitational potential mimicking a travelling tidal wave 5 4 3 New control files rhd dump and rhd snap to request a snapshot of current model 2005 03 08 2006 07 28 New control parameter dtime_out_end 5 4 16 Preparation for major code release beta version with the new modules CHEM 5 7 and HION 5 8 including new parameters 5 4 9 and switches for the configure script 3 5 2006 08 14 2007 02 12 coordinate MHD section MHD parameters 5 4 7 Hydro section with new modii and parameters heat mode 5 4 4 rotating system possible hydrodynamics iteration 5 4 7 new pressure correction scheme 3 6 unsplit hydrodynamics operator possible 5 4 7 2007 10 22 2007 12 18 Double precision time as additional scalar in model file Rather stable version and parameter rearrangements for dust model dustscheme dust_k3mon_03 5 4 11 and dustscheme dust_bins_01 5 4 12 2008 03 13 Expansion Courant number
72. H 90 test f90 Dependencies on used modules ULOPATH 90 UI0 cd UIOPATH f 90 make UIO FYOFLAGS FYOFLAGS 4 5 4 Sample Calls of Fortran UIO Routines The needed modules have to be declared by a use statement 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 pss 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 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 call 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
73. Kutta step is used RungeKutta3 A three step Runge Kutta step is used For possible combinations see 11 e character hdsplit With this parameter the type of the hydrodynamics operator directional splitting scheme can be specified as in character hdsplit f A80 b 80 n Hydrodynamics directional splitting scheme amp c0 123 directional splitting default amp cl unsplit unsplit direct operator c2 CTU Colellas Corner Transport Upwind scheme 1990 123 Possible values are o 123 default The standard directional splitting is activated where the 1D operators for the individual directions are applied in the given order So far only the order 123 is possible o unsplit The standard solver is applied However the changes from the individual steps are computed from and applied to the same model configuration The result is an unsplit scheme 5 4 Parameter File rhd par 89 o CTU Use Colella s Corner Transport Upwind scheme CTU 1990 It first com putesand stores the changes from hydrodynamics in x1 x2 and x3 direction Then half of the contributions from the steps in x1 and x2 direction are used as sort of a predictor step for the full corrector step in x3 direction and accordingly for the two other directions At the end the three corrector step contributions are added That means that two hydrodynamics steps have to be performed in each direction with
74. PM for Gas Dynamical Simulations J Comp Phys 54 174 201 Freytag et al 2002 Freytag B Steffen M amp Dorch B 2002 Astron Nachr 323 213 link to ADS 148 REFERENCES Freytag and H fner 2008 Freytag B H fner S 2008 Three dimensional simulations of the atmosphere of an AGB star A amp A 483 571 583 link to ADS Freytaget al 2010 Freytag B Allard F Ludwig H G Homeier D Steffen M 2010 The role of convection overshoot and gravity waves for the transport of dust in M dwarf and brown dwarf atmospheres A amp A 513 19 link to ADS Freytag et al 2012 Freytag B Steffen M Ludwig H G Wedemeyer B hm S Schaffen berger W Steiner O 2012 J Comp Phys Special Issue Computational Plasma Physics ed Barry Koren 231 919 959 link to ADS link to publisher Janhunen 2000 Janhunen P 2000 J Comput Phys 160 649 Leenaarts amp Wedemeyer B hm 2005 Leenaarts J amp Wedemeyer B hm S 2005 A amp A 431 687 Schaffenberger et al 2005 Schaffenberger W Wedemeyer B hm S Steiner O amp Freytag B 2005 in ESA SP 596 Chromospheric and Coronal Magnetic Fields ed D E Innes A Lagg amp S A Solanki Stone amp Pringle 2001 Stone J M amp Pringle J E 2001 Mon Not R Astron Soc 322 461 Wedemeyer et al 2004 Wedemeyer S Freytag B Steffen M Ludwig H G amp Holweger H 2004 A amp
75. Superbee Piecewise Parabolic PP o Hybridization of Ist and 2nd order flux to ensure positivity of pressure and density e Use of Roe solver 2 2 Magnetohydrodynamics W Schaffenberger 9 e Flux interpolated constrained transport step e Small violation of strict energy conservation after the constrained transport step to keep the pressure positive term of Balsara 1999 e Electric conductivity and additional energy diffusion e Use of thermal energy equation instead of total energy equation possible for HLL solver only e Use of both thermal energy equation and total energy equation possible dual energy method HLL solver only e Reduction of Alfv n speed to avoid small time steps with HLL solver only and in combi nation with thermal energy equation or dual energy method only e Use of multiple MHD substeps e Boundary conditions for the magnetic field can be specified independently from the hydro boundary conditions e Diffusive boundary layers possible e Dimensional splitting or unsplit scheme possible The magnetic field is located at the cell boundaries rather than in the cell centers Therefore the format of the magnetic field arrays is slightly different from that of the other hydrodynamic variables Staggered grid representation of the magnetic field in 2 dimensions 47 494 4 9494 l l l gt gt gt gt Rx gt gt gt l l l 4 7 4 94
76. _101 uio_switch_ieeele_101 uio_switch_native_101 uio_switch_open_101 uio_switch_system_101 EEE configure script 23427 control variables F90_BASEPATH F90_CHEM F90_COMPILER F90_DEBUG 25 F90_DUST F90_HION F90_LHDRAD F90_MACHINE F90_MHD 26 F90_MSRAD F90_PARALLEL F90_POSTFLAGS F90_PREFLAGS F90_SHORTRAD 25 Coriolis force craSHi Cray BS 16 7 137 CTU 150 data format UIO directional splitting 6 double precision dust 6 entropy fix environment variables EOS equation of state files data files table of Fortran files table of HION IDL UIO input chem dat EOS opacities rhd cont 129 rhd dump 129 rhd par rhd stop output rhd done rhd out rhd snap 129 rhd exe fluxes formatted Fortran 6 895 46 efortran HD Hewlett Packard HION input output Hitachi HP 147 hydrodynamics 6 hydrodynamics routines hydrogen ionization 6 IBM IDL CAT combox pro eosbox pro UIO routines uio_data pro uio_datasetlist_rd pro INDEX uio_dataset_rd pro uio_dataset_rd pro uio_init pro uio_struct_rd pro inlining alpha Cray VXI IBM Intel compiler on Linux PGI compiler on Linux SGI Sun input chemical reaction network HION Intel Itanium Lured Linux little_endian 39 44 46 47 Loadleveler Macintosh magnetic fields 6 magnetohydrodynamics makefil
77. _out_ful1 122 real dtime_out_mean 122 real dtime_start 118 real endtime real gamma 126 real grav 76 real luminositypervolune 80 real mass_star 76 real nu_rotation real plustime 117 real qmol real r0_core 77 real r0_grav 76 real ri_grav 77 real ri_rad 77 real r2_grav 77 real rho_min 83 real s_inflow 80 real starttime 116 real teff 76 real va_max 99 tensor viscosity 100 time step 118 rhd snap 129 rhd stop 129 Roe solver rotation 78 SGI short characteristics SHORTrad 6 single precision Sparc 147 Sun tensor viscosity 100 tensor viscosity routine thermodynamic relations adiabatic gradient enthalpy entropy 153 internal energy polytropic gas sound speed specific heats time step 111 timing statistics total energy flux uro conversion type example format Fortran IDL makefile record length unit uiocat uio_datasetlist_rd pro uio_dataset_rd pro uio_dataset_rd pro uioinfo uio_init pro 65 uiolook uio_mac_module uio_struct_rd pro UNIX scripts UKAFF unformatted UNIX viscosity point to point 102 tensor 24 32 100 xb1 69 xb2 xb3 69 xc1 XC2 xc3
78. _reccontsteep f E15 8 b 4 amp n Enhanced reconstruction continuation parameter 1 for steepening amp c0 0 0 off 0 1 reasonable value 0 5 Typical choices are o 0 0 No attempt is made to make the reconstruction more continuous The original reconstruction is used o 0 01 Make the transition to a smoother reconstruction steeper at even lower Mach numbers o 0 1 Reasonable value o 1 0 Make the transition to a smoother reconstruction smoother While the resulting scheme works for solar simulations the parameters are really of benefit only in the case of brown dwarfs or exoplanets or the deep layers of M dwarfs e character hdtransvelomode This parameter controls the treatment of advection of transverse velocities It can be set e g with 92 5 CONTROL AND DATA FILES character hdtransvelomode f A80 b 80 amp n Mode for transverse velocity advection amp c0 Normal default CA1 CA2 CA3 CA4 CA4 The choices are o Normal Compute flux of transversal momentum with standard Roe treatment old default o CA1 Compute flux of transversal momentum with consistent advection version 1 Use mass flux and upwind density to determine flow speed Actually recompute transversal velocities o CA2 Compute flux of transversal momentum with consistent advection version 2 Use mass flux and Roe mean density to determine flow speed Actually recompute transversal velocities o CA3 Compu
79. ac_module F90 uio switch system list 01 Category I O account for property of machine Sometimes it is useful to have in the header of UIO file information about the system that wrote the file How Fortran gets this information depends on the machine Values o 0 Read information from file uioenvfile txt Don t write or delete the file o 1 Call external function system to produce the file uioenvfile txt Read and delete the file default 30 3 PROGRAM FILES INSTALLATION COMPILATION o 2 Call routine system to produce uioenvfile txt Read and delete the file o 3 Call external routine HF_SH to produce uioenvfile txt Read and delete it o 4 Call external function uname to get system information o 5 Call external routine pxfuname to get system information e uio_switch_native_101 in uio_mac_module F90 uio switch native list 01 Category I O account for property of machine All machines can read and write their native format only that it might differ from one to the other It is there if needed but should be avoided in practise Values o 1 Get information about word lengths from uio_deform default o 0 2 Set word lengths explicitely uio_switch_ieeebe_101 in uio_mac_module F90 uio switch ieee big endian list 01 Category I O account for property of machine This is the standard for files read of written by CO5BOLD All machine compiler combi nations should support
80. ains dummy names File Sect I O Type Description rhd exe executable main program rhd par I control data UIO central control file rhd stop I control file to force controlled stop of simulation rhd cont I control file to force continuation after stop rhd dump I control file to request output of current model 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 file of last 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 chul O data UIO small chunk of full dataset written often rhd snap O data UIO file with model snapshot if requested rhd out O data text human readable text output data dat I data text chemical reaction data data atom I data text HION data file model atom edens dat I data UIO HION data file electron density table abundance input I data text HION data file abundances pf_kurucz dat I data UIO HION data file partition functions HION time H out O data UIO HION additional output HION step H out O data UIO HION additional output Table 10 List of all control and data files of COSBOLD 5 1 Model Files rhd sta rhd end rhd full If the UIO scripts Sect 4 6 are properly installed you can view the contents more prec
81. ake make install sequence is described in Sect Without these scripts an UIO file in ASCII format can be examined with any text editor or with more To get an overview about the contents of a binary file the command strings 30 uio_example_file dat can be useful 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 system 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 I3 b 4 n This is the answer 4 3 Structure of UIO Files 53 42 complex ca f E13 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 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
82. al point to point tensor viscosity parameter u 1 0 0 5 4 Parameter File rhd par 103 This parameter is equivalent to real c_visartificial see 5 4 8 with the classical imple mentation of the viscosity tensor A value of 0 0 switches it off Values of 0 3 to 1 0 are reasonable The viscosity controlled with this parameter is meant to act mostly on shocks e real c_visp2phypexpansion This parameter can be set with e g real c_visp2phypexpansion f E15 8 b 4 amp n Parameter for point to point expansion tensor viscosity u 1 0 0 This parameter is equivalent to real c_visexpansion see with the classical implemen tation of the viscosity tensor A value of 0 0 switches it off The viscosity controlled with this parameter is meant to limit or smooth strong expansion events where density pressure temperature and or entropy can drop significantly This parameter is not frequently set to non zero values e real c_visp2phypdivrhov This parameter can be set with e g real c_visp2pdivrhov f E15 8 b 4 amp n Point to point mass flux divergence viscosity coefficient u 1 0 0 A value of 0 0 switches it off Values of 0 5 or even 2 0 are reasonable The viscosity controlled with this parameter acts only on compressible flow configurations i e in near incompressible low Mach number flows it should have hardly any effect Still it can be used in exacly such a case to dampen spurious sound waves for example at the very top o
83. ale compiler NEC SX 5 SGI and Sun Problems might arise with the transition to records larger than 2 GByte which require an extension of the current standard The GNU Fortran compilers particularly g95 might introduce a 64 bit system that does not allow to read older 32 bit files even small ones Each file entry is a header data unit The header contains information to identify the entry and to specify the format and size of the following data block This 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 It still exists However further development was done with the Fortran90 versions Therefore the use of the FORTRAN 77 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 6 0 is used Amazingly the UIO routines also used to work under PV WAVE Version 6 01 sun4 solaris sparc 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 The installation of these scripts with a configure m
84. an be canceled with licancel n34 56789 0 3 7 10 Linux PGI Compiler Under Linux the compiler of the Portland Group was first used to compile COSBOLD 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 compiler version 4 0 on this option can be used instead of the three previous ones It contains and supersedes them e Minline Optimization the routines that should be inlined are listed in Sect e DMSrad_raytas 2 Optimization choose non default version of loop in SUBROUTINE raytas in file MSrad3D F90 See Sect e Drhd_hyd_roe1d_101 0 Optimization choose standard set of routines for Roe solver See Sect 5 4 17 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 7 11 Linux Intel Compiler With Version 7 0 and 7 1 of the Intel compiler CO5BOLD compiled with tricks see below Version 8 0 still caused trouble
85. ansport 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 c0 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 c0 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 convergence 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 1 116 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 d
86. ant ionising or exciting another species The reaction coefficients are needed to calculate the chemical rates at runtime The basic rate is then given by k a Ta gus 97 where T7399 T 300 K with T the gas temperature For catalytic reactions which involve a representative metal also the number density nm of the metal enters NM Q Tooo gut 98 An input file could look like this 5001 H H H2 H2 H2 9 00E 33 0 6 0 0 5002 H H H H2 H 4 43e 28 4 0 0 0 4069 H2 H2 H2 H H 1 00e 08 0 00 84100 0L 4071 H2 OH 0 H2 H 6 00e 09 0 00 50900 0L 66 C OH 0 CH 2 25e 11 0 50 14800 0L 67 C OH co H 1 81e 11 0 50 0 0 3707 C 0 co PHOTON 1 58e 17 0 34 1297 4C 7001 C 0 H co H 2 14e 29 3 08 2114 0D 4076 CO M 0 Cc M 2 79e 03 3 52 128700 0D Refer to Wedemeyer Bohm et al 2005 for more details 5 8 HION Input Several input files are required for the time dependent treatment of hydrogen ionization Cur rently they need to be stored in the same input directory as specified with the parameter hion_datapath There are four input files e model atom The following formatting rules apply Currently we only provide a hydrogen atom file H_6 2 atom The module might be extended for other species in a future version e electron density look up table edens dat as function of total number density of hydrogen in cm or m gas temperature in K and ionization degree of hydrogen e chemical abundances abundance input e partition functions pf_
87. arameter 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 76 5 CONTROL AND DATA FILES 5 4 3 Fundamental Model Parameters e 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 e character grav_mode 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 cO constant central central Three values are possible so far o constant In the standard solar case the constant gravity specified with real grav is directed downward in x8 direction o localboxtide This activates a simple model for the action of a tidal wave on con vection in a local box model It adds to the case of constant gravity a potential Pox which is harmonic in space and time according to Dex Dex cos kyx1 wt 96 It is
88. arts 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 the short example ierr 0 delvar listdata Loop over all datasets while ierr eq 0 do begin amp Read the next dataset ful uio_datasetlist_rd testmodel_0 full listdata listdata ierr ierr if ierr eq 0 then begin amp 4 7 IDL UIO Routines 67 print ful z time format A E15 8 amp Now do the data handling demo print Mean density avg ful z rho amp endif amp endwhile or in the more detailed example model st33gm06n03 modelident _ amp parmodelident _01 modeldisk getenv HOME dat rhd d model modelfile modeldisk model modelident fulls 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 listdata ierr ierr uio_c
89. ary o vertical2 constant extrapolation for the vertical component The transversal cell centered field is set to zero o oblique magnetic fields with a given inclination at the boundary The inclination is specified through parameters C_magthetaB and C_magphiB character bottom_bound_mag The boundary condition at the bottom of the model is given by for instance character bottom_bound_mag f A80 b 80 n bottom boundary conditions magnetic inoutflow Possible values are o constant constant extrapolation of all magnetic field components into the ghost cells o periodic periodic continuation of all magnetic field components into the ghost cells o fixed the component normal to the boundary is kept fixed at its inital value Con stant extrapolation applies for the transversal components o vertical constant extrapolation for the vertical component The transversal cell centered field is mirrored with the opposite sign That should result in transversal components of the boundary centered field being zero at the boundary o vertical2 constant extrapolation for the vertical component The transversal cell centered field is set to zero o oblique magnetic fields with a given inclination at the boundary The inclination is specified through parameters C_magthetaB and C_magphiB o inoutflow magnetic field can be advected into the computational domain by ascend ing material flow Its strength can be specified with the para
90. ata 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 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 precision 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 or linefeeds The first term is the entry type e g real see table 5 followed by an identifier This identifier should follow the standard rules for variables lowercase letters numbers underscore starting with letter It is a name as e g rho v_1 The rest of the terms come in the form keyword value See Tab 6 for some pre defined keywords A header line has a maximum length of 80 characters A continuation line is indicated by u amp at the end of the line A header consists of 20 lines at maximum It can be preceded by empty
91. ays 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 x1 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 OpenMP Determine position 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 36 3 PROGRAM FILES INSTALLATION COMPILATION o 1 Also partially implicit Lambda iteration allowed e rhd_shortrad_formal_t01 in rhd_shortrad_module F90 rhd sh
92. by 2a T Fa f I cos sin d d 14 0 0 The energy change can than be computed from the flux divergence with Opei OF wad OF y2 rad OF y3 rad gt z i 2 1 ap etd 911 Ox 013 15 2 2 Magnetohydrodynamics W Schaffenberger The MHD module solves the equations of ideal MHD given in compact vector form Op ake y 0 a T V lev B B am v ows P 5 jr BB pg 3B 16 t B B ret y petot P 4 5 v V B B Fraa Here B is the magnetic field vector where the units are such that the magnetic permeability u is equal to one I is the identity matrix and a b gt gt a b the scalar product of the two vectors a and b The dyadic tensor product of two vectors a and b is the tensor ab C with elements Cmn ambn and the nth component of the divergence of the tensor C is V C Y im OCmn OLm The total energy is given by v v B B petot pei p_ 3 pd 17 where ei is the internal energy per unit mass The additional solenoidality constraint V B 0 18 must also be fulfilled The aim was to create a stable and easy to use module see Schaffenberger et al 2005 The module has the following features e Use of the HLL solver with the Janhunen source terms Janhunen 2000 o Extension to 2nd order with linear or parabolic reconstruction and a Hancock predictor step or Runge Kutta TVD timeintegration scheme o The following limiters are available Minmod vanLeer
93. ch is always the case so far it should be chosen 5 4 17 Additional Information Obsolete and Test Parameters real abux This optional information parameter can be specified with real abux f E15 8 b 4 n hydrogen abundance number fraction u 1 amp cO 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 real abuy This optional information parameter can be specified with real abuy f E15 8 b 4 n helium abundance number fraction u 1 Y c0 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 real qmol This optional information parameter can be specified with real qmol f E15 8 b 4 n mean molecular weight u u amp c0 standard solar mixture 0 13018000E 01 126 5 CONTROL AND DATA FILES It has no practical consequences because the actually used chemical composition is deter mined by the files for equation of state and opacity 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 consequences because the actually used chemical composition is deter mined by the files for equation of state and o
94. cified as in character hdscheme f A80 b 80 n Hydrodynamics scheme amp cO Roe approximate Riemann solver of Roe type c1 RoeMagKin Roe solver kinetic magnetic field transport amp c2 RoeMHD HLLMHD MHD solver amp c3 None skip hydrodynamics step entirely Roe 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 approximate Riemann solver of Roe type is activated This value will be chosen in most cases 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 For proper MHD simulations use HLLMHD instead o RoeMHD Use the MHD Roe solver o HLLMHD Use the MHD HLL solver the current recommend value for MHD simula tions e real c_hydlowmachcsfactor For very low Mach numbers the over sensitive sound wave detection of the Roe solver for 2D and 3D cases can be suppressed by choos ing a non zero value for real c_hydlowmachcsfactor This is in fact a tiny modification of the Roe solver but changes its behavior signifi cantly and requires for C_hydLowMachcsFactor gt 0 0 hdsplit unsplit and hdtimeintegrationscheme RungeKutta2 or hdtimeintegrationscheme Rungekutta3 The value can be set e g with
95. ctivated o 1 SHORTrad routines are recognized by the compiler e 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 e rhd_rad3d_fromray_101 in rhd_1hdrad_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 one big loop is to be preferred Values o undefined default One big loop o defined Two smaller loops e rhd_rad3d_r02 in rhd_lhdrad_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 e rhd_rad3d_solve_t01 in rhd_lhdrad_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 f
96. ctory cd WRKDIR tt Loop execute RHD code possibly several times in one job for IRUN in 1 do echo echo CO5BOLD Run IRUN date Clear up work directory set e rm set e HEAHEA EEH A HEEE HEHE AE HEE BEHE HEEE E EEE TE EE E EE ME HEEE HETE TE HEE EE HE HETE HE BEHE E DETERE BEE TE EE ETE HE PETE TETE HE HEE HE EHE TEHETE PEHE H EEHEHE REE Get old command file select actual command line and read variables from command line cp p STADIR rhd1 cmd rhdi cmd awk X print next print next print next DONE T print gt cmdline printf 77s n 0 DONE T next print rhdi cmd cat gt dummy_nrhd cmd read INFILE OUTFILE PARFILE ACT lt cmdline mv dummy_nrhd cmd OUTFILE _nrhd cmd echo INFILE echo QUTFILE echo PARFILE echo ACT HEHE HEHE HH HH if ACT dum then FEE EEE HH RARA RAR RHD execution Copy parameter file cp p STADIR PARFILE rhd par Copy start file if test s BAKDIR INFILE then cp p BAKDIR INFILE rhd sta else cp p STADIR INFILE rhd sta cp p rhd sta BAKDIR INFILE 138 6 RUNNING A SIMULATION fi Copy executable cp p RHDEXE rhd exe Execute RHD rhd exe gt rhd out RHD_EXIT if RHD_EXIT 0 s rhd done then Exit status not zero
97. d 0 gt output every time step amp 0 Q c2 dtime_out_end gt 0 gt output every dtime_out_end seconds and at end 1 0E 04 Allowed values are o lt 0 0 Output only at very end of run classical behavior o 0 0 Output at every time step Attention This can produce lots of I O operations and can take a long time However it will not produce a large file Instead the end file is written over and over again o gt 0 0 Output to end file approximately every dtime_out_end seconds and at the very end of the simulation The standard value is 1 0 not enabling any additional output into this file A value a reasonable factor smaller than real dtime_out_full seems appropriate 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 Output time step u s amp cO0 dtime_out_mean lt 0 0 gt no output 0 5E 06 Allowed values 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 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 integer n_outslicedim_mean The index of the optional slice in the mean output file can be specified with e g 5 4 Parameter File rhd par 123 integer n_outslicedim_mean f I4 b 4 n index of slice in
98. 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 amp 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 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 Y 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 readability 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
99. d above result in a very robust scheme which guarantees positivity of pressure and density under almost all conditions However this does not mean that these values are accurate The pressure and temperature distribution may be very inaccurate in regions with strong magnetic fields This may be relevant if one includes special chromospheric physics such as dynamic hydrogen ionization and CO formation in the simulation A possibility to get more accurate pressure and temperature would consist in the use of the entropy equation instead of the energy equation for the computation of the internal energy in regions with strong magnetic field This was included in the original test version of the MHD module In the present version we mak use of the equation for the thermal energy itself depending on the ratio of thermal to magnetic pressure i e the plasma P The limiting P can be specified by the model parameter beta_inv This is the dual energy approach used in many MHD codes Its advantage goes at the expense of violation of strict conservation of the total energy Due to the Courant condition the time step in case of MHD can become considerably smaller than in the hydrodynamic case This happens because the time step is also limited by the Alfv n speed which is large in regions with strong magnetic field and low density small plasma To avoid an extreme time step reduction the Alfv n speed can be artificially limited This this is done by reduc
100. drodynamics equations including source terms due to gravity are the mass con servation equation Op pvi Apv2 Apv3 _ 0 3 06 0x1 0x2 0x8 3 the momentum equation pul a pvlvl P a pul v2 a pvl v3 pgl A pv2 Po pv2 vl 92 pv2v2 P 553 pv2 v3 p92 pv3 pv3 vl g pv3 v2 pv3 v3 P p 93 4 and the energy equation including radiative heating term Qrad Opeik 9 peik P v1 0 peik P v2 0 peik P v3 H 1 vl g2 v2 g3 v3 raa E 5 t axl 912 913 p gl vl 92 v2 93 v3 Qrad 5 The pressure P is computed from density p and internal energy ei via a tabulated equation of state P P p ei 6 For local models the gravity field is simply given by 0 g 0 7 g For global models it is given by 2 u ag J ca ica a 6 8 93 923 with EM d 9 40 VTEC Here M is the mass of the star to be modeled ro and r are free smoothing parameters In addition there are equations for the non local radiation transport If grey opacity tables are used the opacities x are a simple function of e g temperature T and pressure P k K T P 10 and the source function S is given by S Bis 11 8 2 EQUATIONS The change in optical depth Ar along a path with length Ar is than Arsrp r 12 The variation of the intensity J with optical depth 7 along a ray with orientation 0 4 can be described by the simple differential equation d I S 13 dr 2 The radiative energy flux is given
101. e configure script UIO MHD molecules 6 29 103 142 MSrad G PABI BIETA 25 ET BA 109 100 cell centering NEC SX 5 SX 6 SX 8 OMP_NUM_THREADS OMP_SCHEDULE opacities OpenMP activation in configure script chunk size KMP_AFFINITY KMP_STACKSIZE 46 bi OMP_NUM_THREADS 37 OMP_SCHEDULE 37 46 OMP_THREADS on Cray VX1 on Hitachi on HP on Linux gfortran INDEX on Linux Intel on Linux Pathscale on NEC on SGI on Sun thread affinity operator splitting 6 output chunk data sets full data sets HION mean data PathScale PGI precision double single que 26 29 90 132 radiation transport README rhd cont rhd done 129 rhd dump 129 rhd exe 18 20 rhd out 129 rhd par 68 74H128 boundary conditions character bottom_bound 79 character bottom_bound_mag character centrifugal_force 77 character chem_reacfile 105 character chem_reacpath 105 character description character dustreconstruction character dustscheme dust_bins_01 dust_k3mon_03 dust_moment04_c2 character dustschene 104 character eosfile 85 character eospath 85 character file_id 75 character grav_mode 76 character hdcheckflux character hdenthalpyavgmode character hdentropywavemode character hdscheme 87 character hdsplit character hdtimeintegrationscheme character hdtransvelomode character heat_mode 80 151
102. e character chem_reacpath The path of the input file containing the chemical reaction network character chem_reacpath f A80 b 80 n path of reaction table data sven cobold dat chem e real chem_abumetal Abundance of the representative metal M if present relative to hydrogen eM M H A value of 1 0E 04 means there are 10 hydrogen atoms for every metal atom The metal number density for each grid cell is then derived via ny em p my assuming a pure hydrogen gas This parameter is ignored when a quc array for the metal is found in the input model real chem_abumetal f E15 8 b 4 n Chemical abundance of repres metal 1 0E 04 e character hion_datapath The path of all input files for HION character hion_datapath f A80 b 80 n HION data path data sven cobold dat hion e character hion_atomfile The file name of the model atom for HION character hion_atomfile f A80 b 80 n HION atom file name H_6 atom e character hion_abufile The name of the HION input file containing the chemical abundances character hion_abufile f A80 b 80 n HION abundance file name abundance input e character hion_edensfile The name of the HION input file containing the electron density table character hion_edensfile f A80 b 80 n HION electron density file name edens dat e character hion_pffile The name of the HION input file containing the partition functions character hion_pffile f A80 b 80
103. e 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 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 zi 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 5 3 File with Additional Data rhd mean 71 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 the 12 plane z3 and over
104. e 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 compiler_flags info in a form ready to be included in a Fortran program The environment variables that control the script are e F90_COMPILER Fortran compiler o a machine dependent default is chosen individually for each architecture o f90 general default e F9O_PREFLAGS Compiler flags to be put at the beginning of the list Usually the list of compiler flags produced by the configure 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 e F9O_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 e F9O_PARALLEL Parallelization scheme 24 3 PROGRAM FILES INSTALLATION COMPILATION File and path Abb Description hd rhd rhd F90 RHD main program hd rhd rhd_hyd_module F90 RHD hydrodynamics routines hd rhd rhd_1hdrad_module F90 RHD radiative transfer routines long characteristics
105. eal real real real real real real real real real real real real real real real real real real real INDEX c_hydlowmachcsfactor c_hydpredfactor 94 c_hydsdiffvelo 94 c_hydsoundcourant 119 c_hydsoundcourantmax 119 c_hydtdifflin c_hydtdiffmach c_hydvdiffvelo 95 c_magphib 85 c_maxeichange 120 c_pchange cputime cputime_remainlimit c_radcourant c_radcourantmax 120 c_raddcool c_raddinci c_radhtautop c_radimplicitmu 115 c_raditereps 115 c_raditerstep 115 c_radmaxeichange 121 c_radscool c_radtcool c_radthintimefac 121 c_radtinci c_radtintminfac c_radtsmooth c_radtvis 116 c_radtvisdtau 115 c_reccontshift c_reccontsteep c_resB c_resBconst 98 c_rescourant c_rescourantmax c_resepsilon c_rhochangetop c_schange c_slopered c_tchange c_tminlimit 116 c_tsurf c_v3changelinbotton c_v3changesqrbotton c_visartificial 100 c_visbound 97 c_viscourant c_viscourantmax c_visdrag c_visexpansion 100 c_vislinear 100 c_visneul 126 c_visneu2 126 INDEX real c_visp2pcoeff 102 real c_visp2pincl1 103 real c_visp2pincl12 103 real c_visprturb L01 real c_vissmagorinsky 100 real c_vistensordiag 101 real c_vistensordiv 101 real c_vistensoroff 101 real dtime_out_hion 106 134 real dtime_incmax 118 real dtime_max real dtime_min 118 real dtime_min_stop 118 real dtime_out_end 122 real dtime
106. eal c_vissmagorinsky and real c_visartificial But the parameter 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 Off 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 parameters like 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 This is not really parameter one would try to adjust The total amount of viscosity should be controlled with parameters like 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_v
107. easons to be able to use the existing EOS Fortran routines the table is provided o eos_gamma166 eos EOS table for simple gas with constant T 5 3 o cpheos_mm00 eos Copenhagen EOS for their solar composition 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 c0 astro b bf for eos dat home a_bf for eos dat 86 5 4 6 Opacities e character opafile The opacity file can be specified with e g 5 CONTROL AND DATA FILES character opafile f A80 b 80 n opacity file name amp c0 g2va opta big_grey opta amp ci empty gt no radiation transport phoenix_opal_grey opta So far there exist already a couple of files o davmf opta o 5v opta o g2va opta o g2v_lowhe opta o g2v_m20 opta o g2v opta o hmin_p00 opta o opal_lowhe opta o opal_m05 opta o opal_m10 opta o opal_m20 opta o phoenix_dust_grey opta phoenix_dust_ob4 opta phoenix_opal_grey opta o ross_m05 opta o ross_m10 opta o ross_m20 opta o sunur1 opta o sunur2 opta o t5000g44mm20 o t5000g47mm20 o t6300g40mm20 o t6500g44mm20 opta opta opta opta o zzcetilg opta o zzcetil opta e character opapath The opacity file does not have to be in the working directory Instead its path can be specified e g with character opapath
108. ed CPU time which is given by e_time etime tarray in timing_module F90 from the specified total CPU time for the job e real cputime_remainlimit Because COSBOLD 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 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
109. efficients Olnp 2 7 one 29 Xo Ga Kp 30 12 2 EQUATIONS en XT aT 31 Ge Xp 82 It can be shown that 2 P 9 P P a Cy T K 2 Cp Cy a T Kp dd Xp op OXT DT Xt Xe 32 Definition of adiabatic exponents _ Olnp ar Gay m _ OMT _ famT _T2 1 Ves dur Ta er 2 3 3 CO5BOLD equation of state CO5BOLD equation of state input CO5BOLD equation of state output Op Op OT P T ee All required thermodynamic coefficients can be expressed in terms of 22 22 27 e 3p X0e p 2 3 4 Derived thermodynamic coefficients First the missing derivative can be found from the relation e 38 which is obtained from the equality of the mixed derivatives in Eq 20 written as 1 p Then o o 1 o p 40 e p p Tj Oe Tp A First adiabatic exponent 41 This relation is obtained by combining Eq 20 with the identity 0 o dp 2 dp 3 de 42 e p 2 3 A collection of thermodynamic relations M Steffen AIP 13 The adiabatic sound speed is then obtained as Third adiabatic exponent This relation is obtained by combining Eq 20 with the identity OT OT ar 57 ap T 52 e 45 and then using Eq 38 Adiabatic temperature gradient OmT OMT Olnp _Vs 1 47 O0mp Olnp Olnp r Adiabatic energy changes We define the coefficients c and c through the relation
110. enhancement Choose type of short characteristics tau coupling operator Values 3 6 Compiler Macros 35 o1 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 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 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 a 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_dir1_101 in rhd_shortrad_module F90 rhd short characteristics radiation direction 1 loop 01 Category performance enhancement Choose routine version for r
111. er 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 some cases 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 o 2 case distinction with masks weights 0 0 or 1 0 o 3 case distinction with if then else construct slope reduction of source function o 4 case distinction with masks weights 0 0 or 1 0 slope reduction of source function o 5 case distinction with if then else construct 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
112. er of grid points with optically thick diff approximation amp c0 0 no diffusion approximation 0 The value should be choosen so that for all points in that region Ar gt 1 is valid Setting this value to O means that the diffusion approximation is not used in any part of the model e 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 I4 b 4 amp n Refinement factor 0 e 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 I4 b 4 n Number of frequency bins amp c0 1 grey opacities amp c1 2 non grey opacities if available from table amp c2 3 two bands 1 grey 2 CO density via XC0 amp c3 4 two bands 1 grey 2 CO density from chemistry Allowed values are Oo 1 Use the grey part of the table o 2 Use the other possibly non grey frequency dependent part of the table o 3 Use a continuum band plus an infrared band with CO opacity calculated with CO equilibrium density o 4 Use a continuum band plus an infrared
113. 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 At the beginning of every time step COSBOLD checks in the working directory whether the file rhd dump exists If it has been generated e g with touch rhd dump and the file rhd snap does not exist the current model is written into rhd snap It has the same file properties format and conversion as the regular rhd end file The run of the simulation itself is not modified This feature might be useful for debugging purposes If a run was successful i e it was completed because one of the regular termination conditions was fulfilled e g the requested number of time step
114. export OMP_NUM_THREADS 16 46 3 PROGRAM FILES INSTALLATION COMPILATION for a machine with 16 threads e g 2 processors 4 cores per processor 2 threads per core Experimenting with the scheduling e g with export OMP_SCHEDULE DYNAMIC 1 or export OMP_SCHEDULE GUIDES 2 might improve the performance see Sect 3 7 1 The last two OpenMP variables are recognized by several compiler However there are Intel specific ones In some cases it might be helpful to set export LD_ASSUME_KERNEL 2 4 19 when encountering problems with OpenMP However that seems not to be necessary with recent compiler versions Still often the stack memory per thread is too small which can be increased e g with export KMP_STACKSIZE 300000000 To optimize the performance particularly on many core systems the thread affinity see Intel Thread Affinity Interface can specified e g with export KMP_AFFINITY verbose granularity core compact 3 7 12 Linux PathScale Compiler Some experiments with the PathScale compile have been made It is called with pathf90 The result is not entirely satisfying yet Important switches are e byteswapio With this flag set binary files in big_endian format the standard for UIO files are automatically transformed to 1ittle_endian and vice versa e 03 General optimization flag More aggressive optimization can be activated with Ofast or Ofast ipa e mp Parallelization OpenMP directives are act
115. f A80 b 80 n path of opacity file amp c0 astro b bf for opa dat home a_bf for opa dat 5 4 Parameter File rhd par 87 hdScheme hdTimelntegrationScheme hdSplit Ccour Csnacour comment Roe Single 123 1 old default Roe Single unsplit 1 D Roe Single CTU 1 1 2 for D 3 recommended Roe RungeKutta2 unsplit 1 D Roe RungeKutta3 unsplit 1 D HLLMHD Hancock 123 HLLMHD Hancock unsplit HLLMHD RungeKutta2 unsplit HLLMHD RungeKutta3 unsplit Table 11 List of reasonable combinations of options for HD and MHD solver The columns are the type of the M HD scheme see Sect 5 4 7 the time integration scheme see Sect the directional splitting method see Sect 5 4 7 the maximum Courant number where D is the dimension of the computational box see Sect 5 4 15 the maximum sound Courant number where D is the dimension of the computational box only specified for the case where it is actually a new constraint in addition to the normal Courant condition see Sect and a comment 5 4 7 Hydrodynamics Control HD and MHD Many parameters in the parameter file that are valid for the HD module also apply for the MHD module Only a few parameters for the hydrodynamics control character hdscheme Sect 5 4 7 character reconstruction Sect 5 4 7 real c_slopered Sect 5 4 7 are slightly modified or extended for the MHD module e character hdscheme With this parameter the type of the hydrodynamics scheme can be spe
116. f iterations can be specified e g with integer n_radmaxiter f I4 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 value somewhat larger than the recommended number of iterations n_raditer or to 0 which disables 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 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 c0 SHORTrad unity random randomgroup alternate amp c1 MSrad lobatto dblgaus random Allowed values for radscheme SHORTrad are o unity default During all time 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 112 5 CONTROL AND DATA FILES o randomg
117. f 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 _fu11 full 2D 3D model dumps huge see Sect or into the file described by the parameters with suffix mean additional information see Sect 5 3 122 5 CONTROL AND DATA FILES 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 Output time step u s amp c0 dtime_out_full lt 0 0 gt no output amp ci 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 30 sec 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_end The interval between outputs into the end file can be set e g with real dtime_out_end f E15 8 b 4 n Output time step u s amp c0 dtime_out_end lt 0 0 gt output only at very end amp c1 dtime_out_en
118. f the computational box e real c_visp2pincll The interaction with the edge neighbor cells with indices 1 1 0 can be specified with e g real c_visp2pincll f E15 8 b 4 amp n Point to point viscosity inclined cell factor 1 1 1 0 Common values are 1 0 interaction is considered and 0 0 no interaction with these cells The usual value is 1 0 e real c_visp2pincl2 The interaction with the corner neighbor cells with indices 1 1 1 can be specified with e g real c_visp2pincl2 f E15 8 b 4 amp n Point to point viscosity inclined cell factor 2 u 1 0 0 Common values are 1 0 interaction is considered and 0 0 no interaction with these cells The usual value is 0 0 to save some computation time 5 4 9 Dust Molecules Hydrogen Ionization General 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 104 5 CONTROL AND DATA FILES e character dustscheme A scheme for dust or molecule formation and transport can be selected e g with character dustscheme f A80 b
119. file creates a sub directory for in the local directory and possible overwrites existing files You get sub sub directories as described in Sect 3 3 and files as listed in Tables 2 and 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 19 to see if you find one that fits your machine The directory for hd rhd conf should 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 5 Check if there is a configure script or a link to it with ls og configure which should give something like lrwxrwxrwx 1 If it is not there create the link with In s conf configure 17 2002 12 04 17 39 configure gt conf configure 6 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 No parallelization requested assume default No debugging requested assume default No LHDrad module requested assume default No MSrad module requested assume default No SHORTrad module requested assume default No CHEM module requested assume default No HION module requested assume defa
120. gt 222 ee ee 47 re re te a a alone ee a ee ee 48 3 7 17 SGI Origin 2000 3800 at UKAFF cocos 2 2 122 02 20 04 48 3 77 18 sun Sunkire 2 2 3 4 a 2 ee ner aaa ri re 49 4 UIO Data Format 52 A Be ne Sa a RA a A a a E E 52 eet dng fe ete gach se ae we E ee 52 4 3 Structure of UIO Filesl 2222 Co ee 53 4 3 1 Data Representation ASCII or Binary 53 4 3 2 Data File Structural 54 4 3 3 Tablesl 2 2 24 4 25 2k a 20 ee aaa na we nee 55 4 3 4 Recommendations for Standard File Structure 57 4 4 Files amp Directories amp Pathsl Co onen 57 45 ROrtranGD e x u ee a wesen ee ee a ee ee aa 98 4 5 1 __Eiles ema vn ok 8 a Da ek 58 4 5 2 Use of UIO Modules in Fortran Ol 2 22 2 EEE nn nen 59 SE EE E E S es Go ees ae eee Ge ens E 59 4 5 4 Sample Calls of Fortran UIO Routines 60 CONTENTS 3 ne Ge uh eae oe o o aoe en of ene ee io an een tee 61 4 6 1 Installation of UIO UNIX Seriptsl 222222 oo nn nn 61 4 6 2 Quick Examination of Files wiolook 2 2 2 22 2 mn nennen 62 4 6 3 Transformation of Files uiocatl 2 2 2 nn nn 62 4 6 4 Information about Conversion Types uioinfo 63 4T IDE UIO Routines lt s s eca oe od 2 a u ana we ee ee ee 63 4 7 1 Initialization of UIO Routines under IDL 65 Mein shoe Boe pam ee he Bere 65 un 66 5 Control and Data Files 68 5 1 Model Files rhd sta rhd end
121. hange 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 A couple of macros only activate timing measurements and result in additional output Some of them are not thread save und should only be activated 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
122. hangetop f E15 8 b 4 amp n Rate of density change for open upper boundary u 1 0 2 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 3 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 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 H
123. he coalescence rate is specified with e g real c_dust08 f E15 8 b 4 n Sticking coefficient for coalescence u 1 amp c0 Typically between O and 1 1 0 Typical values are between 0 0 deactivating this process and 1 0 The default value is 0 0 e real c_dust09 The sticking coefficient for the nucleation rate is specified with e g real c_dust09 f E15 8 b 4 n Sticking coefficient for nucleation u 1 c0 Typically between O and 1 1 0 Typical values are between 0 0 deactivating this process and 1 0 The default value is 0 0 The standard choice is 1 0 5 4 13 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 LHDrad module is not maintained very much anymore 110 5 CONTROL AND DATA FILES Parameter Section LHDrad MSrad SHORTrad radscheme si e n_radminiter 5 4 13 n_raditer 5 4 13 z n_radmaxiter 5 4 13 t radraybase 5 4 13 i li radraystar 5 4 13 x A n_radtheta 5 4 13 l n_radphi 5 4 13 n_radsubray 5 4 13 ia n_radthinpoint n_radthickpoint n_radtaurefine 5 4 13 si n_radband 5 4 13 n_radrsyslevel 5 4 13 y n_rad
124. he computation for the current time step is stopped and resumed with a smaller one Usually n_hydmaxiter will either be set to a value somewhat larger than the recommended number of iterations n_hyditer or to 0 which disables the check for too many iterations completely This can be safely allowed in many cases To disable the iteration of the hydrodynamics sub step set n_hyditer 0 In case of the MHD module this parameter sets the maximum number of MHD substeps If this parameter is set to zero the number of MHD substeps is not limited 5 4 Parameter File rhd par 97 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 19 b 4 amp n Number of cells per hydro chunk amp c0O 0 gt one 2D slice at a time c1 1 gt minimum chunk size inefficient amp c2 2500 reasonable value amp c3 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 memory but
125. hin which can be activated with character radpressure f A80 b 80 n Radiation pressure mode amp c0 on off on Allowed values are 5 4 Parameter File rhd par 127 o on Radiation pressure on o off Radiation pressure off The scheme is pretty slow and wrong in the optically thick Do not use However the SHORTrad version is much more advance and can be used even if it might require some more testing e 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 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 e 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 Output time step number u 1 amp cO dtimestep_out_fine lt 0 gt no output 1 e character outfile_fine The name of the file for the output of additional information at regular small intervals can be specified with e g character outfile_fine f A80 b 80 n Output file name
126. hin 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 e 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 c0O range 0 0 lt C_visCourant typically 0 5 1 0 better 0 25 0 5 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 e 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 c0O 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 4 16 Input Output Control With this group of parameters the start model and the type and amount o
127. hydrodynamics 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 5 CONTROL AND DATA FILES 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 o inoutflow2 variant of the open lower boundary condition The parameters real s_inflow real c_schange real c_pchange have to be specified In this ver sion the extrapolation of quantities should be smoother than for inoutflow In simulations of a solar like star with the MSrad radiation transport module the bot tom boundary is typically of type inoutflow A supergiant simulation will have a transmitting lower boundary e character heat_mode The mode in which energy is supplied can be adjusted with this parameter The classical choice is to leave it empty in which case the mode is chosen from s_inflow see Sect and luminositypervolume see Sect 5 4 4 Example character heat_mode f A80 b 80 n Heating mode amp c0 bottom_entropy1 bottom_energy1 bottom_entropyi Possible values so far o empty The classical value For local models the energy comes through the lower boundary either by radiation for a closed bottom boundary closedbottom or by convection radiation for an open bottom boundary inoutflow
128. hydrodynamics radiation o transmitting transmitting boundary for hydro and outward radiation exponential decrease of density standard open boundary condition o transmitting2 transmitting boundary for hydro and outward radiation exponential decrease of density and extra velocity treatment o transmitting3 transmitting boundary for hydro and outward radiation constant density extrapolation 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 Possible values are o reflective closed wall no gravity no radiation The velocity vector is mirrored at the boundary 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 closedbottom2 closed wall handles gravity radiation in diffusion approxima tion In this version the extrapolation of quantities should be smoother than for closedbottom o periodic periodic boundaries for
129. iation The velocity vector is mirrored at the boundary 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 radiation o transmitting transmitting boundary for hydro and outward radiation 5 4 Parameter File rhd par 79 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 The velocity vector is mirrored at the boundary 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 periodic periodic boundaries for
130. ies of start model time time s xci x1 coordinates of cell centers cm xc2 x2 coordinates of cell centers cm xc3 x3 coordinates of cell centers cm xb1 x1 coordinates of cell boundaries cm xb2 x2 coordinates of cell boundaries cm xb3 x3 coordinates of cell boundaries cm rho Density g cm 3 ei Internal energy erg g vi Velocity 1 cm s v2 Velocity 2 cm s v3 Velocity 3 cm s quc001 Number density of CO 1 cm 3 advect 1 bb1 Magnetic field 1 G bb2 Magnetic field 2 G bb3 Magnetic field 3 G It might follow ACTION Initialize MS radiation And finally transport routines lt lt lt lt lt lt lt lt ACTION Open output files lt lt lt lt lt lt lt lt 5 6 Text Output rhd out 131 which indicates that the rhd full file see Sect B 1 and the rhd mean file see Sect 5 3 have been opened and now contain a header The end of the initialization phase and the beginning of the proper simulation is marked by e g 2 2 2 Start Computation Time step number itime 47050 time 2 5821813E 08 t_job 8 510000E 00 The output for a typical simulation time step can look like for a supergiant model with SHOR Trad radiation transport Time step number itime 49048 time 2 6822680E 08 t_job 1 272180E 06 dtime 5 3047E 03 HD 1 4838E 04 RAD 5 3047E 03 VIS 1 0723E 05 Luminosity per core vo
131. ifferent discretization It should conserve angular momentum exactly and guarantee positivity of dissipated energy for sufficiently small time steps The current version should only be used for equidistant grids same spacing in all directions as for the su pergiant models by experienced users The point to point viscosity can be used in addition to the standard one or without e real c_visp2pcoeff The strength of the viscosity can be controlled with e g real c_visp2pcoeff f E15 8 b 4 amp n Point to point viscosity coefficient 1 0 20 This parameter is somewhat analogous to real c_visartificial see 5 4 8 But it acts on compression expansion and shear flows A value of 0 0 switches it off e real c_visp2phypsmagorinsky This parameter can be set with e g real c_visp2phypsmagorinsky f E15 8 b 4 amp n Smagorinsky parameter for point to point viscosity u 1 0 3 This parameter is equivalent to real c_vissmagorinsky see 5 4 8 with the classical im plementation of the viscosity tensor A value of 0 0 switches it off Values of 0 3 or 0 5 are reasonable Although the underlying formula and theory is more complex the effects are rather similar to that of real c_visp2pcoeff If additional smoothing is required either of these parameters or both can be set to non zero values e real c_visp2phypartificial This parameter can be set with e g real c_visp2phypartificial f E15 8 b 4 amp n Artifici
132. iffusion 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 3 b 4 n Temperature viscosity u 1 1 6 For well resolved models it should be switched off with c_radtvis lt 0 0 real c_tminlimit A minimum temperature can be set that is enforced by the radiation transport module MSrad3D and SHORTrad by adding energy to the too cool cells e g with real c_tminlimit f E15 8 b 4 amp n Enforced minimum temperature for radiation transport step u K amp c0 lt 0 0 off default 500 0 reasonable value 400 0 5 4 14 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 files 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 real starttime The start time of a simulation is usually taken from the start model file But sometimes is simulation is to be started
133. ine uio_inf_module information 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 8 Contents of uio_base_module f90 4 5 Fortran90 4 5 1 Files The Fortran UIO package is a collection of Fortran90 modules and programs described in Table 7 The file uio_base_module f90 contains the basic set of modules see Table 8 In older version of CO5BOLD the files uio_mac _module f90 Tab 7 contained machine dependent routines collected in the module uio_mac_module see Tab p routine purpose uio_getenv Get information about environment ulo_mkcvls Make list with possible conversion types uio_uopen Open file with special handling for conversion type uio_uclose Close file with special handling for conversion type Table 9 Contents of uio_mac_module In the current version of CO5BOLD there is only one file uio_mac_module F90 with a capital F90 that can be changed during the compilation by preprocessor switches see 3 6 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 manipula
134. ing objects o off This skips the application of the centrifugal force in case of a non zero rotation rate In this case only the Coriolis force is applied By default the centrifugal force is activated e real nu_rotation To transform onto a coordinate system rotation around the x3 axis a rotation rate can be specified with e g real nu_rotation f E15 8 b 4 n Rotation frequency u 1 s 0 0 The potential is modified by adding terms due to a centrifugal force unless centrifugal_force is set to off In addition a Coriolis force are applied during the hydrodynamics step e real ar_RotationAxis The radii of the dust grains are specified with e g real ar_rotationaxis f E10 4 b 4 p 1 d 1 3 n Rotation axis u 1 1 0 0 0 0 0 The default value is 0 0 0 0 1 0 5 4 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 and a top boundary and four side boundaries All boundary conditions of the hydrodynamic case are available in the MHD module e character side_bound The boundary condition at all four sides is given by e g character side_bound f A80 b 80 n side boundary conditions amp cO closed transmitting periodic transmitting Possible values are o reflective closed wall no gravity no rad
135. ing the Lorentz force in the momentum equation by a factor f This factor is calculated with the following formula vr max 19 f v3 V max gt 2 3 A collection of thermodynamic relations M Steffen AIP 11 where va is the original Alfv n speed and v4 max is the desired maximum value of the Alfv n speed Currently this feature works only with the HLL solver It is advisable to use this feature only in combination with either the thermal energy equation beta_inv 0 0 or the dual energy method In the latter case beta_inv should be chosen small enough so that the region where the Lorentz force reduction is active is handled by the thermal energy equation This is obtained with beta_inv S yv4 2 where cs is the speed of sound and y the adiabatic exponent This module has been extensively tested It should be able to handle many MHD flows of astrophysical interest Bugs and problems can be reported to werner schaffenberger gmx at 2 3 A collection of thermodynamic relations M Steffen AIP 2 3 1 Basic thermodynamic equations Differential relations u p de Tds dp 20 p where e is the internal energy 1 dh Tds aor 21 where the specific enthalpy h is defined as h e p p 22 28 en Dr ea E as a 2 3 2 Definition of often used thermodynamic coefficients This implies Definition of specific heats E en ar 7 ar ur A Definitions of further thermodynamic co
136. input routine They can be used to provide comments additional information about the model or control parameters for further processing 5 4 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 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 4 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 4 16 5 Check modify the fundamental parameters including boundary condition specifiers see Sections and 5 4 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
137. integer endtimestep f I11 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 118 5 CONTROL AND DATA FILES 5 4 15 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 and 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 3 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 explici
138. intended to mimic a travelling tidal wave Since the setup is considered experi mental the parameters are set by the C_test parameters according Dex C_testi amplitude of potential variations kn C_test2 horizontal wavenumber w C_test3 frequency Boundary conditions in order to be compatible with periodic lateral boundaries kp should be an integer multiple of 27 times the inverse lateral box size o central For the supergiant 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 e 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 e 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 e 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 5 4 Parameter File rhd par 77 real r0O_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 e real ri_grav The density in an atmosphere in hydrostatic equilibrium can decline to very low values To artificial enlarge the pressure
139. iocat f formatted o rhd_ascii sta rhd_binary sta New start models could be written in double precision binary UIO format directly using the double_flag in the IDL routine rhd_wrboxdata pro For the EOS table eos_mm00_15 eos there exists a double precision binary version 3 7 4 Cray SV1 On craSHi in Kiel a CRAY SV1 20 32768 SN9542 now out of service COSBOLD 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 e F Enable macro expansion e Otaski Parallelization Enable tasking in this case OpenMP e Oinline3 Optimization enable high level of inlining e Ovector3 Oscalar3 General optimization http www cray com craydoc 3 7 Optimization Compiler Switches 39 e Drhd_hyd_roe1d_101 1 Optimization Choose non standard set of routines for Roe solver See Sect 5 4 17 e Drhd_hyd_entropyfix_p01 1 Optimization version with masks weights See Sect 3 6 e Drhd_hyd_upwind_p01 1 Optimization version with masks weights e Drhd_shortrad_operator_101 2 Optimization short characteristics operator with masks weights e Drhd_shortrad_dir_102 1 Optimization OMP PARALLEL statement outside of ou
140. ions All routines that should be inlined are contained in the same modules as the calling routines Therefore no inter procedure inlining is needed 3 7 3 General Single versus double precision Usually the files containing the hydrodynamics and EOS data use 4 byte to represent a single number and most of the computations within CO5BOLD are performed in single precision except for certain routines in e g MSrad or some dust modules To switch to double precision everywhere one has to deal with the binary files and force the transformation of single precision variables to double precision during the compilation Compiling all COSBOLD files with such a switch produces problems with the UIO modules there would be a name conflict between the routines that usually deal with double precision reals and those that are written to deal with single precision reals and are now forced to pretend to be also a double precision version Therefore one should compile the UIO routines and the rest with separate settings e g for the Intel compiler configure make UIO export F90_PREFLAGS r8 fpconstant configure make Code compiled in this way cannot read anymore single precision binary UIO files However there are no problems with the opacity tables ASCI files and formatted UIO files To make existing single precision binary UIO files readable one could transform them to the formatted version with uiocat see 4 6 3 e g like u
141. isely 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 UoK 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 label dataset n RHD model version f A80 b 80 n Program version date 02 01 2002 16 17 26 043 character dataset_id f A10 b 10 n Type of box hierarchy 5 2 Files with additional chunks of data rhd chul 69 real modeltime f E13 6 b 4 n time u s real modeltime_db f E23 15 b 8 n time u s integer modelitime f I11 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 real time_db f E23 15 b 8 n time u s integer itime f 111 b 4 n time step number u 1 real xc1 d 63 63
142. istensordiv 0 333333 in 3D c_vistensordiv 0 5 in 2D is usually switched off 102 5 CONTROL AND DATA FILES e 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 for an Intel Macintosh with integer n_viscellsperchunk f 19 b 4 amp n Number of cells per viscosity chunk amp c0 0 gt old chopping amp c1 12000 reasonable value 32000 It can be adjusted to improve cache efficiency and to modify the work load distribu tion onto the threads in case of parallel 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 An example is given for the Hitachi SR8000 in Sect In addition to the standard tensor viscosity described above there is a point to point vis cosity It relies on a completely d
143. it either natively or via some conversion process Values o 0 Don t include this conversion type default o 1 Get information about word lengths from uio_deform o 2 Set word lengths explicitely uio_switch_ieeele_101 in uio_mac_module F90 uio switch ieee little endian list 01 Category I O account for property of machine Values o 0 Don t include this conversion type default o 1 Get information about word lengths from uio_deform o 2 Set word lengths explicitely uio_switch_ieee_101 in uio_mac_module F90 uio switch ieee list 01 Category I O account for property of machine This is a fallback for reading of UIO files that should be activated for compilation if either of the Endian formats above is allowed It should not be used for writing Values o 0 Don t include this conversion type default o 1 Get information about word lengths from uio_deform o 2 Set word lengths explicitely 4 byte words o 3 Set word lengths explicitely 8 byte words uio_switch_crayxmp_101 in uio_mac_module F90 uio switch cray x mp list 01 Category I O account for property of machine This is the native format on old Cray X MP and Cray TS machines Values o 0 Don t include this conversion type default o 1 Get information about word lengths from uio_deform uio_switch_open_101 in uio_mac_module F90 uio switch open list 01 Category I O account for propert
144. ivated 3 7 13 Linux GNU g95 Compiler One of the available GNU Fortran compilers is the g95 compiler with the g95 home pagd It is called with g95 Important switches are e fendian big 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 03 General optimization flag In the preprocessor switches are listed that control the modern single version uio_mac_module F90 OpenMP is not there yet The binary I O format unformatted is incompatible with the one used before in COSBOLD no existing UIO files can be read http www g95 org 3 7 Optimization Compiler Switches 47 3 7 14 Linux GNU gfortran Compiler The Fortran compiler of the GNU project is called with gfortran Important switches are e fconvert big endian frecord marker 4 With this flag set binary files in big_endian format the standard for UIO files are automatically transformed to little_endian and vice versa In addition the old 32 bit record marker convention is maintained and existing UIO files can be read e 03 General optimization flag e fopenmp Activates the OpenMP directives In the preprocessor switches are listed that control the modern single version uio_mac_module F90 I haven t found out how to use the standard modules yet OpenMP does not work yet And the scalar code is significantly slower than code c
145. kurucz dat The first two files are always needed whereas the files containing chemical abundances and partition functions are required the initial LTE electron densities for very first time step of a model sequence and for creating electron density tables Once the first time step has been calculated the last two input files are obsolete We plan to implement another initial guess for the LTE densities so that only the model atom and the electron density look up table are necessary Refer to Leenaarts amp Wedemeyer Bohm 2005 for more details AK DBDDG72 28034 16964 4934 W80 BDD90 DBDDG76 CBDDG76 134 5 CONTROL AND DATA FILES 5 9 HION Output The HION module can produce two types of output The first is the standard output ofthe quc ar raysinthe full and end files holding the level populations This is all that is needed to restart a computation The second optional output is a HION specific output system that generates files in UIO format after a prescribed number of simulation timesteps or alternatively after a pre scribed time interval see parameter dtime_out_hion Output after a fixed number of timesteps is mainly useful for debugging The files are named HION aaaa bb cccc out with aaaa either step or time indicating output after a fixed number of timesteps or a fixed amount of solar time bb the atom identifier and cccc the number of the output file e g HION step H 0001 out The HION files can be
146. l in cases were strong localized expansions cause problems e real c_vislinear Another viscosity can be activated e g with real c_vislinear f E15 8 b 4 amp n Linear viscosity tensor parameter 1 1 2 5 4 Parameter File rhd par 101 In the formulae for the standard artificial compression Smagorinsky viscosity velocity gradients appear That means that in regions with smooth small amplitude flows these types of viscosity essentially vanish Here the linear viscosity comes in It uses RgasT as approximation for the sound speed that is used in the formula for the kinematic viscosity Ususally it is not activated c_vislinear 0 0 It might be useful to damp small amplitude almost linear waves 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 u 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 cO typically 1 0 120 This is not really parameter one would try to adjust The total amount of viscosity should be controlled with parameters like r
147. lative dust opacity factor u 1 1 0 5 4 11 Dust dustscheme dust_k3mon_03 In this section the parameters for dustscheme dust_k3mon_03 simple 2 bin dust scheme for Forsterite dust are described e integer n_dustgrainradius The number of dust grain radius bins including one for the monomers is specified with integer n_dustgrainradius f I8 b 4 n Number of dust grain radius bins amp ci Includes bin for monomers 2 5 4 Parameter File rhd par 107 The default value is 1 to avoid an empty array The value should be the same as the upper dimension in real ar_dustgrainradius For the current dust scheme there should always be exactly two bins e real ar_dustgrainradius The radii of the dust grains are specified with e g real ar_dustgrainradius f E10 4 b 4 p 1 d 1 2 n Dust grain radii u cm 0 0 1 0E 04 The default value is 0 0 e real c_dust0l The density of the grain material is specified with e g real c_dust01 f E15 8 b 4 n Density of grain material u g cm 3 3 3E 00 e real c_dust02 The atomic weight of the dust monomer is specified with e g real c_dust02 f E15 8 b 4 n Atomic weight of dust monomer u u 140 71 The value 140 71 should be appropriate for Forsterite Mg28104 The unit is the atomic mass unit The default value is 0 0 e real c_dust03 The number fraction of the rarest component is specified with e g real c_dust03 f E15 8 b 4 n Number fraction of rare
148. le can be set with real c_rescourantmax f E15 8 b 4 n maximum resistivity Courant factor u 1 amp c0 range C_resCourant lt C_resCourantmax typically 1 0 0 95 Its value should be slightly above c_rescourant real c_resB This parameter specifies the electric resistivity Values between 0 0 and 1 0 may be rea sonable Higher values are possible but drastically reduce the time step The default value is 0 0 Example real c_resb f E15 8 b 4 Q n Parameter for numerical resistivity 1 0 0 The artificial electric resistivity of Stone amp Pringle 2001 is used It is given by n c_resB j Ax p where ng is the magnetic diffusivity j the current density Az a mean width of the grid cell and p is the density Values lt 0 disactivate this feature real c_resBconst This parameter specifies a constant magnetic diffusivity 7m The default value is 0 0 Example real c_resbconstant f E15 8 b 4 amp n Parameter for constant magnetic diffusivity u cm 2 s 0 1 A reasonable value can be found by choosing a reasonable value for the magnetic Reynolds number Remas ovo Nm Values lt 0 disactivate this feature 5 4 Parameter File rhd par 99 e real c_resepsilon This parameter controls an additional numerical energy diffusion Typical values are be tween 0 0 and 1 0 The default value is 0 0 Example real c_resepsilon f E15 8 b 4 amp n Parameter for additional energy diffusion
149. lines except for the file header entry Example real time f F9 2 b 4 n Time u s cO 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 4 3 Structure of UIO Files 55 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 5 UIO entry types In an unformatted file each header line is an individual record containing a string with exactly 80 characters The following data block scalar or array is one single record 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 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 sec
150. ll flush 6 e 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 e Oparallel Dopenmp Onoautopar Try to enable parallelization with OpenMP direc tives disable auto parallelization e Onoinline Disables inlining This can simplify things With a proper choice of routine versions inlining is not really necessary anymore e 03 0limit General optimization with limited resource usage during compilation Some modules should only be compiled with 02 others compile even with 03 Onolimit 40 3 PROGRAM FILES INSTALLATION COMPILATION The UIO modules and the string handling module should be compiled in debug mode A proposed compiling sequence is MSrad does not compile all other modules are activated export F90_LHDRAD 1 export F90_MSRAD 0 export F90_SHORTRAD 1 export F90_DUST 1 export F90_MHD 1 export F90_PARALLEL openmp export F90_DEBUG 1 configure make UIO STR export F90_DEBUG 0 configure make 3 7 7 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 disk space The single processor performance of COSBOLD 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 parame
151. llowing 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 8287a0c gt 9 tags length 78404128 refs 1 TYPE STRING u10 HEAD STRUCT gt lt Anonymous gt Array 1 DATASET_ID STRING single_box MODELTIME FLOAT 10050 1 MODELITIME LONG 64088 DTIME FLOAT 0 176381 TIME_OUT_FULL_LAST FLOAT 10050 1 TIME_OUT_MEAN_LAST FLOAT 10040 0 Z STRUCT gt lt Anonymous gt Array 1 If the command in Sect has been performed the following substructures are present EOS STRUCT gt lt Anonymous gt Array 1 OPA STRUCT 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 v3 Structure lt 8274184 gt 16 tags length 78403900 refs 2 TYPE STRING uio BOX_ID STRING zZ DIMENSION LONG Array 2 3 TIME FLOAT 10050 1 ITIME LONG 64088 XC1 FLOAT Array 140 1 1 XC2 FLOAT Array 1 140 1 XC3 FLOAT Array 1 1 200 XB1 FLOAT Array 141 1 1 XB2 FLOAT Array 1 141 1 XB3 FLOAT Array 1 1 201 RHO FLOAT Array 140 140 200 EI FLOAT Array 140 140 200 vi FLOAT Array 140 140 200 V2 FLOAT Array 140
152. losrd 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 1err 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 I4 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 All necessary counter information is stored in the structure listdata Note that you can specify an entire group of files with e g modelident _ modelident _ modelident _3 or modelident _ 29 3 0 2 68 5 Control and Data Files 5 CONTROL AND DATA FILES Table 10 shows a list of all files necessary to run CO5BOLD Figure 6 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 control files rhd par rhd stop rhd cont and rhd dump 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 10 only cont
153. lume 4 49999049E 02 HYD 1 N_cellsperchunk n_chunks 10000 1410 HYD 2 N_cellsperchunk n_chunks 10000 1410 HYD 3 N_cellsperchunk n_chunks 10000 1410 VIS3D N_cellsperchunk n_chunks 10000 1360 Start of rhd_shortrad_step n_subdtime 1 minmax T 1 111651E 03 1 630733E 05 Main 1 3 ray direction 2 0 000000 1 000000 0 000000 Main 2 3 ray direction 3 0 707105 0 000000 0 707109 Main 3 3 ray direction 3 0 707105 0 000000 0 707109 Time step ratio dtime dtime_rad 1 750409E 01 dtime_ rad drhoei limit_this all 6 667E 02 2 510E 03 6 276E 02 0 000E 00 n_subdtime 2 minmax T 1 116348E 03 1 630658E 05 Main 1 3 ray direction 1 1 000000 0 000000 0 000000 Main 2 3 ray direction 3 0 000000 0 707105 0 707109 Main 3 3 ray direction 3 0 000000 0 707105 0 707109 Time step ratio dtime dtime_rad 1 836970E 01 dtime_ rad drhoei limit_this all 6 353E 02 3 188E 03 7 971E 02 6 276E 02 n_subdtime 8 minmax T 1 118540E 03 1 630164E 05 Main 1 3 ray direction 2 0 707105 0 707109 0 000000 Main 2 3 ray direction 2 0 707105 0 707109 0 000000 Main 3 3 ray direction 3 0 000000 0 000000 1 000000 Time step ratio dtime dtime_rad 1 791384E 01 dtime_ rad drhoei limit_this all 6 515E 02 3 894
154. mance especially 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 rhd_hyd_roeld_101 in rhd_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 5 5 Additional Control and Status Files rhd stop rhd cont rhd done and rhd dump 129 5 5 Additional Control and Status Files rhd stop rhd cont rhd done and rhd dump Before each time step COSBOLD checks in the working directory 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
155. mation common uio_chainf convert type list of current machine common uio_cvlist names of types keywords identifiers default formats common uio_defnam length of strings size of tables trmtab lintab empty table structure common uio_taborg SES Most of the routines are low level ones and do not have to be worried about because they 4 7 IDL UIO Routines 65 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 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 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 amp endelse if strtrim addpath 2 ne then path addpath 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 Or one just copies
156. matted default fast compact possibly machine dependent output strongly recommended o formatted slow machine independent output big files character outconv_full The conversion type see Sect 4 3 1 of the full model files can be specified e g with 5 4 Parameter File rhd par 125 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 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 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 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 whi
157. me 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 The model range has been extended to sub stellar objects brown dwarfs and to white dwarfs CO5BOLD solves the coupled non linear equations of compressible hydrodynamics in an ex ternal gravity 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 further simplified with directional splitting usually 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 boundarie
158. mean output file u 1 amp c0 0 no output of slice amp ci 1 2 3 output of slice with plane perpendicular to this direction 2 With a value of 0 the output is suppressed A value of 1 2 3 indiciates the direction of the normal to the output plane for instance in a local 3D box in a star model with gravity along direction 3 a value of 3 gives a horizontal plane in the middel of the model useful only in special cases whereas a value of 2 or 1 gives a vertical slice with a horizontal and the vertical axis useful for movies of 2D slices The grid index of the slice cannot be specified e integer outdim_chul The dimension of an additional output chunk into a separate file can be specified with this parameter a 2x3 integer array The output of a horizontal slice at the 20th layer from the bottom can be requested with integer outdim_chul d 1 2 1 3 f I5 b 4 p 6 n Chunk 1 dimension u 1 amp c0 0 start from first 9999 end with last 0 9999 0 9999 20 20 The index ranges go from 1 to the number of elements in that dimension Specifying a lower first or a larger last dimension as in the example means that all elements will be taken The output sampling rate is the same a for mean files Attention a high sampling frequency of large chunks can produce large files very quickly e character infile_start The filename of the initial model is specified e g with character infile_start f A80 b 80 n
159. meter b1_inflow The boundary condition for the hydrodynamic variables must be set to inoutflow too otherwise this boundary condition is the same like constant In the case of inoutflow the magnetic field which is advected into the computational domain has a unique component which is in the x1 direction and it is only present where a velocity in the positive x3 direction exists In all other places the magnetic field components are constantly extrapolated into the ghost cells real bi_inflow This parameter controls the strength of the inflowing horizontal magnetic field at the lower boundary in connection with bottom_bound_mag inoutflow The default value is 0 0 Example 5 4 Parameter File rhd par 85 real bi_inflow f E15 8 b 4 amp n Strength of inflowing horizontal magnetic field G 10 0 The unit of this parameter is gauss no factor y4m e real C_magtheta This parameter specifies the angle between the magnetic field vector and the x3 axis in radians in the case of oblique boundary conditions The default value is 0 0 Example real c_magthetab f E15 8 b 4 amp n angle magnetic field w r to the vertical direction amp u rad cO used in combination with oblique conditions 0 523598775598299 e real C_magphiB This parameter specifies the angle between the horizontal component of the magnetic field vector and the x1 axis in radians in the case of oblique boundary conditions The default value is 0 0
160. ms from a list 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 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 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 5 4 Parameter File rhd par 113 integer n_radphi f 14 b 4 amp n NPHI Number of ray sets in phi direction c0 2 2 e 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 I4 b 4 n KPHI Number of rays per cell c0 2 2 e 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 I4 b 4 amp n Numb
161. n HION partition function file name pf_kurucz dat 106 5 CONTROL AND DATA FILES e real dtime_out_hion Time increment for additional HION output Positive values specify the time increment in seconds negative values the increment in computational time steps Setting the parameter to zero suppresses the output real dtime_out_hion f E15 8 b 4 n Output file time step HION 10 0 e integer hion_chunks Number of chunks to use for HION in order to limit the required memory Do not make it bigger than the number of points in the x2 direction integer hion_chunks f I9 b 4 n Number of HION chunks 1 5 4 10 Dust dustscheme dust_moment04_c2 In this section the parameters for dustscheme dust_moment04_c2 4 bin 4 moments dust scheme for carbon rich dust are described e real c_dust01 The carbon to oxygen ratio is specified with e g real c_dust01 f E15 8 b 4 n C to O ratio 1 1 4 Larger values mean more dust Values below 1 make no sense for the current dust model e real c_dust02 The oxygen abundance is specified with e g real c_dust02 f E15 8 b 4 n Oxygen abundance u 1 6 606934E 04 e real c_dust03 The cutoff for the integration of the degree of condensation is specified with e g real c_dust03 f E15 8 b 4 n cutoff for integration of degree of condensation amp u 1 1 0E 05 e real c_dust04 The relative dust opacity factor is specified with e g real c_dust04 f E15 8 b 4 n Re
162. n with local rho limited new average pressure o 4 Correction with local rho new different formula average pressure o 5 default Correction with local rho new limit new average pressure o 6 Modification of 5 with different geometry factors in case of non equidistant grid e rhd_hyd_entropyfix_p0l1 in rhd_hyd_module F90 rhd hydrodynamics entropy fix 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 e rhd_hyd_upwind_p01 in rhd_hyd_module F90 rhd 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 e 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 Use standard method to compute the Roe states o defined Use non standard method to compute the Roe states 32 3 PROGRAM FIL
163. nMP support even if they do not contain any OpenMP directives themselves e fast General optimization flag to choose close to optimum optimization for the local machine However on AMD machines this works less than perfect because the features of the processors are not well recognized e i_dynamic Helpful against undefined reference to __ctype_b errors e r8 fpconstant Useful to force compilation in double precision see 3 7 3 On Macintosh machines the typical optimization flags are 03 no prec div fno alias ip A big problem is the tiny stack size on those ma chines large arrays taken from the stack should be avoided For the SHORTrad module this can be achieved by setting Drhd_arrays_101 2 during compilation In addition relatively small chunk sizes should be specified in rhd par see Sect and Sect Using the Intel compiler before version 9 1 there was a problem with the UIO modules when OpenMP is activated This was a bit weird because the UIO modules do not contain any OpenMP directives However this means that OpenMP can be safely deactivated for these modules A proposed compiling sequence is all modules activated export F90_LHDRAD 1 export F90_MSRAD 1 export F90_SHORTRAD 1 export F90_DUST 1 export F90_MHD 1 export F90_PARALLEL scalar configure make UIO export F90_PARALLEL openmp configure make For OpenMP see Sect 3 7 1 the number of threads can be set for instance with
164. ndary condition tends to produce a slight reduction of the horizontal velocities at the very bottom As the HD solver does not apply any extra viscosity at the bottom layers the MHD solver has this option there is a tendency to produce a slight predominance of vertical velocities in the regions where matter enters the computational box through the lower boundary By introducing a little bit of damping of the vertical velocity component this tendency can be significantly reduced Guide values are o 0 0 off no linear damping o 0 002 small reasonable value o 0 005 large possible useful value e real c_v3changesqrbottom For the open lower boundary condition inoutflow and inoutflow2 an additional damp ing of the vertical velocity at the open boundary can be specified e g with real c_v3changesqrbottom f E15 8 b 4 n Quadratic velocity reduction rate at bottom u 1 0 002 This damping is stronger for velocities that exceed the rms value of the velocities averaged over the entire bottom layers 82 5 CONTROL AND DATA FILES e real c_rhochangetop The transmitting upper boundary condition can smooth density fluctuations with this parameter It is locally adjusted towards the global average to damp out possible instabil ities It appears to be useful for the HLLMHD solver For simulations without magnetic fields there is no need to set this parameter so far The adjustment rate can be specified e g with real c_rhoc
165. ne Look into the header and if necessary the rest of the configure script or into Sect 3 5 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 With e g export F90_MACHINE dummy export F90_PREFLAGS Oprettyfast Qsomethingelse configure it is possible to specify all machine dependent settings yourself see Sect 3 5 and Sect 3 5 This is useful when dealing with a compiler hitherto unknown to the configure script Start the compilation with make to produce the executable rhd exe 3 3 Directory Structure 21 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 Ho Expand the tar file tar zxvf for tar gz Go into default master directory 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 If you want to compile in a directory in a completely different place not in a sub directory of for as described above you have to set the environment variable F90_BASEPATH see Sect 3 5 to make
166. ng _r_type in timing_module F90 timing rate type Category account for property of machine During a COS5BOLD run the total execution time is measured and printed after each time step The type of clock used can be chosen with o 1 Use call system_clock default o 2 Use call Date_and_Time o 3 Use t etime Sun version used in most cases o 4 Use call etime gfortran version o 5 Use call tremain Cray version o 6 Use call clock Hitachi version gasinter_101 in gasinter_routines F90 gas interpolation 101 Category performance enhancement This switch determines how temporary arrays are handled 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 o 2 No temporary coefficient arrays gasinter_102 in gasinter_routines F90 gas interpolation 102 Category performance enhancement This switch determines how coefficient arrays are handled to improve performance Values o 0 Coefficients are stored as pointer arrays old version o 1 default Coefficients are stored as allocatable arrays rhd_box_arrays01 in rhd_box_module F90 rhd box arrays 01 Category performance enhancement Switch to choose between the classical use of pointer arrays within the box structure to store arrays or the new version with allocatable
167. ng here 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 4 7 3 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 After having read the model data FUL and the tables for the equation of state EOS and opacity OPTA_COMMON see Sects 7 2 3 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 Based on the thermodynamic quantities now present in the FUL structure further quantities can be computed with combox pro as for instance in IDL gt cs combox cs ful 142 7 DATA ANALYSIS WITH IDL 7 3 IDL Data Structure The data structure FUL contains the fo
168. nsists of exactly two items separated by a blank No additional blanks are allowed Use copylist with as above 6 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 4 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 Sun0S 5 5 1 Last change 12 January 1998 1 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 aa aaa ae a aaa ae ae a ae ae ae aa ae ae aaa a ICI IK a ak A IK ae a aa kkk kkk a aka ae ae a kkk kkk kkk ak ak ak kkk kkk kk kk Routines functions uio_ pro most important user routine comfortable useful adkeyl Add one keyword to term table keyword value no link character 5 s adkey2 Add one keyword to term table with keyword value 3 adkey3 Add one keyword to term table with keyword value or default j cheonv Actualize list of conversion types for all channels CcHpos Give current file positi
169. ocity x1 amp u cm s real v2_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 Y n Velocity x2 u cm s real v3_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 Y n Velocity x3 amp u cm s real vi_xmean2 d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Velocity x1 Q u cm s real v2_xmean2 d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Velocity x2 amp u cm s real v3_xmean2 d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Velocity x3 amp u cm s 72 real real real real real real real real real real real real real real real real real real real real real real 5 CONTROL AND DATA FILES rhovi_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 Y n Mass Flux x1 amp u g cm 2 s rhov2_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 Y n Mass Flux x2 amp u g cm 2 s rhov3_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 Y n Mass Flux x3 amp u g cm 2 s bc1_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Magnetic field 1 amp u G bc2_xmean d 1 1 1 1 1 120 E13 6 p 4 b 4 amp n Magnetic field 2 amp u G bc3_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 Y n Magnetic field 3 u G bc1_xmean2 d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Magnetic field 1 amp u G bc2_xmean2 d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Magnetic field 2 u G bc3_xmean2 d 1 1 1 1 1 120 f E13 6 p 4 b 4 Y n Magnetic field 3 amp u G ei_xmean d 1 1 1 1 1 120 f E
170. ode content uio_data mode files 66 4 UIO DATA FORMAT 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 mod1 plot_oi uio dp uo 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 parameter file or for the UIO table file in Sect 14 3 3 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 st
171. of pressure reduction terms amp c1 1 0 Activation of pressure reduction terms default 0 0 Possible choices are o 0 0 Deactivation of pressure reduction terms in waves 3 and 6 in Roe solver o 1 0 Activation of pressure reduction terms in waves 3 and 6 in Roe solver default This parameter is not recognized by the MHD module real c_hydsdiffvelo With this parameter an extra energy diffusion down an entropy step after reconstructing the entropy can be activated For the diffusion velocity all three velocity components are used i e there is a diffusion even transversal to the flow speed This makes the diffusion more isotropic and lets numerical solutions to the Sedov blast wave problem look smoother The value can be set e g with real c_hydsdiffvelo f E15 8 b 4 amp n Parameter for energy diffusion down an entropy step u 1 amp cO typically 1 0 1 0 Possible choices are for example o 0 0 No extra energy diffusion down an entropy gradient default o 0 2 Small value o 1 0 Reasonable value 5 4 Parameter File rhd par 95 o 3 0 Large value It acts on the entropy but only on the fraction of the jump that is still there after the reconstruction unlike C_hydTdiffLin and C_hydTdiffMach that act on local temperature minima see below This parameter is not recognized by the MHD module e real c_hydvdiffvelo With this parameter an extra diffusion of the transversal velocities
172. ome very small To artificially increase the effect of radiative heating the parameter real ri_rad can specify a radius beyond which only positive 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 e real r0_core To insert energy in a sphere different with a radius other than r0_grav the heating radius r0_core can be specified separately e g with real r0_core f E15 8 b 4 n Core Radius u cm 9 45833e 12 If this parameter is not specified rO_grav is used as the radius of the core e character centrifugal_force Usually a centrifugal force is applied if nu_rotation40 To switch it off even for non zero rotation rate the parameter centrifugal_force can be used e g by setting 78 5 CONTROL AND DATA FILES character centrifugal_force f A80 b 80 n Switch on off the centrifugal force amp cO on default off no centrifugal force even for non zero nu_rotation off Three values are possible so far o on This is the default and can be set even for non rotat
173. ompiled e g with the Intel compiler see Sect However the factor is not prohibitive For not too demanding test runs the gfortran compiler can already be useful 3 7 15 NEC SX 5 SX 6 SX 8 First attempts to compile COSBOLD on neSH at the Rechenzentrum Kiel and on hwwsx5 at HLR Stuttgart 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 sunsrv or crossi is called with sxf90 Thus the environment variable F90_COMPILER sx90 has to be set before running the configure script No optimized version of COSBOLD has been achieved yet Some maybe useful switches are e sx5 generate instructions for SX 5 Use sx6 or sx8 when appropriate 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 of a list of routines see Sect e dw floatO no special environment variable use internally and in files the 4 Byte big_endian format For the SX 5 the compiler flags in the configure script are FOOFLAGS C hopt sx5 dw floatO Wf L nostdout L fmtlist L inclist L mrgmsg L transform M noflunf M noinv M noinexact M setall pi exp rhd_shortrad_operator exp rhd_shortrad_dtauop F9OMODULES FOOTIME DMSrad_raytas 1 For the SX 8 the configure scripts gives the
174. on or jump to specified position lt Ghunaits Initialize store and actualize a list of free and occupied unit E numbers 64 closrd closwr cpentr di data dataset_rd 4 UIO DATA FORMAT 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 Read uio file and put data into anonymous structure datasetlist_rd Read data from list of files and put it into an structure deform dim2st exkeyw exitrm exmtrm filcon getenv init meitrm memtrm mkcvls nc2nt openrd openwr pptrmt qmaadd qmadel rd rdtifo rdhdex rdhead rdlabl rdtab skipda slhdex st2dim str ct id tabo tabc tabm tabr tabw uclose uopen vnanrm wf2rf wr wrfifo wrhdme wrhead wrlabl wrtab Determine the default output format for numbers Compose dimension string Extract value of keyword from table Extract one term from the input line Transform 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
175. ongbranch_limit 60000 This switch limits needed compiler resources It is sug gested by the compiler on the CINES machines itself e Drhd_roeid_step_101 1 Slight performance improvement 3 7 17 SGI Origin 2000 3800 at UKAFF CO5BOLD has been also compiled and tested on up to 22 processors on the machines of the UK Astrophysical Fluids Facility UKAFFJP in Leicester England UKAFF operates two machines an SGI Origin 3800 with 128 processors named ukaff and an older SGI Origin 2000 with 22 processors named grand which is mainly used for development and test purposes Both machines are binary compatible At the time of testing April 2003 the SGI MIPSpro Compilers Version 7 4 was installed Most of the compiler switches given in the previous section were used except for the following modifications which either gave empirically a better performance or were recommended by the UKAFF Hints for users e Ofast Replaces 03 gave better performance e LNO cs1 32k 1s1 32 cs2 8M 1s2 128 Explicit cache architecture added The option Ofast is now the default selected by the configure script for all SGIs with IP35 architecture The cache architecture settings are activated for the UKAFF machines only A glitch in the system libraries made it necessary to add a work around to the source code file rhd F90 A bus error occurred whenever the system routine flush was trying to flush an empty file buffer The temporary wo
176. opt ss e pvfunc 2 References the pseudo vectorizing mathematical function and applies the tem porary array to reference the pseudo vectorizing mathematical function e omp parallel 1 parallelize based on OpenMP directives only e procnum 8 generated code for 8 processors on one node e orphaned 1 Checks if the regions sequentially executed contain orphaned directives dur ing run time when PROCNUM 8 is specified If a sequentially executed region contains an orphaned directive the system outputs a message and terminates the program e 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 e pmpar Collects the performance monitor information for each parallelization unit e pmfunc Collects the performance monitor information for each procedure e Drhd_hyd_roe1d_101 1 Optimization Choose non standard set of routines for Roe solver See Sect 5 4 17 e DMSrad_raytas 0 Optimization choose default version of loop in SUBROUTINE raytas in file MSrad3D F90 See Sect e 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 A proposed compiling sequence is only default modules activated export
177. orm 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 e 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 e 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 you have to adjust the size specification d 1 4 in the example above e character history The file history has a similar purpose as the previous entry It can be used to keep infor mation about the parent p
178. ort characteristics radiation formal timing 01 Category additional output 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 performance loss Values o undefined default no timing information o defined call subroutines to measure elapsed time MSrad_raytas in MSrad3D F90 Matthias Steffen radiation ray tau s Category performance enhancement Values o 0 default Loop with IF THEN ELSE o 1 Loop with ABS SIGN o 2 Loop with MIN MAX 3 7 Optimization Compiler Switches In this section some mandatory or useful compiler flags are described These have different functions e 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
179. ous fortran datasheet html ttp www uppmax uu se somputerSystems AngstromSunCluster SunCluster html 52 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 for short files The binary representation uses the Fortran unformatted read and write routines provides much faster I O gives smaller files and the IEEE format is a quasi standard among many platforms compilers On all machines the native binary representation can be chosen On some platforms additional conversion types are offered IEEE on most machines CRAY format an CRAYs The Fortran standard does not guarantee that unformatted i e also UIO files are 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 of one common format IEEE big_endian on all machines and compilers tested Compaq alpha Cray Hitachi HP V2500 HP Itanium2 IBM Intel AMD with Linux OS and PGI Intel or Pathsc
180. output 5 4 13 E c_radtcool 5 4 13 j c_raddcool 5 4 13 c_radscool 5 4 13 c_radtinci 5 4 13 c_raddinci 5 4 13 si c_radimplicitmu 5 4 13 2 i c_raditereps 5 4 13 i c_raditerstep 5 4 13 i i c_radtvisdtau 5 4 13 c_radtvis c_radhtautop c_radcourant c_radcourantmax c_radmaxeichange a ES Ol x XK XA XX a ES Ol x 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 c0 LHDrad MSrad SHORTrad amp c1 None skip radiation transport step entirely SHORTrad Possible values are O O None Skip radiation transport entirely 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 6 MSrad solar module It uses long characteristics The lateral boundaries have to be periodic Top and bottom can be closed or open Note that the switch Drhd_r02 1 has to be set during compilation see Sect 3 6 SHORTrad new supergiant module It uses short characteristics and is restricted to an equidistant grid and open boundaries at all surfaces Note that the s
181. p as H H 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 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 1 60 0E 05 5 4 Parameter File rhd par 83 Possible values are o C gt 0 0 Older version To x1 x2 C x x xz1 22 o C lt 0 0 New version 79 1 72 abs C x H x1 x2 k x1 1x2 In this case a value of C_radHtautop 1 0 might be a good choice e real rho_min During long 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 belo
182. p strict monotonicity whereas PP is strictly monotonic and achieves low dissipation from avoiding jumps at cell boundaries wherever possible However it chops off flattens extrema like all TVD schemes and it shows Gibbs wiggles near a jump that is not surrounded by constant plateaus but lies in a slope The new 2nd order scheme FRmono is designed to suppress these wiggles too The highest resolution scheme is PP It is implemented in the MHD module too By specifying e g reconstruction FRweno PP it is possible to use the FRweno scheme for the hydrodynamics scheme as such and the monotonic PP only for the advection of additional quc quantities real c_slopered A new extra stabilization mechanism can be activated that reduces the slope and flattens the reconstruction function in case of a strong density contrast Poneside Potherside gt 2 between neighboring cells This value can be set e g with real c_slopered f E15 8 b 4 amp n Slope reduction parameter in case of strong density contrast u 1 amp c0 0 00 off default 0 02 reasonable value 0 10 large value 0 02 Typical choices are 5 4 Parameter File rhd par 91 o 0 0 Slope reduction switched off Original reconstruction is used o 0 02 Moderate slope reduction in case of large density jumps o 0 10 More pronounced slope reduction in case of strong density contrast The default is not to use this trick and leave the parameter at 0 0 However if numerical
183. pacity real c_visneul 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 down 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 t
184. pecified that is based only on the sound speed c e g with real c_hydsoundcourantmax f E15 8 b 4 amp n maximum HD sound speed Courant factor u 1 amp c0O range c_hydsoundcourant lt c_hydsoundcourantmax lt 0 5 typically 0 5 0 5 The pair c_hydsoundcourant c_hydsoundcourantmax works together in a the same way as described above for c_courant c_courantmax 120 5 CONTROL AND DATA FILES e real c_hydexpcourant In addition to the usual Courant condition one could restrict the maximum expansion between two adjacent grid cells with e g real c_hydexpcourant f E15 3 b 4 n HD expansion Courant factor u 1 cO range 0 0 lt C_hydExpCourant lt C_hydExpCourantmax typically 0 3 0 2 real c_hydexpcourantmax This parameter can be set e g with real c_hydexpcourantmax f E15 8 b 4 n HD max expansion Courant factor u 1 amp cO range 0 0 lt C_hydExpCourant lt C_hydExpCourantmax typically 0 5 0 3 The pair c_hydexpcourant c_hydexpcourantmax works analogously to the pair c_courant c_courantmax 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 e c0 range 0 1 1 0 typically 0 5 off 20 0 0 5 The default is 0 9 Nevertheless since the Roe solver is constructed to handle shocks and rapid changes in density and energy
185. plus kinetic energy and multiply with the computed mass flux This is a more experimental version and not generally recom mended o CA4 Averaging the enthalpy and multiply with the computed mass flux This is a more experimental version and not generally recommended Here CA1 and CA2 behave in a similar way whereas CA3 and CA4 are essentially just for tests I prefer the CA1 variant for the time being However both CA1 and CA2 work only well for small fluctuations and Mach numbers Therefore one of the modified schemes should be used Again they are rather similar even if the implemented creteria are rather different While most of the versions work for ordinary main sequence models the comparably pooly resolved red supergiant models with large entropy step and Mach numbers require a combination of the criteria above Therefore CA1gMps is recommended for all type of models in general This parameter is not recognized by the MHD module real c_hydpredfactor The hydrostatic pressure correction terms in the two acoustic waves are always present However for the entropy wave and the ionization wave it is not quite clear if the terms should be there the classical default or if they should be set to zero The value of a factor in front of these terms can be set e g with real c_hydpredfactor f E15 8 b 4 amp n hydrostatic pressure reduction in waves 3 and 6 u 1 amp c0 0 0 Deactivation
186. r is then called with Drhd_chem01 F9O_HION HION module time dependent hydrogen ionization o 0 do not activate compile and link this module default o 1 activate this source step module Setting this variable to 1 will set F90_DUST 1 The compiler is then called with Drhd_hion01 F90_DUST DUST module o 0 do not activate compile and link this module default o 1 activate this source step module If this variable is set to 1 the compiler is called with Drhd_box_quc01 1 see Sect F9O_MHD MHD module o 0 do not activate compile and link this module default o 1 activate this magnetohydrodynamics module MHD HLL solver If CO5BOLD is compiled with the MHD module your start model should include magnetic fields otherwise zero magnetic fields are created and used In the latter case the magnetic field arrays are not written into the output files F90_MACHINE Explicit machine specification This is usually not necessary use local or y instead o local machine suntu Sun Oo 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 dependent flags but use module selections o empty Compiler flags are composed from F90_PREFLAGS and F90_POSTFLAGS only F90_BASEPATH Path for CO5BOLD base directory o gt The configure script tries to determine the base directory name automatically de fault This
187. r outfile_chul The name of the file for the output of an additional data chunk at regular intervals the same as for mean file can be specified with e g character outfile_chul f A80 b 80 n Output file name for chunks rhd chui The UIO format is the same as specifiec for mean files Leaving the name 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 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 character outconv_end The conversion type see Sect 4 3 1 of the final model files can be specified e g with character outconv_end f A80 b 80 n QOutput 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 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 Output file format amp cO formatted unformatted unformatted Allowed values are o unfor
188. r to get the magnetic field strength in gauss The CO5BOLD analysis tool CAT does this automatically when reading the model data so that CAT outputs the field strength in gauss Positivity of pressure and density A special problem of MHD simulations is that pressure or density can become negative in some circumstances This problem is also present in pure hydrodynamic simulations but gets worse for MHD The original hydrodynamic version of CO5SBOLD tries to fix this problem by reducing the time step In hydrodynamics this works in most cases In MHD however reduction of the time step often does not help and other methods are necessary to avoid this problem Therefore the MHD module uses a HLL solver instead of a Roe solver which is used in the hydrodynamic module It was shown numerically by Janhunen 2000 that using a HLL solver together with additional source terms in the induction equation keeps pressure and density positive under all circumstances Because the constrained transport step which is performed after the 1D sweeps with the MHD solver changes the magnetic field a correction of the internal energy in each cell is necessary to keep the total energy conserved Because this correction can lead to negative pressure it is omitted if the internal energy would become too small Therefore the total energy is not exactly conserved but this affects only a few cells in the simulation box See also on this topic The methods describe
189. red supergiant mod els o FRcont 2nd order continuous version of FR unstable except for low Mach numbers Usually the VanLeer reconstruction has been a good choice If a more stable and diffusive scheme is needed take Minmod However the variants of the new 2nd order Frankenstein s Method are a better choice if the additional computational cost is acceptable The PP reconstruction gives the highest accuracy However there is the possibility that it produces somewhat noisy models with small wiggles e g in the velocity for extreme cases solar models look fine with PP The options Constant SuperBee and FRcont are just for testing purposes they have either too much sometimes the wrong sign of or too little diffusion respectively The order of decreasing diffusivity and increasing accuracy is roughly schemes on a line are similar schemes in brackets are for testing only Constant MinMod FRmimo PPmimo vanLeer FRmono FRweno Superbee PP FRcont However there are differences how the increase in accuracy is achieved vanLeer uses potentially dangerous anti diffusion in contrast to MinMod but needs only a 3 point stencil whereas PPmimo and FRmimo don t have anti diffusion but need a more expensive 5 point stencil FRweno achieves actually a 2nd order accurate reconstruction also near extrema for reasonably resolved structures e g sufficiently long wavelengths of sine waves Le it gives u
190. requently The timing measurement might slow it down somewhat It should not be used in conjunction with OpenMP Values o undefined default no timing information 34 3 PROGRAM FILES INSTALLATION COMPILATION o defined call subroutines to measure elapsed time e rhd_rad3d_dir_t01 in rhd_lhdrad_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 o undefined default no timing information o defined call subroutines to measure elapsed time rhd_rad3d_step_t01 in rhd_lhdrad_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 ov
191. rhd fine Leaving it empty means that no file of this type is written Specifying it means the same yet e 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 Output 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 e 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 Output file conversion amp c0 ieee_4 ieee_8 crayxmp_8 native ieee_4 128 5 CONTROL AND DATA FILES 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 CO5SBOLD yet 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 wi
192. rk around was simply to add a write statement before every call of flush This made the log file look less nice but did the job Now the few flush statements that are not necessarily preceded by a write statement are removed The main goal was to investigate the scaling of the performance of COSBOLD with the number of processors This was done only for the MSrad module considering local surface convection http www nsc liu se systems sgi3k http techpubs sgi com library tpl cgi bin init cgi 1 3 7 Optimization Compiler Switches 49 models Two model sizes were tested a small one with 125x125x81 grid points employing non grey radiative transfer 4 frequency bands and a large one with 315x315x81 grid points employing grey radiative transfer Rather short runs of 10 small model and 3 large model time steps were performed Even for the large model the memory demand was ca 800Mb which is very modest considering that every sub node of the machine consisting of 4 processors has 2Gb of memory The results are summarized in the following three figures The black lines give the scaling of the total time the green lines the scaling of the time needed by the hydrodynamics routines and the red lines the scaling of the radiative transfer routines The scaling is presented as the increase of processing time per processors as the problem is distributed among more and more processors The times are normalized to the
193. roperties 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 The axes xc1 xc2 and xc3 describe the positions of the cell centers The axes xb1 xb2 and xb3 contain the positions of the cell boundaries they have one element more than the corresponding cell centered quantity Cell boundaries should be centered in the middle between cell centers for the best represen tation of radiative fluxes with MSrad3D 5 2 Files with additional chunks of data rhd chul If specified the file rhd chu1 contains parts of full data sets written with the same sampling rate as mean files see below 5 3 File with Additional Data rhd mean 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 70 5 CONTROL AND DATA FILES 5 3 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 file_id f A8 b 3 n Fil
194. roup At each new time step a new base axis system is chosen at random It is kept for all radiative sub steps o alternate Alternate between unity and random orientation matrix o drift01 Slow drift algorithm 1 o drift02 Slow drift algorithm 2 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 Allowed values for radscheme MSrad are o lobatto o dblgaus 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 c0 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 x1 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 o oktaeder N 3 default octahedron o tetraeder N 4 tetrahedron o cube N 4 o ikosaeder N 6 icosahedron o dodekaeder N 10 dodecahedron o list 01 list 01 3 Choose ray syste
195. ry format this can be changed to ASCII for matted in rhd par Their contents can be read and analyzed with IDL routines see Sect 14 7 3 For machines with batch queue there is a script which can handle an entire sequence of simulations see Sect 6 2 136 6 RUNNING A SIMULATION 6 2 Running CO5SBOLD on a Machine with Batch System For longer simulations it is inconvenient to restart the individual jobs by hand This task is done by a script originally from Hans G nter Ludwig Its basic function is sketched in Fig 6 CO5BOLD function diagram A D IES 11 Figure 6 Program scheme Here comes an example of the script rhd1 job for a system without dedicated batch system The submission of a job is done via nohup rhd1 job amp bin sh PBS N rhdi PBS 1 walltime 72 00 00 PBS 1 nodes 1 ppn 4 Job file for the execution of RHD on gunnar Itanium 2 de Source rhd1 job original from HGL Last modification 2002 12 13 6 2 Running CO5BOLD on a Machine with Batch System 137 set xv BASEDIR users bf dat job j1 STADIR BASEDIR sta Start directory contains par rhdi cmd rhd1 job WRKDIR BASEDIR wrk Work directory BAKDIR BASEDIR bak Backup and output directory RHDEXE STADIR rhd exe RHD program to be executed export NCPUS 4 echo NCPUS export OMP_NUM_THREADS 1 Jump into work dire
196. s UIOPATH EOSPATH bin f90 man gas f90 ULOSRCPATH YGASPATH EOSSRCPATH MAC YUICEXEPATH MAC MAC GASEXEPATH JEOSEXEPATH violok 90 exe Unix shell scripts Figure 1 Old directory scheme rad hdrad SRADPATH MAC RADEXEPATH 3 5 Configure Script 23 Paths Abb Description HOME for con f90 CON constants and units HOME or dust f90 DUST source terms due to dust or molecules HOME for hion f90 HION time dependent hydrogen ionization HOME for chem CHEM chemical reaction network 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 f90 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 3 5 Configure Script The configure script produces a Makefile It 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 ar
197. s 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 The code was supplemented with an optional MHD version Schaffenberger et al 2005 that can treat magnetic fields There are also modules for the formation and advection of dust available The current version now contains the treatment of chemical reaction networks mostly used for the formation of molecules Wedemeyer Bohm et al 2005 and hydrogen ionization Leenaarts amp Wedemeyer B hm 2005 too 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 B 1 Introduction to UIO Sect 4 1 How to Make a Proper Parameter File Sect 5 4 1 How to Run CO5BOLD Sect 6 1 2 Equations 2 1 Basic Equations The hydrodynamics equations are expressed as conservation relations plus source terms for p pul pv2 pu3 peikg 1 the mass density the three mass fluxes and the total energy density per volume respectively Each quantity q has its corresponding flux f q and possibly source term s q For convenience p vi v2 v3 ei 2 are chosen as independent quantities The conserved quantities are purely algebraic combinations of these The 3D hy
198. s far below the 2 GByte limit might run However experienced IBM users might experiment instead with the compiler switches bmaxstack bmaxdata and qsmallstack with the UNIX commands limit or ulimit or with the settings in the header of the batch script e 03 Choose optimization level Higher levels that involve interprocedural analysis cause the compiler to stop with an error message e qarch auto qtune auto qcache auto To allow optimization specific for the local machine default in the configure script Cross compilation can be activated e g with qarch pwr3 qtune pwr3 or qarch pwr4 qtune pwr4 by setting an environment vari able e g F90_MACHINE pwr3 before calling configure e Q Q To activate inlining and to specify the list of routines that should be inlined see Sect 13 7 2 e qsmp noauto omp Parallelization OpenMP directives are activated A job script rhd job on the Loadleveler batch system on io cines fr can be submitted with llsubmit rhd job http www 306 ibm com software awdtools fortran xlfortran library http publib boulder ibm com infocenter comphelp index jsp http os cc biu ac il documentation http os ce biu ac il documentation xIf_8 1 1 html http pcf nersc gov computers SP craytoSP htm 44 3 PROGRAM FILES INSTALLATION COMPILATION The jobs in the queue for user testuser can be checked with llq u testuser A job with ID n34 56789 0 c
199. s 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 simulation was successful and should be continued Note the existence of an rhd end file only indicates that CO5BOLD managed to exit gracefully due to an error or in a regular way 5 6 Text Output rhd out During execution expecially during the initialization phase CO5BOLD writes lots of informa tion to standard output After the header its with a block Compiler call e g pgf90 byteswapio fast Mvect sse Mcache_align Minfo inline Minline rhd_hyd_a vg rhd_hyd_upwind rhd_hyd_pred0 rhd_hyd_predm rhd_hyd_predp rhd_hyd_alpha rhd_h yd_constanteq rhd_hyd_minmodeq rhd_hyd_minmod rhd_hyd_vanleereq rhd_hyd_vanleer rhd_hyd_superbeeeq rhd_hyd_superbee rhd_hyd_ppeq rhd_hyd_pp rhd_hyd_hdflux rhd _hyd_entropyfix Minline rhd_rad3d_raylhd rhd_rad3d_solve rhd_rad3d_solveeq rhd _shortrad_operator rhd_shortrad_dtauop Drhd_hyd_roeid_101 0 Drhd_r02 Drhd_r0 3 DMSrad_raytasi Drhd_hyd_entropyfix_p01 1 Drhd_roeid_step_t01 Drhd_roeid_f lux_t01 Drhd_vis_t01 Drhd_bound_t01 Drhd_shortrad_step_t01 Drhd_shortrad_fo rmal_t01 Drhd_shortrad_lambda_t01 These lines were produced by the configure script see Sect 3 5 and written into the file compiler_flags info which is accessed from rhd F90 via include during compilation Various modules now ha
200. seful 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 Installation of UIO UNIX Scripts The installation procedure for the UIO scripts has been updated to make use of its own configure script Therefore the procedure should now look like tar zxvf for tar gz cd for uio f90 YOUR_MACHINE configure make make install or tar zxvf for tar gz cd for uio f90 mkdir YOUR_MACHINE cd YOUR_MACHINE In s conf configure configure make make install 62 4 UIO DATA FORMAT Some of the environment variables that control the CO5BOLD configure script are also rec ognized see the header of the UIO configure script The command make install generates a directory HOME local and sub directories An init script is put into HOME bin And the resource files cshrc and bashrc are modified to call it Therefore this installation step is potentially dangerous because its effect is not restricted to the local directory 4 6 2 Quick Examination of Files uiolook The shell script uiolook calls 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 filename AVAILABILITY DESCRIPTION The routine uiolook reads each filename file in
201. 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 6 Compiler Macros 27 3 6 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 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 5 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 c
202. some overhead for copying and adding the contributions Still together with e g reconstruction FRweno there is a dramatic improvement for convection at small Mach numbers compared to 123 vanLeer This parameter is recognized by hdscheme Roe and hdscheme HLLMHD although hdscheme HLLMHD does not know hdsplit CTU e character hdcheckflux With this parameter the CheckFlux routine of the HLLMHD solver can be des activated as e g in character hdcheckflux f A80 b 80 n Switch to activate checking of MHD fluxes amp c0 on off off This parameter is only recognized by the HLLMHD scheme Leaving it on might be safer but is definitely slightly slower 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 PPmimo c3 FRmimo FRmono 2 FRweno 2 FRcont FRweno Possible values are 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 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 VanLeer default The recommended first order reconstruction method Superbee The most aggressive
203. spherical shells r and a 2D slice through the model z 5 3 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 real time_db f E23 15 b 8 n time amp u s integer itime f 110 b 4 n time step number amp u 1 real xci d 1 1 1 1 1 1 f E13 6 p 4 b 4 n x1 coordinates of cell centers amp u scm amp ds 0 0 0 1 0 1 real xc2 d 1 1 1 1 1 1 f E13 6 p 4 b 4 n x2 coordinates of cell centers amp u cn amp ds 0 1 0 0 0 1 real xc3 d 1 1 1 1 1 120 f E13 6 p 4 b 4 n x3 coordinates of cell centers amp u cm amp ds 0 1 0 1 0 0 real xb1 d 1 2 1 1 1 1 f E13 6 p 4 b 4 n x1 coordinates of cell boundaries amp u cn amp ds 0 1 0 1 0 1 real xb2 d 1 1 1 2 1 1 f E13 6 p 4 b 4 n x2 coordinates of cell boundaries amp u cn amp ds 0 1 0 1 0 1 real xb3 d 1 1 1 1 1 121 f E13 6 p 4 b 4 n x3 coordinates of cell boundaries amp u cm amp ds 0 1 0 1 0 1 real rho_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Density amp u g cm 3 real vi_xmean d 1 1 1 1 1 120 f E13 6 p 4 b 4 amp n Vel
204. st component u 1 amp cO For Mg25i04 Mg is the rarest its fraction is 3 1187E 05 amp c1 Mg2Si04 contains 2 Mg gt 1 2 gt 1 55935e 05 1 55935e 05 For MgaSiO4 the rarest component is usually Mga So half the magnesium abundance is required as value The default value is 0 0 e real c_dust04 The lower dust limit fraction is specified with e g real c_dust04 f E15 8 b 4 n Lower dust limit fraction u 1 1 0E 10 It is used in the calculation of the settling velocity where a division by the total density of monomers and dust is required To prevent this denominator to become zero a term Cdusto4 P is added The default value is 0 0 e real c_dust05 The minimum number of monomers during condensation is specified with e g real c_dust05 f E15 8 b 4 n Minimum number of monomers during condensation u 1 10 0 For very small grains just one or very few monomers the condensation rates can be very small in this dust model nucleation that would form already small clumps of monomers is not considered Therefore to speed things up a minimum number of monomers can be given that is considered for the condensation rate With 1 0 or smaller values the enhancement is switched off The default value is 0 0 108 5 CONTROL AND DATA FILES e real c_dust06 The sticking coefficient for the condensation rate is specified with e g real c_dust06 f E15 8 b 4 n Sticking coefficient u 1 amp c0 For C rich dus
205. 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 hd mhd rhd_mhd_module F90 MHD magnetic fields 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 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 dust rhd_dust_module F90 DUST dust molecule formation hd dust dust_k3mon_module f DUST 1 or 2 component dust model hd dust dust_bins_module f90 DUST multi bin dust model dust_momentc2_module f DUST 4 moment dust model C2 INC DUST dust include file Ca molecule C2H INC DUST dust include file CoH molecule C2H2 INC DUST dust include file CoH molecule CHPAR_CT INC DUST dust include file DINDEX INC DUST dust include file DKSPLINT INC DUST dust include file H2 INC DUST dust include file H molecule chem_rn_module F90 CHEM chemical reaction network chem_rn_dvode F
206. t 0 37 can be between O and 1 1 0 The default value is 0 0 5 4 12 Dust dustscheme dust_bins_01 In this section the parameters for dustscheme dust_bins_01 multi size bin dust scheme for Forsterite dust are described e integer n_dustgrainradius The number of dust grain radius bins including one for the monomers is specified with integer n_dustgrainradius f I8 b 4 n Number of dust grain radius bins amp ci Includes bin for monomers 8 The default value is 1 to avoid an empty array The value should be the same as the upper dimension in real ar_dustgrainradius e real ar_dustgrainradius The radii of the dust grains are specified with e g real ar_dustgrainradius f E15 8 b 4 p 1 d 1 8 n Dust grain radii u cm 0 00390625E 04 0156250E 04 06250E 04 25000E 04 00000E 04 00000E 04 16 0000E 04 fe oO Oo Oo o 6 The default value is 0 0 e real c_dust01 The density of the grain material is specified with e g real c_dust01 f E15 8 b 4 n Density of grain material u g cm 3 3 3E 00 e real c_dust02 The atomic weight of the dust monomer is specified with e g real c_dust02 f E15 8 b 4 n Atomic weight of dust monomer u u 140 71 The value 140 71 should be appropriate for Forsterite Mg25i04 The unit is the atomic mass unit The default value is 0 0 e real c_dust03 The number fraction of the rarest component is specified with e g real c_dust03 f E15
207. t 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 3 7 then the procedure should be fairly easy The general compilation procedure is now tar zxvf for tar gz cd for hd rhd mkdir p YOUR_MACHINE cd YOUR_MACHINE In 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 1 All Fortran files are listed in Tables 2 and 3 3 2 Compilation Procedure for CO5BOLD The installation procedure has changed significantly since the last release now there is a configure script see Sect that creates the complete temporary makefile which can be used to compile CO5BOLD and produce the executable rhd exe 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 On a restricted UNIX you might be forced to use gunzip for tar gz tar xvf for tar instead Unpacking the tar
208. t 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 PRE Korn shell kshrc f MLO UIOPATH HOME uio export UIOPATH PATH PATH UIOPATH bin export PATH MANPATH MANPATH UIOPATH man export MANPATH xk 58 4 UIO DATA FORMAT File contents uio_base_module f90 Collection of basic modules uio_mac_module F90 Machine dependent routines for all machines current 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 7 UIO Fortran90 files module contents uio_cst_module channel status information uio_cvl module convert type list of current mach
209. t_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 7 2 CO5BOLD Data in IDL 141 IDL gt uio_openrd nc modelfile outstr ierr IDL gt for i 0 ntime 1 do begin IDL gt ful uio_dataset_rd modelfile channel nc ierr ierr outstr err_msg IDL gt endfor amp IDL gt 126 losrd ne 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 amp IDL gt if ierr eq 0 then begin amp IDL gt Do the data processi
210. table to test the table routines integer inti f 15 b 4 n Integer 1 column real reali f F5 1 b 4 n Real 2 column character chari f A16 b 16 n Char 3 column real real2 f E13 6 b 4 n Real 4 column integer int2 f 15 b 4 n Integer 5 column inti reall chart real2 int2 i 2 0 a 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 While 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
211. te flux of transversal momentum with consistent advection version 3 Use mass flux and upwind density to determine flow speed Compute transversal momentum fluxes from mass flux and diffusive momentum flux o CA4 Compute flux of transversal momentum with consistent advection version 4 Use mass flux and Roe mean density J to determine flow speed Compute transversal momentum fluxes from mass flux and diffusive momentum flux recommended For instance for a 2D Sedov blast wave problem the new modes give less artifacts close to the axes than the old mode Normal The four new advection types are made of to choices for the way to compute the effective flow speed across a cell boundary different density values can be used and two ways to compose the final transversal momentum fluxes Version CA4 is recommeded This parameter is not recognized by the MHD module character hdentropywavemode This parameter controls the computation of the Roe correction flux for the entropy wave It can be set e g with character hdentropywavemode f A80 b 80 amp n Mode for entropy wave type amp c0 Normal Entropy1 Entropy2 Entropy3M Entropy3Ms Entropy3gMps recommended Entropy3gMps The choices are o Normal Compute entropy wave flux with standard Roe treatment from pressure and density old default o Entropy1 Compute entropy wave flux from entropy This only works well for small Mach numbers o Entropy2 Compute entropy wa
212. teger integer integer integer integer integer integer integer integer integer integer integer integer integer integer n_radband 115 n_raditer ITT n_radmaxiter 111 n_radminiter 111 n_radoutput n_radphi 112 n_radrsyslevel n_radsubray n_radtaurefine 113 n_radtheta 112 n_radthickpoint 113 n_rescellsperchunk 97 n_viscellsperchunk 102 outfile_chul plustimestep starttimestep luminosity MHD 87 molecules 103 opacities process management 116 radiation transport 109 reading in IDL 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 abux 125 abuy 125 ar_dustgrainradius ar_RotationAxis bi_inflow beta_inv c_magthetab c_radkappasmooth c_visp2phypartificial c_visp2phypdivrhov 103 c_visp2phypexpansion 103 c_visp2phypsmagorinsky 102 c_coredrag c_courant c_courantmax 119 c_dust01 10611108 c_dust02 1061108 c_dust03 1061108 c_dust04 c_dust05 c_dust06 c_dust07 109 c_dust08 109 c_dust09 109 c_dustoX chem_abumetal 105 c_hptopfactor c_hydexpcourant 120 c_hydexpcourantmax 120 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 r
213. temperature minimum u 1 amp c0 typically 0 2 if activated usually 0 0 0 0 96 5 CONTROL AND DATA FILES It just acts on the temperature gradient in the neighborhood of a local minimum whereas C_hydTdiffMach see below has an additional factor that takes velocity gradients into account which prevent this type of diffusion from acting in deeper convective layers I rec ommend as a default C_hydTdiffLin 0 0 and non zero values only in case of an emergency and C_hydTdiffMach 1 0 or 2 0 as a default These parameters are not recognized by the MHD module real c_hydtdiffmach Analogously to c_hydtdifflin an additional energy dissipation down a temperature gra dient but only in cells adjacent to a local temperature minimum in 1D can be applied that has a scaling factor derived from the Mach number This Mach number dependent diffusion can be set e g with real c_hydtdiffmach f E15 8 b 4 amp n Parameter 1 for energy diffusion near local temperature minimum u 1 amp cO typically 0 2 if activated usually 0 0 1 0 I recommend as a default C_hydTdiffLin 0 0 and non zero values only in case of an emer gency and C_hydTdiffMach 1 0 or 2 0 as a default These parameters are not recognized by the MHD module integer n_hyditer After each complete hydiative time step the recommendation for the next time step will be chosen so that n_hyditer iterations will probably needed The parameter can be set e g with
214. ter file Therefore OpenMP should not be activated currently The compiler settings are somewhat similar to the settings of the HP V2500 system in Sec tion 3 7 6 e U77 Link proper library to make the machine understand e g call flush 6 e 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 e Ofast High optimization level And 0faster is even higher e 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 A proposed compiling sequence is LHDrad DUST MHD do not compile export F90_MSRAD 1 export F90_SHORTRAD 1 configure make 3 7 8 Hitachi SR8000 Some information about the Hitachi compiler is herd In the preprocessor switches are listed that control the modern single version uio_mac_module F90 e conti199 Up to 199 continuation lines can be interpreted otherwise not more than 39 continuation lines are accepted 3 7 Optimization Compiler Switches 41 e limit Limits the amount of time and memory for compilation e opt ss use highest possible optimization level e 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
215. ter loop in rhd_shortrad_dirX 3 7 5 Compaq alpha The UIO module allows the reading and writing of files in little_endian and big_endian format In 3 6 the preprocessor switches are listed that control the modern single version uio_mac_module F90 of this file e assume byterecl Necessary for the UIO routines specify that the length of a record is measured in bytes and not in words e cpp invoke the preprocessor on all source files e inline speed V Force automatic inlining optimized for speed e 04 General optimization e Drhd_hyd_roe1d_101 0 Optimization Choose standard set of routines for Roe solver See Sect 5 4 17 e DMSrad_raytas 0 Optimization choose default version of loop in SUBROUTINE raytas in file MSrad3D F90 See Sect 3 7 6 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 CO5SBOLD Yet when running on several processors only some routines e g rhd_shortrad_dirsimplel in CO5BOLD 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 very good partly because the achievable optimization level is not very high Some macros which seem to be necessary e U77 Link proper library to make the machine understand e g ca
216. terpolation 2 Possible values o 1 Simple arithmetic average of fluxes default o 2 Quadratic interpolation of fluxes to the cell edges This parameter is only recognized by the hdscheme HLLMHD 98 5 CONTROL AND DATA FILES e integer n_rescellsperchunk The approximate number of grid cells per chunk in the 3D resistivity scheme can be specified e g with integer n_rescellsperchunk f 19 b 4 amp n Number of cells per chunk in resistivity routine amp c0 0 gt one 2D slice at a time amp c1 1 gt minimum chunk size inefficient amp c2 10000 typical value 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 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 real c_rescourant The tensor resistivity routines have their own time step restriction The recommended typical time step can be set e g with real c_rescourant f E15 8 b 4 n resistivity Courant factor u 1 c0 range 0 0 lt C_resCourant typically 0 5 0 5 real c_rescourantmax The absolute upper limit for the resistivity time sca
217. th 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 rhd_roeid_slope_101 in rhd_hyd_module F90 rhd roe 1 dimension slope loop 01 Category feature activation When this compiler switch is set a new extra stabilization mechanism can be activated If one of the reconstruction methods VanLeer Superbee or PP see Sect is activated the slope can be reduced by averaging with the results from a MinMod reconstruction by setting c_slopered see Sect 5 4 7 to a positive non zero value This can improve the stability without significantly reducing the effective numerical resolution Switch values o 0 default no slope reduction o 1 slope reduction in case of expansion wave o 2 slope reduction in case of strong density contrast 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 perfor
218. the data part After the reading of the header e g with use uio_siz_module use uio_nam_module integer ntt characterx let termt 2 nttmx call uio_rdhd ncin termt ntt 4 6 UNIX Scripts 61 the identifier type and dimension if any of the entry is 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 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 a 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 a 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 and of course CO5BOLD 4 6 UNIX Scripts So far there exist three UNIX shell scripts u
219. the paths to the source files known to the configure script That might look like mkdir SOME_REMOTE_PLACE cd SOME_REMOTE_PLACE export F90_BASEPATH HOME f or In s F90_BASEPATH hd rhd conf configure configure The variable F90_BASEPATH also has to be set explicitely if the main directory for should have another name Renaming the sub directories with the source files is not a good idea it requires modifications of the configure script itself 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 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 Fortran Files Tables 2 and 3 show a list of all source files necessary to compile the complete version of CO5BOLD 22 setarodeppaths csh setarcdeppaths sh mat MATPATH str f90 STRPATH MA TSRCPATH MAC MAC ISTREXEPATH ISTREXEPATH 3 PROGRAM FILES INSTALLATION COMPILATION FMAC MAC RHDEXEPATH HSTEXEPATH rhd af15 RHDPATH HSTPATH MAC MAC HDWEXEPATH MEANEXEPATH hdw mean HDWPATH MEANPATH Main directory FORTRANDISK uio eo
220. the tensor viscosity routines 25446 400391 sec Some of these values are split further 5 7 Chemistry Input The number densities of the chemical species must be provided as cell centred quantities quc in cm see Sect 3 6 The array UIO headers must be named following this example Number density of H2 The chemistry input file contains all data for the reaction network It is a text file with a strict format following the UMIST 99 ratefile standard FORMAT 14 5 A8 1X 2 1X A4 1X 1PE8 2 3X 0PF5 2 2X 0PF8 1 A16 It consists of 12 columns with the following meaning 5 8 HION Input 133 col meaning format 1 reaction ID IA 2 4 reactants max 3 symbols with 8 characters 3 A8 1X 5 8 products max 4 symbols first two with 2 A8 1X 2 1X A4 8 characters last 2 with 4 characters 2 A8 1X 2 1X A4 9 reaction coefficient a 1PE8 2 10 reaction coefficient 6 0PF5 2 11 reaction coefficient y OPF8 1 12 reference A16 The symbols are usually the chemical symbols of the involved species e g C for carbon The present species are recognised automatically Molecules consisting of more than one atom of the same chemical element e g Ha are also possible H2 A special case is the representative metal M which is a catalytic element only i e it must appear as reactant and product The special symbol PHOTON represents a photon as reaction product Currently no photon can be used as react
221. tion 4 2 The dimension keyword gives the number of columns and rows in the form d 1 columns l rows The Holweger M ller 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 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 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_ eff 5780 0 table atmosphere 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 amp 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 1og10 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
222. tion of a certain table format see the example in section 4 2 The latest extension comes within the modules uio_var_module f90 and 4 5 Fortran90 59 uio_varfile_module f90 The module uio_var_module f90 contains a type definition for a variable uio flexible 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 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 label enddataset A typical case for the use of
223. tities density arrays o 1 handling of additional density arrays is activated To actually include dust formation in a simulation it is necessary to 1 set the switch Drhd_box_quc01 1 during compilation this is done by the configure script if the environment variable F90_DUST is set to 1 see the description of the variable in Sect 2 put arrays specifying the initial conditions of the additional density into the start model as real quc001 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 fields 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 13 5 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 Input output UIO e uio_switch_system_101 in uio_m
224. tly the minimum time step with e g real dtime_min f E15 8 b 4 n Minimum time step u s amp c0 dtime_min 0 0 gt no restriction Tg 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 3 b 4 n Maximum time step uss amp c0 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 prevent 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 c0 dtime_min_stop 0 0 gt no restriction amp ci dtime lt dtime_min_stop gt program stop 1
225. tmax 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 us1 amp cO range C_radCourant lt C_radCourantmax typically 2 0 Bic This value will typically be somewhat larger than real c_radcourant 5 4 Parameter File rhd par 121 e 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 c0 ramge 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 e real c_radthintimefac In the LHDrad module only the radiative time step restriction due to energy changes can be relaxed further in the optically t
226. u 1 0 5 The diffusion coefficient of the additional energy diffusion is given by ng c_resepsilon j Av p analog to the magnetic diffusivity c_resB Values lt 0 disactivate this feature e real beta_inv This parameter is used for the dual energy method It determines which cells are updated with the thermal energy equation Example real beta_inv f E15 8 b 4 amp n 1 beta dual energy parameter u 1 1 0 The criterion is as follows if 8 lt 1 beta_inv the equation for the thermal energy is used if 8 gt 1 beta_inv the equation for the total energy is used b is the plasma i e the ratio of the gas pressure to the magnetic pressure If beta_inv is set to zero the thermal energy equation is used for all cells A reasonable value may be 100 0 To deactivate this feature set beta_inv to a negative value If not specified this parameter is set to 1 0 This parameter works only with hdscheme HLLMHD When va_max gt 0 then a reasonable value is given by beta_inv S UAmax2 Cs2 where cs is the speed of sound in the region where 8 lt 1 beta_inv e real va_max This parameter limits the Alfv n speed to va_max by an arbitrary reduction of the Lorentz force Example real va_max f E15 8 b 4 amp n maximum Alfven speed u cm s amp 1 0 This parameter is only recognized in conjunction with hdscheme HLLMHD va_max 5 0E 06 might be a reasonable value for some specific applications to the solar photosphere If
227. 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 Sun0S 5 5 1 Last change 27 November 1996 1 4 6 3 Transformation of Files uiocat The shell script uiocat calls the Fortran program uiocat f90 The man page UIOCAT 1V Misc Reference Manual Pages UIOCAT 1V NAME uiocat concatenate file s in uio form SYNOPSIS uiocat c conversion format h 1 copylist o outputfilename filename DESCRIPTION The routine uiocat reads each filename file in uio form in sequence 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 G Conversion type native ieee_4 machine dependent its specification is only relevant if an output file is specified with the o option and output 4 7 IDL UIO Routines 63 format unformatted f Output format formatted or unformatted Its specification is only relevant if an output file is specified with the o option H Help print usage of uiocat 1 List of entries to be copied E g uiocat 1 real rho ulocat 1 real rho integer i uiocat 1 label real rho integer i uiocat 1 label real rho i Here copylist is a list separated by Each item co
228. ult No dust module requested assume default No MHD module requested assume default No TWEAK module requested assume default No explicit machine requested assume default List of control environment variables F90_COMPILER F90_PREFLAGS F90_POSTFLAGS F9O_PARALLEL scalar F90_DEBUG 0 F90_LHDRAD 0 F90_PARALLEL scalar F90_DEBUG 0 F90_LHDRAD 0 F90_MSRAD 0 F90_SHORTRAD 1 F90_CHEM 0 F90_HION O F90_DUST 0 F90_MHD 0 F90_TWEAK 0 F9O_MACHINE 1ocal 20 3 PROGRAM FILES INSTALLATION COMPILATION F90_MSRAD F90_SHORTRAD F90_CHEM F90_HION F90_DUST F90_MHD F90_TWEAK F90_MACHINE local gt MACHINE i686 MACMODEL Intel Pentium F90_BASEPATH home bf for Il Go OOO Or Oo Linux system with i686 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 osu cdi aa cca aaa nee 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 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 5 with env grep F90_ Obs at the beginning there might be no
229. ve a routine XXX_switchinfo that prints the values of the compiler switches used during the compilation of that particular module The output can look e g like Compiler switches rhd hyd module corres as IDF 0 130 5 CONTROL AND DATA FILES rhd_hyd_gravcorr_p01 5 rhd_hyd_entropyfix_p01 1 rhd_hyd_upwind_p01 0 rhd_hyd_roeid_101 0 rhd_roeid_step_101 0 rhd_roeid_slope_101 0 rhd_roeid_flux_101 undefined rhd_bound_t01 defined rhd_roeid_flux_t01 defined rhd_roeid_step_t01 defined See Sect 3 6 for more information about the meaning of the values The reading of the parameter file starts with ACTION Read parameter file lt lt lt lt lt lt lt lt After a parameter is read its value is printed see Sect 5 4 The line ACTION Load EOS data lt lt lt lt lt lt lt lt indicates the start of the reading of the equation of state data It is followed by some information about the EOS table in use Similarly the line ACTION Load opacity tables lt lt lt lt lt lt lt lt indicates the start of the reading of the opacity data The information that follows is taken directly from the header of the opacity table Currently the last file to be read is the start model which is announced by ACTION Read start model lt lt lt lt lt lt lt lt and followed by some information about the start model e g the number of grid points and a new section showing the quantities actually read e g Propert
230. ve flux from entropy and pressure o Entropy3M Compute entropy wave flux from entropy pressure and density In fact an cases Normal and Entropy1 are interpolated according to the Mach number o Entropy3Ms Compute entropy wave flux from entropy pressure and density In fact an cases Normal and Entropy1 are interpolated according to the Mach number and entropy fluctuations o Entropy3gMps Compute entropy wave flux from entropy pressure and density In fact an cases Normal and Entropy1 are interpolated according to the Mach number and fluctuations in pressure directly and after subtracting the hydrostatic pressure correction and entropy This case is recommended 5 4 Parameter File rhd par 93 The Normal computation with the standard Roe procedure is optimized for shocks and works also for small fluctuations in density and pressure However in the case of a nearly adiabatic stratification the density and pressure fluctuations between adjacent depth points induce some spurious fluxes These are avoided by reconstructing the entropy directly Entropy1 However that does not work well for shocks Therefore an interpolation between the standard reconstruction based on pressure and density and another one based on entropy is recommended Entropy3gMps This parameter is not recognized by the MHD module e character hdenthalpyavgmode This parameter controls the type of averaging used to get from the cell centered enthalphy flux the
231. w this value A value of 0 0 default or below deactivates this feature e real c_coredrag To damp the flow in the core of models with central potential a drag force restricted to the inner part of the model r lt r0_grav can be applied It is controlled e g with real c_coredrag f E15 3 b 4 n Core drag force parameter u 1 1 0 A value of 0 0 default or below deactivates this feature The following parameters are specific to MHD simulations For MHD calculations they must be set additional to the hydrodynamic boundary parameters e character side_bound_mag_x1 and character side_bound_mag_x2 The boundary condition at the sides perpendicular to the x1 direction and perpendicular to the x2 direction respectively They are given by e g character side_bound_mag_x1 f A80 b 80 n side boundary conditions magnetic x1 fixed character side_bound_mag_x2 f A80 b 80 n side boundary conditions magnetic x2 periodic Possible values are o constant constant extrapolation of all magnetic field components into the ghost cells o periodic periodic continuation of all magnetic field components into the ghost cells o fixed the component normal to the boundary is kept fixed at its inital value Con stant extrapolation applies for the transversal components o vertical constant extrapolation for the vertical component The transversal cell centered field is mirrored with the opposite sign That should result in transversal
232. which is optimized for a specific architecture Tell the compiler if and what to inline Improve the general performance 3 7 Optimization Compiler Switches 37 3 7 1 General OpenMP settings To activate OpenMP you have to set the corresponding environment variable see 3 5 before calling the configure script like export F90_PARALLEL openmp configure make This will insert the corresponding compiler switch e g openmp omp mp confer the following sections into the compiler calls in the makefile see Sect 3 5 The calls to the timing routines that would be executed in parallel are removed by not setting the appropriate compiler macros see Sect 3 6 In addition the switch rhd_shortrad_dir_102 see 3 6 might be set according to experience about performance enhancements The user has to find optimum values for the parameters n_hydcellsperchunk for the Roe solver module see Sect 5 4 7 and n_viscellsperchunk for the tensor viscosity module see Sect to optimize the size of the chunk given to one thread per time For several modules the environment variable OMP_SCHEDULE can be set before running CO5BOLD to control its OpenMP scheduling behavior Important parallel loops in the SHORT rad module have a SCHEDULE RUNTIME modifier that allows this external control The old default is achieved by not defining the variable or by setting export OMP_SCHEDULE STATIC 1 On some machines e g Intel Xeon with Linux
233. witch Drhd_r03 1 has to be set during compilation see Sect 3 6 5 4 Parameter File rhd par 111 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 I4 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 I4 b 4 amp n Number of radiation transport iterations c0 10 8 For a simulation of a solar type star with comparatively long radiative time scales it will typically be set to 1 For stars 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 o
234. 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 Al 0 Allowed values are o gt 0 Set the initial time step of the simulation to this value and override value from start model 5 4 Parameter File rhd par 117 o lt 0 default Take the initial time step count from start model e real cputime Because of the long simulation time usually COS5BOLD will run in some sort of batch mode which might impose limits on the execution time per run On a CRAY the CPU time that is left can be accessed with a special subroutine in call tremain in timing_module F90 On other machines it is possible to specify the allowed total time for the job e g with real cputime f E15 8 b 4 n CPU time u s 1000000 0 During the run of CO5BOLD the leftover CPU time is computed by subtracting the us
235. y 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 c_visexpansion c_vislinear c_visp2pcoeff 0 0 skips the tensor viscosity step entirely e real c_visartificial A standard artificial viscosity can be activated e g with 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 Larger values 1 2 in the example above are only necessary for some nasty under resolved supergiant models e real c_visexpansion An additional viscosity can be activated e g with real c_visexpansion f E15 8 b 4 amp n Expansion viscosity tensor parameter u 1 1 2 While the standard artificial viscosity acts on compressed regions this viscosity acts in expansion areas Ususally it is not activated c_visexpansion 0 0 However it might be usefu
236. y of machine Many compilers support a transparent conversion between number representations during reading and writing This is not a Fortran standard though and has to be activated in different ways 3 6 Compiler Macros 31 o 0 No conversion default Oo 1 Use the convert keyword in the open statement Intel and gfortran compilers on Linux machines standard compiler on Dec Alphas o 2 Use asnunit Cray X MP style o 3 Use asnunit Cray TS style Hydrodynamics Roe solver e rhd_hyd_gravcorr_po0l1 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 o 0 No pressure correction terms in Roe solver o 1 Simple correction with rhomean no new average pressure o 2 Simple correction with rhomean new average pressure o 3 Correctio

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