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University of Hamburg Planet Simulator User's Guide Version 16.0

1. a a eee ee Ludo A TIE heh ee 8 em Bou oie d 122 Vig S hs Ae Bee oe MN NEM Eee Sa E s r eo Sp ha OD rrr 4 CONTENTS 45 5 1 _ 45 45 5 8__ 46 Ud HTYPE 2 a Eu GE SORE oe RA E Wes 53d peces 46 b MVIYPbB u 25424254 le Bee A Dee Be a we Wenn 46 Sy ee ee 46 TTC 4T be ee M 47 T 4T 5 10 SERVICE format 48 249 5 Sod d p 48 za go wb soe ve Rem hom XOU ovo Ru 48 519 MARS Lue amp b brace Peur OE US e pL het est we S dd wet 48 DA MULGI ommo weed edu X Re 48 hoe al 6 oe ccr 49 5 16 Troubleshooting 444444624464 8ob8 Sew OR OE RO Gos 49 51 6I Gra ds 2222455 e x de rad UN re Xx UE CK Ge ob Ae ie 51 Denm 5 EM EAM 54 57
2. EXCHANGE PUMA MAIN LOOP puma f90 LANDSTEP 7 landmod f90 SURFSTEP surfmod f90 SEASTEP seamod f90 CPLEXCHANGE ICE intermod atm f90 ICESTEP icemod f90 CPLEXCHANGE OCEAN CPLEXCHANGE ATMOS iintermod ice f90 intermod ice f90 OCEANSTEP oceanmod f90 Figure 2 2 Subroutine flow when no external coupler is used 2 14 SEA ICE AND OCEAN MODULES 2 15 icemod f90 General The module icemod f90 contains subroutines to compute sea ice cover and thickness interface to the main PLASIM module is given by the subroutine icestep which is called by cplexchange defined in intermod atm f90 which is called by seastep defined in seamod f90 Input Output icemod f90 requires the file ice flxcor if NFLXCORR is set to a negative value If NOUTPUT is set to 1 the output files fort 75 containing global fields of ice model data and the file fort 76 containing diagnostic ice data are produced for details see the reference manual Both output files are in service format module is controlled by the namelist icepar in the file ice namelist Parameter Type Purpose default NDIAG INTEGER Diagnostic output every NDIAG 160 time steps NOUT INTEGER data output every NOUT 82 time steps NOUTPUT INTEGER Icemodel output 0 1 1 NFLXCORR INTEGER Time constant for restoring gt
3. ice Input Output oceanmod f90 requires the file ocean flxcor if NFLX CORRSST or NFLXCORRMLD is set to a negative value If NOUTPUT is set to 1 the output file fort 31 containing global fields of ocean model data in service format is produced for details see the ice modul section of the ref erence guide The module is controlled by the namelist oceanpar in the file ocean namelist Parameter Type Purpose default NDIAG INTEGER Diagnostic output every NDIAG 480 time steps NOUT INTEGER Model data output every NOUT 32 time steps NOUTPUT INTEGER Oceanmodel output 1 0 no 1 yes NFLXCORRMLD INTEGER Time constant for restoring 60d mixed layer depth gt 0 no flux correction 0 use fluxcorrec tion from file 0 NFLXCORRSST INTEGER Time constant for restoring sea 60d surface temperature gt 0 no flux correction 0 use fluxcor rection from file 0 Structure oceanmod f90 uses the module oceanmod which is not dependent on the module pumamod Subroutine oceanini reads the namelist and when required the flux corrections from the file ocean flxcor Subroutine oceanstep calls mixocean which calculates mixed layer depth and temperature If an ice cover is present mixed layer depth is set to the climatological value and the sea surface temperature is set to the freezing temperature For details of the mixed layer model see the Planet Simulator Reference Manual
4. kg m2 University of Hamburg Planet Simulator 15 m 20 5 m ECUECGUE RE 3E 0 ET 990 995 m1000 m1005 m1010 E1015 m1020 m1025 _ University of Hamburg Planet Simulator Earth Fraedrich Kirk amp Lunkei fRpr i X Zonal Mind m s SSOP coe da 02 360 08 B Spherical Harmonics Ps T iture C 6501 0 1367 0 XIPrecipitable Mater kg m2 DAWN 0 000 IX Zonal Wind m s X Meridional Wind m s IXPs Hovmoeller 128 steps X Timeseries 128 steps Tables Meridional Wind m s Latitude 59N 5 Temperature C 30 m 20m 10m 0 m 10 5 7 Ps Hovmoeller 128 steps Latitude 59N SEE Zonal wind m s Level 4 aj Timeseries 128 steps 27 574 m s 10 9 20 25 m 30 EE SSS eC Eg Le 2 OTET E 2 edi Pum EP ge B 5 88 9093 SA Bg e 7 Le Xun cin 22 55 9 OSS ig Suo User s Guide Version 16 0 Frank Lunkeit Simon Blessing Klaus Fraedrich Heiko Jansen Edilbert Kirk Ute Luksch Frank Sielmann The Planet Simulator User s Guide is a publication of the Theoretical Meteorology at the Meteorological Institute of the University of Hamburg Address Prof Dr Klaus Fraedrich Meteorological Institute University of Hamburg Bundesstrasse 55 D 20146 Hamburg Contact Klaus FraedrichOzmaw de Frank Lunkeit zmaw de E KirkOgmx
5. ature NVDIFF Integer Switch for vertical diffusion 0 off 1 1 on VDIFF LAMM Real Tuning parameter for vertical diffusion 160 VDIFF_B Real Tuning parameter for vertical diffusion 5 VDIFF_C Real Tuning parameter for vertical diffusion 5 VDIFF D Real Tuning parameter for vertical diffusion 5 ZUMIN D Real Minimum surface wind speed m s 1 Structure Internally fluxmod f90 uses the FORTRAN 90 module fluxmod which uses the global common module pumamod from pumamod f90 Subroutine fluxini reads the namelist and if the parallel version is used distributes the namelist pa rameters to the different processes Subroutine fluxstep calls the subroutine to compute the surface fluxes and calls the subroutine vdiff to do the vertical diffusion Subroutine fluxstop is a dummy subroutine since there is nothing to do to finalize the computations in fluxmod f90 The computation of the surface fluxes surflx is spitted into several parts After initializing the stability dependent transfer co efficients the subroutines mkstress mkshfl and mkevap do the computations which are related to the surface wind stress the surface sensible heat flux and the surface evaporation respectively 2 2 miscmod f90 General The module miscmod f90 contains miscellaneous subroutines which do not fit well to other modules interface to the main module plasim f90 is given by the subroutines miscini miscstep and miscstop which
6. Chapter 3 Parallel Program Execution 3 1 Concept The Planet Simulator is coded for parallel execution on computers with multiple CPU s or networked machines The implementation uses MPI Message Passage Interface that is available for nearly every operating system http www mcs anl gov mpi In order to avoid maintaining two sets of source code for the parallel and the single CPU version all calls to the MPI routines are encapsulated into a module Users that want to compile and execute the parallel version use the module mpimod f90 and the commands mpif90 for compiling and mpirun for running If MPI is not implemented or the single CPU version is sufficient mpimod stub f90 is used instead of mpimod f90 Also remove or comment the line use mpi and set the number of processors to 1 parameter NPRO 1 3 2 Parallelization in Gridpoint Domain The data arrays in gridpoint domain are either three dimensional e g gt NLON NLEV referring to an array organized after longitudes latitudes and levels or two dimensional e g gp NLON NLAT The code is organized such that there are no dependencies in latitudinal direction while in gridpoint domain Such dependencies are resolved during the Legendre Transformations So the the partitioning of the data is done in latitudes The program can use as many CPU s as latitudes with the extreme of every CPU doing the computations for a single latitude There is the restriction how
7. parameter in Magnus Teten formula ra4 35 86 real parameter in Magnus Teten formula solar day 86400 0 real length of solar day siderial day 86164 0 real length of siderial day ww 7 29 5 real 2m siderialday yplanet Earth char name of planet 1 3 Namelist MISCPAR Name Def Type Description nfixer 1 int 1 correct negative moisture nudge 0 int 1 temperature relaxation in the uppermost level tnudge 10 0 Time scale d of the temperature relaxation 67 68 APPENDIX C NAMELISTS 1 4 Namelist FLUXPAR Name Def Type Description nevap 1 int 1 turn on surface evaporation nshfl 1 int 1 turn on surface sensible heat flux nstress 1 int 1 turn on surface wind stress nvdiff 1 int 1 turn on vertical diffusion vdiff lamm 160 0 real tuning parameter for vert diff vdiff b 5 0 real tuning parameter for vert diff vdiff c 5 0 real tuning parameter for vert diff vdiff d 5 0 real tuning parameter for vert diff zumin 1 0 real minimum surface wind speed m s C 1 5 Namelist RADPAR Name Def Type Description acl2 3 0 05 0 1 0 2 real cloud absorptivities spectral range 2 acllwr 0 1 real mass absorption coefficient for clouds lwr clgray 1 0 real cloud grayness co2 360 0 real co2 concentration ppmv dawn 0 0 real zenith angle threshhold for night 55010 1365 0 real sola
8. 1 or climatology 0 nperpetual_ocean 0 int perpetual climate conditions day nprhor 0 int gridpoint for debug printout nprint 0 int switch for debug printout taunc 0 0 real time scale for newtonian cooling vdiffk 1 0 4 real vertikal diffusion coeff m 2 s C 5 File ice namelist 5 1 Namelist ICEPAR Name Def Type Description newsurf 0 int 1 read surface data after restart nfluko 0 int switch for flux correction nice 1 int sea ice model 1 or climatology 0 nout 32 int model data output every nout time steps nperpetual_ice 0 int perpetual climate conditions day nprhor 0 int gridpoint for debug printout nprint 0 int switch for debug printout nsnow 1 int allow snow on ice yes no 1 0 ntskin 1 int compute skin temperature 0 clim ncpl_ice_ocean 1 int ice ocean coupling time steps taunc 0 0 real time scale for newtonian cooling xmind 0 1 real minimal ice thickness m NAMELISTS
9. ILL SED ah eee A OUR Ruf ko Web owe dod die ed 57 7 1 1 Basie switches for column 57 7 1 2 Boundary Conditions and 57 7 2 Graphical User Interface GUD 58 59 63 65 C 1 File puma namelist 2 a eae opo 55 4 cho ge Hu ke Row Roe e dy 66 111 Namelst INP s ess 66 C 1 2 Namelist PLANET aoaaa aaa 67 C 1 3 Namelist MISCPAR 67 Cla ELUXPAH 24 8 4 3 4 oe EE RE OX E xs 68 C 1 5 Namelist 68 C 1 6 Namelist RAINPAR 68 C 1 Namelist SURFPAR 69 C 2 Fieland namelst ll s 69 2 11 Namelist 69 C 3 File sea namelist 0 70 3 1 Namelist 70 4 File ocean 70 C 4 1 Namelist 70 C 5 File namelist 2 2l ll Rs 70 C 5 1 Namelist ICEPAR 70 Chapter 1 Installation The whole package containing the models Planet Simulator and PUMA along with MoSt the Model Starter comes in a single file usually named Most n tgz with n specifying a versio
10. The parameters that are exchanged are listed in Table 2 1 sea ice and ocean model use a time step of one day Thus atmospheric coupling to the sea ice model is performed every 32 time steps while the sea ice and ocean model are coupled every time step The coupling scheme is shown in Fig 2 1 Fig 2 2 shows how the subroutines are placed when no external coupler is used Parameter Atmosphere Ice Ice Ocean Ice cover Ice thickness Snow thickness Surface temperature Deep sea temperature Mixed layer depth Net precipitation runoff gt Salinity Melt and freeze volume Heat fluxes gt d Heat fluxes dT gt Radiation Wind stress gt Ta To Tab Table 2 1 Parameters to be exchanged between models Arrows denote the direction in which the parameter is passed e g the atmosphere receives ice cover information from the ice model 2 14 SEA ICE AND OCEAN MODULES 31 32 Timesteps Timesteps surface temperature net precipitation ice cover runoff snow thickness total heatflux ice thickness sensible heatflux radiation wind stress sea surface temperature deep sea temperature mixed layer depth net precipitation salinity runoff total heatflux wind stress freeze and melt volume Figure 2 1 Schematic illustration of the model coupling 32 CHAPTER 2 MODULES FLOW DIAGRAM ATMOSPHERE ICE OCEAN
11. 0 3604 no flux correction 0 use flux correction from file 0 Structure icemod f90 uses the module icemod which is not dependent on the module pumamod Subroutine 2ceini reads the namelist and when re quired the flux correction from the file flxcor Subroutine cestep calls cplerchange_atmos defined in intermod ice to get the atmospheric forcing fields If the sea namelist parameter NICE is set to 1 the subroutine subice is called which calculates ice cover and thickness Otherwise climatologi cal data interpolated to the current time step by iceget are used If an ice cover is present the surface temperature is calculated in skintemp Otherwise the surface temperature is set to the sea surface temperature calculated by the ocean model Every NCPL ICE OCEAN defined in sea namelist time steps the external subroutine cplerchange_ocean defined in intermod_ice is called to pass the atmospheric forcing to and retrieve oceanic data from the ocean module oceanmod f90 The oceanic data is used for ice calculations in the next time step 33 34 CHAPTER 2 MODULES 2 16 oceanmod f90 General The module oceanmod f90 contains a mixed layer ocean model i e subroutines to compute sea surface temperature and mixed layer depth The interface to the main PLASIM module is via the module icemod f90 given by the subroutine oceanstep which is called by cplexchange ocean defined in
12. 0 indicating the December of the preceding year an mm 13 for the January of the following year may be included for interpolation during transient simulations If there are some fields not present in the surface txt default values will be used which can be set in the namelist The use of some fields depend on the setting of some namelist parameters The restart file plasim restart is an unformatted file which contains all variables needed to continue the run landmod f90 is controlled by the namelist landpar given in the namelist file land namelist Parameter Type Purpose Default NLANDT Integer Switch for surface tempera 1 ture 1 computed 0 cli matology NLANDW Integer Switch for soil wetness 1 1 computed 0 clima tology NBIOME Integer Switch for biome model 0 SIMBA 1 on 0 off ALBLAND Real Background albedo 0 2 DZOLAND Real Roughnesslength m 2 0 DRHSLAND Real Wetness factor 0 25 ALBSMIN Real Minimum albedo for snow 0 4 ALBSMAX Real Maximum albedo for snow 0 8 Parameter Type Purpose Default NWATCINI Integer Switch to initialize soil 0 water content manually 1 on 0 off DWATCINI Real Soil water content m for 0 0 manual initialization ALBGMIN Real Minimum albedo for 0 6 glaciers ALBGMAX Real Maximum albedo for 0 8 glaciers WSMAX Real Maximum field capacity of 0 5 soil water bucket size m DRHSFULL Real Threshold above which wet 0 4 ness factor is 1 DZGLAC Real Threshold of o
13. Qm snow melt heat flux Wm Qo oceanic heat flux Wm ds surface specific humidity keke s t saturation specific humidity keke R refexivity albedo Rs surface albedo Ra gas constant for dry air 287 05 surface long wave radiation W m Rs surface short wave radiation Wm R gas constant for water vapor 461 51 JE UR Ro zeroth moment of the temperature distribution Km first moment of the temperature distribution K m Ri Richardson number Sw salinity of sea water 34 7 psu 61 Symbol Definition Value Unit t time S t scaled time step T transmissivity temperature K y temperature anomaly T To Ta deep ocean temperature at 400m K sea ice surface temperature K IG freezing temperature 271 25 K T surface temperature K Ta sea surface temperature K melting point 273 16 K Toss mixed layer temperature K T onis climatological mixed layer temperature K Tref asymptotic reference temperature K To oceanic temperature profile K To reference temperature profile 250 0 K U scaled zonal wind u cos o u zonal wind ms Ux friction velocity ms V scaled meridional wind v cosy U meridional wind ms 0 horizontal wind vector msg Wir cloud liquid water path gm Wow mass of snow water kg W oi soil water m z height m Zo roughness length m At time increment S Az height increment m thermal expansion coefficient p 2 41 107 K t p back scatterin
14. de Contents 1 Installation ee Aus os a eG eee dons MEAG EA eee Reed aoe be oS ae eee be pee ES 2 Modules 2 1 fluxmod f90 e eaei araoa e Ona Rs 2 2 misemod f90 aaa 2 3 surfmod f90 2 4 90 991 00 2 5 landmod f90 2 0 0000 26 Neorg TOO sc AEE OES SOROS Be KS 2 7 xupimod 90 mpimod stub f90 1 seek eee Sb eee YD eared een 28 OUtmMOdAIO uu uox 73 Be ee a Raw eae Poe Ae Oe de ZH les 2 nus oh eA e g ee we Roi ACE DEUS BE 2 10 plasimumid I9U oe de ele ae Bo xoxo Eo bom om ob OES mom 45 6 E dox 6 90 eR tr PUN UE a 2 12 00 2 13 01 2 14 Sea and ocean modules 2 a a a a aa 2 15 icemod 90 muse ex mee ox ese ox mox we X X ge ho e d 2 16 1090 3 1 Concept 5525555 e Rock teh Kok UR SESE oH KS et Di T CD TIME Wow iios dd deo dd dinh SEES code se ss s a ma mia Aa e aa a Boa a Graphical user interface
15. map you have the following choices If e your data is raw PUMA output you need to process it with the pumaburner postprocessor see section 5 in order to transform it to either NETCDF option or namelist parameter NETCDF 1 or GRIB option g or namelist parameter GRIB 1 and proceed from there e your data is in SERVICE format you need to convert it to either GRIB for instance with the PINGOs 6 2 VIS5D 55 grb copy2 data srv data with grib metainfo grb output grb or NETCDF using the program puma2cdf which is available with the PUMA postprocessing tools Despite of its name this program cannot process raw PUMA output but takes SERVICE format as input It can as well be called as srv2cdf which changes its behaviour oddities of model output such as the existence of February 30 are then no longer removed Once the format is changed proceed from there e your data is in NETCDF format it can easily transformed to Vis5D s native format by means of the program cdf2v2d which is available with the PUMA postprocessing tools e your data is in GRIB format you can find a transformation tool named Grib2V5d at lt http grib2v5d sourceforge net gt which offers various practical features Once the conversion to Vis5D s native format is achieved please follow the instructions from the Vis5D documentation or if Vis5D is already installed on your system try finding your own way by typing visbd my data v5d 56 CHAPTE
16. of surface pressure GU Three dimensional grid of zonal wind GV Three dimensional grid of meridional wind GP Grid of surface pressure DQVI Vertically integrated humidity GUCOL sounding of eastward wind at a grid point GVCOL sounding of northward wind a grid point GTCOL sounding of temperature at a grid point DQCOL sounding of humidity at a grid point DQLCOL sounding of liquid water at a grid point DCCCOL sounding of cloud cover at a grid point SCALAR Selected scalars for timeseries and tables window number 0 8 width height left top 4 2 GUI CONFIGURATION 43 4 2 2 Plot Name Description ISOHOR Isolines and colouring of horizontal grids ISOCS Isolines and colouring of cross sections ISOHOV Colouring of Hovmoeller diagram ISOTS Timeseries ISOTAB Tables ISOSH Coloured amplitudes ISOLON Isolines and colouring of longitude height section ISOCOL vertical Hovmoeller diagram for soundings 4 2 3 Palette Name Range Description AUTO automatic rainbow colours U 10 50 rainbow colours V 10 10 rainbow colours 50 50 blue red P 985 1025 blue red Q 0 60 rainbow colours DCC 0 100 rainbow colours MARST 90 0 blue red AMPLI 0 12 blue green red VEG 0 100 shades of green 4 2 4 Title title item may contain any text but keep it short the length of the window s title bar is limited The words Latitude and Level
17. parallel program execution original files in the src directory are not changed by Most program modules are then compiled and linked using the make command in bld most plasim build also issued by Most Most provides a makefile named make plasim for building the executable For modules that exist in more than one version the selection of the module to use is done by environment variables that are set automatically by MoSt but may be changed manually by the user Look into the make plasim for further information The resolution and CPU parameters are coded into the filename of the executable in order to have different names for different versions E g the executable most plasim t21 110 p2 x is an executable compiled for a horizontal resolution of T21 a vertical resolution of 10 levels and 2 CPU s The executable is copied to the models bin directory after building Each time Most is used to setup a new experiment it checks the bin directory for a matching executable If it s there it s used without rebuilding otherwise a new executable with the selected parameters is created Rebuilding may be forced by using the cleanplasim command in the Most directory The build directory is not cleared after usage user may want to modify the makefile or the build script for his own purposes and start the building directly by executing most plasim build For permanent user modifications the contents of the bld directories
18. sea level pressure c151 and the albedo c175 refer to appendix B for a list of codes The GrADS program is started by typing grads in a terminal window Then data is visualised either by typing commands line by line or preferably by using scripts The following script called tglob gs displays the monthly mean surface temperature tglob gs function pass m reinit open puma m enable print print mf set t m c set gxout shaded d c139 273 16 cbar gs set gxout contour d c139 273 16 draw title Surface Temperature deg C month m print disable print lgxps i print mf o tglob m ps variable m at the beginning of the script defines the month which should be displayed It is passed from the terminal with the script call Note that in this line no quotation marks are present since only GrADS specific commands are framed by quotation marks Script commands like variable definitions if clauses etc are used without quotation marks The script is executed by typing its name without the ending and the number of the month to be shown For example tglob 7 displays the monthly mean surface temperature in July The resulting output file is called tglob7 ps following script thh displays the time dependent surface temperature of Hamburg Here two variables are passed to GrADS the first and last day to plot note that here the file puma gra is opened which conta
19. 0 General The module legmod f90 contains all subroutines necessary to perform the Legendre transformation and its inverse The interface to the main module plasim f90 is given by the subroutines legini inigau fc2sp fc9sp and sp2gp which are called in plasim f90 from the subroutines prolog and gridpoint Input Output legmod f90 does not use any extra input file or output file No namelist input is required The following subroutines are included in legmod f90 Subroutine Purpose inigau compute Gaussian abscissas and weights legini compute Legendre polynomials fs2sp Fourier to Spectral transformation sp2fc Spectral to Fourier transformation sp fc Simultaneous transformation of T Div and Vort dirlega Compute and transform adiabatic tendencies dirlegd Compute and transform diabatic tendencies invlega Spectral to Fourier adiabatic part invlegd Spectral to Fourier diabatic part 2 7 mpimod f90 mpimod stub f90 General The module mpimod f90 contains interface subroutines to the MPI Mes sage Passing Interface needed for massive parallel computing Several MPI rou tines are called from the module The interface to other modules are given by nu merous subroutines which names starts with mp Subroutines from mpimod f90 are called in sveral other modules There are no direct calls to MPI other than in mpi mod f90 This encapsulation makes it possible to use mpimod_stub f90 for single CPU runs without c
20. 0 off 1 on NO3 Integer Switch for ozone 0 off 1 1 idealized distribution 2 externally presrcibed CO2 Real CO concentration ppmv 360 0 GSOLO Real Solar constant W m 1367 0 IYRBP Integer Year PB reference is 1950 50 to calculate orbit from NSWR Integer Switch for short wave radi 1 ation 0 off 1 NLWR Integer Switch for long wave radia 1 tion 0 off 1 on NSOL Integer Switch for incoming solar 1 radiation 0 off 1 on NSWRCL Integer Switch for computed short 1 wave cloud properties 0 off 1 on NRSCAT Integer Switch for Rayleigh scatter 1 ing 0 off 1 on RCL1 3 Real Array Prescribed cloud albedos 0 15 0 30 0 60 for high middle and low level clouds spectral range 1 25 26 CHAPTER 2 MODULES Parameter Type Purpose Default RCL2 3 Real Array Prescribed cloud albedos 0 15 0 30 0 60 frac for high middle and low level clouds spectral range 2 ACL2 3 Real Array Prescribed cloud absorptiv 0 05 0 10 0 20 ities frac for high middle and low level clouds spec tral range 2 CLGRAY Real Prescribed grayness of 1 0 clouds 1 0 computed TPOFMT Real Tuning for point of mean 0 15 transmission ACLLWR Real Mass absorption coefficient 0 1 for clouds long wave TSWRI Real Tuning of cloud albedo 0 035 spectral range 1 TSWR2 Real Tuning of cloud back scat 0 04 tering spectral range 2 TSWR3 Real Tun
21. 1000 1005 1010 1015 1020 endif set ccols 1 set grads off t 2 54 CHAPTER 6 GRAPHICS d c151 100 title yr ny set vpage 0 5 5 0 4 25 set gxout contour if setlevs 1 set clevs 990 995 1000 1005 1010 1015 1020 endif set ccols 1 set grads off t 3 d 151 100 title yr ny set vpage 5 5 11 0 4 25 set gxout contour if setlevs 1 set clevs 990 995 1000 1005 1010 1015 1020 endif set ccols 1 set grads off t 4 c151 100 draw title yr ny SON print disable print lgxps c i print mf o sm ps 6 2 Vis5D Vis5D is a system for interactive visualization of large 5 D gridded data sets such as those produced by numerical weather models One can make isosurfaces contour line slices colored slices volume renderings etc of data a 3 D grid then rotate and animate the images in real time There s also a feature for wind trajectory tracing a way to make text annotations for publications support for interactive data analysis etc from the Vis5D home page http www ssec wisc edu billh vis5d html This powerful visualisation tool together with its documentation is available through the above home page Vis5D uses its own data format which makes it necessary to transform your data Depending on their format and the flowchart on http puma dkrz de puma download
22. 4 1 MoSt is the fastest way to get the model running It gives access to the most important parameters of the model preset to the most frequently used values The model can be started with a mouse click on the button labelled Save amp Run either with the standard paramater setting or after editing some of the parameters in the MoSt window Some parameters like horizontal and vertical resolution or the number of processors require the building compile link and load of new executables MoSt achieves this by generating and executing build scripts that perform the necessary code changes and create the required executable Other parameters define startup and boundary conditions or settings for parameterisations They can be edited in MoSt and after a check for correct range and consistency with other parameters are written to the model s namelist file Depending on all settings MoSt generates a runscript for the simulation The user has the choice of leaving MoSt and continue with the simulation under control of a GUI right away or to exit MoSt with the scripts prepared to run The second alternative is useful for users who want to modify the setup beyond the scope of MoSt or want to run the Planet Simulator without GUI There s also a simple graphical editor for topograpy Check the box Orography and then use the mouse to mark rectangular areas in the topography display Enter a value for rising positive or lowering the area and press the
23. 5 2 Usage pumaburn4 options InputFile OutputFile lt namelist gt printout option h print available codes and names option d option g option n option m InputFile OutputFile redirected lt stdin gt Unpack the raw data to full real representation Transform variables from the model s representation to a user selectable format e g grids zonal mean cross sections fourier coefficients Calculate diagnostic variables like vertical velocity geopotential height wind compo nents etc Transfrom variables from levels to user selectable pressure levels Compute monthly means and standard deviations Write selected data either in SERVICE GRIB or NetCDF format for further processing option c namelist printout help this output debug mode verbose output Grib output override namelist option NetCDF output override namelist option Mean 1 output override namelist option Planet Simulator or PUMA data file GRIB SERVICE or NetCDF format file redirected lt stdout gt 45 46 CHAPTER 5 POSTPROCESSOR PUMABURNER 5 3 Namelist The namelist values control the selection coordinate system and output format of the post processed variables Names and values are not case sensitive You can assign values to the following names Name Def Type Description Example HTYPE S char Horizontal type HTYPE G VTYPE S char Vertical type VTYPE P MODLEV 0 int Mod
24. R 6 GRAPHICS Chapter 7 Column Mode and Soundings T 1 Setup The column mode of the the Planet Simulator is an integral part of the full Planet Simulator and not a stand alone model The advantage of this approach is that all options and modules available in the full model are automatically included in the column mode and that no extra maintenance is necessary Technically this is realized by switching off horizontal advection and diffusion which leaves us with an independent column for each grid point The inclusion of additional options for boundary conditions allows for runs with synchronized columns Running the Model at the lowest resolution T1 with 8 synchronized columns is efficient enough to run very fast column integrations Using a standard setup with 10 atmospheric layers and a mixed layer ocean one can simulate more than 33500 years per day on a single processor PC 3 3 GHZ CPU To make full use of the computer power one can setup an ensemble of columns by specifying boundary conditions for every grid point separately 7 1 1 Basic switches for column setup We introduce the macro switch COLUMN in the namelist inp which is part of the namelist puma namelist By setting COLUMN 1 a default column mode is initialized by setting YMODE Column KICK 0 0 and NHORDIF 0 One can customize the column setup by keeping the default value COLUMN 0 and by setting the other switches individually For more details see th
25. Unit 110 1 g mixed layer depth m 129 1 S surface geopotential m s 130 NLEV s temperature K 131 NLEV u velocity m s 132 NLEV v velocity m s 133 NLEV 5 specific humidity kg kg 135 NLEV vertical velocity Pa s 138 NLEV 5 vorticity 1 s 139 1 g surface temperature K 140 1 g soil wetness m 141 1 g snow depth water equi m 142 1 ga large scale precipitation m s 143 1 ga convective precipitation m s 144 1 ga snow fall m s 146 1 surface sensible heat flux W m 147 1 surface latent heat flux W m 148 NLEV c horizontal streamfunktion m s 149 NLEV velocity potential m s 151 1 mean sea level pressure Pa 152 1 5 In surface pressure 153 NLEV g cloud liquid water content kg kg 155 NLEV s divergence 1 8 156 NLEV geopotential height gpm 157 NLEV relative humidity frac 159 1 g u m s 160 1 ga surface runoff m s 63 64 v APPENDIX B PLANET SIMULATOR CODES FOR VARIABLES Code Levels Type Variable Unit 162 NLEV cloud cover frac 164 1 ga total cloud cover frac 169 1 ga surface temperature K 170 1 g deep soil temperature K 172 1 g land sea mask 0 sea 1 land 173 1 g surface roughness m 175 1 g surface albedo frac 176 1 ga surface solar radiation W m 177 1 ga surface thermal radiation W m 178 1 ga top solar radiati
26. W m surface zonal wind stress Pa surface meridional wind stress Pa UEM long wave radiation flux density Wm pow short wave radiation flux density Wm g gravitational acceleration 9 81 m7 his mixed layer depth m Iis climatological mixed layer depth m H effective mixed layer depth T 7 m H reduced center of gravity B m 59 60 APPENDIX A LIST OF CONSTANTS AND SYMBOLS Symbol Definition Value Unit Js vertical turbulent moisture flux kgm s vertical turbulent temperature flux kms Ju vertical turbulent flux of zonal momentum Pa Jy vertical turbulent flux of meridional momentum Pa k von Karman constant 0 4 Kn exchange coefficient for heat Km exchange coefficient for momentum L latent heat Ly latent heat of fusion L L 3 28 10 ln mixing length for heat m lm mixing length for momentum m Ls latent heat of sublimation 2 8345 10 Ly latent heat of vapourization 2 5008 10 Jkg P convective precipitation ms large scale precipitation nig P u associated Legendre function of the first kind pressure Pa ps surface pressure Pa Ds scaled surface pressure 4 specific humidity Q total heat flux through sea ice Wm Q flux correction heat flux through sea ice Wm Qa total atmospheric heat flux Wm Qe conductive heat flux through sea ice Wm Qf heat flux available for freezing sea ice W m 0 heat flux into the soil Wm
27. ag nostic 2 d grid point output 0 off 1 on Number of additional diag nostic 3 d grid point output 0 off 1 on Number of additional diag nostic 2 d spectral output 0 off 1 on Number of additional diag nostic 3 d spectral output 0 off 1 on Default 45 1 21 22 CHAPTER 2 MODULES Parameter NDL NLEV NHDIFF NHORDIF NTIME NPERPETUAL DTNS DTROP DTTRP TGR TDISSD NLEV TDISSZ NLEV TDISST NLEV TDISSQ NLEV PSURF RESTIM NLEV Type Integer Array Integer Integer Integer Integer Real Real Real Real Real Real Array Real Array Real Array Real Array Real Real Array Purpose Switch for diagnostic print out of a level 0 off 1 on Cut off wave number for horizontal diffusion Switch for horizontal diffu sion 0 off 1 on Switch for CPU time diag nostics 0 off 1 on Switch for perpetual simu lations 0 annual cycle gt 0 day of the year Equator to pole tempera ture difference for New tonian cooling usually not used North pole to south pole temperature difference for Newtonian cooling usu ally not used height m for Newtonian cooling usually not used Smoothing of the tropopause K for Newto nian cooling usually not used Surface temperature K for Newtonian cooling usually not used time scale 4 for the ho
28. are called in puma f90 from the subroutines prolog gridpointd and epilog respectively subroutine to eliminate spurious negative humidity and an optional subroutine to relax the upper level temperature towards a prescribed distribution is included in miscmod f90 Input Output miscmod f90 does not use any extra output file If the relaxation is switched on a climatological annual cycle of the prescribed upper level temper ature distribution K is read from the external file surface txt The file format is formatted SERVICE format with 8I10 for the headers and 8E12 6 for the tem perature fields assign the field the header needs to have the header information code 130 level 1 and a date identifier of the form yymmdd or mmdd where mm goes from 1 to 12 January to December or from 0 to 14 including the December of the previous year and the January of the following year Fields which are not needed will be skipped The module is controlled by the namelist miscpar which is part of the namelist file puma namelist Parameter Type Purpose default NFIXER Integer Switch for correction of neg 1 ative moisture 0 off 1 on NUDGE Integer Switch for temperature re 0 laxation in the uppermost level 0 off 1 on TNUDGE Real Time scale d of the tem 10 perature relaxation Structure Internally miscmod f90 uses the FORTRAN 90 module miscmod which uses the global common module pumamod from pumamod f90 Subroutin
29. button labelled Preprocess The preprocessor will be built and executed a new topography will be computed and written to a start file Another editor is the mode editor for spherical harmonics Green modes are enabled red modes are disabled This feature can be used to make runs with only certain modes of spherical harmonics being active MB1 MB2 MB3 refer to the left middle and right mouse button You may toggle individual modes or whole lines and columns Currently this mode editor can only be used for Planet Simulator in the T21 resolution The GUI for running the Planet Simulator screenshot in has two main purposes first one is to display model arrays in suitable representations Current implementations are e Zonal mean cross sections 39 40 CHAPTER 4 GRAPHICAL USER INTERFACE ersity of Hamburg A PUMA Planet Simulator Model Namelist PUMA MPSTEP 45 Planet Simulator Earth NDIAG NPRINT Modules C02 Ocean DAWN Ice GSOLO Parallelism of CPUs Resolution Lon 110 170 Lat 45 5 Latitudes 0 Change gpm Levels pherical Harmonics mode selector Options Debug mode Write Output Run with GUI Orography Annual cycle Diurnal cycle Simulation Start year Years to run MB 1 Toggle mode MB 2 Toggle column MB 3 Toggle li
30. cording to the namelist input nitpm and initsi initialize some parameter for the physics and the semi implicit scheme respectively outini starts the output If a file named plasim restart exists all variables and arrays are read by restart otherwise initfd sets the prognostic variables to their initial values Calls to miscini fluxini radini rainini and surfini start the initialization of the respective external modules i Finally the global mean surface pressure is set according to PSURF the observed value is 1011 hPa Trenberth 1981 while 1013 is the ICAO standard and the orography Subroutine master controls the time stepping First if its not a restart initial NKITS explicit forward timesteps are performed main loop is defined by calling gridpointa for the adiabatic tendencies spectrala to add the adiabatic tendencies gridpointd for the diabatic tendencies which are computed by the external modules spectrald to add the diabatic tendencies and the interface routines to the output module outmod f90 run is finalized by subroutine epilog which writes the restart records and calls the respective interface routines of the external modules 23 24 CHAPTER 2 MODULES 2 10 plasimmod f90 General The file plasimmod f90 contains the module pumamod f90 which de clares all parameters and variables which may be used to share information between plasim f90 and other modules No subroutines or programs are include
31. ctral field give information about setup read spectral array from restart file read gridpoint array from restart file write spectral array to restart file write gridpoint array to restart file compute maximum value of an array compute sum of all array elements 2 8 outmod f90 General The module outmod f90 controls the data output of the model The inter face to the main PUMA module puma f90 is given by the subroutines outini outgp outsp outreset and outaccu which are called in puma f90 from the subroutines prolog and master Input Output outmod f90 writes the output data to the file puma output which is unformatted puma output is designed to be post processed by the program burn see section which converts the model variables to useful output in user friendly format There is no separate namelist for outmod f90 but some parameter of namelist inp of plasim f90 are used to control the format and the output interval Structure Internally outmod f90 uses the global common module pumamod from plasimmod f90 in several subroutines Subroutine outinz does the initialization Sub routines outgp and outsp write the grid point and the spectral fields to the output puma output accumulates some output variables over the output interval outreset resets the accumulated arrays to zero 19 20 CHAPTER 2 MODULES 2 9 plasim f90 General The module plasim f90 is the main mo
32. d Input Output pumamod f90 does not use any extra input file or output file No namelist input is required Structure Internally plasimmod f90 is FORTRAN 90 module named pumam od Names for global parameters scalars and arrays are declared and if possible values are preset 2 11 radmod f90 General The module radmod f90 contains subroutines to compute radiative energy fluxes and the temperature tendencies due to long wave and short wave radiation interface to the main PLASIM module plasim f90 is given by the subroutines radini radstep and radstop which are called in plasim f90 from the subroutines prolog gridpointd and epilog respectively Input Output radmod f90 does not use an extra output file If the Switch for ozone see namelist is set to 2 externally prescribed the climatological cycle of the ozone distribution is read from the external file surface txt which name is given in the namelist The file format is formatted SERVICE format with 8I10 for the header and 8E12 6 for the fields To assign the fields the headers need to have the header information code 200 level going from 1 to NLEV and a date identifier of the form yymmdd or mmdd where mm goes from 01 to 12 January to December radmod f90 is controlled by the namelist radpar which is part of the namelist file puma namelist Parameter Purpose Default NDCYCLE Integer Switch for diurnal cycle of 0 insolation
33. data the latter one information on the grid time steps and variable names The program srv2gra is one of the postprocessing tools available at lt http puma dkrz de puma download map gt If you chose to compile it yourself please read the comments in the first few lines of the program text Sometimes the srv2gra tool has difficulties to calculate an appropriate time increment from the date headers of the data records so you should check this In this example the file puma m ct1 should look like this DSET puma m gra UNDEF 9e 09 XDEF 64 LINEAR 0 0000 5 6250 OPTIONS YREV YDEF 32 LEVELS 85 7606 80 2688 74 7445 69 2130 63 6786 58 1430 52 6065 47 0696 5l 52 CHAPTER 6 GRAPHICS 41 5325 35 9951 30 4576 24 9199 19 3822 13 8445 8 3067 2 7689 2 7689 8 3067 13 8445 19 3822 24 9199 30 4576 35 9951 41 5325 47 0696 52 6065 58 1430 63 6786 69 2130 74 7445 80 2688 85 7606 ZDEF 1 LINEAR 1 1 TDEF 12 LINEAR 00 00Z01jan0001 imo VARS 3 c139 0 99 139 0 0 151 0 99 151 0 0 175 0 99 175 0 0 ENDVARS Here the line starting with TDEF ends with 1mo since we are handling monthly mean data When the PUMA output is used without averaging this should correspond to the output interval given by the nafter variable used in the namelist of your PUMA run see section C The number of variables depends on how the pumaburner was called In this example only 3 variables were processed i e the surface temperature c139 the
34. dule of the model It includes the main program plasim and controls the run From plasim f90 the interface routines to the modules miscmod f90 fluxmod f90 radmod f90 rainmod f90 surfmod f90 are called output is done by calling the interface routines to outmod f90 In addition the adiabatic tendencies and the horizontal diffusion are computed in plasim f90 do the necessary transformations calls to the modules fftmod f90 and legmod f90 are used Input Output plasim f90 does not use any extra input file or output file A di agnostic print out is written on standard output plasim f90 is controlled by the namelist inp which is part of the namelist file puma namelist Parameter Type Purpose Default COLUMN Integer 1 Set all parameters for de 0 fault column mode KICK Integer Switch for initial white 1 noise disturbance on sur face pressure 0 none 1 global 2 hemispher ically symmetric 3 one wavenumber only NWPD Integer Number of Writes Per Day 1 for output data NADV Integer Switch for advection 1 0 ofET on NCOEFF Integer Number of spectral coeff 0 cients in diagnostic print out NDEL NLEV Integer Array Order of the horizontal dif 2 fusion NDIAG Integer Time interval for diagnostic 12 print out time steps NKITS Integer Number of initial explicit 3 Euler time steps N RUN YEARS Integer Number of years to run 1 N RUN MONTHS Integer Number of months to run N_RUN_DAYS Int
35. e miscini reads the namelist and if the parallel version is used distributes the namelist param eters to the different processes If the relaxation is switched on the climatological temperature is read from surface txt and distributed to the processors Subroutine miscstep calls the subroutine fixer to eliminate spurious negative humidity arising from the spectral method and if the relaxation is switched on calls the subroutine mknudge to do the temperature nudging Subroutine miscstop is a dummy sub routine since there is nothing to do to finalize the computations in miscmod f90 11 12 CHAPTER 2 MODULES 2 3 surfmod f90 General The module surfmod f90 deals as an interface between the atmospheric part of the model and modules or models for the land and the oceans The interface to the main PUMA module puma f90 is given by the subroutines surfini surfstep and surfstop which are called in puma f90 from the subroutines prolog gridpointd and epilog respectively Calls to subroutines named landini landstep and landstop and seaini seastep and seastop provide the interface to land and the ocean modules respectively Input Output surfmod f90 reads the land sea mask and the orography surface geopotential m s from file surface txt The file format is formatted SERVICE format with 8I10 for the headers and 8E12 6 for the fields To assign the fields the headers need to have the header information code 129 for the
36. e table inp in appendix 7 1 22 Boundary Conditions and forcing For the T1 truncation the following lower boundary conditions are specified by external fields The land sea mask 3002 surf 0172 sra the surface geopotential N002 surf 0129 5 and the surface temperature N002 surf 0169 sra The other fields are set by default within the model Some can be set by namelist parameters see description of standard model surface fluxes of heat and moisture in the column mode can be influenced by the switch ZUMIN the namelist which sets the surface wind speed entering the bulk exchange scheme The default value is set to 1 m s Keeping the standard settings the columns will be forced by the solar forcing corresponding to the grid point where the column is located For the T1 truncation this mean that the columns are located approximately at gaussian latitudes 35 26 The solar forcing corresponds to the default of the full model A daily mean insolation is used with an annual cycle The solar 57 58 CHAPTER 7 COLUMN MODE AND SOUNDINGS forcing is also influenced by the climatological ozon distribution which by default also has an annual cycle 7 2 Graphical User Interface GUI visualize the time evolution of the column model a vertical Hovmoeller plot has been added to the GUI picture type ISOCOL The sounding device can be also used to visualize the vertical profiles at an arbitrary grid point of the ga
37. eger Number of days to run for 1 short test runs N_START_YEAR Integer Start year 1 START MONTH Integer Start month 1 N DAYS YEAR Integer 365 use real calendar with 360 leap years 360 use simple calendar with 12 months of equal length N DAYS PER MONTH Integer Number of days per month 30 for simple calendar Parameter MPSTEP NEQSIG NPRINT NPRHOR NPACKSP NPACKGP NRAD NFLUX NDIAGGP NDIAGSP NDIAGCF NDIAGGP2D NDIAGGP3D NDIAGSP2D NDIAGSP3D Type Integer Integer Integer Integer Integer Integer Integer Integer Integer Integer Integer Integer Integer Integer Integer Purpose Minutes per step length of timestep Switch for non equally spaced sigma levels 1 non equally spaced 1 equally spaced Switch for extended debug print out 0 off 1 on 2 very extended Number of the grid point to be used for very extended debug print out Switch for spectral output 0 normal 1 com pressed Switch for grid point out put 0 normal 1 com pressed Switch for radiation 0 off 1 on Switch for surface fluxes and vertical diffuson 0 off 1 on Switch for additional di agnostic grid point output 0 off T on Switch for additional di agnostic spectral output 0 off 1 on Switch for additional cloud forcing diagnostic 0 off 1 on Number of additional di
38. el levels MODLEV 2 3 4 hPa O real Pressure levels 500 1000 CODE 0 int ECMWF field code CODE 130 152 GRIB 0 int GRIB output selector GRIB 1 NETCDF 0 int NetCDF output selector NETCDF 21 MEAN 1 int Compute monthly means MEAN 0 HHMM 1 int Time format in Service format HHMM 0 HEAD7 0 int User parameter HEAD7 0815 MARS 0 int Use constants for planet Mars MARS 1 MULTI 0 int Process multiple input files MULTI 12 5 4 HTYPE HTYPE accepts the first character of the following string Following settings are equivalent HTYPE S HTYPE Spherical Harmonics HTYPE Something Blanks and the equal sign are optional Possible Values are Setting Description Dimension for T21 resolution HTYPE S Spherical Harmonics 506 22 23 coefficients HTYPE F Fourier Coefficients 32 42 latitudes wavenumber HTYPE Z Zonal Means 32 levels latitudes levels HTYPE Gauss Grid 64 32 longitudes latitudes 5 5 VTYPE V TYPE accepts the first character of the following string Following settings are equivalent VTYPE 5 VTYPE Sigma VTYPE Super Blanks and the equal sign are optional Possible Values are Setting Description Remark VTYPE S Sigma model levels Some derived variables are not available VTYPE P Pressure levels Interpolation to pressure levels 5 6 MODLEV MODLEV is used in combination with VTYPE S If VTYPE is not
39. ever that the number of latitudes NLAT divided by the number of processors NPRO giving the number of latitudes per process NLPP must have zero remainder E g T31 resolution uses N LAT 48 Possible values for NPRO are then 1 2 3 4 6 8 12 16 24 and 48 loops dealing with a latitudinal index look like do jlat 1 NLPP enddo There are however many subroutines with the most prominent called calcgp that can fuse latitudinal and longitudinal indices In all these cases the dimension NHOR is used NHOR is defined as NHOR NLON NLPP in the pumamod module The typical gridpoint loop that looks like 35 36 CHAPTER 3 PARALLEL PROGRAM EXECUTION do jlat 1 NLPP do 1101 1 gp jlon jlat enddo enddo is then replaced by the faster executing loop do jhor 1 NHOR gp jhor aes enddo uo 3 9 Parallelization in Spectral Domain number of coefficients in spectral domain NRSP is divided by the number of processes NPRO giving the number of coefficients per process NSPP The number is rounded up to the next integer and the last process may get some additional dummy elements if there is a remainder in the division operation loops in spectral domain are organized like do jsp 1 NSPP sp jsp enddo 3 4 Synchronization points All processes must communicate and have therefore to be synchronized at following events e Legendre Transformation This involve
40. g coefficient diffusivity factor 1 66 scaled vorticity 0 potential temperature K K Ra Ca K mean heat conductivity in ice and snow Wm K heat conductivity in ice 2 03 W m t K Ks heat conductivity in snow 0 31 n asymptotic mixing length for heat m m asymptotic mixing length for momentum m longitude sin Y 5 Lo cosine of the solar zenith angle p density of air kg m density of sea ice 920 kg m Ps density of snow 330 kg m Pw density of sea water 1030 kg m Po density of fresh water 1000 kg m 62 APPENDIX A LIST OF CONSTANTS AND SYMBOLS Symbol Definition Value Unit normalized pressure coordinate o vertical velocity in system OSB Stefan Bolzmann constant 5 67 1078 Wm K TN cloud optical depth TF time scale for RF TR time scale for NC TT time scale for temperature flux correction S Th time scale for depth flux correction S geopotential height 0 2 m s7 scaled geopotential height p latitude X scaled velocity potential Y scaled streamfunction angular velocity of the earth 7 292 10 2 5 1 0 single scattering albedo Appendix B Planet Simulator Codes for Variables Codes available from PUMA burner adapted from ECHAM Code Levels Type Variable
41. hanging any other part of the model code The selection is done auto matically by using MoSt or manually by editing Most15 plasim src make plasim Input Output mpimod f90 and mpimod stub do not use any extra input file or output file No namelist input is required Structure Internally mpimod f90 uses the FORTRAN 90 module mpimod which uses the global common module pumamod from plasimmod f90 and the MPI module mpi The following subroutines are included in mpimod f90 Subroutine Purpose mpbci broadcast 1 integer mpbcin broadcast n integers mpbcr broadcast 1 real mpbcrn broadcast n reals mpbel broadcast 1 logical mpscin scatter n integers mpscrn scatter n reals mpscgp scatter grid point field mpgagp gather grid point field mpgallgp gather grid point field to all mpscsp scatter spectral field mpgasp gather spectral field mpgacs gather cross section mpgallsp gather spectral field to all mpsum sum spectral field mpsumsc sum and scatter spectral field mpsumr sum n reals mpsumbcr sum and broadcast n reals mpstart initialize MPI mpstop finalize MPI 17 18 CHAPTER 2 MODULES Subroutine mpreadgp mpwritegp mpwritegph mpreadsp mpwritesp mpi info mpgetsp mpgetgp mpputsp mpputgp mpsumval Purpose read and scatter grid point field gather and write grid point field gather and write with header grid point field read and scatter spectral field gather and write spe
42. have special features in conjunction with threedimen sional arrays where the user may scroll the level or latitude The GUI will insert the level number after the world Level or the latitude after the word Latitude 4 2 5 Geometry The four integers following the geometry item describe the size and screen position of the window The first two parameters refer to width and height in screen pixel These are the sizes of the inner window title bar border and other decorations are not counted The third and fourth parameter set the coordinates of the upper left corner of the window x and y again without borders If the geometry item is not defined the GUI will initialize the window s geometry depending on the screen size 44 CHAPTER 4 GRAPHICAL USER INTERFACE Chapter 5 Postprocessor Pumaburner 5 1 Introduction The Pumaburner is postprocessor for the Planet Simulator and the PUMA model family It s the only interface between raw model data output and diagnostics graphics and user software The output data of the Planet Simulator are stored as packed binary 16 bit values using the model representation Prognostic variables like temperature divergence vorticity pressure and humidity are stored as coefficients of spherical harmonics on levels Variables like radi ation precipitation evaporation clouds and other fields of the parameterization package are stored on Gaussian grids The tasks of the Pumaburner are
43. have to be copied elsewhere because each usage of Most overwrites the contents of bld 1 4 MODEL RUN PHASE 7 1 4 Model run phase After building the model with the selected configuration Most writes or copies all necessary files to the model s run directory These are the executable initial and boundary data namelist files containing the parameter and finally the run script itself Depending on the exit from Most either Save amp Exit or Run amp Exit the run script is started from Most and takes control of the model run A checkmark on GUI invokes also the Graphical User Interface for user control and display of variables during the run Again all contents of the run directory are subject of change for the user But it would be wise to keep changed run setups in other user created directories because each usage of Most overwrites the contents of the run directory 1 5 Running long simulations For long simulations make a new directory on a filesystem that has enough free disk space to store the results You may use the df command to check filesystems Hint 1 Don t use your home directory if there are filequotas Your run may crash due to file quota exceeded Hint 2 Use a local disk not NFS mounted filesystems if possible The model runs much faster writing output to local disks Example e cd Most16 e most x e Select model and resolution e Switch GUI off e Switch Output on e Edit number of years to
44. ing of cloud single 0 006 scattering albedo spectral range 2 DAWN Real Threshold for zenith angle 0 0 Structure Internally radmod f90 uses the FORTRAN 90 module radmod which uses the global common module pumamod from plasimmod f90 Additionally the FORTRAN 90 module orbparam is used Subroutine radini reads the namelist and if the parallel version is used distributes the namelist parameters to the different processes Orbital parameters are computed by calling orb_params If is set to 2 the ozone distribution is read from surface txt Subroutine radstep calls the subroutines solang and mko3 to compute the cosine of the solar angle and the ozone distribution respectively The short wave radiative fluxes are calculate in swr while the long wave radiative fluxes are computed in lwr Subroutine radstop is dummy subroutine since there is nothing to do to finalize the computations in radmod f90 2 12 rainmod f90 General The module rainmod f90 contains subroutines to compute large scale and convective precipitation and the related temperature tendencies In addition a parameterization of dry convective mixing of temperature and moisture is included and cloud cover is diagnosed The interface to the main PLASIM module plasim f90 is given by the subroutines rainini rainstep and rainstop which are called in puma f90 from the subroutines prolog gridpointd and epilog respectively Input Output rainmod f90 does not
45. ins data on a daily basis The call thh 91 180 displays the surface temperature of Hamburg for the spring season from April 1st to June 30th thh gs 6 1 GRADS 53 function 41 42 reinit open puma enable print print mf set lat 53 set lon 10 t 741 d2 d 139 273 16 draw title Surface Temperature deg C in Hamburg print disable print lgxps i print mf o thh ps It is possible to have more than one figure in a plot which is illustrated in the following script It plots seasonal means of the sea level pressure The data file is prepared like this srv selcode 151 puma srv slp srv srv seasmean slp srv sm srv srv2gra slp sm srv The commands set vpage sets virtual pages inside the graphic window The full window is 11 inch wide and 8 5 inch high so set vpage 0 5 5 4 25 8 5 defines the upper left corner If setlevs 1 is specified the pressure levels as given are used Otherwise GrADS defines contour levels depending on the data set sm gs setlevs 1 reinit open sm enable print print mf he set vpage 0 5 5 4 25 8 5 set gxout contour if setlevs 1 set clevs 990 995 1000 1005 1010 1015 1020 endif ccols 1 set grads off t 1 d c151 100 draw title SLP hPa yr ny DJF set vpage 5 5 11 4 25 8 5 set gxout contour if setlevs 1 set clevs 990 995
46. le GUI cfg which must be present in the current directory MoSt copies the file GUI cfg from the dat directory to the run directory while building the Planet Simulator After reading GUI cfg an attempt is made to read the file last used cfg This file is always written at the end of a GUI controlled simulation So one may rearrange and position GUI windows during a run and the new layout will be saved to the file GUI last used cfg In order to make this user layout default for following runs just copy this file like Most15 plasim run cp dat GUI cfg dat GUI cfg old Most15 plasim run cp GUI last used cfg dat GUI cfg 42 MoSt will then copy your new layout to the run directory at the next invocation The GUI cfg is a text file that may be also edited manually There is a section for each CHAPTER 4 GRAPHICAL USER INTERFACE window counting from 0 to 8 which looks like Window 00 Array CSU Plot ISOCS Palette U Title Zonal Wind m s 529 299 2 3 Geometry Window 01 Array SPAN Plot ISOSH array name lt picture type lt colour palette lt window title Palette AMPLI Title Spherical Harmonics Ps Geometry 529 299 535 3 Possible values for these items are 4 2 1 Array Name Description CSU Cross Section U Zonal mean zonal wind CSV Cross Section V Zonal mean meridional wind CST Cross Section T Zonal mean temperature SPAN Spherical harmonics coefficients
47. mamod from plasimmod f90 Subroutine seazni reads the namelist and if the parallel version is used distributes the namelist pa rameters to the different processes If it is not a restart i e if NRESTART from inp of plasimmod f90 is 0 the files surface txt and ocean_parameter are being read The climatological sea ice compactness is converted to a sea ice thickness as initial condition and additional surface parameters are set If it is a restart the restart file sea_restart is read Subroutine seastep accumulates the variables used for the coupling between the atmosphere and the ocean The coupling is done via the sea ice model There is no direct connection between atmosphere and ocean model If there is no sea ice the coupling quantities are passed through the ice model without changes Subroutine seastop finalizes the run and writes the restart records 29 30 CHAPTER 2 MODULES 2 14 Sea ice and ocean modules This section describes the modules that represent sea ice and ocean and the necessary interfaces between these modules and the atmospheric modules Conceptually the sea ice model lies inbetween the atmosphere model and the ocean model Thus the PUMA main part and the ocean model are both coupled to the sea ice model but not directly to each other The sea ice model decides whether a given gridpoint is covered with ice or not in the latter case it merely functions as passing the ocean fluxes to the atmosphere and vice versa
48. meter MULTI can bes used to process a series of input data within one run of the pumaburner Setting MULTI to a number n tells the pumaburner to procees n input files The input files must follow one of the following two rules e YYMM rule The last four characters of the filename contain the data in the form YYMM 5 15 NAMELIST EXAMPLE 49 e NNN rule The last four characters of the filename consist of a dot followed ny a 3 digit sequence number Examples Namelist contains MULTI 3 Command pumaburn namelist gt printout run 005 out pumaburn processes the files lt run 005 gt lt run 006 gt lt run 007 gt Namelist contains MULTI 4 Command pumaburn namelist gt printout 0211 out pumaburn processes the files lt 0211 gt lt 0212 gt lt 0301 gt lt 0302 gt 5 15 Namelist example VTYPE Pressure HTYPE Grid CODE 130 131 132 hPa 200 500 700 850 1000 MEAN 0 GRIB 0 NETCDF 0 This namelist will write Temperature 130 u 130 and v 131 on pressure levels 200hPa 500hPa 700hPa 850hPa and 1000hPa The output interval is the same as found on the model data e g every 12 or every 6 hours MEAN 0 The output format is SERVICE format 5 16 Troubleshooting If the pumaburner reports an error or doesn t produce the expected results try the following e Check your namelist especially for invalid codes types and levels e Run the pumaburner in debug mode by using the optio
49. mple calendar or 365 n_run_days 1 int Simulation time days to run months 0 int Simulation time months to run n_run_years 1 int Simulation time years to run n start month 1 int Starting month n start year 1 int Starting year psurf 101100 0 real global mean surface pressure Pa restim NLEV all 15 0 real restoration timescale for each level sigh NLEV all 0 0 real user definable sigmah array sellon 0 0 real longitude of soundings in the GUI tO NLEV all 250 0 real reference Ta temperature profile tfrc NLEV 0 0 0 1 int Rayleigh friction timescale in days tdissd 0 2 real diffusion time scale for divergence days tdissq 5 6 real diffusion time scale for specific humidity days tdisst 5 6 real diffusion time scale for temperature days tdissz 1 1 real diffusion time scale for vorticity days time0 0 0 real start time for performance estimates C 1 2 Namelist PLANET Name Def Type Description akap 0 286 real kappa alr 0 0065 real lapse rate eccen 0 0 real eccentricity for fixed orbits ga 9 81 real gravity gascon 287 0 real gas constant mvelp 0 0 real longitude of vernal equinox for fixed orbits deg nfixorb 0 int 1 fix the planetary orbit obliq 0 0 real obliquity for fixed orbits deg plarad 6371000 0 real planetary radius pnu 0 1 real time filter ral 610 78 real parameter in Magnus Teten formula ra2 17 269 real
50. n d Example pumaburn lt namelist gt printout d data in data out This will print out some details like parameters and memory allocation during the run The additional information may help to detect the problem e Not all combinations of HTYPE and CODE are valid Try to use HTYPE Grid and VTYPE Pressure before switching to exotic parameter combinations 50 CHAPTER 5 POSTPROCESSOR PUMABURNER Chapter 6 Graphics 6 1 Grads In this section visualisation using the graphics package GrADS is described A useful Internet site for reference and installation instructions is X http grads iges org grads grads html Latest versions of GrADS can handle data NETCDF format via the command sdfopen GRIB HDF SDS and in its native binary format The native format can conveniently be derived from SERVICE format In the following it is assumed that the PUMA output has been converted to SERVICE format with the pumaburner and the resulting file is called puma srv Monthly mean data is either obtained directly from the pumaburner namelist parameter MEAN 1 see section or via a PINGO command Srv monmeans puma srv puma_m srv Information on the PINGO package can be found in DKRZ report 11 at lt http www mad zmaw de Pingo repdl htm1 gt The SERVICE file has to be converted to GrADS s native format by the command srv2gra puma_m srv which results in the files puma_m gra and puma_m ctl The first file contains the
51. n number The following subsection gives an example assuming version 16 1 1 Quick Installation tar zxvf Most16 tgz cd 16 configure sh most x if your tar command doesn t support the z option e g on Sun UNIX type instead gunzip Most16 tgz tar xvf Most16 tar cd 16 configure sh most x If this sequence of commands produces error messages consult the FAQ Frequent Asked Questions and README files in the Most16 directory They are plain text files that can be read with the command more or any text editor 1 2 Most16 directory home Mosti6 ls 1G TIW E I 1 1548 check c lt Used by configure sh rwxr xr x 1 57 cleanplasim Delete run bld and bin for PLASIM rwxr xr x 1 51 cleanpuma Delete run bld and bin for PUMA drwxr xr x 2 4096 common lt Topography files rwxr xr x 1 3911 configure sh The configure script rw r r 1 308 csub c Currently unused srw r t 21 234 f90check f90 lt Used by configure sh rw r r 1 3033 FAQ Frequently Asked Questions drwxr xr x 2 4096 images Directory for images rw resr 1 154 makecheck lt Used by configure sh 6 CHAPTER 1 INSTALLATION rw r r 1 85 makefile lt Used to make most x rw r r 1 107844 most c Source for MoSt Model Starter rw r r 1 6399 NEW IN VERSION 16 lt New in this version drwxr xr x 8 4096 plasim lt Planet Simulator directory drwxr xr x 2 4096 postproce
52. ne Zonal Wavenumber Figure 4 1 Screenshot of Model Starter MoSt Spherical Harmonics Ps Water kg m2 138 steps Latitude 55N Ei Zonal Wind m s Level 4 7 fps OAR Shy es ES Figure 4 2 Screenshot of Graphical User Interface GUI 42 GUI CONFIGURATION 41 Horizontal global fields in cylinder projection e Horizontal global fields in polar projection Time longitude Hovmoeller diagrams Amplitudes of coefficients of spherical harmonics e Time series e Numerical values In case of horizontal global grids pressing the MMB Middle Mouse Button toggles between cylinder and polar projection If the grid is just one level from many of a three dimensional field like u or v the level shown can be decreased by the LMB or increased by the RMB For Hovmoeller and longitude height sections the LMB and RMB can be used to select the latitude The second purpose is the interaction part of the GUI which allows the user to change selected model variables during the model run It is not necessary though possible to pause the model while changing variables Changes to model variables are of course monitored in the outputfile and checked by GUI for the appropriate range of values and maximum possible change per timestep because otherwise a rapid parameter change or a choice of values beyond the normal range may blow up the model All model variables which are candidates fo
53. on 48 CHAPTER 5 POSTPROCESSOR PUMABURNER 5 10 SERVICE format The SERVICE format uses the following structure The whole file consists of pairs of header records and data records The header record is an integer array of 8 elements head 1 ECMWF field code head 2 modellevel or pressure in Pa head 3 date yymmdd 00 for monthly means head 4 time hhmm or hh for HHMM 0 head 5 1 dimension of data array head 6 2 dimension of data array head 7 may be set with the parameter HEAD7 head 8 experiment number extracted from filename Example for reading the SERVICE format GRIB 0 NETCDF 0 INTEGER HEAD 8 REAL FIELD 64 32 dimensions for T21 grids READ 10 ERR 888 END 999 HEAD READ 10 ERR 888 END 999 FIELD 888 STOP 21 0 ERR 999 STOP EOF 511 HHMM Setting Description HHMM 0 head 4 shows the time in hours HH HHMM 1 head 4 shows the time in hours and minutes 5 12 HEAD 7th element of the header is reserved for the user It may be used for experiment numbers flags or anything else Setting HEAD7 to a number exports this number to every header record in the output file SERVICE format only 5 13 MARS This parameter is used for processing simulations of the Mars atmosphere Setting MARS 1 switches gravity gas constant and planet radius to the correct values for the planet Mars 5 14 MULTI The para
54. on W m 179 1 ga top thermal radiation W m 180 1 ga u stress Pa 181 1 ga v stress Pa 182 1 m s 183 1 g soil temperature K 199 1 g vegetation cover frac 203 1 ga top solar radiation upward W m 204 1 ga surface solar radiation upward W m 205 1 ga surface thermal radiation upward W m 207 1 g soil temperature level 2 K 208 1 g soil temperature level 3 K 209 1 g soil temperature level 4 K 210 1 g sea ice cover frac 211 1 g sea ice thickness m 212 1 g forest cover frac 218 1 g snow melt water equiv m s 221 1 g snow depth change water equiv m s 230 1 ga vertical integrated spec hum kg m 232 1 g glacier cover frac PUMA spectral field PUMA grid point field computed by PUMA burner accumulated 65 66 Appendix C Namelists APPENDIX C C 1 File puma namelist C 1 1 Namelist INP Name Def Type Description column 0 int 1 initialize PLASIM for column runs kick 1 int 0 no noise initialization p const 1 random white noise 2 Equator symmetric random white noise 3 mode 1 2 no random initialization mars 0 int 1 initialize PLASIM for planet Mars mpstep 45 int minutes per step lenghth of timestep nadv 1 int 1 switches horizontal advection on ncoeff 0 int spectral coefficients to print in wrspam ndel NLEV all 2 int order of hyperdiffusion for each level 2 h ndiag 12 int output interval for diagnostics times
55. precip 1 0 yes no rcrit NLEV real critical relative hum for non conv clouds C 2 FILE LAND NAMELIST C 1 7 Namelist SURFPAR 69 Name Def Type Description noromax model resolution NTRU int resolution of orography nsurf not active int debug switch oroscale 1 0 real scaling factor for orography C 2 File land namelist 2 1 Namelist LANDPAR Name Def Type Description albgmax 0 8 real max albedo for glaciers albgmin 0 6 real min albedo for glaciers albland 0 2 real albedo for land albsmax 0 8 real max albedo for snow albsmaxf 0 4 real max albedo for snow with forest albsmin 0 4 real min albedo for snow albsminf 0 3 real min albedo for snow with forest co2conv 14 0 real co2 conversion factor drhsfull 0 4 real threshold above which drhs 1 frac of wsmax drhsland 0 25 real wetness factor land dsmax 5 00 real maximum snow depth m h20 1 no limit dsoilz NLSOIL real soil layer thickness dwatcini 0 0 real soil water content m for manual initialization nwatcini 1 dzOland 2 0 real roughness length land dzglac real threshold of orography to be glacier 1 dztop 0 20 real thickness of the uppermost soil layer m forgrow 1 0 real growth factor initialization gs 1 0 real stomatal conductance initialization nbiome 0 int switch for vegetation model 1 0 prog clim ncveg 1 int compute new dcveg 0 ini
56. r izontal diffusion of diver gence time scale d for the hori zontal diffusion of vorticity time scale d for the hori zontal diffusion of tempera ture time scale d for the hori zontal diffusion of moisture Global mean sea level pres sure Pal Time scale d for Newto nian cooling usually not used Default NLEV 0 15 0 0 0 0 12000 0 280 NLEV 0 2 Tl NLEV 5 6 NLEV 5 6 101100 00 NLEV 0 0 Parameter Type Purpose Default MARS Integer 1 Set all parameters for 0 Mars atmosphere NGUI Integer Run with 1 or without 0 0 GUI NOUTPUT Integer Global witch for enabling 1 1 or disabling 0 output to file puma output SELLON Real Longitude of soundings in 0 0 the GUI TO NLEV Real Array Reference temperature used NLEV 250 0 in the discretization scheme TFRC NLEV Real Array Time scale 4 for Rayleigh NLEV 0 0 friction 0 0 off Structure Internally plasim f90 uses the FORTRAN 90 global common module pumamod from plasimmod f90 After starting MPI the main program plasim calls prolog for initializing the model Then master is called to do the time stepping Finally subroutine epilog finishes the run In subroutine prolog calls to different subroutines which are part of plasim f90 or are provided by other modules initialize various parts of the model gauaw and inilat build the grid readnl reads the namelist and sets some parameter ac
57. r constant w m2 iyrbp 50 int Year before present 1950 AD default 2000 AD ndcycle 0 int switch for daily cycle 1 on 0 off nlwr 1 int switch for long wave radiation dbug 1 on 0 off no3 1 int switch for ozon 1 on 0 off nrscat 1 int switch for rayleigh scattering dbug 1 on 0 off nsol 1 int switch for solar insolation dbug 1 on 0 off nswr 1 int switch for short wave radiation dbug 1 on 0 off nswrcl 1 int switch for computed or prescribed cloud props 1 com 0 pres rcl1 3 0 15 0 3 0 6 real cloud albedos spectral range 1 rcl2 3 0 15 0 3 0 6 real cloud albedos spectral range 2 th2oc 0 04 real absorption coefficient for h20 continuum tpofmt 1 0 real tuning of point of mean lwr transmissivity in layer tswrl 0 04 real tuning of cloud albedo rangel tswr2 0 048 real tuning of cloud back scattering c range2 tswr3 0 004 real tuning of cloud s scattering alb range2 C 1 6 Namelist RAINPAR Name Def Type Description clwcrit1 0 1 real 1st critical vertical velocity for clouds clwcrit2 0 0 real 2nd critical vertical velocity for clouds kbetta 1 int switch for betta in kuo 1 0 yes no ncsurf l int conv starts from surface 1 0 yes no ndca 1 int dry convective adjustment 1 0 yes no nmoment 0 int momentum mixing 1 0 yes no nshallow 0 int switch for shallow convection 1 0 yes no nprc 1 int large convective precip 1 0 yes no npr 1 int switch for large scale
58. r the display or interactive changes have a special code to communicate with the Planet Simulator The experienced modeller can add new code for more variables using the existing communication code as template Thus all model fields or even fields received via coupling with other models can be put on the GUI display Both MoSt and GUI are implemented using the Xlib X11R5 which is a library of routines for graphics and event communication As this library is part of every UNIX Linux operating system and base of all desktop environments there is no need to install additional software for running MoSt and GUI Another important property of Xlib is the full network transparency display of MoSt and GUI is not locked to the machine running the programs or the model In fact the best performance is obtained in running the Planet Simulator on two or four CPUs of a remote server while displaying the GUI on the user s workstation In summarizing the MoSt and GUI programs automate many tedious tasks minimize the time to become familiar with the Planet Simulator and make debugging and parameter tuning much easier More kinds of presentations coordinate projections and interactivity are being developed A graphical preprocessor with editor for boundary conditions and a graphical postprocessor are future expansions to build an almost complete environment for modellers 4 2 GUI configuration On initialization the GUI reads its configuration from a fi
59. ram should be tested in single and in multi CPU configuration The results of a single CPU run is usually not exactly the same as the result of a multi CPU run due to effects in rounding But the results should show only small differences during the first timesteps e Synchronization points The code is optimzed for parallel execution and minimizes there fore communication overhead necessary communication code is grouped around the Legendre transformations If more scatter gather operations or other communica tion routines are to be added they should be placed just before or after the execution of the calls to the Legendre Transformation Any other place would degrade the overall performance in introducing additional process synchronization 38 CHAPTER 3 PARALLEL PROGRAM EXECUTION Chapter 4 Graphical User Interface 4 1 Graphical user interface GUI The Planet Simulator may be used in the traditional fashion with shell scripts batch jobs and network queuing systems This is acceptable for long running simulations on complex machines and number crunchers like vector computers massive parallel computers and work station clusters T here is now however a much more convenient method by using a graphical user interface GUI for model setup with parameter configurations and for interaction between user and model The Planet Simulator is configured and setup by the first GUI module named MoSt Model Starter screenshot in
60. rography to 1 0 be glacier 1 0 none m DZTOP Real Thickness of the uppermost 0 2 soil layer m DSOILZ 5 Real Array Soil layer thicknesses m 0 4 0 8 1 6 3 2 6 4 Structure Internally landmod f90 uses the FORTRAN 90 module landmod which uses the global common module pumamod from plasimmod f90 Subroutine landini reads the namelist and if the parallel version is used distributes the namelist pa rameters to the different processes If the run is not started from a restart file the initialization file surface txt is being read The soil and the river runoff are ini tialized via soilini and roffini and different variables are set according to the values given by the namelist or the surface txt Additionally the climatological surface temperatures and soil wetnesses are updated from surface txt if NRESTART 2 If NRESTART 3 special application the bucket size the roughness length and the albedo are set to the values given in the namelist Subroutine landstep computes new surface and soil values via sozlstep which calls tands and wandr for the heat and water budgets respectively If NLANDT and or NLANDW are set to 0 climato logical values are used for the surface temperature and the soil wetness Via roffstep the river runoff is computed Finally the biome model s mbastep is called The land model is finalized by landstop which writes the restart record to plasim restart 15 CHAPTER 2 MODULES 2 6 legmod f9
61. run e Click on Save amp Exit e Make a directory e g mkdir data longsim e cp plasim run data longsim e cd data longsim e edit most plasim run for experiment name e edit namelist files if necessary e start simulation with most plasim run amp CHAPTER 1 INSTALLATION Chapter 2 Modules In the following the purposes of the individual modules is given and the general structure and possible input and output opportunities namelist and files are explained 9 10 CHAPTER 2 MODULES 2 1 fluxmod f90 General The module fluxmod f90 contains subroutines to compute the different surface fluxes and to perform the vertical diffusion The interface to the main PUMA module puma f90 is given by the subroutines fluxini flurstep and fluxstop which are called in puma f90 from the subroutines prolog gridpointd and epilog respectively Input Output fluxmod f90 does not use any extra input file or output file and is controlled by the namelist fluxpar which is part of the namelist file puma namelist Parameter Type Purpose Default NEVAP Integer Switch for surface evaporation 0 off 1 1 on NSHFL Integer Switch for surface sensible heat flux 1 0 off 1 on NSTRESS Integer Switch for surface wind stress 0 off 1 1 on NTSA Integer Switch for computing the near surface 2 air temperature which is used for the Richardson number 1 potential tem perature 2 virtual potential temper
62. s changing from latitudinal partitioning to spectral partitioning and such some gather and scatter operations e Inverse Legendre Transformation The partitioning changes from spectral to latitudinal by using gather broadcast and scatter operations e Input Output All read and write operations must be done only by the root process who gathers and broadcasts or scatters the information as desired Code that is to be executed by the root process exclusively is written like if mypid NROOT then endif NROOT is typically 0 in MPI implementations mypid My process identification is assigned by MPI 3 5 SOURCE CODE 3T 3 5 Source code It needs some discipline in order to maintain parallel code Here are the most important rules for changing or adding code to the Planet Simulator e Adding namelist parameters All namelist parameters must be broadcasted after reading the namelist Subroutines mpbci mpbcr mpbcin mpbcrn e Adding scalar variables and arrays Global variables must be defined in a module header and initialized e Initialization code Initialization code that contains dependencies on latitude or spectral modes must be done by the root process only and then scattered from there to all child processes e Array dimensions and loop limits Always use parameter constants NHOR NLAT etc as defined in pumamod f90 for array dimensions and loop limits e Testing After significant code changes the prog
63. s different lengths of months and output intervals correctly Setting Description MEAN 0 Do no averaging all terms are processed MEAN 1 Compute and write monthly mean fields Not for spherical har monics Fourier coefficients or zonal means on sigma levels MEAN 2 Compute and write monthly deviations Not for spherical harmon ics Fourier coefficients or zonal means on sigma levels Deviations are not available for NetCDF output MEAN 3 Combination of MEAN 1 and MEAN 2 Each mean field is fol lowed by a deviation field with an identical header record Not for spherical harmonics Fourier coefficients or zonal means on sigma levels 5 9 Format of output data The pumaburner supports three different output formats e GRIB GRIdded Binary WMO standard for gridded data e NetCDF Network Common Data Format e Service Format for user readable data see below For more detailed descriptions see for example Setting Description GRIB 1 NetCDF 0 The output file is written GRIB format This option can be used only for HTYPE Spherical Harmonics or HTYPE Gauss Grid GRIB 0 NetCDF 1 The output file is written in NetCDF format This op tion can be used for HTYPE Gauss Grid only GRIB 0 NetCDF 0 The output file is written in Service format This is the preferred format for user programs For a detailed description see the following section GRIB 1 NetCDF 1 Illegal combinati
64. set to Sigma the contents of MODLEV are ignored MODLEV is an integer array that can get as many values as there are levels in the model output levels are numbered from top of the atmo sphere to the bottom The number of levels and the corresponding sigma values are listed in the pumaburner printout The outputfile orders the level according to the MODLEV values MODLEV 1 2 3 4 5 produces an output file of five model levels sorted from top to bottom while MODLEV 5 4 3 2 1 sorts them from bottom to top 5 7 HPA AT 5 7 hPa hPa is used combination with P If VT YPE is not set to Pressure the contents of hPa are ignored hPa is a real array that accepts pressure values with the units hectoPascal or millibar All output variables will be interpolated to the selected pressure levels There is no extrapolation on the top of the atmosphere For pressure values that are lower than that of the model s top level the top level value of the variable is taken The variables tem perature and geopotential height are extrapolated if the selected pressure is higher than the surface pressure All other variables are set to the value of the lowest mode level for this case The outputfile contains the levels in the same order as set in hPa Example hpa 100 300 500 700 850 900 1000 5 8 MEAN MEAN can be used to compute montly means and or deviations The Pumaburner reads date and time information from the model file and handle
65. sp Finally diagnostic clouds are calculated in mkclouds Subroutine radstop is a dummy subroutine since there is nothing to do to finalize the computations in radmod f90 27 28 CHAPTER 2 MODULES 2 13 seamod f90 General The module seamod f90 is the interface from the atmosphere to the ocean and the sea ice The interface to the main PLASIM module puma f90 is given by the subroutines seaini seastep and seastop which are called in puma f90 from the subroutines prolog gridpointd and epilog respectively Input Output seamod f90 reads different surface parameters either from the file surface txt see namelist and the file ocean parameter or from the restart file sea restart which is written at the end of an integration The files formats are unformatted for the restart file formatted SERVICE format with 8I10 for the header and 8E12 6 for the fields for surface txt and formatted EXTRA format with 4110 for the header and 6 1X E12 6 for the fields for ocean parameter The file surface txt may include the following fields The climatological annual cycle of the surface temperature and the climatological annual cycle of the sea ice compactness frac To assign the fields the headers need to have the header information code 169 for surface temperature and code 210 for the compactness 1 ice 0 open water a date identifier of the form yymmdd or mmdd where mm goes from 1 to 12 January to December is req
66. ssor lt Postprocessor directory drwxr xr x 8 4096 puma PUMA directory rw r r 1 839 README lt Read this first rw r r 1 191 README USER Notes for MAC user rw r r 1 698 README WINDOWS USER Notes for Windows user directory structure must not be changed even empty directories must be kept as they are the Most program relies on the existence of these directories For each model currently Planet Simulator and PUMA exists a directory plasim and puma with following subdirectories Mosti6 plasim ls lg 128 bin lt model executables 1824 bld lt build directory 280 dat lt initial and boundary data 80 doc lt documentation user s guide reference manual 928 run lt run directory 1744 src lt source code drwxr xr x drwxr xr x drwxr xr x drwxr xr x drwxr xr x drwxr xr x NON O PN PN OIN PN After installation only dat doc and src contain files all other directories are empty Running Most to setup a model configuration and define an experiment uses the directo ries in the following manner 1 3 Model build phase Most writes an executable shell script to the bld directory and executes it directly hereafter It copies all necessary source files from src to bld and modifies them according to the selected parameter configuration Modification of source code is necessary for vertical and horizontal resolution change and for using more than 1 processor
67. subroutines necessary to perform the fast fourier transformation and its inverse The interface to the main module plasim f90 is given by the subroutines and fc2gp which are called in plasim f90 from the subroutine gridpoint Input Output fftmod f90 does not use any extra input file or output file No namelist input is required Structure Internally fftmod f90 uses the FORT RAN 90 module fftmod which uses no other modules Subroutine gp2fc performs the transformation from grid point space into fourier space while the subroutine fc2gp does the transformation from fourier space into grid point space Both routines use several subroutines to do the direct or indirect transformation for different factors When gp2fc or fc2gp is called for the first time fftini is called to do the initialization of the FFT alternate module fft991mod f90 may be used instead of fftmod f90 While fft mod f90 runs faster fft991mod f90 can be used for resolutions that are not supported by fftmod f90 e g T63 or T106 Edit the file Most16 plasim src make plasim for module selection Use either FFTMOD fftmod or FFTMOD fft991mod 13 14 CHAPTER 2 MODULES 2 5 landmod f90 General The module landmod f90 contains parameterizations for land surface and soil processes which include the simple biome model SIMBA and a model for the river runoff The interface to the Planet Simulator is given via the module surfmod f90 by
68. surface geopotential and 172 for the land sea mask 1 0 land 0 0 sea Fractional land sea masks containing other values than 1 0 and 0 0 will be converted with values 0 5 set to 1 0 and all other to 0 0 surfmod f90 is controlled by the namelist surfpar which is part of the namelist file puma namelist Parameter Type Purpose default NSURF Integer Debug switch not active NOROMAX Integer Resolution of orography NTRU OROSCALE Real Scaling factor for orography 1 0 Structure Internally surfmod f90 uses the FORTRAN 90 module surfmod which uses the global common module pumamod from pumamod f90 Subroutine surfini reads the namelist and if the parallel version is used distributes the namelist pa rameters to the different processes If the run is not started from a restart file the land sea mask and the orography are read from file surface txt According to the namelist input the orography is scaled by OROSCALE transfered into spectral space and truncated to NOROMAX Calls to subroutines landini and seaini are the interfaces to the respective initialization routines contained in the land and ocean modules During the run the interface to land and ocean is given by calls to the external subroutines landstep and seastep which are called by surfstep At the end of the integration interface subroutines landstop and seastop are called by surfstop 2 4 fftmod f90 fft991mod f90 General The module fftmod f90 contains all
69. teps ndiagcf 0 int 1 turn on cloud forcing diagnostic ndiaggp 0 int 1 process franks gp diagnostic arrays ndiaggp2d 0 int number of additional 2 d gp diagnostic arrays ndiaggp3d 0 int number of additional 3 d gp diagnostic arrays ndiagsp 0 int 1 process franks sp diagnostic arrays ndiagsp2d 0 int number of additional 2 d sp diagnostic arrays ndiagsp3d 0 int number of additional 3 d sp diagnostic arrays ndl NLEV all 0 1 activate spectral printouts for this level neqsig 1 int 1 use equidistant sigma levels nflux 1 int 1 switches vertical diffusion on ngui 0 int 1 run with active GUI nhdiff 15 lint critical wavenumber for horizontal diffusion nhordif 1 int 1 switches horizontal diffusion on nkits 3 int number of short initial timesteps noutput 1 int enables 1 or disables 0 output file npackgp 1 1 pack gridpoint fields on output npacksp 1 1 pack spectral fields on output nperpetual 0 int radiation day for perpetual integration nprhor 0 int 1 grid point for print out only for checks nprint 0 1 comprehensive print out only for checks nrad 1 int 1 switches radiation on ntime 0 int 1 turn on time use diagnostics nwpd 1 int number of writes per day to puma_output NAMELISTS C 1 FILE PUMA NAMELIST Namelist INP continued Name Def Type Description n days per month 30 int length of month for simple calendar n days per year 360 int length of year for si
70. the subroutines landini landstep and landstop which are called in surfmod f90 from the subroutines surfini surfstep and surfstop respectively Input Output landmod f90 reads several surface and soil parameters either from the initial file surface txt or from the restart file plasim restart which is written at the end of an integration surface txt contains several surface fields which are needed for initialization The file format is formatted SERVICE format with 8110 for the header and 8E12 6 for the fields The file may include the following fields surface geopotential orography m s land sea mask 1 0 0 0 surface roughness m background albedo frac glacier mask frac bucket size m soil temperature climatological annual cycle of the surface temperature K climatological annual cycle of the soil wetness m To assign the fields the headers need to have the header information code 129 for surface geopotential code 172 for the land sea mask 1 land 0 sea 173 for the surface roughness 174 for the background albedo 232 for the glacier mask 1 glacier 0 no glacier 229 for the bucket size 209 for the soil temperature 169 for the surface temperature and 140 for the soil wetness for the climatological annual cycles of surface temperature and soil wetness a date identifier of the form yymmdd or mmdd where mm goes from 1 to 12 January to December is required Two additional months with mm
71. tial state newsurf 0 int dtcl dwcl 1 update from file 2 reset nlandt 1 int switch for land model 1 0 prog clim nlandw 1 int switch for soil model 1 0 prog clim nwatcini 0 int switch for manual soil water setting 1 0 on off rinisoil 0 0 real soil carbon initialization riniveg 0 0 real biomass carbon initialization rlaigrow 0 5 real above ground growth factor initialization rlue 8 0E 10 real rnbiocats 0 0 real tau soil 42 0 real years in landini scaled to seconds tau veg 10 0 real years in landini scaled to seconds wsmax WSMAX EARTH real max field capacity of soil water m 70 max 2 0 real maximum roughness length for vegetation 0 C 3 File sea namelist 3 1 Namelist SEAPAR APPENDIX C Name Def Type Description 32 int atmosphere ice coupling time steps albsea 0 069 real albedo for open water albice 0 7 real max albedo for sea ice dz0sea 1 5 1075 real roughness length sea m 0 1 0 1077 real roughness length ice m drhssea 1 0 real wetness factor sea drhsice 1 0 real wetness factor ice C 4 File ocean namelist C 4 1 Namelist OCEANPAR Name Def Type Description dlayer NLEV 50 0 real layer depth m ndiag 480 int diagnostics each ndiag timestep newsurf 0 int 1 read surface data after restart nfluko 0 int switch for flux correction nocean 1 int ocean model
72. uired Fields which are not needed will be skipped The file ocean parameter includes the following fields The climatological annual cycle of the sea surface temperature K the climatological annual cycle of the mixed layer depth m and the climatological average of the deep ocean temperature m To assign the fields the order must be as described above no header information is used The restart file sea restart contains all variables needed to continue the run seamod f90 is controlled by the namelist seapar given in the namelist file sea namelist Parameter Purpose Default ALBSEA Real Albedo for ice free ocean 0 069 ALBICE Real Maximum albedo for sea ice 0 7 DZOSEA Real Minimum roughness length 1 0 107 m for ice free ocean DZOICE Real Roughness length m for 1 0 10 sea ice DRHSSEA Real Wetness factor for ice free 1 0 ocean DRHSICE Real Wetness factor for sea ice 1 0 NOCEAN Integer Switch for ocean model 1 0 climatological SST 1 ocean model NICE Integer Switch for sea ice model 1 0 climatological 1 sea ice model Parameter Type Purpose Default NCPLICE OCEAN Integer ice ocean coupling time 32 steps NCPL_ATMOS_ICE Integer ice atmosphere coupling 1 time steps TDEEPSEA Real Homogeneous deep ocean 0 0 temperature DHICEMIN Real Minimum sea ice thickness 0 1 im Structure Internally seamod f90 uses the FORTRAN 90 module seamod which uses the global common module pu
73. use any extra input or output file and is con trolled by the namelist rainpar which is part of the namelist file puma namelist Parameter Type Purpose Default KBETTA Integer Switch for betta in Kuo 1 parameterization 0 off 1 on NPRL Integer Switch for large scale pre 1 cipitation 0 off 1 on NPRC Integer Switch for convective pre 1 cipitation 0 off 1 on NDCA Integer Switch for dry convective 1 adjustment 0 off 1 on NSHALLOW Integer Switch for shallow convec 1 tion 0 off 1 on RCRIT NLEV Real Array Critical relative humidity computed for cloud formation CLWCRIT1 Real Critical vertical veloc 0 1 ity for cloud formation Pa s not active if CLWCRIT2 gt CLWCRIT1 CLWCRIT2 Real Critical vertical veloc 0 0 ity for cloud formation Pa s not active if CLWCRIT2 gt CLWCRIT1 Structure Internally rainmod f90 uses the FORTRAN 90 module rainmod which uses the global common module pumamod from plasimmod f90 Subroutine rainini reads the namelist and if the parallel version is used distributes the namelist param eters to the different processes Subroutine rainstep calls the subroutine mkdqdtgp to obtain the adiabatic moisture tendencies in grid point space which are needed for the Kuo parameterization kuo is called to compute the convective precipitation and the respective tendencies Dry convective adjustment is performed in mkdca Large scale precipitation is computed in mkl
74. ussian grid in the full model By clicking the window the sounding goes from grid point to grid point in meridional direction longitude can be selected by the switch sellon which is a parameter of the inp namelist in puma namelist Using the template GUILsounding cfg in folder plasim dat the GUI is configured for soundings In this case sellon can be modified in the control window For more details see chapter 4 Appendix A List of Constants and Symbols Symbol Definition Value Unit a earth radius 6371 10 m A D V Vinp A absorptivity emissivity As surface emissivity B T Planck function Wm cloud cover Char Charnock constant 0 018 transfer coefficient for heat drag coefficient for momentum Cp specific heat of moist air at constant pressure Jkg K Cpd specific heat of dry air at constant pressure 1005 46 Jkg K specific heat of water vapor at constant pressure 1869 46 Jkg K specific heat of sea ice 2070 Wskg K Cp specific heat of snow 2090 W skg t ey specific heat of sea water 4180 Wskg K Cw coefficient for the deep ocean heat flux 4 Wm wetness factor D scaled divergence es E evaporation ime Eo extrateristical solar flux density Wm f Coriolis parameter 20 sin yp st E tendency of the first moment 4 Kms y tendency of the zeroth moment Kms surface moisture flux 267 Fr surface sensible heat flux

University of Hamburg Planet Simulator User's Guide Version 16.0

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