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Regional Climatic Model RegCM User's Guide - gforge

1. Raindrop evap rate coef kg m 2 s 1 1 2 s cevapoce 100E 02 Raindrop evap rate coef kg m 2 s 1 1 2 s caccrlnd 3 000 Raindrop accretion rate m3 kg s caccroce 3 000 Raindrop accretion rate m3 kg s cllwcv 0 3E 3 Cloud liquid water content for convective precip clfrcvmax 1 00 Max cloud fractional cover for convective precip cftotmax 0 75 Max total cover cloud fraction for radiation We found that RegCM4 is especially sensitive to 1 cevap increasing cevap will generally decrease precipitation 2 gulland guloce increase of guland guloce will generally lead to reduce precipitation 6 1 14 microparam namelist This namelist controls the new microphysics scheme amp microparam budget_compute false Verify enthalpy and moisture conservation nssopt 1 Supersaturation Computation 0 gt No scheme 1 gt Tompkins 2 gt Lohmann and Karcher 3 gt Gierens Choose the autoconversion paramaterization gt 1 Klein amp Pincus 2000 gt 2 Khairoutdinov and Kogan 2000 gt 3 Kessler 1969 gt 4 Sundqvist Implicit Explicit control NOT ACTIVATED YET IT DOES NOT WORK ksemi 0 gt scheme is fully explicit ksemi gt scheme is fully implicit kautoconv 4 ksemi 1 0D0 O lt ksemi lt 1 gt scheme is semi implicit vaxr 4 0D0 Rain fall speed default is 4 m s vaxi 0 15D0 Ice fall speed default is 0 15 m s vgxs 1 0
2. e Climate indices We wont make here a comprehensive analysis of this tool but you can find some ideas in the PostProc directory on REGCM_ROOT reading the two sample average and regrid scripts which use a combination of NCO programs and cdo operators to reach goal A very simple usage pattern for example to obtain a monthly mean is cdo monmean test_001_T2M 1990 nc 7 2 GrADS program This tool is the one mostly used at ICTP to analyze and plot model output results It can be used either as an interactive tool either as a batch data analysis tool We have already written in chapter 5 about the helper program GrADSNcPlot which can be used to interactively plot model output results We will here detail why an helper program is needed and how it does work For information regarding the grads program itself a comprehensive guide may be found at http www iges org grads gadoc users html 7 2 1 GrADS limits The grads program is powerful yet has limits 1 Only the equirectangular projection or Plate Carr e is supported Some other projections can be used through a pdef entry in the CTL file using the internal direct preprojection engines but not all RegCM supported projections are supported using direct engine 41 2 NetCDF format allows multidimensional variables while grads supports just four dimensional time level latitude longitude variables Luckily these limits can be exceeded carefully telling grads the RegCM data str
3. ee First RegCM model simulation 2 ee 5 1 3 2 5 3 5 4 39 6 Localizing the model and running your simulation 6 1 The commented namelist 2 2 2 2 2 Comm nn 6 1 1 dimparamnamelist 22 4642 Bra ern E 6 1 2 geoparam n melist u en ee a En a ees 6 1 3 tetrainparam nammelist 2 4 a we md a er neh meh a 6 1 4 debugparam namelist gt sepse CH nn n nn 6 1 5 boundaryparam namelist e 6 1 6 globdatparam namelist 02 0200000000000 00008 6 1 7 dnestparam namelist u oe ae ee wh ee a a a ee eed ey 6 1 8 perturbparam namelist 2 CC nn nn 6 1 9 restartparam namelist 2 2 2 Comm ee ea a 6 1 10 timeparam nammelist o s s im 2 2 Comm nn 6 1 1 oUtparam namelist sss 2 2 4 a ae sed Ka pn a ae an 6 1 12 physicsparam namelist 2 2 Com mn 6 1 13 subexparamnamelist 2 2 Comm nn 10 11 11 12 12 12 13 13 14 14 15 15 16 17 17 18 6 1 14 microparam nammelist s s i s 2 Comm nn 6 1 15 grellparam emanparam tiedtkeparam and kfparam namelists 6 1 16 holtslagparam namelist 2 CC Hmmm nn 6 1 17 Uwparaminamelist saen YA wi ee PR ee in 6 1 18 slabocparam namelist 6 1 19 tweakparam namelist Hmm nn 6 1 20 rrtmparam namelist 20000000020 a 6 1 21 chemparam namelist 2 2 Comm nn 6 2 The CEM Options Para an a ae He PR ee A A S 6 3 The CEM 4 5 options 2a un eh OR a ee de Se wae ai el wi 6 4 Sensitivity experiments h
4. gt cd REGCM_RUN Now we are ready to modify the input namelist file to reflect this directory layout A namelist file in FORTRAN 1s a convenient way to give input to a program in a formatted file read at runtime by the program to setup its execution behaviour So the next step is somewhat tricky as you need to edit the namelist file respecting its well defined syntax Open your preferred text file editor and load the test_001 in file You will need to modify for the scope of the present tutorial the following lines FROM dirter set this to where your domain file is TO dirter input FROM inpter set this to where your surface dataset is TO inpter SREGCM_GLOBEDAT where REGCM_GLOBEDAT is the directory where input data have been downloaded in chapter 4 FROM dirglob set this to where your icbc for model is TO dirglob input 15 FROM inpglob set this to where your input global data is TO inpglob REGCM_GLOBEDAT and last bits FROM dirout set this to where your output files will be written TO dirout output These modifications just reflect the above directory layout proposed for this tutorial and any of these paths can point anywhere on your system disks The path is limited to 256 characters We are now ready to execute the first program of the RegCM model 5 2 Create the DOMAIN file using terrain The first step is to create the DOM
5. o var edtminx_ocn 0 25 Minimum Precipitation Efficiency x var edtmaxx_ocn 0 50 Maximum Precipitation Efficiency x var pbcmax 150 0 Max depth mb of stable layer b twn LCL amp LFC mincld 150 0 Min cloud depth mb htmin 250 0 Min convective heating htmax 500 0 Max convective heating skbmax 0 4 Max cloud base height in sigma dtauc 30 0 Fritsch amp Chappell 1980 ABE Removal Timescale min ip emanparam minsig 0 95 Lowest sigma level from which convection can originate elcrit_ocn 0 0011 Autoconversion threshold water content g g over ocean elcrit_lnd 0 0011 Autoconversion threshold water content g g over land tlerit 55 0 Below tlcrit auto conversion threshold is zero entp 1 5 sigd 0 05 sigs 0 12 Fraction of precipitation falling outside of cloud omtrain 50 0 Fall speed of rain Pa s omtsnow 5 5 Fall speed of snow Pa s Coefficient of mixing in the entrainment formulation Fractional area covered by unsaturated dndraft coeffr 1 0 Coefficient governing the rate of rain evaporation coeffs 0 8 Coefficient governing the rate of snow evaporation cu 0 7 Coefficient governing convective momentum transport betae 10 0 Controls downdraft velocity scale dtmax 0 9 Max negative parcel temperature perturbation below LFC alphae 0 2 Controls the approach rate to quasi equilibrium damp 0 1 Controls the approach rate to q
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7. 1 In case of the mixed schemes 96 97 98 99 both the selected schemes configuration namelist are read in Note in this case for the schemes only the relevant Ocean or Land control values are used 2 Minimum and maximum values of the fraction of reevaporated water in the downdraft for the Grell scheme is essentially a measure of the precipitation efficiency increasing their value generally decrease convective precipitation 3 Again read carefully the Reference Manual before attempting any tuning and report in any work modification of this parameters 6 1 16 holtslagparam namelist You are allowed here to tune the Holtslag PBL scheme selected above in 6 1 12 with the iblt yp number if selected number is 1 amp holtslagparam ricr_ocn 0 25D0 Critical Richardson Number over Ocean ricr_lnd 0 25D0 Critical Richardson Number over Land zhnew_fac 0 25D0 Multiplicative factor for zzhnew in holtpbl 6 1 17 uwparam namelist You are allowed here to tune the UW PBL scheme selected above in 6 1 12 with the ibltyp number if selected number is 2 amp uwparam iuwvadv 0 O standard T QV QC advection 1 GB01 style advection 1 is ideal for MSc simulation but may have stability issues Efficiency of enhancement of entrainment by cloud evap see Grenier and Bretherton 2001 Mon Wea Rev and Bretherton and Park 2009 J Clim Scaling parameter for stable boundary layer eddy length atwo 15 0D0 rstbl 1 5D0 sc
8. GNU gfortran compiler version gt 4 6 2 Linux with Intel ifort compiler version gt 12 0 3 Linux with Portland pgf95 compiler version gt 11 0 4 Mac OsX with gfortran compiler gt 4 6 from MacPorts 5 IBM AIX with x1f2003 compiler The 4 4 version of the RegCM model relies on the standard GNU autotools to configure and build the model code The first step is to change working directory to REGCM_ROOT and run the configure script giving as arguments the chosen compilers gt cd SREGCM_ROOT gt configure CC icc FC ifort To know the list of arguments that can be given to the configure script the script can be launched with the help command line argument gt configure help The useful arguments to successfully build the model are with netcdf Path to NetCDF installation default NETCDF environment with hdf5 Path to HDF5 installation default HDF5 environment with szip Path to SZIP installation default SZIP environment CC C compiler command CFLAGS C compiler flags LDF LAGS linker flags e g L lt lib dir gt if you have libraries in a nonstandard directory lt lib dir gt 10 LIBS libraries to pass to the linker e g 1 lt library gt CPPFLAGS Objective C C preprocessor flags e g I lt include dir gt if you have headers in a nonstandard directory lt include dir gt CPP C preprocessor FC Fortran compiler command FCFLAGS Fortran compiler flags MPIFC MP
9. Incase of a chemistry simulation type CBMZ or DCCB the global emission files must first be interpolate to the RegCM model grid using the following procedure e Create the RegCM model grid description file to be used by cdo to calculate weghts for a conservative remapping interpolation gt cd REGCM_RUN gt bin emcre_grid test_001 in e Interpolate the global data on the RegCM grid with the interpolation script gt cd REGCM_RUN gt bin interp_emissions test_001 in The cdo program installation is mandatory in this case to perform this step The interpolation is mass conservative and is consistent for any ratio of model resolution global emission resolution Note the programs and script uses the same root path of terrain and icbc programs for input and data directory By default we expect the global emission to be at the same level than e g EIN15 in your data path layout This results in a file named _CHEMISS nc of monthly emission for the whole RCP period You dont need to reprocess the file if you change the date of your simulation as long as you are in the RCP temporal windows for now Historical from 1990 2010 Which scenario to use is controlled by the scenario variable in the physicsparam parameter namelist as above in 6 1 12 2 In function of the value of the chemsimtype parameter the relevant boundary conditions will be produced on the RegCM domain by running 34 gt cd REGCM_RUN gt bin chem_icbc tes
10. Mask to eventually disable variables SRF enable_rad_vars 23 true Mask to eventually disable variables RAD enable_sub_vars 17 true Mask to eventually disable variables SUB enable_sts_vars 17 true Mask to eventually disable variables STS enable_lak_vars 18 true Mask to eventually disable variables LAK enable_opt_vars 13 true Mask to eventually disable variables OPT enable_che_vars 24 true Mask to eventually disable variables CHE dirout output Path where all output will be placed lsync false If sync of output files at every timestep is requested Note it has a performance impact Enabled by default if debug_level gt 2 idiag 0 Enable tendency diagnostic output in the ATM file NOTE output file gets HUGE false This enables paralell input do_parallel_netcdf_in Each processors reads its slice in the input file Enable ONLY in case of HUGE input bandwidth This enables paralell output if the hdf5 netcdf libraries support it and do_parallel_netcdf_out false the model is compiled with enable nc4 parallel Things you need to know here 1 The surface fields are the mean values in the interval specified by the frequency values The dynamical fields are instead the point value at the output time Refer to the Reference Manual Giorgi 2011 for a detailed description of the model output fields 2 If the chemistry or lake model are not enabled the values sp
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12. any of the supported models but we will for now for our test run download just the EIN15 dataset for the year 1990 Jan 01 00 00 00 UTC to Dec 31 18 00 00 UTC gt cd SREGCM_GLOBEDAT gt cd EIN15 gt mkdir 1990 gt cd 1990 gt for type in air hgt rhum uwnd vwnd gt do gt for hh in 00 06 12 18 gt do gt curl o type 1990 hh nc gt ICTP_DATASITE EIN15 1990 S type 1990 hh nc gt done gt done With this datasets we are now ready to go through the RegCM Little Tutorial in the next chapter of this User Guide 14 Chapter 5 Running a test simulation using the model We will in this chapter go through a sample session in using the model with a sample configuration file prepared for this task 5 1 Setting up the run environment The model executables prepared in chapter 3 are waiting for us to use them So let s give them a chance The model test run proposed here requires around 100Mb of disk space to store the DOMAIN and ICBC in input and the output files We will assume here that you the user have already established a convenient directory on a disk partition with enough space identified in the following discussion with REGCM_RUN We will setup in this directory a standard environment where the model can be executed for the purpose of learning how to use it gt cd REGCM_RUN gt mkdir input output gt In sf SREGCM_ROOT bin gt cp SREGCM_ROOT Testing test_001 in
13. bugs 8 1 The Gforge site A new welcoming home for the RegCM Community has been built with the help of Italian National Research Council CNR Democritos Group on the e science Lab E Forge web site https gforge ictp it gf project regem Figure 8 1 The Gforge site collaborative work and that It permits an evolving Latest Blog posts RegCM 4 1 released Posted on 201 by co We are proud to say that RegCM 4 1 version has been released RegCM4 1 has the following upgrades Tropical band option officially enabled and documented General bug fixing cleaning in preprocessing main model postprocessing e Lake Model working again Login Register 3 LE Recently Registered Projects 2012 02 09 x 2011 04 0 2010 02 10 R Downloads On this site you have access with a simple registration to a friendly bug tracking system under the tracker link allowing the users to post problems and bugs they discover It allows posting also of files to give you the opportunity to provide as much information as possible about the environment the model is running at your institution helping us better understand and solve efficiently your problems Help us grow the model to fit your requirements giving the broader user community the benefit of a valuable tool to do better research 43 Chapter 9 Appendices We will review here a sample installation session of software neede
14. directory now contains two more files gt ls 1 input test_001_DOMAIN000 nc test_001_ICBC 1990060100 nc test_001_ICBC 1990070100 nc test_001_LANDUSE test_001_SST nc 17 The ICBC files contain the surface pressure surface temperature horizontal 3D wind components 3D temperature and mixing ratio for the RegCM domain for the period and time resolution specified in the input file Again you may want to use the GrADSNcPlot program to look at file content gt bin GrADSNcPlot input test_001_ICBC 1990060100 nc If not familiar with GrADS program enter in sequence the following commands at the ga gt prompt ga gt q file ga gt set gxout shaded ga gt set mpdset hires ga gt set cint 2 ga gt dts ga gt c ga gt set lon 10 ga gt set lat 43 ga gt set t 1 last ga gt d ts ga gt quit this will plot the interpolated surface temperature field on the X11 window first at first time step and then a time section in one of the domain points for a whole month We are now ready to run the model 5 5 First RegCM model simulation The model has now all needed data to allow you to launch a test simulation the final goal of our little tutorial The model command line now will differ if you have prepared the Serial or the MPI version For the MPI enabled version we will assume that your machine is a dual core processor baseline for current machines even for laptops Change the np 2 argument to the number of processors
15. horizontal resolution in km ptop 5 0 Pressure of model top in cbar clat 45 39 Central latitude of model domain in degrees North hemisphere is positive clon 13 48 Central longitude of model domain in degrees West is negative plat 45 39 Pole latitude only for rotated Mercator Proj plon 13 48 Pole longitude only for rotated Mercator Proj Lambert true latitude low latitude side Lambert true latitude high latitude side Use this to enable a tropical band In this case the ds iproj clat clon parameters are not considered truelatl 30 0 truelath 60 i_band 0 The things you need to know here 1 The different projection engines produce better results depending on the position and extent of the domain In particular regardless of hemisphere e Middle latitudes around 45 degrees Lambert Conformal e Polar latitudes more than 75 degrees Polar Stereographic e Low latitudes up to 30 degrees and crossing the equator Mercator e Crossing more than 45 degrees extent in latitude Rotated Mercator 2 The model hydrostatic engine does not allow a resolution lower than 20km If you want a higher resolution consider using the subgridding scheme ICTP plans to introduce in the future a non hydrostatic compressible core to the RegCM model 21 Lowering the top pressure of the model can give you problems in regions with complex topography Touch the default after thinking twice on that Always s
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17. inpglob directory for files without a domname 1 e like ATM YYYYMMDDHH nc j Nesting control amp fnestparam coarse_outdir coarse_domname globdata RegCM EUROPE Coarse domain output dir if FNEST Coarse domain domname 6 1 8 perturbparam namelist This namelist lets you control to which input field and of what fractional level a perturbation is added at ICBC stage on the input fields It is read by the ICBC program if the ensemble_run parameter in the globdatparam namelist is set to true Perturbation control for ensembles amp perturbparam lperturb_topo perturb_frac_top lperturb_ts f perturb_frac_ts lperturb_ps f perturb_frac_ps lperturb_t f perturb_frac_t lperturb_q f perturb_frac_q lperturb_u f perturb_frac_u lperturb_v f perturb_frac_v false o al al al al al al 0 001D0 Se 0 00 Se 0 00 Se 0 00 Se 0 00 Se 0 00 Se 0 00 DO DO DO DO DO DO va Add perturbation Fractional ue Add perturbation Fractiona va ue Add perturbation Fractiona va ue Add perturbation Fractional va ue Add perturbation Fractiona va ue Add perturbation Fractiona va ue Add perturbation Fractional va ue to of to of to of to of to of to of to of S t S t S t t t h je Zz t m t urface el
18. inside RegCM The default is to use the RegCM BATS Land Model 3 3 Build the model executables Now that everything is hopefully configured you may use the make program to build executables gt make This target will builds all model parts The compilation is started in the whole model tree PreProc Main and PostProc Lot of messages will appear on screen abd at the end all executables are built int the source directories To copy them to a bin directory in the model root or into a bin directory in the path specified with the prefix argument to the configure script esplicitly issue the command gt make install Congratulations You can now go to next step and run a test simulation 11 Chapter 4 Accessing global datasets The first step to run a test simulation is to obtain static data to localize model DOMAIN and Atmosphere and Ocean global model dataset to build initial and boundary conditions ICBC to run a local area simulation ICTP maintains a public accessible web repository of datasets on http clima dods ictp it data d8 cordex We will in the following substitute this URL with a shell variable gt export ICTP_DATASITE http clima dods ictp it data d8 cordex As of now you are requested to download required global data on your local disk storage before any run attempt In the future the ICTP ESP team has planned to make available an OpenDAP THREDDS Server to give remote access to global dataset for creating
19. intelsoft I am now ready to compile software 9 4 Pre requisite library installation The help script will build netCDF V4 and MPI libraries to be used to compile the RegCM model Then we can just execute the script gt prereq_install sh This script installs the netCDF mpi librares in the home regcm intelsoft directory If something goes wrong logs are saved in home regcm intelsoft logs Downloading ZLIB library Downloading HDF5 library Downloading netCDF Library Downloading MPICH2 Library Compiling MPI library Compiled MPI library Compiling zlib Library Compiled zlib library Compiling HDF5 library Compiled HDF5 library Compiling netCDF Library Compiled netCDF C library Compiled netCDF Fortran library Done To link RegCM with this librares use 38008870 PATH home regcm intelsoft bin PATH configure Y 47 CC icc FC ifort CPPFLAGS I home regem intelsoft include LDFLAGS L home regcm intelsoft lib Y LIBS 1netcdff lnetcdf lhdf5_hl lhdf5 1z The admins who must compile the pre requisite libraries are invited to look at the script identifying the various steps The normal user should be content of the last printout message which details how to use the just built libraries to compile RegCM model sources against At run time an environment variable must be added to set correct paths gt export PATH home regem intelsoft bin PATH The above is
20. layers in the RRTM radiation model e Model input output of netCDF files is consistent at all stages using a common library e Fix for tracer gases optical properties in the visible spectra e Relaxing upstream scheme for cloud disabled as it may need reworking e The GrADSNC programs now is able to guess when the data are monthly averages calculated with cdo and use Imo as timestep in the ctl file e All model output is now using the write intrinsic instead of print e A long standing bug in the computation of drag coefficient have been fixed Next release V 5 X e New dynamical core from Giovanni Tumolo semi implicit semi Lagrangian p adaptive Discontinuous Galerkin method three dimensional model The model code is in Fortran 2003 ANSI standard The development is done on Linux boxes and the model is known to run on Oracle Solaris platforms IBM AIX platforms MacOS Mplatforms No porting effort has been done towards non Unix like Operating Systems We will for this User Guide assume that the reference platform is a recent Linux distributon with a bash shell Typographical convention is the following Table 1 1 Conventions S gt gt SSHELL VARIABLE normal shell prompt root shell prompt a Shell variable Any shell variable is supposed to be set by the User with the following example syntax gt export REGCM_ROOT home user RegCM4 4 rc13 Hope you will find this document useful Any error found
21. pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall 45 nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm sse4_1 sse4_2 popent lahf_lm ida dts tpr_shadow vnmi flexpriority ept vpid bogomips 3467 81 clflush size 64 cache_alignment 64 address sizes 36 bits physical 48 bits virtual power management repeated eight time with Processor Ids from 0 to 7 I have a Quad Core Intel with Hyperthreading on this multiply by 2 the reported processor list The processor reports here also to support Intel Streaming SIMD Extensions V4 2 which can be later used to speed up code execution vectorizing floating point operation on any single CPU core 9 2 Chose compiler Depending on the processor we can chose which compiler to use On a Linux box we have multiple choices e GNU Gfortran e G95 Intel ifort compiler e Portland compiler e Absoft ProFortran e NAG Fortran Compiler and for sure other which I may not be aware of All of these compilers have pros and cons so I am just for now selecting one in the pool only to continue the exposition I am not selecting the trivial solution of Gfortran as most Linux distributions have it already packaged and all the other required software as well most complete distribution I am aware of for this is Fedora all needed software is packaged and it is a matter of yum inst
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23. you have on Your platform on my laptop QuadCore I use np 4 e MPI version gt cd REGCM_RUN gt mpirun np 8 bin regcmMPI test_001 in e Serial version 2 gt cd REGCM_RUN gt bin regcmSerial test_001 in Now the model will start running and a series of diagnostic messages will be printed on screen As this is a simulation known to behave well no stoppers will appear so you may want now to have a coffee break and come back in 10 minutes from now At the end of the run the model will print the following message RegCM V4 simulation successfully reached end The output directory now contains four files gt ls output test_001_ATM 1990060100 nc test_001_SRF 1990060100 nc test_001_RAD 1990060100 nc test_001_SAV 1990070100 nc Use regemMPICLM if the CLM version has been configured 2Deprecated Support will be dropped in future releases 18 the ATM file contains the atmosphere status from the model the SRF file contains the surface diagnostic variables and the RAD file contains radiation fluxes information The SAV file stores the status of the model at the end of the simulation period to enable a restart thus allowing a long simulation period to be splitted in shorter simulations To have a look for example at surface fields you may want to use the following command gt bin GrADSNcPlot output test_001_SRF 1990060100 nc Assuming the previous crash course in using GraDS was received you should be a
24. 23 Maximum sigma spacing only used if kz is not 14 18 or 23 nsg 1 For subgridding number of points to decompose If nsg 1 no subgridding is performed CLM3 5 does NOT work with subgridding enabled The things you need to know here 1 In the current version 4 4 the model parallelizes execution dividing the work between the processors with the minimum work per processor is 9 points or a box 3x3 so the maximum number of processors which can be used in a parallel run for the above configuration is roughly 180 2 If a custom number of sigma level is chosen not 14 18 or 23 the actual sigma values are calculated mimimizing the a b coefficients for the equation dsig i dsmax ae epee a 6 1 derived from the recursive relation 20 dsig i a i dsig i 1 6 2 where a i bxa i 1 We at ICTP normally use 18 levels 3 Specifying an nsg number greater than one triggers the subgrid BATS model on There is no plan to extend this feature to CLM3 5 model This affects only surface variable calculations All dynamical variables are calculated still on the coarser grid Rain in the current implementation is also calculated on the coarser grid 6 1 2 geoparam namelist This namelist is used by the terrain program to geolocate the model grid on the earth surface The RegCM model uses a limited number of projection engines The value here are used by the other model programs to assert consistency with the geolocatio
25. AIN file to localize the model on a world region The program which does this for you reading the global databases is terrain To launch the terrain program enter the following commands gt cd REGCM_RUN gt bin terrain test_001 in If everything is correctly configured up to this point the model should print something on stdout and the last lines will be Grid data written to output file Successfully completed terrain fields generation In the input directory the program will write the following two files gt ls input test_001_DOMAINO00 nc test_001_LANDUSE The DOMAIN file contains the localized topography and landuse databases as well as projection information and land sea mask The second file is an ASCII encoded version of the landuse used for modifying it on request We will cover it s usage later on To have a quick look at the DOMAIN file content you may want to use the GrADSNcPlot program gt bin GrADSNcPlot input test_001_DOMAINO000 nc If not familiar with GrADS program enter in sequence the following commands at the ga gt prompt ga gt q file ga gt set gxout shaded ga gt set mpdset hires ga gt set cint 50 ga gt d topo ga gt c ga gt set cint 1 ga gt d landuse ga gt quit this will plot the topography and the landuse on the X11 window 16 5 3 Create the SST using the sst program We are now ready to create the Sea Surface Temperature for the model reading a global datas
26. CT The Abdus Salam International Centre for Theoretical Physics Strada Costiera 11 I 34151 Trieste Italy Earth System Physics Section ESP Regional Climatic Model RegCM User s Guide Version 4 4 Trieste Italy June 4 2015 Filippo Giorgi Nellie Elguindi Stefano Cozzini Fabien Solmon Graziano Giuliani Contents 1 Release Notes 2 Obtaining the model 2 1 Simple Model User 2 8 344 eh Dae eG REE ee ee ee ee eG ee eee ee 2 2 Model Developer s oa ti oh ble Ee SUN cote Se ee Ba eA te eS 3 Installation procedure 3 1 Software requirements s s as 2 28 eRe RPE ie A A E ROPER OR eR Os 3 2 Configuring build 2 eee SA ERE eH eA Ad be 3 2 1 Model configuration at build stage 2 ee ee 3 3 Build the model executables 20 00 0000 000000000000 0004 4 Accessing global datasets Global dataset directory LayoUt en Static Surface Dataset ee ee ee CEM Dataset it aa Sot Becks AR go De WOR badd ie Se a oe oe a hee le CEM 4S Dataset ita et sone ee eA ee Eee ee hele SE ees Sea Surface Temperat re 2 2 44 2 We ea Bar Dear Atmosphere and Land temperature Global Dataset o o n 4 1 4 2 4 3 44 4 5 4 6 5 Running a test simulation using the model Setting up the run environment 2 0 00000 2 eee Create the DOMAIN file using terran aoaaa Create the SST using the sst progra Create the ICBC files using the icbc program 1 2
27. D0 Snow fall speed default is 1 m s zauto_rate_khair 0 355D0 Autoconversion coefficient for kautoconv 2 Autoconversion coefficient for kautoconv 3 Autoconversion coefficient for kautoconv 1 zauto_rate_kessl 1 D 3 zauto_rate_klepi 0 5D 3 rkconv 1 666D 4 rcovpmin 0 1D0 rpecons 5 547D 5 Autoconversion coefficient for kautoconv 4 Minimum precipitation coverage Evaporation constant Kessler 29 6 1 15 grellparam emanparam tiedtkeparam and kfparam namelists You are allowed here to tune the convection scheme selected above in 6 1 12 with the icup_1nd or icup_ocn number if selected number is 2 4 5 amp grellparam shrmin 0 25 Minimum Shear effect on precip eff shrmax 0 50 Maximum Shear effect on precip eff edtmin 0 25 Minimum Precipitation Efficiency edtmax 0 50 Maximum Precipitation Efficiency edtmino 0 25 Minimum Precipitation Efficiency o var edtmaxo 0 50 Maximum Precipitation Efficiency o var edtminx 0 25 Minimum Precipitation Efficiency x var edtmaxx 0 50 Maximum Precipitation Efficiency x var shrmin_ocn 0 25 Minimum Shear effect on precip eff OCEAN points shrmax_ocn 0 50 Maximum Shear effect on precip eff edtmin_ocn 0 25 Minimum Precipitation Efficiency edtmax_ocn 0 50 Maximum Precipitation Efficiency edtmino_ocn 0 25 Minimum Precipitation Efficiency o var edtmaxo_ocn 0 50 Maximum Precipitation Efficiency
28. DOMAIN and ICBC without the need to download the global dataset but just the required subset in space and time using the ICTP web server capabilities to create that subset Our advice to you is to use handy transfer program such as uget but below we will show you how to use command line download tools curl and wget to get data 4 1 Global dataset directory Layout You are suggested to establish a convenient location for global datasets on your local storage Keep in mind that required space for a year of global data can be as large as 8 GBytes Having this in mind we will now consider that you the user have identified on your system or have network access to such a storage resource to store say 100 GB of data and have it reachable on your system under the SREGCM_GLOBEDAT location On this directory you are required to make the following directories gt cd SREGCM_GLOBEDAT gt mkdir SURFACE CLM CLM45 SST EIN15 This does not fill all possible global data sources paths but will be enough for the scope of running the model for testing its capabilities 4 2 Static Surface Dataset The model needs to be localized on a particular DOMAIN The needed information are topography land type classification and optionally lake depth to run the Hostetler lake model and soil texture classification to run the chemistry option with DUST enabled This means downloading four files which are global archives at 30second horizontal resolution on a glob
29. I Fortran compiler command 3 2 1 Model configuration at build stage 1 Enable debug enable debug Enable debugging flags and per processor log file If enabled the model will be compiled using debug flags for the compiler which will allow the use of a debugger such as gdb More diagnostics will also be generated during model run The default is to build production binaries with all optimization flags turned on 2 Serial code using stub MPI library enable mpiserial Use the included MPI replacement library for single processor The model is coded to use an MP library to run in parallel mode using multiple cores processors or run on a cluster To enable instead a serial compilation option a stub MPI library with empty callbacks needs to be compiled and linked to the executable The RegCM team strongly suggest to build MPI enabled model also on standalone systems to take advantage of the multicore capabilities of any modern processor 3 CLM option enable clm Supply this option if you plan on using CLM option This option switches off the default Land model of RegCM derived from BATS1e and enables the use of the Community Land Model V3 5 inside RegCM The default is to use the RegCM BATS Land Model 4 CLM 4 5 option enable clm45 Supply this option if you plan on using CLM45 option This option switches off the default Land model of RegCM derived from BATS 1e and enables the use of the Community Land Model V4 5
30. The domname will control the output file naming convention all generated files will add this prefix to the old V3 naming convention giving you the capability to recognize different runs Try to use always meaningful names 22 2 You can control the final land water mask using the h2opct parameter This parameter can be used to have more land points than calculated by the simple interpolation engine Try it with different values to find best land shapes A zero value means use just the interpolation engine higher values will extend into ocean points the land at land water interface The h2ohgt parameter allows also water points to have elevation greater than zero to avoid wall effects on the coasts 3 A number of flags control the capability of the terrain program to modify on request the class type variables in the DOMAIN file You can modify on request the landuse the texture and the lake land interface Running once the terrain program it will generate for you aside from the DOMAIN file a series of ASCII files you can modify with any text editor Running the terrain program the second time and setting a fudge flag will tell the program to overwrite the selected variable with the modified value in the ASCII file This can be useful for sensitivity experiments in the BATS surface model or to design a scenario experiment 4 Some of the land surface types in BATS have been little tested and used or are extremely simplified and thus should be us
31. adiative forcing is calculated and outputted but there is NO aerosol radiative feedback on climate This can be viewed as a control run option e if equal to 2 there is a feedback of aerosol radiative forcing on climate fields via perturbation of the temperature tendency This can be view as the perturbed run option ichdustemd Choice for parametrisation of dust emission size distribution e if set to 1 the standard scheme s used Alfaro et al Zakey et al 2006 e if set to 2 the revised soil granulometry Kok et al 2011 emission size distribution is used rdstemfac Scaling factor erodibility for tuning DUST emission flux Sparse notes 1 2 Outputs are in netCDF so process with your favorite software The flux and tendency variables as well as radiative forcings are accumulated and averaged between 2 output time steps like precipitations The concentration burden and aerosol optical depth are instantaneous The outputs size can be huge especially for full chemistry and diagnostic options In the future we might have the choice of outputting selected variables only 35 Not every possible dynamical configuration has been tested for the chemistry option so bugs might appear please report CLM enables to calculate on line biogenic volatile hydrocarbon emissions as well as chemical deposition that can be used in RegCM There are some flags to activate when compiling CLM we will update the documentation when
32. al latitude longitude grid of the above data 12 gt cd SREGCM_GLOBEDAT gt cd SURFACE gt curl o GTOPO_DEM_30s nc ICTP_DATASITE SURFACE GIOPO_DEM_30s nc gt curl o GLCC_BATS_30s nc ICTP_DATASITE SURFACE GLCC_BATS_30s nc Optional Lake and Texture datasets gt cd REGCM_GLOBEDAT gt cd SURFACE gt curl o ETOPO_BTM_30s nc ICTP_DATASITE SURFACE ETOPO_BTM_30s nc gt curl o GLZB_SOIL_30s nc ICTP_DATASITE SURFACE GLZB_SOIL_30s nc 4 3 CLM Dataset If you are planning to enable the CLM option in the model you will need a series of files with global land surface characteristics datasets gt cd SREGCM_GLOBEDAT gt cd CLM gt curl o mksrf_fmax nc ICTP_DATASITE CLM mksrf_fmax nc gt curl o mksrf_glacier nc ICTP_DATASITE CLM mksrf_glacier nc gt curl o mksrf_lai nc ICTP_DATASITE CLM mksrf_lai nc gt curl o mksrf_lanwat nc ICTP_DATASITE CLM mksrf_lanwat nc gt curl o mksrf_navyoro_20min nc ICTP_DATASITE CLM mksr f_navyoro_20min nc gt curl o mksrf_pft nc ICTP_DATASITE CLM mksrf_pft nc gt curl o mksrf_soicol_clm2 nc ICTP_DATASITE CLM mksrf_soicol_clm2 nc gt curl o mksrf_soitex 10level nc ICTP_DATASITE CLM mksrf_soitex 10level nc gt curl o mksrf_urban nc ICTP_DATASITE CLM mksrf_urban nc gt curl o pft physiology c070207 ICTP_DATASITE CLM pft physiology c070207 gt curl o pft physiology c070207 readme gt S ICTP_DATASITE CLM pft phy
33. al boundary conditions typically for wind components temperature water vapor and surface pressure These are obtained by interpolation from output from reanalysis of observations or global climate model simulations which thus drive the regional climate model The lateral boundary conditions LBC are provided through the so called relaxation diffusion technique which consists of 1 selecting a lateral buffer zone of n grid point width nspgx 2 interpolating the driving large scale fields onto the model grid 3 applying the relaxation diffusion term da ot where Q is a prognostic variable wind components temperature water vapor surface pressure The first term on the rhs is a Newtonian relaxation term which brings the model solution mod towards the LBC field F n Fi Onc Omod F n F2 A2 QLBC Omod 6 4 23 LBC and the second term diffuses the differences between model solution and LBC F n is an exponential function given by anf ed F n exp ist 6 5 Where n is the grid point distance from the boundary varying from 1 to nspgx n 1 is the outermost grid point n 2 the adjacent one etc The anudge array determines the strength of the LBC forcing and depends on the model level k In practice F n is equal to 1 at the outermost grid point row and decreases exponentially to 0 at the internal edge of the buffer zone nspgd at a rate determined by anudge Larger buffer zones and larger values of
34. ale Higher values mean stronger mixing in stable conditions Czero constant in UW PBL eqn 44a and pgs 856 857 czero 5 869D0 6 1 18 slabocparam namelist Here you define parameter and stage fot the Ocean q flux adjusted mixed layer model amp slabocparam do_qflux_adj false Activate SLAB Ocean model surface fluxes adjust from an already created climatology do_restore_sst true Create during the run the SLAB Ocean model surface fluxes climatology to be used in a subsequent run sst_restore_timescale 5 0D0 Time interval in days in building the g flux adjustment 50 0D0 Depth in meters of the Ocean mixed layer mixed_layer_depth 31 6 1 19 tweakparam namelist This namelist controls the tweaking of the model to obtain custom scenarioes Is enabled if itweak is 1 in 6 1 12 amp tweakparam itweak_sst 0 itweak_temperature 0 itweak_solar_irradiance itweak_greenhouse_gases sst_tweak 0 0D0 temperature_tweak 0 0D0 solar_tweak 0 0D0 0 0 Enable adding sst_tweak to input TS Enable adding temperature_tweak to input T Add solar_tweak to solar constant Multiply gas_tweak_factors to GG concentrations In K In K In W m 2 1367 0 is default solar gas_tweak_factors 1 0D0 1 0D0 1 0D0 1 0D0 1 0D0 co2 CH4 N20 CFC11 CFC12 6 1 20 rrtmparam namelist You are allowed here to tune the RRTM radiative scheme selected above in 6 1 12 with the irrtm number
35. all So let us assume I have licensed the Intel Composer XE Professional Suite 13 0 0 on my laptop My system administrator installed it on the default location under opt intel and I have my shell environment update loading vendor provided script gt source opt intel bin compilervars sh intel64 With some modification the path the script the arguments to the script same step is to be performed for all non GNU compilers in the above list and is documented in the installation manual of the compiler itself In case of Intel to check the correct behaviour of the compiler try to type the following command gt ifort version ifort IFORT 13 0 0 20120731 Copyright C 1985 2012 Intel Corporation All rights reserved I am skipping here any problem that may arise from license installation for any of the compilers so I am assuming that if the compiler is callable it works As this step is usually performed by a system administrator on the machine I am assuming a skilled professional will take care of that 46 9 3 Environment setup We will now use the prereq_install shell script provided in the Tools Scripts directory Given the above environment we can edit the file and decomment the lines relative to the selected compiler Working CC Compiler CC gcc CC icec CC pgcc Working C Compiler CXX g CXX icpc CXX pgCC Working Fortran Compiler FC gfortran FC ifort FC pgf90 Destination directory DEST home regem
36. anudge will yield a greater forcing by the LBC Typically for domain sizes of 100 grid points we use a buffer zone width of 10 12 grid points for large domai In ns this buffer zone can increase to values of 15 or even 20 the model anudge has three increasing values from the lower to the mid and higher troposphere For example for nspgx 10 we use anudge equals to 1 2 3 for the lower mid and upper troposphere respectively This allows a stronger forcing in the upper troposphere to insure a greater consistency of large scale circulations with t he forcing LBC while allowing more freedom to the model in the lower troposphere where local high resolution forcings e g complex topography are more important For nspgx of 15 20 for example anudge values could be increased to 2 3 4 As a rule of thumb the choice of the maximum anudge value should follow the conditions nspgx 1 es anudge k amp boundaryparam nspgx 12 nspgx 1 represent the number of cross point slices on the boundary sponge or relaxation boundary conditions nspgd 12 nspgd 1 represent the number of dot point slices on the boundary sponge or relaxation boundary conditions high_nudge 3 0 Nudge value high range medium_nudge 2 0 Nudge value medium range low_nudge 1 0 Nudge value low range 6 1 6 globdatparam namelist This namelist is used by the sst and icbc ICBC programs You can tell them how to build initial and b
37. aracteristics datasets to the RegCM projected grid The content of the pft physiology c070207 file are described in the pft physiology c070207 readme file All the other pre processing steps are just equal to the one detailed in chapter 5 To run the CLM option in the RegCM model just substitute the executable name gt mpirun np 2 bin regcmMPICLM regcm in Note that the CLM land model is much heavier than the BATS1e model and computing time increases 6 3 The CLM 4 5 options We will now discuss from the user point of view how to use the model setup which need to be activated at configure stage The CLM 4 5 option if activated allows the user to run a simulation using the CLM version 4 5 surface model instead of the default BATS le model We will not here go in deep in the difference between the two models read the Reference Manual for this The executable of the model is different in the case of the CLM 4 5 and is named regcmMPICLM45 Note that in the CLM 4 5 case only the MPI enabled compilation is supported no serial Enable At configure stage see 3 2 1 the option is to be enabled with the right command line argument to the configure script enable clm45 Supply this option if you plan on using CLM45 option This will enable a preprocessing flag and build a different model executable Note that no modifications are needed for any other part of the model but this triggers the building of another pre processing program mksu
38. belongs to me and can be reported to be corrected in future revisions Enjoy Chapter 2 Obtaining the model 2 1 Simple Model User A packed archive file with the model code can be downloaded from http gforge ictp it gf project regem frs and it can be later on decompressed and unpacked using gt tar zxvf RegCM 4 4 0 tar gz 2 2 Model Developer If you plan to become a model developer source code can be obtained via svn The RegCM team strongly encouragethe contributing developers to enroll on the gforge site to always be up to date and to check on line all the news of the package https gforge ictp it gf project regem The correct procedure is first to register on the G forge site then ask the ICTP scientific team head Filippo Giorgi to be enrolled as a model developer After being officially granted the status you will gain access to the model subversion repository Check that Subversion software is installed on your machine typing the following command gt svn version If your system answers command not found refer to your System Administrator or software installation manual of your OS to install the subversion software As an example on Scientific Linux the command to install it as root is gt yum install subversion If Subversion is installed just type the following command gt svn checkout https gforge ictp it svn regem branches regcm core Chapter 3 Installation procedure Whate
39. ble for modifications made by others This License is a kind of copyleft which means that derivative works of the document must themselves be free in the same sense It complements the GNU General Public License which is a copyleft license designed for free software We have designed this License in order to use it for manuals for free software because free software needs free documentation a free program should come with manuals providing the same freedoms that the software does But this License is not limited to software manuals it can be used for any textual work regardless of subject matter or whether it is published as a printed book We recommend this License principally for works whose purpose is instruction or reference 1 APPLICABILITY AND DEFINITIONS This License applies to any manual or other work in any medium that contains a notice placed by the copyright holder saying it can be distributed under the terms of this License Such a notice grants a world wide royalty free license unlimited in duration to use that work under the conditions stated herein The Document below refers to any such manual or work Any member of the public is a licensee and is addressed as you You accept the license if you copy modify or distribute the work in a way requiring permission under copyright law A Modified Version of the Document means any work containing the Document or a portion of it either copied verbatim or with
40. ble to plot the variables in the file This is the end of this little tutorial and in the next chapter we will examine how to configure the model for your research needs 19 Chapter 6 Localizing the model and running your simulation We will examine in this chapter in more detail the namelist configuration file to give you the User a deeper knowledge of model capabilities 6 1 The commented namelist In this section we will show you the commented namelist input file you will find under REGCM_ROOT Doc with the name README namelist All model programs seen so far with the exception of the GrADS helper program use as input this namelist file which is unique to a particular simulation The model input namelist file is composed by a number of different namelists each one devoted to configuring the model capabilities A namelist in the namelist file is identified with a starting amp character followed by namelist name and ends on a single line with the character 6 1 1 dimparam namelist This namelist contains the base X Y Z domain dimension information used by the model dynamic memory allocator to request the Operating System the memory space to store the model internal variables amp dimparam iy 34 This is number of points in the N S direction jx 48 This is number of points in the E W direction kz 18 Number of vertical levels dsmin 0 01 dsmax 0 05 Minimum sigma spacing only used if kz is not 14 18 or
41. ced in all copies and that you add no other conditions whatsoever to those of this License You may not use technical measures to obstruct or control the reading or further copying of the copies you make or distribute However you may accept 52 compensation in exchange for copies If you distribute a large enough number of copies you must also follow the conditions in section 3 You may also lend copies under the same conditions stated above and you may publicly display copies 3 COPYING IN QUANTITY If you publish printed copies or copies in media that commonly have printed covers of the Document numbering more than 100 and the Document s license notice requires Cover Texts you must enclose the copies in covers that carry clearly and legibly all these Cover Texts Front Cover Texts on the front cover and Back Cover Texts on the back cover Both covers must also clearly and legibly identify you as the publisher of these copies The front cover must present the full title with all words of the title equally prominent and visible You may add other material on the covers in addition Copying with changes limited to the covers as long as they preserve the title of the Document and satisfy these conditions can be treated as verbatim copying in other respects If the required texts for either cover are too voluminous to fit legibly you should put the first ones listed as many as fit reasonably on the actual cover and continue
42. d to install the RegCM model The starting point is here a Linux system on a multicore processor box and the final goal is to have an optimized system to run the model I will use bash as my shell and assume that GNU development tools like make sed awk are installed as part of the default Operating System environment as is the case in most Linux distro I will require also for commodity a command line web downloader such as cur1 installed on the system along its development libraries to be used to enable OpenDAP remote data access protocol capabilities of netCDF library Standard file management tools such as tar and gzip and wget are also required The symbol gt will stand for a shell prompt I will assume that the process is performed as a normal system user which will own all the toolchain I will be now just the regcm user 9 1 Identify Processor First step is to identify the processor to know its capabilities gt cat proc cpuinfo This command will ask to the operating system to print processor informations A sample answer on my laptop is processor 2 0 vendor_id Genuinelntel cpu family 6 model 30 model name Intel R Core TM i7 CPU Q 740 1 73GHz stepping w5 cpu MHz 933 000 cache size 6144 KB physical id 0 siblings 8 core id 0 cpu cores 4 apicid 0 initial apicid 0 fpu yes fpu_exception yes cpuid level TI wp yes flags fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
43. e and inflow outflow dependent 4 gt Sponge Perkey amp Kreitzberg MWR 1976 5 gt Relaxation exponential technique isladvec 0 Semilagrangian advection scheme for tracers and humidity 1 0 gt Disabled 1 gt Enable Semi Lagrangian Scheme ibltyp 1 Boundary layer scheme 0 gt Frictionless 1 gt Holtslag PBL Holtslag 1990 2 gt UW PBL Bretherton and McCaa 2004 icup_Ind 4 Cumulus convection scheme Over Land icup_ocn 4 Cumulus convection scheme Over Icean 1 gt Kuo 2 gt Grell 1 3 gt Betts Miller 1986 DOES NOT WORK 4 gt Emanuel 1991 5 gt Tiedtke 1996 6 gt Kain Fritsch 1990 Kain 2004 igce 1 Grell Scheme Cumulus closure scheme 1 gt Arakawa amp Schubert 1974 2 gt Fritsch amp Chappell 1980 ipptls 1 Moisture scheme 1 gt Explicit moisture SUBEX Pal et al 2000 2 gt Explicit moisture Nogherotto Tompkins iocnflx 2 Ocean Flux scheme 1 1 gt Use BATSle Monin Obukhov 2 gt Zeng et al 1998 3 gt Coare bulk flux algorithm snowice only activated with coupling iocnrough 1 Zeng Ocean model roughness formula to use 1 gt 0 0065 ustar ustar egrav 2 gt 0 013 ustar ustar egrav 0 11 visa ustar ipgf 0 Pressure gradient force scheme 0 gt Use full fields 1 gt Hydrostatic deduction with pert temperature iemiss 0 Use computed long wave emissivity lakemod 0 Use lake
44. ecified in the control flags are not considered If nsg is not greater than one in dimparam at 6 1 1 the ifsub flag is not considered 3 For the output directory the path variable has a limit of 256 characters This path must be a local path on disk where the user running the model has write permissions granted 4 The enablevar logical arrays can be used to avoid saving one of the time dependent variables in the output file in the order they are saved in the output file itself Note that geolocation and pressure variables cannot be disabled 27 6 1 12 physicsparam namelist This namelist controls the model physics You have a number of option here and the best way to select the right set is to carefully read the the Reference Manual Giorgi 2011 We are for the purposes of this User Guide not going in detail in here except in saying that probably you will need to run some experiments especially with different cumulus convection schemes before finding out the best model setting Although the mixed convection scheme Grell over land and Emanuel over ocean seems to provide an overall better performance our experience is that there is no scheme that works best everywhere therefore we advice to always do some sensitivity experiments to select the best scheme for your application amp physicsparam iboudy 5 Lateral Boundary conditions scheme 0 gt Fixed 1 gt Relaxation linear technique 2 gt Time dependent 3 gt Tim
45. ed cautiously Specifically the types are sea ice bog marsh irrigated crop glacier If such types are present in a domain the user is advised to carefully check the model behavior at such points and eventually substitute these types with others 5 The inpter directory is expected to contain a SURFACE directory where the actual netCDF global dataset are stored The overall path is limited to 256 characters 6 If the netCDF library is compiled with OpenDAP support an URL can be used as a path in the dirter and inpter variables Note that the 256 character limit for paths holds in the whole program For terrain program you may want to try the following URL http clima dods ictp it thredds dodsC 6 1 4 debugparam namelist This namelist is used by all RegCM programs to enable disable some debug printout In the current release this flag is honored only by the model itself If you are not a developer you may find this flags useless amp debugparam debug_level 0 Currently value of 2 and 3 control previous DIAG flag dbgfrq 3 Interval for printout if debug_level gt 3 Just note that with current implementation the output file syncing is left to the netCDF library If You want to examine step by step the output while the model is running set the debug_level at value 3 6 1 5 boundaryparam namelist Being a limited area model in order to be run RegCM4 requires the provision of meteorological initial and time dependent later
46. et The program which does this for you is the sst program which is executed with the following commands gt cd REGCM_RUN gt bin sst test_001 in If everything is correctly configured up to this point the model should print something on stdout and the last line will be Successfully generated SST The input directory now contains a new file S gt ls input test_001_DOMAINO00 nc test_001_LANDUSE test_001_SST nc The SST file contains the Sea Surface temperature to be used in generating the Initial and Boundary Conditions for the model for the period specified in the namelist file Again you may want to use the GrADSNcPlot program to look at file content gt bin GrADSNcPlot input test_001_SST nc If not familiar with GrADS program enter in sequence the following commands at the ga gt prompt ga gt q file ga gt set gxout shaded ga gt set mpdset hires ga gt set cint 2 ga gt d sst ga gt quit this will plot the interpolated sst field on the X11 window 5 4 Create the ICBC files using the icbc program Next step is to create the ICBC Initial Condition Boundary Conditions for the model itself The program which does this for you is the icbc program executed with the following commands gt cd REGCM_RUN gt bin icbe test_001 in If everything is correctly configured up to this point the model should print something on stdout and the last line will be Successfully completed ICBC The input
47. et al 2011 ichdiag 0 enable writing of additional tracer tendency diagnostics in the output idirect 1 CHoice to enable or not aerosol feedbacks on radiation and dynamics aerosol direct and semi direct effects possible choice 1 or 2 no coupling to dynamic and thermodynamic However the clear sky surface and top of atmosphere aerosol radiative forcings are diagnosed 2 allows aerosol feedbacks on radiative thermodynamic and dynamic fields iindirect 0 Enable sulfate first indirect effect in radiation scheme based on Qian et al 2001 rdstemfac 1 0 Dust emission adjustment factor soil erodibility linearly reduce or increase the dust flux The chemsimtype parameter select one in a number of fixed sets which define the nature and number of chemical species and or transported aerosols together with wich relevant scheme is to be used in the simulation The implemented possible simulation types for the aerosol chemistry options are 1 2 DUST Activate 4 dust bins scheme with on line emission transport and removal SSLT Activate 2 sea salt bins scheme with on line emission transport and removal DUSS Activate Dust and seasalt scheme 6 tracers CARB Activate 4 species organic and black carbon in both hydrophobic and hydrophilic aerosol scheme with on line emission transport and removal SULF Activate SO2 and SO4 tracers with simple sulfate oxidation from oxidant climat
48. evation e perturbation on topo urface temeprature e perturbation on ts urface pressure e perturbation on ps emperature e perturbation on t umidity mixing ratio e perturbation on q onal velocity e perturbation on u eridional velocity e perturbation on v 25 Things you need to know here 1 The perturb_frac should not exceed a percent of the field value The algorithm detail of the applied noise can be found in O Brien et al 2011 6 1 9 restartparam namelist This namelist lets you control the time period the model is currently simulating in this particular run You may want to split longer runs for which you have prepared the ICBC s into shorter runs to schedule HPC resource usage in a more collaborative way with other researcher sharing it the regem model allows restart so be friendly with other research projects which may not have this fortune unless you are late for publication amp r if md md md estartparam rest false If a restart ate0 1990060100 Global start is gdatel most probably atel 1990060100 Start date of this run ate2 1990060200 End date for this run Things you need to know here 1 After the simulation starts on restart NEVER change the mdate0 value The correct scheme for restart is e Set ifrest to true e Set mdatel to the value in mdate2 e Define the new value for mdate2 2 Consider that current RegCM convention is to place midnight of first day of m
49. fully tested The Tiedke and Emmanuel schemes when activated offer a more detailed treatment of convective transport than the simple mixing hypothesis used with other schemes The UW planetary boundary layer option integrate directly the emission and deposition flux terms as part of the calculation of trurbulent tracer tendency 6 2 The CLM options We will now discuss from the user point of view how to use the model setup which need to be activated at configure stage The CLM option if activated allows the user to run a simulation using the CLM surface model instead of the default BATS le model We will not here go in deep in the difference between the two models read the Reference Manual for this The executable of the model is different in the case of the CLM and is named regcmMPICLM Note that in the CLM case only the MPI enabled compilation is supported no serial and no subgridding is possible nsg is always 1 Enable At configure stage see 3 2 1 the option is to be enabled with the right command line argument to the configure script enable clm Supply this option if you plan on using CLM option This will enable a preprocessing flag and build a different model executable Note that no modifications are needed for any other part of the model but this triggers the building of another pre processing program clm2rcn Prepare and run The CLM configuration requires a separate namelist in the namelist input file amp clmpa
50. ghted Averager A comprehensive user guide can be found at http nco sourceforge net nco html Sample usage patterns 1 Get value of tas variable at a particular point for all timesteps with a prescribed format one per line on stdout ncks C H s 6 2f n v tas d iy 16 d jx 16 test_001_SRF 1990060100 nc 2 Extract one timestep of tas from a file and save into a new netCDF file ncks c v tas d time 6 test_001_SRF 1990060100 nc test_001_SRF 1990060212 nc 3 Cat together a year worth of output data for the single tas variable into a single file nercat c v tas test_001_SRF 1990 0100 nc test_001_T2M 1990 nc 40 4 Get the DJF mean value of the tempertaure from a multiyear run test_001_DJF_T2M nc We strongly encourage you to read the on line user guide of the NCO tools You will for sure get a boost on your data manipulation and analysis skills 7 1 3 Climate data Operators CDO The monolithic cdo program from the Max Planck Institut fur Meteorologie implements a really comprehensive collection of command line Operators to manipulate and analyse Climate and NWP model Data either in netCDF or GRIB format There are more than 400 operators available covering the following topics e File information and file operations e Selection and Comparision e Modification of meta data e Arithmetic operations e Statistical analysis e Regression and Interpolation e Vector and spectral Transformations e Formatted I O
51. hysical reality Do not underestimate what you can do at this early stage having a good representation of the surface can lead to valuable results later when the model calculates climatic parameters amp terrainparam domname AQWA Name of the domain Controls naming of input files smthbdy false Smoothing Control flag true gt Perform extra smoothing in boundaries lakedpth false If using lakemod see below produce from terrain program the domain bathymetry ltexture false If using DUST tracer see below produce from terrain program the texture soil dataset lsmoist false Use Satellite Soil Moisture Dataset for initialization of soil moisture fudge_1nd false Fudging Control flag for landuse of grid fudge_lnd_s false Fudging Control flag for landuse of subgrid fudge_tex false Fudging Control flag for texture of grid fudge_tex_s false Fudging Control flag for texture of subgrid fudge_lak false Fudging Control flag for lake of grid fudge_lak_s false Fudging Control flag for lake of subgrid h2opct 50 Surface minimum H20 percent to be considered water h2ohgt false Allow water points to have elevation greater than 0 ismthlev 1 How many times apply the 121 smoothing dirter input Output directory for terrain files inpter globdata Input directory for SURFACE dataset The things you need to know here 1
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53. idt 200000000 0002p eee a S Postprocessing tools TA sCommand Une tools ei aes 5 2 A Ba Eee See a ve Ok See ee ce TA 7 1 1 netCDFlibrary tools e a e e e e a a a e 7 1 2 NetCDF operators NCO 22 2 2 20 Sr eR ne he ee S 7 1 3 Climate data Operators CDO 2 000000 0 00000004 7 2 GrADS program vicio a ee ee BA ee en ee ee Bae eG gt 22 OTADS MS 0 2 4 00 8d ae Ei Pete ile Sede oo eh 7 3 CISL s NCL NCAR Command Language aoaaa 7 4 R Statistical Computing Language CC m nun nn 1 3 Non tres tod Sii 1 Rd ln Benge laa rn on Getting help and reporting bugs 8 1 The Gforge site sore cee Bed E a A Appendices 9 1 Identify Processor 5 2 2 2 we o e e re 9 2 Chose compiler uva u Brenn er Br eh Rare ek aber in Bye 9 3 Environment setup 2 2 2 2 2222 ee Sana Dura Andere Weck fee ie 9 4 Pre requisite library installation 2 2 aaa 2b ee ee Chapter 1 Release Notes RegCM 4 4 is a new step in recoding the RegCM model after the effort put into the RegCM4 version The code base now is actively developed by a community of developers internal and external to ICTP and this work is merged on the Gforge site on gforge ictp it site The main new technical features of the code are summarized in the following points e A number of new global models input layers have been added to preproc stage and we plan to support any request to add a new layer What is needed is just send u
54. if selected number is 1 amp rrtmparam inflgsw 2 0 use the optical properties calculated in prep_dat_rrtm same as standard radiation 2 use RRTM option to calculate cloud optical properties from water path and cloud drop radius iceflgsw 3 Flag for ice particle specification 0 gt ice effective radius r_ec Ebert and Curry 1992 r_ec must be gt 10 0 microns 1 gt ice effective radius r_ec Ebert and Curry 1992 r_ec range is limited to 13 0 to 130 0 microns 2 gt ice effective radius r_k Key Streamer Ref Manual 1996 r_k range is limited to 5 0 to 131 0 microns 3 gt generalized effective size dge Fu 1996 dge range is limited to 5 0 to 140 0 microns dge 1 0315 r_ec ligflgsw 1 Flag for liquid droplet specification 0 gt Compute the optical depths due to water clouds in ATM currently not supported I 1 gt The water droplet effective radius microns is input and the optical depths due to water clouds are computed as in Hu and Stamnes J Clim 6 728 742 1993 inflglw 2 Flag for cloud optical properties as above but for LW iceflglw 3 Flag for ice particle specification as above but for LW ligflglw 1 Flag for liquid droplet specification as above but for LW idrv 0 Flag for calculation of dFdT the change in upward flux as a function of surface temperature 0 off 1 on icld 1 Cloud Overlap hypothesis irng 1 mersenne
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56. ion is in a form called CDL network Common Data form Language that can be viewed edited or serve as input to ncgen thus ncdump and ncgen can be used as inverses to transform data representation between binary and text representations ncdump may also be used as a simple browser for netCDF datasets to display the dimension names and lengths variable names types and shapes attribute names and values and optionally the values of data for all variables or selected variables in a netCDF dataset Sample usage patterns 1 Look at the structure of the data in the netCDF dataset ncdump c test_001_SRF 1990060100 nc 2 Produce a fully annotated one data value per line listing of the data for the variables time and tas using FORTRAN conventions for indices and show the floating point data with only four significant digits of precision and the time values with ISO format ncdump v time tas p 4 t f fortran test_001_SRF 1990060100 nc ncgen program the reverse of the ncdump program generates a netCDF file or a C or FORTRAN program that creates a netCDF dataset from a CDL input Sample usage patterns 1 From a CDL file generate a binary netCDF file ncgen 0o test_001_SRF 1990060100_modif nc test_001_SRF 1990060100 cdl 2 From a CDL file generate a Fortran program to write the netCDF file ncgen f test_001_SRF 1990060100 cdl gt prog f nccopy utility copies an input netCDF file to an output netCDF file in any of the four for
57. l perturbations are introduced in the initial or lateral boundary conditions the model will generally produce different patterns of e g precipitation that appear as sometimes seemingly organized noise when compared to the control simulation This noise depends on domain size and climatic regimes for example it is especially pronounced in warm climate regimes e g tropics or during the summer season and large doamins When doing for example sensitivity experiments to model modifications e g to land use change this internal variability noise can be misinterpreted as a model response to the factor modified Users of RegCM4 should be aware of this when they do sensitivity experiments The best way to filter out this noise is to perform ensembles of simulations and lok at the ensemble averages to extract the real model response from the noise 38 Chapter 7 Postprocessing tools The new netCDF output format allows users to use a number of general purpose tools to postprocess model output files We will in this section do a quick review of some of the Open Source and Free Software ones 7 1 Command line tools Three major set of tools may help you do even complex calculation just from command line prompt 7 1 1 netCDF library tools The netCDF library itself offers three basic tools to play with netCDF archived data ncdump program generates a text representation of a specified netCDF file on standard output The text representat
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59. mat variants if possible and in function of the selected output format add compression filter and or data chunking Sample usage patterns 39 1 Convert a netCDF dataset to a netCDF 4 classic model compressed data file using shuffling to enhance compression level nccopy k 4 d 9 s test_001_SRF 1990060100 nc test_001_SRF 1990060100_compressed nc You can also find in the Tools Programs RegCM_read directory under REGCM_ROOT a sample program to read an output file using the netCDF library you can modify to fit your needs 7 1 2 NetCDF operators NCO This set of tools can be considered a swiss army knife to manage netCDF datasets There are multiple operators and Each operator takes netCDF files as input then operates e g derives new data averages hyperslabs manipulates metadata and produces a netCDF output file The single command style of NCO allows users to manipulate and analyze files interactively or with simple scripts that avoid some overhead of higher level programming environments The major tools are e ncap2 netCDF Arithmetic Processor e ncatted netCDF Attribute Editor e ncbo netCDF Binary Operator e ncea netCDF Ensemble Averager e ncecat netCDF Ensemble Concatenator e ncflint netCDF File Interpolator e ncks netCDF Kitchen Sink e ncpdq netCDF Permute Dimensions Quickly Pack Data Quietly e ncra netCDF Record Averager e ncrcat netCDF Record Concatenator e ncrename netCDF Renamer e ncwa netCDF Wei
60. model ichem 1 Use active aerosol chemical model scenario A1B IPCC Scenario to use in A1B A2 B1 B2 RCP Scenarios in RPC2 6 RCP4 5 RCP6 RCP8 5 idesst 0 Use diurnal cycle sst scheme iseaice 0 Model seaice effects idesseas 0 Model desert seasonal albedo variability iconvlwp 0 Use convective liquid water path as the large scale liquid water path irrtm 0 Use RRIM radiation scheme instead of CCSM iclimao3 0 Use 03 climatic dataset from SPARC CMIP5 isolconst 1 Use a constant 1367 W m 2 instead of the prescribed TSI recommended CMIP5 solar forcing data 28 islab_ocean 0 Activate the SLAB ocean model itweak 0 Enable tweak scenario 6 1 13 subexparam namelist This namelist controls the SUBEX moisture scheme Please consider carefully reporting in your work the tuning you perform on this parameters The parameters below are the ones currently used at ICTP amp subexparam ncld 1 of bottom model levels with no clouds acklland 250E 03 Autoconversion Rate for Land qckloce 250E 03 Autoconversion Rate for Ocean gulland 0 4 Fract of Gultepe eqn qcth when precip occurs guloce 0 4 Fract of Gultepe eqn qcth for ocean rhmax 1 01 RH at whicn FCC 1 0 rh0oce 0 90 Relative humidity threshold for ocean rh0land 0 80 Relative humidity threshold for land tc0 238 0 Below this temperature rh0 begins to approach unity cevaplnd 100E 02
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62. n information written by the terrain program in the DOMAIN file The first step in any application is the selection of model domain and resolution There are no strict rules for this selection which in fact is mostly determined by the nature of the problem and the availability of computing resources The domain should be large enough to allow the model to develop its own circulations and to include all relevant forcings and processes and the resolution should be high enough to capture local processes of interest e g due to complex topography or land surface On the other hand the model computational cost increases rapidly with resolution and domain size so a compromise needs to be usually reached between all these factors This is usually achieved by experience understanding of the problem or trial and error however one tip to remember is to avoid that the boundaries of the domain cross major topographical systems This is because the mismatch in the resolution of the coarse scale lateral driving fields and the model fields in the presence of steep topography may generate spurious local effects e g localized precipitation areas which can affect the model behavior at least in adjacent areas amp geoparam iproj LAMCON Domain cartographic projection Supported values are LAMCON Lambert conformal POLSTR Polar stereographic Doesn t work NORMER Normal Mercator ROTMER Rotated Mercator ds 60 0 Grid point
63. needed to be repeated for any shell which is used to run RegCM programs and can be appended for convenience on the user shell startup scripts 48 Bibliography Giorgi F Regcm version 4 1 reference manual Tech rep ICTP Trieste 2011 O Brien T A L C Sloan and M A Snyder Can ensembles of regional climate model simulations improve results from sensitivity studies Climate Dynamics 37 1111 1118 doi 10 1007 s00382 010 0900 5 2011 R Courant K F and H Lewy ber die partiellen differenzengleichungen der mathematischen physik Mathematische Annalen 100 1 3274 1928 Rew R K and G P Davis Netcdf An interface for scientific data access IEEE Computer Graphics and Applications 10 4 76 82 1990 49 50 GNU Free Documentation License Version 1 3 3 November 2008 Copyright C 2000 2001 2002 2007 2008 Free Software Foundation Inc lt http fsf org gt Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed 0 PREAMBLE The purpose of this License is to make a manual textbook or other functional and useful document free in the sense of freedom to assure everyone the effective freedom to copy and redistribute it with or without modifying it either commercially or noncommercially Secondarily this License preserves for the author and publisher a way to get credit for their work while not being considered responsi
64. o leap year the HadCM has a length of 360 days 30 day months The RegCM4 length of the year has to be the same as in the forcing fields and this can be set in the variable dayspy Please remember to always check the consistency of the length of the year 2 Even if listed not all the input engines are fully tested Some of them need data which have been reformatted by ICTP they are not in the original format with which they are distributed by the institution producing them Some input data are not freely distibutable by ICTP and you need a special agreement with the owner to use them Hopefully the situation is changing and data exchange is becoming more and more the basis for good science in the climatic field 3 For notes on path you can see the above in terrainparam namelist description at 5 6 1 7 fnestparam namelist This namelist is read if the FNEST is selected as dattyp in globdatparam namelist see above in 6 1 6 and permits the user to specify the output directory of the coarse resolution run already completed and the name of the coarse domain i e the domname namelist parameter used in the terrainparam coarse namelist see above in 6 1 3 The nested domain must be contained inside the coarse domain and possibly the nested domain should not overlap the boundary region of the coarse run Those checks are left to the user If nothing is specified or namelist not present default is to search for a directory RegCM inside
65. ology with on line emission transport and removal SUCA Activate both SULF and CARB AERO Activate all DUST SSLT CARB and SULF CBMZ Activate CBMZ gas phase only option 37 tracer are considered here DCCB Activate CBMZ DUST CARB sulfate nitrate ammonium aerosol calculated with the ISORROPIA gas aerosol thermodynamical scheme 50 tracers are considered here The more tracer are used the heavier computationally are the simulations and the outputs The chemistry outputs consist of one netCDF file per tracer named explicitely and containing concentration fields different diagnostics and one netCDF file giving the optical properties of the total aerosol mixture i e aerosol optical depth and radiative forcing For a big domain this can require a huge amount of disk space to store the model results We will now detail the steps required to run a chemistry aerosol simulation with the RegCM model 33 Pre Processing We need to perform a couple of operations in the pre processing stage to prepare input datasets for an aerosol chemistry simulation 1 In the case of a DUST AERO or DCCB simulation we need the model to prepare soil type dataset to be used for dust emission calculation at the terrain program stage The ltexture parameter in the terrainparam namelist see above in 6 1 3 should be set to true 2 After having prepared the static and boundary condition data with the icbc program for the atmosphere we need also
66. ondary conditions amp globdatparam ibdyfrg 6 boundary condition interval hours ssttyp OI_WK Type of Sea Surface Temperature used One in GISST OISST OI2ST OI_WK OI2WK FV_A2 FV_B2 EH5A2 EH5B1 EHA1B EIN75 EIN15 ERSST ERSKT CCSST CA_XX HA_XX EC_XX IP_XX GE_XX l CN_XX dattyp EIN15 Type of global analysis datasets used One in ECMWF ERA40 EIN75 EIN15 EIN25 ERAHI NNRP1 NNRP2 NRP2W GFS11 FVGCM FNEST EH5A2 EH5B1 EHA1B CCSMN ECEXY CA_XX HA_XX EC_XX IP_XX GF_XX CN_XX MP_XX gdatel 1990060100 Start date for ICBC data generation gdate2 1990070100 End data for ICBC data generation calendar gregorian Calendar to use gregorian noleap or 360_day dirglob input Path for ICBC produced input files inpglob globdata Path for ICBC global input datasets ensemble_run false If this is a member of a perturbed ensemble run Activate random noise added to input Look http users ictp it pubregcm RegCM4 globedat htm on how to download them 24 Things you need to know here 1 The gdate time window to build ICBC must be always greater or equal to the time window you plan to run the model in Different GCMs and reanalysis products have different length of the year For example the reanalysis products employ the real year length 365 days real leap years i e and average length of 365 2422 the CCSM has a length of 365 days n
67. onsortium need conversion from GRIB to netCDF e Institut Pierre Simon Laplace CMSA MR f NOAA Geophysical Fluid Dynamics Laboratory ESM2M g Centre National de Recherches Mtorologiques CM5 model h Max Planck Institut fr Meteorologie MPI ESM MR 4 ECHAM 5 dataset A1B in binary format from ICTP A2 converted from GRIB to netCDF using cdo 5 33 years Era Interim average available from ICTP Code for FV model and some CAM 2 4 is present but is obsolete or untested Boundary conditions emissions for tracers both aerosols and chemically active creation from different sources 2D model decomposition is fully tested and model scales easily up to 512 processors what was scaling previously up to 64 processors RCP standard 2 6 4 5 6 0 and 8 5 Greenhouse gas concentration data for historical and future scenarios A new option to use measured total solar irradiance from SOLARIS instead of the previously used hardcoded solar constant Climatological and future 2 6 4 5 and 8 5 scenario data for ozone concentration The CLM 4 5 surface scheme basic physics option is coupled to the RegCM model The Ocean coupling is now hadled with a module which allows the RegCM code to be used as an external library into the RegESM package Experimental new empirical cumulus cloud representation option In the model output each file tipology can be disabled and in each file each output 2D 3D variable can be disable The default is to write all
68. onth as the last timestep in previous month except on first model output file ifrest false It is for this reason better to use as start and end time a month boundary We usually consider a month data file the basic unit of output each time you cross a month a new output file will be created for you 6 1 10 timeparam namelist This namelist contains model internal timesteps used by the model as basic integration timestep and triggers for calling internal parametric schemes amp t dt dt dt dt imeparam 150 time step in seconds rad 30 time interval solar radiation calculated minutes abem 18 time interval absorption emission calculated hours srf 600 time interval at which land model is called seconds Things you need to know here 1 The dynamical hydrostatical core of RegCM requires a fixed timestep and you need to manually find the correct value which permits not to break the CourantFriedrichsLewy condition considering R Courant and Lewy 1928 A good rule of thumb is to have a dt not greater than three times the ds value in km specified in the geoparam namelist at 6 1 2 A greater value may lower computing time but in case of strong advection may lead to non accurate computation or even the violation of CFL condition and the divergence of the solution 2 All the other internal timesteps need to be multiples of the base timestep Note that the units are different so you need to convert the
69. ool from NCAR is an interpreted language designed for scientific data analysis and visualization Noah Diffenbaugh and Mark Snyder have created a website dedicated to visualizing RegCM3 output using the NCAR Command Language NCL These scripts where built using RegCM3 model output converted to netCDF using an external converter They have been adapted to serve as very basic example scripts to process a native RegCM 4 2 output data file or do some data analysis using the NCL language and are available in the Tools Scripts NCL examples directory Travis O Brien from the User Community also contributed sample scripts which may be found under the Tools Scripts NCL directory 7 4 R Statistical Computing Language The R statistical computing language is able with an add on package to load into interal data structure a meteorological field read from a netCDF RegCM output A sample script to load and plot the 2m Temperature at a selected timestep can be used as a reference to develop a real powerful statistical analysis of model results it is under Tools Scripts R 7 5 Non free tools Note that the netCDF format using plugins or native capabilities allows clean access to model output from a number of non free tools like Matlab or IDL For a more complete list of tools you are invited to scroll down the very long list of tools at http www unidata ucar edu software netcdf software html 42 Chapter 8 Getting help and reporting
70. other timesteps in seconds before the check 3 In case of strong surface gradients a low value for the surface timesteps may help the model better describe the interaction with the atmosphere and obtain a stable solution 4 If you hit a non stable condition the restart capability of the model may help find the correct timestep just for a particular period using a different timestep at different times 26 6 1 11 outparam namelist This namelist controls the model output engine allowing you to enable disable any of the output file writeout or to modify the frequency the fields are written in the files goutparam ifsave true Create SAV files for restart savfrq 48 Frequency in hours to create them ifatm true Output ATM atmfrq De Frequency in hours to write to ATM ifrad true Output RAD radfrq 6 Frequency in hours to write to RAD ifsts true Output STS frequence is daily ifsrf true Output SRF srffrq Sir Frequency in hours to write to SRF ifsub true Output SUB subfrq 6 Frequency in hours to write to SUB iflak true Output LAK lakfrq 6 Frequency in hours to write to LAK ifchem true Output CHE ifopt false Output OPT chemfrq 6 Frequency in hours to write to CHE enable_atm_vars 64 true Mask to eventually disable variables ATM enable_srf_vars 30 true
71. pecify clat and clon the central domain point and do fine adjustment of the position moving it around a little bit A little shift in position and some tests can help you obtain a better representation of coastlines and topography at the coarse resolutions If using LAMCON projection take care to place the two true latitudes at around one fourth and three fourth of the domain latitude space to better correct the projection distortion of the domain The pole position for the rotated mercator position should be as near as possible to the center domain position For the i_band parameter selecting this will enable the tropical band experiment and the horizontal resolution will be calculated from the number of jx points The projection is set to Normal Mercator the center of the projection is set to clat 0 0 clon 180 0 and the grid point resolution is calculated as 2 x Tx 6370 0 jx 6 3 Just remember a The model for a tropical band simulation is heavy as the number of points is usually huge to obtain a good horizontal resolution Check any memory limit is disabled on your platform before attempting a run b The model scales well on a cluster with a large number of processors 6 1 3 terrainparam namelist This namelist is used by the terrain program to know how you want to generate the DOMAIN file You can control its work using a number of parameters to obtain what you consider the best representation of the p
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73. ram dirclm input CLM path to Input data produced by clm2rcm If relative It should be how to reach the Input dir from the Run dir Frequency for CLM own output write For CLM Type of land surface parameterization 1 gt using DOMAIN INFO for landmask same as BATS 2 gt using mksrf_navyoro file landfraction for landmask and perform a weighted average over clmfrq 12 imask 1 ocean land gridcells for example tgb tgb_ocean 1 landfraction tgb_land landfraction Things you need to know here 1 The inpter path defined in terrainparam namelist described in 6 1 3 is used also by the clm2rcm program See at 4 3 how to obtain needed datasets 2 The file pft physiology c070207 should be manually copied in the dirclm directory before running the model 3 The clmfrq is relative to the output produced by the CLM model itself and does not control the RegCM model output To know the CLM output file content refer to CLM 3 5 documentation 4 The imask 2 option cannot be used with the icup_1nd or icup_ocn cumulus convection schemes 2 which rely on the BATS le landmask 36 In the case of CLM run the user needs to run after the terrain program the clm2rcm program and copy the pft physiology c070207 in the input directory gt cd REGCM_RUN gt bin terrain regcm in gt bin clm2rcm regcm in gt cp REGCM_GLOBEDAT CLM pft physiology c070207 input The clm2rcm program interpolates global land ch
74. rfdata Prepare and run The CLM45 configuration requires a separate entries in the namelist input file amp clm_inparm fpftcon pft physiology cl30503 nc fsnowoptics snicar_optics_5bnd_c090915 nc fsnowaging snicar_drdt_bst_fit_60_c070416 nc hist_nhtfrg 0 amp clm_soilhydrology_inparm h2osfcflag 1 origflag 0 amp clm_hydrologyl_inparm oldfflag 0 Things you need to know here 1 The namelist 6 1 6 is used also by the mksurfdata program See at 4 4 how to obtain needed datasets 37 2 The hist_nhtfrq is relative to the output produced by the CLM 4 5 model itself and does not control the RegCM model output 3 To know the CLM 4 5 output file content refer to CLM 4 5 documentation In the case of CLM 4 5 run the user needs to run after the terrain program the mksurfdata program gt cd REGCM_RUN gt bin terrain regcm in gt bin mksurfdata regcm in gt cp REGCM_GLOBEDAT CLM pft physiology c070207 input All the other pre processing steps are just equal to the one detailed in chapter 5 To run the CLM 4 5 option in the RegCM model just substitute the executable name gt mpirun np 2 bin regcmMPICLM45 regcm in 6 4 Sensitivity experiments hint Although the LBC forcing does provide a constraint for the model as any RCM RegCM4 is characterized by a certain level of internal variability due to its non liner processes e g convection For example if smal
75. rms of section 4 Replacing Invariant Sections with translations requires special permission from their copyright holders but you may include 55 translations of some or all Invariant Sections in addition to the original versions of these Invariant Sections You may include a translation of this License and all the license notices in the Document and any Warranty Disclaimers provided that you also include the original English version of this License and the original versions of those notices and disclaimers In case of a disagreement between the translation and the original version of this License or a notice or disclaimer the original version will prevail If a section in the Document is Entitled Acknowledgements Dedications or History the requirement section 4 to Preserve its Title section 1 will typically require changing the actual title 9 TERMINATION You may not copy modify sublicense or distribute the Document except as expressly provided under this License Any attempt otherwise to copy modify sublicense or distribute it is void and will automatically terminate your rights under this License However if you cease all violation of this License then your license from a particular copyright holder is reinstated a provisionally unless and until the copyright holder explicitly and finally terminates your license and b permanently if the copyright holder fails to notify you of the violation by some rea
76. s a couple of months worth of data specify format if not netCDF fix a naming convention Just ask we will help you Now supported at SST stage 1 7 3 4 GISST Met Office s Global Ice coverage and Sea Surface Temperatures This data required a pre processing from ASCII to binary and are available from ICTP up to 2002 from clima dods server NOAA Optimal Interpolation SST dataset ECMWF Era Interim SST dataset CMIPS global ocean model datasets a Canadian Centre for Climate Modelling and Analysis CanESM2 b Met Office Hadley Centre HadGEM2 ES c Commonwealth Scientific and Industrial Research Organization Mk3 6 d EC EARTH consortium need conversion from GRIB to netCDF e Institut Pierre Simon Laplace CMSA MR f NOAA Geophysical Fluid Dynamics Laboratory ESM2M g Centre National de Recherches Mtorologiques CM5 model h Max Planck Institut fr Meteorologie MPI ESM MR 5 ECHAM 5 dataset A1B in binary format from ICTP A2 converted from GRIB to netCDF using cdo 6 33 years Era Interim average available from ICTP Code for FV model and some CAM 2 4 is present but is obsolete or untested Supported at ICBC stage 1 ERA Interim and ERA 40 reanalysis 2 NNRP reanalysys V1 and V2 3 CMIPS global atmosphere model datasets a Canadian Centre for Climate Modelling and Analysis CanESM2 b Met Office Hadley Centre HadGEM2 ES c Commonwealth Scientific and Industrial Research Organization Mk3 6 d EC EARTH c
77. siology c070207 readme gt curl o rdirc 05 061026 ICTP_DATASITE CLM rdirc 05 061026 This is the input file for the clm2rcm program see at 6 2 4 4 CLM 4 5 Dataset If you are planning to enable the CLM 4 5 option in the model you will need a series of files with global land surface characteristics datasets gt cd SREGCM_GLOBEDAT gt cd CLM45 gt mkdir megan pftdata snicardata surface gt for dir in megan pftdata snicardata surface do cd dir wget S ICTP_DATASITE CLM45 Sdir 0 A wget A nc 11 no parent base ICTP_DATASITE CLM45 Sdir nd Fri done This is the input file for the mksurfdata program see at 6 3 13 4 5 Sea Surface Temperature The model needs a global SST dataset to feed the model with ocean temperature You have multiple choices for SST data but we will for now for our test run download just CAC OISST weekly for the period 1981 present gt cd SREGCM_GLOBEDAT gt cd SST gt CDCSITE ftp cdc noaa gov pub Datasets noaa oisst v2 gt curl o sst wkmean 1981 1989 nc gt ftp SCDCSITE sst wkmean 1981 1989 nc gt curl o sst wkmean 1990 present nc gt ftp SCDCSITE sst wkmean 1990 present nc 4 6 Atmosphere and Land temperature Global Dataset The model needs to build initial and boundary conditions for the regional scale interpolating on the RegCM grid the data from a Global Climatic Model output The GCM dataset can come from
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79. sonable means prior to 60 days after the cessation Moreover your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means this is the first time you have received notice of violation of this License for any work from that copyright holder and you cure the violation prior to 30 days after your receipt of the notice Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License If your rights have been terminated and not permanently reinstated receipt of a copy of some or all of the same material does not give you any rights to use it 10 FUTURE REVISIONS OF THIS LICENSE The Free Software Foundation may publish new revised versions of the GNU Free Documentation License from time to time Such new versions will be similar in spirit to the present version but may differ in detail to address new problems or concerns See http www gnu org copyleft Each version of the License is given a distinguishing version number If the Document specifies that a particular numbered version of this License or any later version applies to it you have the option of following the terms and conditions either of that specified version or of any later version that has been published not as a draft by the ree Software Foundation If the Document does not specify a ver
80. t_001 in That will result in 6 hourly chemical boundary conditions in your input directory _CHBC nc and or _AEBC nc Run time parameters The other chemparam namelist parameters let you control run time behaviour of the model chemistry and aerosol schemes 1 10 ichsolver relevant for gas phase chemistry options activate the chemical solver CBMZ If different from 1 there is no chemical reactions and the tracer are only emitted transported and removed ichsursrc if set different from 1 the emission term is suppressed and only boundary conditions are generating tracer in the domain ichdrdepo if set different from 1 the dry deposition and sedimentation of tracers is disabled for chemistry species ichremlsc if set different from 1 rainout of chemical species is disabled ichremcvc if set different from 1 washout of chemical species is disabled ichcumtra if set different form 1 the convective transport of tracers is disabled ichdiag if set to 1 the writing of additional diagnostics in the chemistry output is enabled Particularly all the 3D tendency terms advection turbulence convection boundary condition chemistry removal etc of the tracer equation are outputted at the frequency ichfreq This is usefull for budget and sensitivity studies as well as debugging This potentially can generate HUGE files idirect Enable aerosol feedbacks on radiation e if equal to 1 only aerosol r
81. the defined variables but the user may play with the enable_xxx_vars flags to eventually disable variables Some variables cannot be disabled xlat xlon mask topo ps Those are needed for model geolocation Model input is read now in parallel by all processors i e a complete diskless model for computing nodes is not supported each processor needs access to the input data directory Model output can be written in parallel by the model taking advantage of a parallel file system and the mpiio capability of the HDF5 library Model must be compiled with the enable nc4 parallel flag and the namelist option do_parallel_netcdf_io must be set to true As to take advantage from this a particular harware software stack is needed this is NOT the default option Model output files contain when applicable geolocation informations following the CF 1 6 convention IDV can now use this informations except for the rotated mercator projection which is unsupported in the java IDV library Model output variable naming convention and unit of measure shouldi respect the CORDEX experiment guidelines User should report any non conformity The Kallen 1996 algorithm is used to compute Mean Sea Level pressure A Gauss Seidel smoothing has been applied to the Mean Sea Level and the Geopotential Height post processing calculation subroutines Bug Fixing e Cressman type interpolation is used for all Gaussian grids in SST ICBC e Added extra stratospheric
82. to define chemical emissions and chemical boundary conditions The data needed for this second task come from different sources both measurements data or GCM model with a chemistry parametrization active 1 Emission dataset The pre processor can manage CMIP5 RCP and IASA anthropogenic emissions for present day and future emission For this the global RCP emission dataset have first been processed by ICTP to match the species considered in the chemical solver CBMZ and to aggregate different sector of emissions that are present in the RCP fields e g CO emission from biomass burning fossil fuel ship The resulting global files as well as grid informations are publicly available on ICTP site http clima dods ictp it data d8 cordex RCP_EMGLOB_PROCESSED 2 Chemical boundary conditions for important tracersare available through ICTP We use monthly boundary condition coming from global simulations CAM EC EARTH for aerosols following different RCP scenarios HIST future For gas phase species we now have 6 hourly chemical boundary conditions issued from the MOZART CTM Alternatively we can use a climatology representative of monthly average concentrations over the period 2000 2007 coming from the MOZART CTM The oxidant fields used in the simple sulfate scheme is also a climatology coming from MOZART CTM The data are available on ICTP site The steps to prepare the chemistry boundary conditions data are the following 1
83. to permit their use in free software 57
84. ts released under this License under the terms defined in section 4 above for modified versions provided that you include in the combination all of the Invariant Sections of all of the original documents unmodified and list them all as Invariant Sections of your combined work in its license notice and that you preserve all their Warranty Disclaimers The combined work need only contain one copy of this License and multiple identical Invariant Sections may be replaced with a single copy If there are multiple Invariant Sections with the same name but different contents make the title of each such section unique by adding at the end of it in parentheses the name of the original author or publisher of that section if known or else a unique number Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work In the combination you must combine any sections Entitled History in the various original documents forming one section Entitled History likewise combine any sections Entitled Acknowledgements and any sections Entitled Dedications You must delete all sections Entitled Endorsements 6 COLLECTIONS OF DOCUMENTS You may make a collection consisting of the Document and other documents released under this License and replace the individual copies of this License in the various documents with a single copy that is included in the collection provided that you fol
85. twister random generator for McICA COH 6 1 21 chemparam namelist This namelist controls the chemistry and aerosol options in the RegCM model amp chemparam chemsimtype CBMZ a Which chemical tracers to be activated One in DUST Activate 4 dust bins scheme SSLT Activate 2 bins Sea salt scheme DUSS Activate DUST SSLT CARB Activate 4 species black anthropic carbon simulations SULF Activate S02 and S04 tracers SUCA Activate both SUKF and CARB AERO Activate all DUST SSLT CARB and SULF CBMZ Activate gas phase and sulfate 32 ichsolver 1 ichsursre 1 ichdrdepo 1 DCCB Activate CBMZ DUST CARB POLLEN Activate POLLEN transport scheme Activate the gas phase chemical solver CBMZ Enable the emissions fluxes 1 enable tracer surface dry deposition For dust it is calculated by a size settling and dry deposition scheme For other aerosol a dry deposition velocity is simply prescribed further ichebdy 1 Enable reading of chemical boundary conditions otherwise put 0 in boundary conditions ichcumtra 1 enable tracer convective transport ichremlsc 1 enable tracer rainout ichremcve 1 enable tracer washout ichdustemd 1 Choice for parametrisation of dust emission size distribution use the standard scheme Alfaro et al Zakey et al 2 use a revised soil granulometry ref Kok et al emission size distribution Menut et al 2012 Kok
86. uasi equilibrium epmax_ocn 0 999 Maximum precipitation efficiency ocean epmax_l1nd 0 999 Maximum precipitation efficiency land amp tiedtkeparam Actual used scheme Max entrainment iconv 1 2 3 iconv 4 entrmax 1 75D 3 entrdd 3 0D 4 entrpen 1 75D 3 entrscv 3 0D 4 entrmid 1 0D 4 cprcon 1 0D 4 detrpen 0 75D 4 entshalp 2 0D0 rcuc_Ind 0 05D0 rcuc_ocn 0 05D0 Convective cloud cover for rain evporation iconv 4 rcpec_lnd 5 55D 5 Coefficient for rain evaporation below cloud iconv 4 Entrainment rate for cumulus downdrafts Entrainment rate for penetrative convection Entrainment rate for shallow convection iconv 1 2 3 Entrainment rate for midlevel convection iconv 1 2 3 Coefficient for determining conversion iconv 1 2 3 Detrainment rate for penetrative convection iconv 4 shallow entrainment factor for entrorg iconv 4 Convective cloud cover for rain evporation iconv 4 rcpec_ocn 5 55D 5 Coefficient for rain evaporation below cloud iconv 4 rhebc_1lnd 0 7D0 Critical rh below cloud for evaporation iconv 4 rhebc_ocn 0 9D0 Critical rh below cloud for evaporation iconv 4 30 rprc_ind 1 4D 3 conversion coefficient from cloud water iconv 4 rprc_ocn 1 4D 3 conversion coefficient from cloud water iconv 4 amp kfparam kf_trigger 3 Trigger mechanism Allowed values 1 and 3 kf_entrate 0 03D0 Entrainment rate Things you need to know here
87. ucture using the CTL file and one ancillary proj file 1 The grads program allows usage of the pdef BILIN option in the CTL file which allows the user to specify a supplementary file name In this file are stored three lat lon floating point grids which have for each point on the equirectangular grid the indexes i j on the projected grid as well as wind rotation values 2 The grads program allows identifying four dimentional slices of a multidimensional variable as new variables providing them a unique name This is how we are able to see in grads chemical output variables While the GrADSNcPlot program allows interactive plotting and after quitting the grads program removes the CTL file and the proj file the GrADSNcPrepare program only creates this two files allowing share of the proj file between multiple CTL files sharing the same RegCM domain i e it creates just only once the proj file To use the grads program you need to have both this ancillary files together with the data netCDF file To create the CTL file for the history CLM output file you need to provide to the helper programs the path to both the history CLM and the RegCM DOMAIN file as in GrADSNcPrepare clmoutput clm2 h0 2000 07 30 00000 nc test_DOMAIN000 nc A collection of sample grads scripts commonly used at ICTP to plot simulation results can be found in the Tools Scripts GrADS directory under SREGCM_ROOT 7 3 CISL s NCL NCAR Command Language This awesome t
88. ver method is chosen to download the code we assume that you have now on your working directory a new directory named RegCM 4 4 x That directory will be for the rest of this guide referred as REGCM_ROOT All the operations to build the model binaries will be performed in this directory 3 1 Software requirements In order to configure and install the RegCM code the following software are needed 1 2 3 GNU Make program Fortran 2003 compiler One in a C compiler for the serial option enable mpi serial at configure b MPI2 Message Passing Library compiled with the above fortran compiler for parallel runs using multiple core single machines or cluster of machines default Source code for the implementation code was tested with can be obtained at http www open mpi org netCDF Rew and Davis 1990 Format I O library compiled with the above Fortran compiler Source code can be found from ftp ftp unidata ucar edu pub netcdf Optional requirements strongly suggested are 1 HDF5 Format I O Library compiled with the above fortran compiler to enable netCDF V4 features Source code can be obtained at http www hdfgroup org ftp HDF5 current sre Note that some of the input datasets available from ICTP from 2012 DO require this option as we distribute data in the netCDF V4 format Note that current netCDF version 4 3 1 1 4 2 is dependent on HDF5 1 8 12 NCO netCDF Operators for manging netCDF file Most Linu
89. x distribution have this already packed and you should refer to your System Administrator or OS Software Installation manual to obtain it Source code is at http nco sourceforge net sre CDO Climatic data Operators for managing netCDF file Most Linux distribution have this already packed and you should refer to your System Administrator or OS Software Installation manual to obtain it Source code is at https code zmaw de projects cdo files 4 A Scientific Plotting and Data Analysis Software such as e IGES GrADS 2 0 Graphical Analysis and Display System Convenient helpers are packed in RegCM to use GrADS with RegCM netCDF output files Binaries and source code can be obtained from http www iges org grads downloads html e NCL NCAR CISL Command Language The NCL can read netCDF output files and sample scripts can be found in the Tools Scripts NCL directory Binaries and source code can be obtained from http www ncl ucar edu 5 A quick viewer for netCDF files like NcView http meteora ucsd edu pierce ncview_home_page html A script is shipped in the RegCM codebase in the Tools directory to help user compile and install required packages and its usage is detailed in chapter 9 3 2 Configuring build The RegCM Version 4 4 is configured by a configure script which will select the known working configuration for the supported architectures Currently tested and supported configurations OS Compiler are 1 Linux with

Regional Climatic Model RegCM User's Guide - gforge

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