Scripps Coupled Ocean-Atmosphere Regional
Contents
1. User modifiable section Please specify the appropiate sponge area by increasing its horizontal mixing coefficients if defined ADRIAO2 elif defined SPINUP_HCS HUMBOLDT CURRENT SYSTEM taken from Southern California Bight sponge areas i fac 4 0 r8 if defined UV VIS2 SOUTH DO j JstrR MIN 6 JendR cff visc2 ng REAL 6 j r8 facxvisc2 ng visc2 ng 6 0_r8 DO i IstrR lendR visc2 r i j cff visc2 p i j cff END DO END DO NORTH DO j MAX JstrR Mm ng 1 6 JendR cff fac visc2 ng amp REAL Mm ng 1 j r8 visc2 ng fac visc2 ng 6 0 r8 DO i IstrR IendR visc2 r i j cff visc2 p i j cff END DO END DO IWEST DO i IstrR MIN 6 IendR DO j MAX JstrR i MIN Mm ng 1 i JendR 13 cff visc2 ng REAL 6 i r8 fac visc2 ng visc2 ng 6 0 r8 visc2 r i j cff visc2 p i j cff END DO END DO endif if defined TS_DIF2 DO j JstrR MIN 6 JendR cff1 tnu2 itemp ng amp REAL 6 j r8 fac tnu2 itemp ng tnu2 itemp ng 6 0 r8 cff2 tnu2 isalt ng amp REAL 6 j r8 fac tnu2 isalt ng tnu2 isalt ng 6 0 r8 DO i IstrR IendR diff2 i j itemp cffi diff2 i j isalt cff2 DO itrc 3 NT ng diff2 i j itrc cffi 4 0 r8 ENDDO END DO END DO DO j MAX JstrR Mm ng 1 6 JendR cff1 fac tnu2 itemp ng amp REAL Mm ng 1 j r8 tnu2 itemp ng amp fac tnu2 itemp ng 6 0 r8 cff2 fac tnu2 isalt ng amp REAL Mm ng 1 j r8 tnu2 isalt ng fac tnu2 isalt ng 6 0 r8 DO i Istr2. scp usr comp cluster Couple_RsmRoms Model ROMS spinup_hes avg_0010 nc One can use ncview to see which initial file to use and which initial month to pick 24 vi coldstart_init m cd Research SCOARv2 Lib preparerun ROMS hcs coldstart gerd rnt_gridload roms20_hcs initfile roms20_hes spinup nc climfile avg_0010 nc rnc_CreatelniFile grd initfile timeindex 3 1 to length t 12 June May 3 is for September matlab coldstart_init exit 7 Folders and files in their appropriate places e Archive folders local machine cd storage mkdir SCOAR output cd mkdir hcs cd mkdir ROMS RSM cd RSM mkdir 2008 cd ROMS mkdir avg dia forc his e Create folders to place files needed for the SCOAR application run LINUX machine cd Couple RsmRoms Model misc mkdir hes cd Couple RsmRoms Lib grids mkdir hcs cd mkdir ROMS RSM cd Couple RsmRoms Lib exec mkdir ROMS hcs RSM hcs e Create folder that would contain the scripts for the application run cd Couple RsmRoms Shell mkdir hcs cp couple Nday sh hes cp Rsm2Roms bulk sh hes cp prepareROMS sh hcs 25 cp uauo sh hcs cp Roms2Rsm sh hcs cp sst_t0 sh hcs e Edit the driver script according to your application needs cd Couple RsmRoms Shell main couple cp main couple sh main couple hcs sh vi main couple hcs sh YYYYS 2008 start year MMS 09 start month DDS 15 start day YYYYE 2008 end year MME 12 end month DD
3. www myroms org 443 gt Subversion Repository Password for username e Type in your password and download of ROMS will commence Directories created Atmosphere Compilers Data Lib Master ROMS svn User Waves makefile e Ensure that your netcdf path and mpif90 location is correct cd Compilers vi Linux pgi mk ifdef USE NETCDF4 NETCDF INCDIR opt pgisoft netcdf4 include NETCDF LIBDIR opt pgisoft netcdf4 lib HDF5 LIBDIR opt pgisoft hdf5 lib else NETCDF_INCDIR share apps netcdf pgi include NETCDF_LIBDIR share apps netcdf pgi lib endif ifdef USE_MPIF90 FC share apps mpich1 pgi bin mpif90 LD FC else LIBS Bdynamic lfmpi pgi Impi pgi Bstatic endif e Turn on MPI and 64 bit setting cd vi makefile USE MPI on USE_MPIF90 on USE LARGE on make c Coupler Need to copy over shell scripts coupler code and auxiliary files e cd Couple RsmRoms Shell scp user home comp Research SCOARv2 102910_Shell tar tar xvf 102910 Shell tar e cd Lib aux files scp user home comp Research SCOARv2 090808_aux tar tar xvf 090808_aux tar e cd codes scp user home comp Research SCOARv2 102910_code tar tar xvf 102910_code tar e Make sure path and directories in compilecode sh is correct then compile compilecode sh 2 Grid Set up The domain is to be created in RSM first since there are certain requisites that must be met for RSM to run smoothly with a given
4. gt amp 1spinuphcs log 4 Executables for RSM and ROMS With the spin up running we now prepare for the SCOAR run Beginning with RSM a RSM e Create folders for RSM model that is specific to our case study cd Couple RsmRoms Model RSM cp r rruns hcs cp r rsm hcs cd hes mv rruns runs 64cpu mv rsm rsm_64cpu cd rem 64cpu def cp r rsm6228r160199 rsm6228r128237 e Specifying number of grid points for domain cd Couple RsmRoms Model RSM hcs rsm 64cpu def rsm6228r128237 vi define h define _igrd_ 128 define jgrd 237 e Specifying definitions for the physics package cd Couple RsmRoms Model RSM hcs rsm 64cpu def vi physics h define CLDSLINGO Slingo cloud scheme define INSA CLD Insa s cloudiness adjustment to Slingo scheme undef CLDADJ empirical cloudiness adjustment define INTERACTIVE STRATUS cloudiness based on cloud water and RH 17 only applicable for predicted cloud water define ICECLOUD cloud water feed into radiation define RAS Relaxed Arakawa Schubert scheme define CLD3 Song You Hong prognostic qc qi qr qs define NEW MPHYS additional option for CLD3 CLD5 CLDWSMMPS define VCI additional option for CLD3 CLD5 CLDWSMMPS define DIFFQ horizontal diffusion of moisture define DIFUC strong horizontal diffusion of cloud water variables to stabilize cloud water prediction schemes and allow for larger time step undef RASC2 RAS wit
5. E 16 end day RESTART no restart option LastNDay Model day for restart gridname hcs name of application rsmNCPU 64 number of CPUs used for RSM romsNCPU 64 number of CPUs used for ROMS Nameit_RSM rsm20_hcs model resolution grid name Nameit ROMS roms20 hcs model resolution grid name BCFile SODA Boundary conditions for ocean model archive yes archive in local computer not cluster archive dir rsm storage SCOAR output hcs RSM archive dir roms storage SCOAR output hcs ROMS nd 30 number of vertical layers in ocean model SSTt0 yes Zuse ROMS SST from spin up run as initial forcing for RSM filterSST no smoothing of SST fields at each coupling needinterp no interpolation between ROMS and RSM grids tiling no tiling between ROMS and RSM grids e NOTE At this point you should check the rest of the shell scripts to make sure you ve accounted for any changes e Transfer grid information files cd Couple_RsmRoms Lib grids scp r userQhome comp Research SCOARv2 Lib grids hcs ROMS Couple RsmRoms Lib grids hcs scp r userQhome comp Research SCOARv2 Lib grids hcs RSM Couple RsmRoms Lib grids hcs If tiling was used then we must also transfer the required file Example scp user home comp Research SCOARv2 Lib grids hces hcs tile txt Couple RsmRoms Lib grids hes e Transfer ROMS initial and template files cd Couple RsmRoms Model misc hcs 26 sftp user home comp cd Research SCOARv2 Lib preparerun ROMS hcs col
6. NUP HCS with HCS ifdef SPONGE if defined ADRIAO2 elif defined HCS Now to make the ROMS executable file oceanM will be created in Couple RsmRoms Model ROMS hcs Od E make Create input file ocean_hcs in Also pretty similar to ocean_spinuphcs in with some adjustments cd Couple RsmRoms Model ROMS hcs cp spinup hcs ocean spinuphcs in ocean hcs in vi ocean hcs in TITLE HUMBOLDT CURRENT SYSTEM MyAppCPP HCS VARNAME varinfo dat Lm 127 Number of I direction INTERIOR RHO points Mm 236 Number of J direction INTERIOR RHO points N 30 Number of vertical levels 20 Ntilel 8 I direction partition NtileJ 8 J direction partition NTIMES 144 DT 600 0d0 NDTFAST 30 NRREC D LcycleRST T NRST 145 LDEFOUT NHIS 145 NDEFHIS 0 NTSAVG 1 NAVG 144 NDEFAVG NTSDIA 1 NDIA 145 NDEFDIA DSTART 0 0d0 days TIDE START 0 0d0 days TIME_REF 0 0d0 yyyymmdd dd GRDNAME ocean grd nc ININAME ocean_ini nc CLMNAME ocean_clm nc BRYNAME ocean_bry nc NFFILES 1 number of forcing files FRCNAME ocean_fre nc forcing file 1 grid 1 RSTNAME ocean rat ne HISNAME ocean bis ne AVGNAME ocean avg nc APARNAM Couple RsmRoms Model ROMS upwelling ROMS External s4dvar in SPOSNAM Couple RsmRoms Model ROMS upwelling ROMS External stations in 21 FPOSNAM Couple_RsmRoms Model ROMS upwelling ROMS Exte
7. R IendR diff2 i j itemp cffi diff2 i j isalt cff2 DO itrc 3 NT ng diff2 i j itrc cffi 4 0 r8 ENDDO END DO END DO DO i IstrR MIN 6 IendR DO j MAX JstrR i MIN Mm ng 1 i JendR cff1 tnu2 itemp ng amp REAL 6 i r8 fac tnu2 itemp ng tnu2 itemp ng 6 0 r8 14 cff2 tnu2 isalt ng amp amp REAL 6 i r8 fac tnu2 isalt ng tnu2 isalt ng 6 0 r8 diff2 i j itemp cffi diff2 i j isalt cff2 DO itrc 3 NT ng diff2 i j itrc cffi 4 0 r8 ENDDO END DO END DO endif e Now to make the ROMS executable file ocean M will be created in Couple RsmRoms Model ROMS spinu hes ed af make e Create input file ocean_spinuphcs in to ensure that ROMS takes in all the right values according the the domain model and cpu specifications Myriad examples can be found in Couple RsmRoms Model ROMS ROMS External Take one for them and modify ac cordingly cd Couple RsmRoms Model ROMS spinup hcs cp 7 Couple RsmRoms Model ROMS ROMS External ocean upwelling in ocean_spinuphcs in vi ocean spinhcs in TITLE HUMBOLDT CURRENT SYSTEM MyAppCPP SPINUP_HCS VARNAME ROMS External varinfo dat Lm 127 Number of I direction INTERIOR RHO points Mm 236 Number of J direction INTERIOR RHO points N 30 Number of vertical levels Ntilel 8 I direction partition NtileJ 8 J direction partition NTIMES 518400 DT 600 0d0 NDTFAST 30 LDEFOUT T NHIS 4820 NDEFHIS 51840 15 NTSAVG NA
8. Scripps Coupled Ocean Atmosphere Regional SCOAR Model User Manual Dian Putrasahan Art Miller and Hyodae 500 This manual shows how to install set it up and run a simple case SCOAR has 3 main components RSM ROMS and the SST flux coupler For help with RSM you can refer to http g rsm wikispaces com For help with ROMS you can refer to https www myroms org wiki index php Documentation_ Portal Check that you have C compiler Fortran90 compiler and adequate space in your system Other programs and toolbox you may want to have for verification purposes and or to prepare the files before running the coupled model would include Matlab R ROMS toolbox IRD and Manu s toolbox GrADS ncview For the purposes of this manual the colors are coded as follows Red is for emphasis Blue for commands in unix linux environment Brown for commands statements in vi editor Green for commands in Matlab or GrADS Black for normal text or comments Some fortran code in vi mode are in black for easier reading with indentations Let s set up and place SCOAR in a directory called Coupled RsmRoms There are 5 main folders for SCOAR Lib Model Run Shell log e Lib contains any auxiliary files codes for the coupler all executable files and all grid preparation files Model as it the name suggests holds all the source code for ROMS and RSM Shell contains all the shell scripts for calling each executable at the appropriate tim
9. VG 4320 NDEFAVG 51840 TNU2 20 0d0 20 0d0 m2 s TNU4 0 0d0 0 0d0 m4 s VISC2 5 0d0 m2 s VISC4 0 0d0 m4 s BLK ZQ 2 0d0 air humidity BLK_ZT 2 0d0 air temperature THETAS 6 5d0 0 lt THETAS lt 20 THETA B 0 0d0 0 lt THETAB lt 1 TCLINE 75 0d0 m DSTART 15 0d0 days TIDE START 0 0d0 days TIME REF 1 0d0 yyyymmdd dd TNUDG 30 0d0 30 040 30 0d0 30 040 30 0d0 30 0d0 days ZNUDG 30 0d0 days M2NUDG 30 0d0 days M3NUDG 30 0d0 days OBCFAC 10 0d0 nondimensional GAMMA2 1 0d0 GRDNAME hcs grid nc ININAME hcs init nc CLMNAME hcs clim nc BRYNAME hes bry nc NFFILES 1 number of forcing files FRCNAME hcs forc nc forcing file 1 grid 1 RSTNAME rst nc HISNAME his nc AVGNAME avg nc e Transfer of files from home computer to cluster home computer 16 cd ROMS IRD toolbox Roms tools Preprocessing tools hcs scp hcs grid nc user comp cluster Couple RsmRoms Model ROMS spinup hcs scp hcs forc nc user comp cluster Couple RsmRoms Model ROMS spinup hcs scp hcs init nc user comp cluster Couple RsmRoms Model ROMS spinup hcs scp hcs bry nc user comp cluster Couple RsmRoms Model ROMS spinup hcs e Initiate spin up run of ROMS LINUX machine cd Couple RsmRoms Model ROMS spinup hcs vi launch64 share apps mpich1 pgi bin mpirun nolocal np 64 machinefile node list oceanM ocean spinuphcs in launch64
10. cotru truth co truth latitude delx delx cos truth rad rerth rad e Make RSM set model up cd Couple RsmRoms Model RSM hcs rsm 64cpu make e Create RSM executable cd Couple RsmRoms Model RSM hcs runs 64cpu configure scr rsim scoar e Account for change in time step in Southern Hemisphere because seasons are in reference to Northern Hemisphere Only needed when doing SH Winter requires shorter time steps because of the the storms passing through vi rsim scoar DELTAT_REG_SPRING 90 DELTAT REG SUMMER 60 DELTAT_REG_FALL 90 DELTAT REG WINTER 100 0 ROMS This is very similar to the ROMS spin up set up except the application name is now HCS instead of SPINUP HCS All conducted in the linux machine e Create folder for ROMS application cd Couple RsmRoms Model ROMS mkdir hcs cd spinup hcs cp r Compilers hcs cp r Master hcs cp r ROMS hcs cp makefile hcs ed 19 cp launch64 hes cp node list hcs Modify makefile provide a name for ROMS application cd hes vi makefile ROMS APPLICATION HCS Create apps h file Similar to spinup hcs h but with some adjustments as noted below for this case study cd ROMS Include mv spinup_hcs h hcs h vi hcs h undef QCORRECTION undef SCORRECTION define BULK FLUXES define COOL_SKIN define LONGWAVE OUT define EMINUSP Ensure that sponge layer is turned on and applied to the case cd Functionals vi ana hmixcoef h Substitute SPI
11. dstart get roms spinup nc cd general forcing mget nc exit e Transfer ROMS files to run ocean model cd Couple RsmRoms Model ROMS hcs cp node list Couple RsmRoms Lib exec ROMS hcs vi launch64 share apps mpich1 pgi bin mpirun nolocal np 64 machinefile node list oceanM ocean in cp launch64 Couple RsmRoms Lib exec ROMS hcs launch64 cp ocean_hes in Couple_RsmRoms Lib exec ROMS hcs ocean64_roms30_day_hes in cp oceanM Couple RsmRoms Lib exec ROMS hcs e Transfer RSM executable file to run atmospheric model cd Couple RsmRoms Model RSM hcs runs 64cpu cp rsim scoar Couple RsmRoms Lib exec RSM hcs rsm 64cpu day 1168 e Create a log dir for keep your log files cd Couple RsmRoms log mkdir hcs log 8 Running SCOAR Now at last we can run the model Typically you would want to run it on a background cd Couple RsmRoms Shell main_couple main couple hcs sh gt amp log hcs log logl amp 27
12. ed to RSM for coupler to work cd Couple RsmRoms Model RSM expser rsm scp user home comp Research SCOARv2 rsim_scoar in cd Couple RsmRoms Model RSM libs etc scp user home comp Research SCOARv2 ieee2grb sst_scoar in cd Couple RsmRoms Model RSM libs etc utils scp user home comp Research SCOARv2 ieee2grb _sst_scoar F Compile added codes cd Couple RsmRoms Model RSM libs etc utils vi Makefile in EXECS date x ifdef x ieee2grb sst x ieee2grb_sst_scoar x mpiset x incdte x ed uf configure libs cd etc utils make Adjustment to allow RSM to use ROMS SST at time t 0 cd Couple RsmRoms Model RSM rsm src rsml vi rsmsmf F Line 215 insert 6 c Kei amp Dian addition May 13 2009 c Attempting to call sfc F so as to use the sfc field at beginning of integration 6 ifdef MP if mype eq master then endif print surface update fhour is fhour print surface update idate is idate ifdef MP endif endif 6 thour 0 call sfc nrsmoi idate 4 idate 2 idate 3 idate 1 fhour 6 c end of addition May 13 2009 C a NS make b ROMS In order to download ROMS you would need to register with the ROMS community http www myroms org Once you have a username and password ROMS maybe downloaded using SVN e svn checkout username username https www myroms org svn src trunk Couple RsmRoms Model ROMS Authentication realm lt https
13. elp for help PRESS ENTER TO PROCEED lt return gt Model choices gsm rsm crsm nhm roms scm gdas cpl return gsm gt rsm Machine architecture Type single thread mpi hybrid return single gt mpi Institution Enter INSTITUTION for list return sio gt sio ecpc esc navo ncar ncep ncsa nersc tacc sdsc or any name return ecpc gt sio Machine CPU type Type MACHINE for list return linux 2 sgi origin ibmsp sun dec nec hp cray t90 t3e es linux mac gt linux Machine nickname Type the machine nickname return atlas gt atlas Compiler Enter COMPILER for list return pgi gt pgi or intel gt pgi Additional options If you need to change mpi version 1 compile in 64 bit no linux distribution 1 linux vsn 0 netcdf vsn 3 debug option no username m0101 enter yes else press enter or no gt lt return gt Model resolution and domain specification 1 through 43 options Type the number associated with your model dimension specification If there is no choice available type 999 return 36 gt 9 Number of pes rsm type number of cpus to use return 4 e 64 Choice of run script rsm Which script do you want to run rcases rsim rsm rsmrt test return test gt e rsm Creates libs rsm rsm runs hist and tmp 14054 You have compiled RSM Node list in your home directory is important cd vi nodelist Files that need to be add
14. er computation e Create forcing and initial nc file template for ROMS cd Research SCOARv2 Lib preparerun ROMS mkdir hcs 23 cd mkdir general forcing coldstart bdry clim ed aj cp create bulk forc init m ROMS hcs general forcing cp coldstart_init m ROMS hcs coldstart cp create clim bdry m ROMS hcs bdry clim cd ROMS hcs general forcing vi create bulk forc init m cd Research SCOARv2 Lib preparerun ROMS hcs general forcing nameit roms20_hcs nameit2 hcs matlab create_bulk_forc_init exit Create boundary files for ROMS Assumes climatology file was already made from SODA products and is named roms20_hcs clim nc cd Research SCOARv2 Lib preparerun ROMS hcs bdry _clim vi create_clim_bdry m nameit roms20_hcs nameit2 hcs dataset 0 96 O dataset for general clim and bdry that has been made from IRD toolbox dataset 1 96 1 WOA2001 Uses IRD toolbox dataset 2 2 SODA Uses Manu s toolbox dataset 3 96 3 Levitus Uses Manu s toolbox BC_dir Research SCOARv2 Lib preparerun ROMS hces bdry_clim elseif dataset nameit roms20_hcs BC _dir Research SCOARv2 Lib preparerun ROMS hcs bdry clim grd rnt gridload nameit clmfile nameit clim nc bryfile nameit bry nc matlab create_clim_bdry exit Create very first initial file for ROMS from spin up run cd Research SCOARv2 Lib preparerun ROMS hcs coldstart
15. es log keeps all the standard outputs that come from running the shell scripts Once SCOAR starts running everything is placed and carried out in the Run folder mkdir Couple RsmRoms cd Couple RsmRoms mkdir Lib Model Run Shell log cd Lib mkdir aux files codes exec grids cd exec mkdir Coupler RSM ROMS cd Model mkdir ROMS RSM misc 1 Download and Installation Check that netcdf has been installed If not go to http www unidata ucar edu software netcdf and download netcdf version tar file tar xvf netcdf 3 6 1 tar cd netcdf 3 6 1 src configure prefix home username netcdf make check make install Set environment for NETCDF a RSM You would need CVS in your system to download RSM You can check this by typing cvs If CVS is not installed in your system go to http www nongnu org cvs and have it installed e Set your environment for CVSROOT example setenv CVSROOT pserver anoncvs rokka ucsd edu rokkal kana cvs server root cpscvs Note that password for user anoncvs is return e Be sure to add current directory to your path in cshrc or equivalent e cd Couple RsmRoms Model RSM e cvs co INSTALL Creates several different directories CVS def expscr instscr makefiles and install executable Interactive installation proceed as follow e install Install G RSM library source and run scripts from cvs repository The default version of this run is trunk install h
16. grid In choosing the number of grid points certain contraints apply e igrd x direction should be a product of the integer powers of 2 3 and 5 Also the integer power of 3 cannot be more than 2 e jgrd y direction must be an odd number To learn more details on this go to http g rsm wikispaces com Choosing a regional domain For the purpose of this study let s take the case for the Humboldt Current System a I Setting up domain in RSM LINUX MACHINE For the Humboldt Current System hcs we want to include 3 upwelling centers 20 228 32 348 36 38S You would want to consider sponge layer when you create your domain So say you want 5S 405 then you d make your domain from 0S to 45S We d like to get at least 600km offshore that would put it to 90W cd Couple RsmRoms Model RSM cd rsm vi define h define _igrd_ 128 define _jgrd_ 237 cd rruns vi rsm RPROJ 0 RTRUTH 20 RORIENT 80 RDELX 20000 RDELY 20000 RCENLAT 20 RCENLON 80 RLFTGRD 63 RBTMGRD 142 prmap rsm ga gt d lat ga gt quit Check the domain Keep changing your number of grid points resolution location of cenlat and cenlon and number of grid points from left and bottom till you get the domain you desire view prmap ctl xdef 129 linear 268 037 0 191 ydef 238 levels 42 842 42 701 42 561 b II Setup domain in ROMS and RSM local computer Here we create grid nc files Note that grdname must NOT con
17. h detarained cloud water like RASV2 vi misc h undef STDAMP Spectral tendency damping scheme for rsm undef STDAMP3 area average log ps correction to be used with stdamp undef NFDR national fire danger rating system Z define SPNG_WID wide original sponge zone in rsml rltbini F undef SPNG NRW narrow sponge zone in rsml rltbini F Configure RSM model cd Couple RsmRoms Model RSM hcs rsm_64cpu make clean configure model Build file directories in RSM that pertains to application case While doing so several things to check for The grid must match and allow SST from ROMS to be used on the initial step t t0 in RSM Edit makefile for source code cd src vi makefile GSM_PROGS share co2 mtn cher sfcl fest pgb sgb sfc0 p2sig RSM_PROGS share rsml sfcl rgsm rmtn rinpg rfcst rpgb 002 5100 p2sig mtn RESCON co2 mtn Check for matching grid especially with rtruth 0 cd sfcl vi rgetarea F Originally on line 53 60 delx rlon2 rlon1 float kgds 02 1 6 delx kgds 12 dx meter on truth latitude dely kgds 13 dy meter on truth latitude orient rloni truth kgds 09 1 e 3 truth latitude cotru truth co truth latitude 18 delx delx cos truth rad rerth rad Modified to include rtruth 20 c delx rlon2 rlon1 float kgds 02 1 delx kgds 12 dx meter on truth latitude dely kgds 13 dy meter on truth latitude orient rloni truth kgds 09 1 e 3 truth latitude truth 20
18. km gridindo grdfile ROMS IRD toolbox Roms _tools Preprocessing tools hcs hcs grid nc gridindo N 30 gridindo thetas 6 5 gridindo thetab 0 0 gridindo tcline 75 gridindo hc 10 gridindo cstfile ROMS Manu _toolbox matlib rgrd rgrd_WorldCstLinePacific mat case roms20_hcs gridindo id gridid gridindo name HCS ROMS 20km gridindo grdfile Research SCOARv2 Lib grids hcs ROMS roms20_hcs grid nc gridindo N 30 gridindo thetas 6 5 gridindo thetab 0 0 gridindo tcline 75 gridindo hc 10 gridindo cstfile ROMS Manu_toolbox matlib rgrd rgrd_WorldCstLinePacific mat case rsm20 hcs gridindo id gridid gridindo name HCS RSM 20km gridindo grdfile Research SCOAR v2 Lib grids hcs RSM rsm20 hcs grid nc gridindo N 30 gridindo thetas 6 5 gridindo thetab 0 0 gridindo tcline 75 gridindo hc 10 gridindo cstfile ROMS Manu _toolbox matlib rgrd rgrd_WorldCstLinePacific mat Create climatology boundary and initial files for ROMS spin up run cd ROMS IRD toolbox Roms tools Preprocessing tools hcs matlab grd rnt gridload hes indir ROMS IRD toolbox Roms tools Preprocessing tools hcs nameof hcs clmfile indir nameof clim nc bryfile indir nameof bry nc initfile indir nameof init nc forcfile indir nameof forc nc rnc_CreateBryFile grd br
19. ne NONLIN EOS define CURVGRID define MASKING define SOLVE3D define SPLINES define OUT DOUBLE define AVERAGES define AVERAGES FLUXES Hifdef NL MODEL define LMD MIXING undef MY25 MIXING ifdef LMD MIXING ii undef DIURNAL SRFLUX define SOLAR SOURCE define LMD RIMIX define LMD CONVEC define LMD NONLOCAL define LMD_SKPP endif else undef LMD_MIXING endif undef CLIM_NUDGING 11 undef CLOSED_OBC ifndef CLOSED_OBC define EASTERN_WALL undef NORTHERN_WALL undef SOUTHERN_WALL undef WESTERN WALL endif undef CLAMPED_BC ifndef CLAMPED_BC define SPONGE define WEST_VOLCONS define SOUTH_VOLCONS define NORTH_VOLCONS define RADIATION 2D ii define WEST FSGRADIENT define WEST M2RADIATION define WEST M2NUDGING define WEST M3RADIATION define WEST M3NUDGING define WEST TRADIATION define WEST TNUDGING define NORTH FSGRADIENT define NORTH M2RADIATION ii define NORTH M2NUDGING define NORTH M3RADIATION define NORTH M9NUDGING define NORTH TRADIATION ii define NORTH TNUDGING define SOUTH FSGRADIENT define SOUTH M2RADIATION define SOUTH M2NUDGING define SOUTH M3RADIATION define SOUTH M3NUDGING define SOUTH TRADIATION define SOUTH TNUDGING endif define ANA BSFLUX define ANA BTFLUX e Ensure that sponge layer is turned on and applied to the case 12 cd Functionals vi ana hmixcoef h ifdef SPONGE
20. rnal floats in BPARNAM Couple RsmRoms Model ROMS upwelling ROMS External bioFasham in SPARNAM Couple_RsmRoms Model ROMS upwelling ROMS External sediment in USRNAME Couple RsmRoms Model ROMS upwelling ROMS External MyFile dat 5 Files containing grid information for ROMS RSM and coupler e Create grid nc files for ROMS and RSM local machine cd Research SCOARv2 Lib grids mkdir hes cd hes mkdir Coupler matlab ROMS RSM grid nc files the same as the one created previously hcs grid nc since grid for ocean and atmosphere is the same Note that grid nc files are named as model resolution_gridname grid nc cp ROMS IRD toolbox Roms tools Preprocessing tools hcs hcs grid nc Research SCOARwv2 Lib gri hcs grid nc cp ROMS IRD toolbox Roms tools Preprocessing tools hcs hcs grid nc Research SCOAR hcs grid nc e Create associated files grid info for ROMS and RSM Since we ll use Manu s toolbox for this check that ROMS Manu_toolbox matlib rnt rnt_ gridinfo m contains the correct locations of the grid nc files cd Research SCOARv2 Lib grids cp gen grid m hcs Coupler cp gridmask m hcs matlab cd hcs Coupler vi gen grid m cd Research SCOARv2 Lib grids hcs Coupler Ensure that all are correctly named model resolution gridname Example in vi editor you can do substitution of all word1 into word2 1 s rsm20_pcr rsm20_hes g 1 s roms10 pcr roms20 hcs g cd matlab vi gridmask m cd Research SCOARv2 Lib grid
21. s hcs matlab rgn1 rsm20 besi rgn2 roms20_hcs cd Coupler matlab gen_grid 22 cd matlab gridmask exit Make text file for tiling purposes No tiling in this case so skip this But below is an example if needed cd Research SCOARv2 Lib grids hcs vi hes_tile txt il Make text file rgrd dat for input into ieee2grib_sst_scoar f rgrd txt contains xlonla xlon2a xlatla xlat2a delx dely ortru idrt ortru gt real orientation of regional polar projection or truth for regional mercater projection needs a at the end idrt gt integer data representation type 0 latlon 1 mercater 2 3 lambert 4 gaussian 5 polar if lonla 95 695 then xlon1a 3604 95 695 264 305 delx and dely are horizontal resolution in metres cd Research SCOARv2 Lib grids hcs RSM vi rgrd dat 268 037 292 485 42 842 2 140 20000 20000 20 1 6 Initial forcing and boundary files for ROMS and RSM RSM only requires initial SST forcing from ROMS spin up run Initial state and boundary condi tions for RSM are provided by NCEP Reanalysis II R2 making RSM a dynamical downscaling of NCEP ROMS on the other hand can use boundary conditions from a variety of sources including Levitus SODA OFES etc Initial state of ROMS can be taken from the spin up run Forcing for ROMS comes from RSM but dependent upon which options are chosen bulk parameterization or not RSM can provide the necessary variables needed for eith
22. tain for the region part Also note that roms and rsm grid is the same This is part of the preparation for ROMS spin up run We will use a mix of ROMS toolboxes IRD toolbox and Manu s toolbox e Set parameters and file names cd ROMS IRD toolbox Roms tools cp r Preprocessing_tools Preprocessing_tools_hcs cd vi romstool_param m title Humboldt Current System Ocean Spin Up config hcs values for dl lonr and latr are taken from prmap ctl dl 0 191 lonr 268 037 0 191 268 037 0 191 129 1 latr 42 842 42 701 42 561 N 30 theta_s 6 5 theta_b 0 he 10 hmin 75 vi make_grid m erdname hcs grid nc vi make_forcing m title Forcing COADS erdname hcs grid nc frcname hes forc nc vi make_clim m title Climatology erdname hcs grid nc frcname hes forc nc clmname hcs clim nc ininame hcs init nc oaname hcs oa nc Preparing the files using matlab matlab make_grid close all make_forcing close all make_clim close all exit Set information of grids in rnt_gridinfo m This is to ensure that matlab would search for the right grid files 3 cases must be provided gridname besi model_resolution_gridname roms20_hcs and rsm20_hcs cd ROMS Manu_toolbox matlib rnt vi rnt gridinfo m case hcs gridindo id gridid gridindo name Humboldt Current System Ocean Spinup 20
23. yfile rnc_SetBryFromClim grd clmfile bryfile rnc CreatelniFile grd initfile If you want to set initial month to June imon 6 rnc_SetInitFromClim grd clmfile initfile imon exit 3 ROMS spin up A spin up for the ocean model is required in order for the ocean state to be stable Typically we would give it a 10 year spin up run The atmosphere itself only requires about 2 days for spin up e Create folder for ROMS application LINUX machine cd Couple RsmRoms Model ROMS mkdir spinup_hcs cp r Compilers spinup_hcs cp r Master spinup_hcs cp r ROMS spinup hcs cp makefile spinup_hcs cp node_list spinup_hcs e Modify makefile provide a name for ROMS application cd spinup_hcs vi makefile ROMS_APPLICATION SPINUP_HCS e Create apps h file to specify all the definitions for the ROMS application Listing of defini tions that can be used are located in Couple RsmRoms Model ROMS ROMS Include cppdefs h Many examples of apps h are located in the same folder Below is a sample for this case study cd ROMS Include vi spinup_hcs h define NL MODEL ifdef NL MODEL undef ADJOINT undef TANGENT endif 10 define UV_ADV define UV COR define UV VIS2 define UV LDRAG undef MIX GEO UV define MIX S UV define TS U3HADVECTION define TS CAVADVECTION define TS DIF2 undef TS_DIF4 undef MIX_GEO_TS define MIX_S_TS define DJ GRADPS define SALINITY define QCORRECTION define SCORRECTION defi
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