Preparation of forcing files ============================ Mesh building with BMGTOOLS ---------------------------- #. Get BMGTOOLS here :: mkdir BMG cp /home/datawork-mars/TOOLS/BATHY/BMGTOOLS/bmg-linux64b-rev1489.tar.gz . tar -xzvf bmg-linux64b-rev1489.tar.gz #. Open the **Create module** in a terminal :: cd create_bmg-5.0.0 ./CreateBMG.sh .. warning :: If a memory is requested put 4GO #. Get the appropriate coastline to build your configuration here :: /home/datawork-croco/datarmor-only/DATA/COASTLINE/BMGTOOLS_FORMAT/france.line /home/datawork-croco/datarmor-only/DATA/COASTLINE/BMGTOOLS_FORMAT/europa.closed.line /home/datawork-croco/datarmor-only/DATA/COASTLINE/BMGTOOLS_FORMAT/med_sea.line #. Create a new project (Top left button) #. Create a grid with the following features (Button on the top right bar) and follow the instructions * Click and drag on the map to define approximatively your domain * In the popup window you can define : * The limits of your area of interest * If you want to choose your grid resolution by meters choose the option **Grid defined by curvilinear mesh size** #. Save your project and check in the directory that you have a file head.TEST with the features of your grid :: TEST0 65.0000000 40.0000000 15.0000000 -20.0000000 0.0500000 0.0833333 5662.40 5563.84 421 501 167 158 190 180 TEST .. image :: FIG/FORMATION/formation_bmg1.png :width: 800px :height: 600px #. Interpolation of the bathymetry on the grid * Get the fortran executable, the associated namelist and the batch :: /home/datawork-mars/TOOLS/BATHY/INTERP/interp_bathy/INTERP_BATHY.exe /home/datawork-mars/TOOLS/BATHY/INTERP/interp_bathy/namelist /home/datawork-mars/TOOLS/BATHY/INTERP/interp_bathy/batch_interp * Build a text file which list the MNT files you want to use and pickup from here :: cat catalog.dat : /home/datawork-croco/datarmor-only/DATA/MNT_HOMONIM/MNT_ATL100m_HOMONIM_WGS84_NM.nc * Edit the namelist :: Choose the grid2grid mode &flags l_interp_soundings2grid=.false. l_interp_grid2grid=.true. l_smooth=.false. l_connect=.false. / &interp_soundings2grid coastfile='/home/datawork-croco/datarmor-only/DATA/TDC/france.line' &interp_grid2grid data_catalog='catalog.cat' l_bathy_bmg=.true. l_closed_line=.true. landvalue=-999 grid_file='RootGrid.nc' nivmoypath='' l_bathy_threshold=.true. bathy_threshold=2.0 mask_method='HXHY' / * Launch the executable :: qsub batch_interp #. Open in another terminal the **Check BMG** module to view and edit (if needed) your bathymetry * Open :: cd check_bmg-5.0.0 ./CheckBMG.sh * Load your grid file (*RootGrid.nc*) and your coastline file * You can edit your grid with the button in the top right pannel with different ways * Single (one mesh ) * Sequential (several meshes in sequential) * Polygon (group of meshes within a polygon) * Rectangle (groupe meshes within a rectangle) You juste have to select the nodes and edit the bathymetry values .. image :: FIG/FORMATION/formation_bmg2.png :width: 600px :height: 400px .. image :: FIG/FORMATION/formation_bmg3.png :width: 600px :height: 400px .. warning :: dont forget to save your project to take into acount your modifications #. Convert the bathymetry and the grid to CROCO framework Preprocessing of files are based on a set of python scripts. On Datarmor you can get a python with vacumm :: module load vacumm/3.4.0 * Get the python script from CROCO directory :: cp -r /home/datawork-croco/datarmor-only/TRAININGS/TRAINING_2021/MARS2CROCO/BATHY . cd BATHY * Edit the python script **convert_bathymars2croco.py** and set user parameters * Launch the script :: python convert_bathymars2croco.py bathy_file.nc ==> You get croco_grd.nc * Check if your bathy seems ok :: ncview croco_grd.nc Build tidal atlas on CROCO grid -------------------------------- To get tide on your OBC, you need an atlas with harmonic constituents on your model grid **croco_grd.nc** * First you also need the following script :: cp /home/datawork-croco/datarmor-only/TRAININGS/TRAINING_2021/MARS2CROCO/TIDES/convert_fes2croco.py . cp /home/datawork-croco/datarmor-only/TRAININGS/TRAINING_2021/MARS2CROCO/TIDES/tides.txt . cp /home/datawork-croco/datarmor-only/TRAININGS/TRAINING_2021/batch_python . * Edit the python script to set the list of constituents you want in your Atlas * The script need the **croco_grd.nc** file so you need to link it the directory :: ln -s ../BATHY/croco_grd.nc . * Run the script :: qsub batch_python .. _OBCIC: 3D Initial and Boundary conditions ----------------------------------- This part deals with generation of OBC and IC for your grid, from an Ocean General Circulation Model (exemple :MERCATOR, HYCOM ..) #. First you have to get the numerical solution which covers your grid and your period of simulation :: /home/datawork-croco/datarmor-only/DATA/MERCATOR_SOLUTION #. The second step is to interpolate this file on your grid. We use a fortran programm for this : * Get the following directory :: cp -r /home/datawork-croco/datarmor-only/TRAININGS/TRAINING_2021/EXTRACT_CROCO . cd EXTRACT * Edit the namelist :: vi IN/namelist * Change the mode (IC or OBC at once) :: &extractmode l_extract_obc=.false. ! compute Open Boundaries Conditions (set to true) l_extract_ic=.false. / ! compute Initial Conditions (set to true) * Change the name of the input file with the MERCATOR file :: &namcoarse file_coarse = 'MERCATOR_PSY2V4.nc' ! name of file containing data to be interpolated * In this section set the name of init and obc file, input bathy file and activate which obc you want to extract :: &namfine head_fine = 'head.useless' ! head.CONF file (a line of the one used in MARS) file_ic='init.nc' ! name of ic output file file_fine_w = 'obc_west.nc' ! name of west obc output file file_fine_e = 'obc_east.nc' ! name of east obc output file file_fine_s = 'obc_south.nc' ! name of south obc output file file_fine_n = 'obc_north.nc' ! name of north obc output file l_obc_west = .false. ! Interpolate west obc ? l_obc_east = .false. ! Interpolate east obc ? l_obc_south = .false. ! Interpolate south obc ? l_obc_north = .false. ! Interpolate north obc ? obc_width = 2 ! width of obc domain, must the same than in MARS file_bathy_fine = 'bathy_rang1_2500_final.nc' * Adpat the parameters for interpolation : * Set l_interpxyz to .false. ==> it enables 2D interpolation with SCRIP and vertical interpolation with splines * If your OGCM model is in SIGMA coordinates set your own intermediate Z vertical profile (used for vertical interpolation sigma to sigma) :: Z=(0:immersion1:dh1_ref,immersion1:immersion2:dh2_ref,immersion2:immersion3:dh3_ref) :: ¶m_interp l_interpxyz = .false. ! rapdist = 6.0 ! only if l_interpxyz=.true. must be <= 6 radius = 20.0e+3 ! only if l_interpxyz=.true. aspect_ratio = 10 ! only if l_interpxyz=.true. dh1_ref=1.0 ! only if OGCM in Sigma (dz between 0 and immersion1) immersion1 =40.0 ! only if OGCM in Sigma (first immersion below 0 in z profil) dh2_ref= 2.0 ! only if OGCM in Sigma (dz between immersion1 and immersion2) immersion2 =60.0 ! only if OGCM in Sigma (second immersion in z profil) dh3_ref=5.0 ! only if OGCM in Sigma (dz between immersion2 and immersion3) immersion3=200.0 ! only if OGCM in Sigma (last immersion in z profil : must be >= MAX(H0) !!!) nextrap = 10 ! 2D spatial extrapolation iteration l_correct_rho=.false. ! correct vertical density instabilities l_complete_prof_first=.false. ! extrapolate Z profils before doing interpolation l_interp_conserv=.true. / ! perform conservative vericale interpolation instead of splines * Launch the executable in batch mode :: qsub batch_extract Build a new configuration with CROCO ===================================== Open a terminal and login to Datarmor :: ssh -X login@datarmor Environment and source code ---------------------------- #. Setup environment * Source this file to set some environment variables :: cd $HOME cp /home/datawork-croco/datarmor-only/TRAININGS/TRAINING_2021/croco_env.* . source croco_env.csh * Build a "CROCO" directory on your $DATAWORK :: cd $work mkdir TRAINING_2021 cd TRAINING_2021 mkdir croco mkdir CONFIGS #. Get the source code :: cp -r $CROCO_DIR/../../SOURCE_CODES/CROCO/croco_git/croco_master/croco croco/. cp -r $CROCO_DIR/../../SOURCE_CODES/CROCO/croco_git/croco_tools croco/. #. Create a new config * Build a directory for your new configuration and get the following scripts from the source code directory :: cd $confs mkdir my_config cd my_config mkdir CROCO_FILES cp $croco/OCEAN/param.h . cp $croco/OCEAN/cppdefs.h . cp $croco/OCEAN/jobcomp . cp $CROCO_DIR/job* . Edit your configuration parameters files ---------------------------------------- #. Setup **param.h** * First section : define your domain dimensions (get xi_rho and eta_rho from **croco_grd.nc**) :: LLm0 = xi_rho-2 ; MMm0=eta_rho-2 #elif defined REGIONAL # elif defined SEINE parameter (LLm0=410, MMm0=180, N=20) ! SEINE * Second section : define your MPI decomposition :: Choose your decomposition so number_procs=NP_XI*NP_ETA #ifdef MPI integer NP_XI, NP_ETA, NNODES parameter (NP_XI=14, NP_ETA=6, NNODES=NP_XI*NP_ETA) * If you are using WET_DRY set the critical depth :: #ifdef WET_DRY real D_wetdry ! Critical Depth for Drying cells # else parameter (D_wetdry=0.4) * Third section :: Number of harmonic components :: #else parameter (Ntides=114) * Fourth section :: Number of river :: #if defined PSOURCE || defined PSOURCE_NCFILE integer Msrc ! Number of point sources parameter (Msrc=9) ! ====== == ===== ======= #endif #. Edit **cppdef.h** : Simple config with only tides at boundaries * Activate *REGIONAL* case :: #define REGIONAL /* REGIONAL Applications */ * Set configuration name (same as **param.h**) :: /* Configuration Name */ # define MEDI5KM * Set MPI parallelisation :: # define MPI * Activate TIDES and define Open boundary conditions according to your domain :: /* Open Boundary Conditions */ # define TIDES # undef OBC_EAST # define OBC_WEST # define OBC_NORTH # undef OBC_SOUTH * In **preselected options** only change these ones : * vertical mixing :: /* Vertical Mixing */ # define GLS_MIXING * Analytical surface fluxes :: /* Surface Forcing */ # undef BULK_FLUX /* Suppression des termes atmospheriques */ # define ANA_SSFLUX /* analytical salinity flux */ # define ANA_STFLUX /* analytical Latent and Sensible flux */ # define ANA_SMFLUX /* surface momentum flux = wind */ # define ANA_SRFLUX /* surface short surface radiative */ # define ANA_SST /* climatological surface temperature */ # define ANA_SSS /* climatological surface salinity */ # undef ANA_TCLIMA /* climatological surface for others tracers */ * Lateral Forcing :: /* Lateral Forcing */ # undef CLIMATOLOGY # define ANA_INITIAL # define ANA_BRY # define FRC_BRY # ifdef FRC_BRY # define Z_FRC_BRY # define M2_FRC_BRY # undef M3_FRC_BRY # undef T_FRC_BRY # endif * Bottom Forcing :: /* Bottom Forcing */ # define ANA_BSFLUX # define ANA_BTFLUX * Desactivate source :: /* Point Sources - Rivers */ # undef PSOURCE # undef PSOURCE_NCFILE # ifdef PSOURCE_NCFILE # define PSOURCE_NCFILE_TS # endif #. Compile the model in batch mode * Edit your job comp and set the source code path :: SOURCE=$croco/OCEAN * Launch the compilation :: qsub job_comp_datarmor.pbs .. note :: you should get a **croco** executable file #. Edit the config input file **croco.in** * Time stepping :: time_stepping: NTIMES dt[sec] NDTFAST NINFO 594000 40 10 1 * **NTIMES** : Number of global time step (dt) you can use this script to get NTIMES given your start and end date :: /home/datawork-croco/datarmor-only/FORMATION/PREPROC/calc_steps.py Duration of your simulation == NTIMES*dt * **dt** : baroclinic time step (depend on your mesh grid size) * **NDTFAST** : number of fast time step in one baroclinic time step * Sigma distribution :: S-coord: THETA_S, THETA_B, Hc (m) 0.0d0 0.0d0 2000.0d0 * Origin date (only) for Netcdf :: start_date: 01-01-1900 00:00:00 * Set the path to your inputs files which should be in a **CROCO_FILES** directory :: grid: filename CROCO_FILES/croco_grd.nc forcing: filename CROCO_FILES/croco_frc_manga16.nc bulk_forcing: filename CROCO_FILES/bidon.nc climatology: filename CROCO_FILES/croco_clm.nc boundary: filename CROCO_FILES/croco_bry.nc initial: NRREC filename -1 CROCO_FILES/croco_ini.nc restart: NRST, NRPFRST / filename 9000 -2 CROCO_FILES/croco_rst.nc history: LDEFHIS, NWRT, NRPFHIS / filename T 90 0 CROCO_FILES/croco_his.nc averages: NTSAVG, NAVG, NRPFAVG / filename 1 2140 0 CROCO_FILES/croco_avg.nc * Choose which variables you want to save in your output (T/F to activate/desactivate) :: primary_history_fields: zeta UBAR VBAR U V wrtT(1:NT) T F F T T 30*T auxiliary_history_fields: rho Omega W Akv Akt Aks Visc3d Diff3d HBL HBBL Bostr Wstr Ustr Vstr Shfl Swfl rsw rlw lat sen HEL F F F F F F F F F F F F F F F F 10*F gls_history_fields: TKE GLS Lscale F F F primary_averages: zeta UBAR VBAR U V wrtT(1:NT) F F F F F 30*T auxiliary_averages: rho Omega W Akv Akt Aks Visc3d Diff3d HBL HBBL Bostr Wstr Ustr Vstr Shfl Swfl rsw rlw lat sen HEL F F F F F F F F F F F F F F F F 10*F gls_averages: TKE GLS Lscale F F F * Set lateral viscosity (ONLY if UV_VIS2 or UV_VIS4 cpp key are enabled) :: lateral_visc: VISC2, VISC4 [m^2/sec for all] 6.34 0. * Set lateral diffusivity (ONLY if UV_DIFF2 or UV_DIFF4 cpp key are enabled) :: tracer_diff2: TNU2(1:NT) [m^2/sec for all] 30*1.d-2 tracer_diff4: TNU4(1:NT) [m^4/sec for all] 30*0.d11 * Set bottom drag :: bottom_drag: RDRG [m/s], RDRG2, Zob [m], Cdb_min, Cdb_max 0.0d-4 5.d-3 3.5d-3 1.d-4 1.d-1 * Barotropic mode :: RDRG superseded by RDRG2 * Baroclinc mode :: RDRG superseded by RDRG2 superseded by Z0B #. Edit **batch_mpt** to set the right number of nodes and walltime (1node=28 procs) :: #PBS -q mpi_3 #PBS -l mem=8gb #PBS -l walltime=10:00:00 #PBS -N CROCO_SEINE #. Launch the model :: qsub batch_mpt #. Visualize * First use ncview :: module load ncview ncview CROCO_FILES/croc_his.nc Custom you configuration ========================== Add a source for a river discharge ----------------------------------- * In **cppdefs.h** you should activate * *PSOURCE* : activate tracer for sources * PSOURCE_NCFILE : if you want to use a chronological discharge (dont use it for now) :: /* Point Sources - Rivers */ # define PSOURCE # undef PSOURCE_NCFILE # ifdef PSOURCE_NCFILE # define PSOURCE_NCFILE_TS # endif * In **param.h** set the number of source points :: #if defined PSOURCE || defined PSOURCE_NCFILE integer Msrc ! Number of point sources parameter (Msrc=5) ! ====== == ===== ======= #endif * Compile your model * Edit **croco.in** file First line is for the number of sources then there should be one line by source :: psource: Nsrc Isrc Jsrc Dsrc Qbar [m3/s] Lsrc Tsrc 1 310 23 0 -900. T T 0. 0. * **Isrc,Jsrc** : Coordinates of point sources * **Dsrc** : Direction of outflow (0 along u, 1 along v) * **Qbar** : Average discharge in m3/s (positive to the North/East, negative to the South/West) * **Lsrc** : Logical for associate tracers to the source (here Temp,Sal) * **Tsrc** : Tracer value (here Temp,Sal) Add a real Atmospheric forcing ------------------------------- * In **cppdefs.h** you should activate * *ONLINE* : Use online interpolation (spatial and temporal) from an meteo model on different grid * *AROME* : data are formatted in MeteoFrance framework * *BULK_FLUX* : Compute bulk fluxes * *BULK_FAIRALL* : use FAIRALL formulation for bulk * *BULK_SMFLUX* : compute surface momentum flux (from wind stress) * *READ_PATM* : Read atmospherical pressure in atm file and use it in the code for bulk and surface pressure gradient :: # define BULK_FLUX # ifdef BULK_FLUX # define BULK_FAIRALL # undef BULK_LW # undef BULK_EP # define BULK_SMFLUX # ifdef BULK_SMFLUX # define BULK_SM_UPDATE # endif # undef SST_SKIN # undef ANA_DIURNAL_SW # define ONLINE # define AROME # define READ_PATM # undef ERA_ECMWF # undef RELATIVE_WIND # else # undef QCORRECTION # undef SFLX_CORR # undef ANA_DIURNAL_SW # endif * Dont forget to remove analytical bulk fluxes :: /* Suppression des termes atmospheriques */ # define ANA_SSFLUX /* surface salinity */ # define ANA_STFLUX /* surface temperature */ # undef ANA_SMFLUX /* surface momentum flux = wind */ # undef ANA_SRFLUX /* surface short surface radiative */ # define ANA_SST # define ANA_SSS * Recompile the model * Go to your configuration directory and make a link to this file :: cd /home1/datawork/login/CROCO/config cd CROCO_FILES ln -s /home/datawork-croco/datarmor-only/DATA/METEOROLOGICAL_FORCINGS/ARPEGE-HR_2017_final.nc . * Now edit the **croco.in** file (see bottom of file) Set begin year, end year and mont, number of records per day in your dataset and the path of the file :: online: byear bmonth recordsperday byearend bmonthend / data path 2017 1 24 2017 12 CROCO_FILES/ARPEGE-HR_2017_final.nc Add 3D IC and OBC ------------------ * First you need to get your IC and OBC files see :ref:`OBCIC` * Edit **cppdefs.h** to activate BRY conditions: * undefine analytical Init and boundary conditions * activate BRY for Tracers (T_FRC_BRY) :: # undef ANA_INITIAL # undef ANA_BRY # define FRC_BRY # ifdef FRC_BRY # define Z_FRC_BRY # define M2_FRC_BRY # undef M3_FRC_BRY # undef T_FRC_BRY # endif * Compile the model * Copy you croco_ic.nc and croco_bry.nc files in the CROCO_FILES diretory * Edit **croco.in** file Set the path to your IC/OBC files :: boundary: filename CROCO_FILES/croco_bry.nc initial: NRREC filename -1 CROCO_FILES/croco_ini.nc .. note :: When you start from an init file the start date of your simulation is the date of the file