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
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
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
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) ! SEINESecond 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 MPIActivate 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 3D Initial and Boundary conditions
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