5.2. Set up you own test case#

Example: set up a convection test case: test case that mimic the winter convection happening in the North-Western Mediterranean sea

Create a configuration directory:
```
mkdir ~/CONFIGS/CONVECTION
```

Copy the input files from croco sources:

cd ~/CONFIGS/CONVECTION
cp ~/croco/croco/OCEAN/cppdefs.h .
cp ~/croco/croco/OCEAN/param.h .
cp ~/croco/croco/OCEAN/jobcomp .
cp ~/croco/croco/OCEAN/croco.in .

Edit cppdefs.h, param.h, and croco.in for your new CONVECTION case:
- Add a dedicated key for this test case CONVECTION (in cppdefs.h)
- Set up a flat bottom; 2500 m deep (variable depth in ana_grid.F and follow what is performed under the key BASIN, for instance)
- Set up your grid: 1000x1000x200 grid points (respectively in xi, eta and vertical directions) (parameters LLm0, MMm0, and N in param.h)
- Specify a length and width of 50km in both directions (xi, eta) (variables Length_XI, Length_ETA in ana_grid.F)
- Set up an almost cold start with velocity component fields set to white noise (see in ana_initial.F what is performed for other test cases and fill in arrays u,v) around 0.1 mm/s
- Set up the initial ssh fields to zero (arrays zeta in ana_initial.F)
- Set up the initial stratification (i.e. the temperature and salinity fields) (in ana_initial.F: array t)
- Set up the wind stress forcing (svstr, sustr in analytical.F ; you may follow what is set for INNERSHELF; not necessary)
- Set the permanent heat surface flux (stflx= -500 w/m2 (-500/rho0*Cp) in analytical.F in subroutine ana_stflux_tile)
Warning

In cppdefs.h define your own cpp key CONVECTION, which might be a clone of the key BASIN ; in case we add the salinity (concerning the BASIN case), do not forget to add the keys ANA_SSFLUX and ANA_BSFLUX .

Warning

In croco.in in case we add (with respect to the BASIN case) the salinity do not forget to modify the number of tracers written 2*T and the number of Akt (2*.1.0e-6)

Warning

In croco.in we adjust the time step and ndtfast to reach the stability

Edit the compilation script jobcomp:

# set source, compilation and run directories
#
SOURCE=~/croco/croco/OCEAN
SCRDIR=./Compile
RUNDIR=`pwd`
ROOT_DIR=$SOURCE/..

#
# compiler options
#
FC=$FC

#
# set MPI directories if needed
#
MPIF90=$MPIF90
MPIDIR=$(dirname $(dirname $(which $MPIF90) ))
MPILIB="-L$MPIDIR/lib -lmpi -limf -lm"
MPIINC="-I$MPIDIR/include"

# set NETCDF directories
#
#-----------------------------------------------------------
# Use :
#-lnetcdf           : version netcdf-3.6.3                --
#-lnetcdff -lnetcdf : version netcdf-4.1.2                --
#-lnetcdff          : version netcdf-fortran-4.2-gfortran --
#-----------------------------------------------------------
#
#NETCDFLIB="-L/usr/local/lib -lnetcdf"
#NETCDFINC="-I/usr/local/include"
NETCDFLIB=$(nf-config --flibs)
NETCDFINC=-I$(nf-config --includedir)

Compile the model:
```
./jobcomp > jobcomp.log
```
If compilation is successful, you should have a croco executable in your directory.
Run the model:
- Classical launch command is (but should probably be launched in a dedicated submission job in clusters… see next item):
```
mpirun -np NPROCS croco croco.in
```
  where NPROCS is the number of CPUs you want to allocate. mpirun -np NPROCS is a typical mpi command, but it may be adjusted to your MPI compiler and machine settings.
- OR by using a batch script (e.g. PBS) to launch the model (in clusters), examples are provided:
```
cp ~/croco/croco_tools/job_croco_mpi.pbs .
```
  Edit job_croco_mpi.pbs according to your MPI settings in param.h and launch the run:
```
qsub job_croco_mpi.pbs
```
  Warning
  
  NPROCS needs to be consistent to what you indicated in param.h during compilation
If you want to try another mixing parameterization:
- Add in cppdefs.h, in your CONVECTION case, the following cpp keys dedicated to the closure:
```
#define GLS_MIXING
```
- In croco.in add this lines for GLS history and averages fields
```
gls_history_fields:   TKE  GLS  Lscale
                F     F    F
gls_averages:   TKE  GLS  Lscale
                F     F    F
```
- Recompile, and re-run the model

If you want to add stflux as tanh signal:

in analytical.F:

real*4 r2,RR2
!  Set kinematic surface heat flux [degC m/s] at horizontal
!  RHO-points.
!
    r2= 10**2
    ic = LLm0/2.
    jc = MMm0/2.
    do j=JstrR,JendR
      do i=IstrR,IendR
        RR2 =  (i+iminmpi-ic)*(i+iminmpi-ic)+(jminmpi-jc)*(jminmpi-jc)
        stflx(i,j,itemp)=(-200. -200. * tanh((r2-RR2)/1000.))/rho0/Cp
      enddo
    enddo

Recompile and re-run the model.