7.3. Climatological pre-processing#

First we will start by preparing surface and boundary conditions from climatological datasets. Those datasets can be downloaded on CROCO website:

https://www.croco-ocean.org/download/

CARS2009	CSIRO Atlas of Regional Seas database. Annual, seasonal and monthly climatology for temperature, salinity, nitrate, phosphate and oxygen
COADS05	Directory of the surface fluxes global monthly climatology at resolution (Da Silva et al., 1994)
GOT99.2	Atlas of the loading tide for M2 S2 N2 K2 K1 O1 P1 Q1
QuikSCAT_clim	QuickSCAT monthly climatology of wind stress
RUNOFF_DAI	River discharge monthly climatology in $m.s^{-3}$ for the 925 largest rivers reaching the ocean (from Dai en Trenberth, 2000)
SST_pathfinder	SST global monthly climatology at a finer resolution (9.28 km) than COADS05, computed from AVHRR-Pathfinder observations from 1985 to 1997 [Casey and Cornillon, 1999]
SeaWifs	Surface chlorophyll-a climatology based on SeaWifs observations
TPX07	Directory of the global model of ocean tides TPXO7 [Egbert and Erofeeva, 2002]
Topo	Location of the global topography dataset at 2° resolution (Smith and Sandwell, 1997). Original data can be found at: http://topex.ucsd.edu/cgi-bin/get_data.cgi
WOA2009	World Ocean Atlas 2009 global datase References list: http://www.nodc.noaa.gov/OC5/WOA09/pubwoa09.html
WOAPISCES	A global dataset for biogeochemical PISCES data (annual and seasonal climatology). References are : Fe and DOC : Aumont and Bopp [2006] Si, O2, NO3, PO4 from WOA2005, DIC and Alkalinity come from Goyet et al.

First you may need to edit start.m, which contains the path to all useful croco_tools Matlab scripts:
```
disp(['Add the paths of the different toolboxes'])
tools_path=['~/croco/croco_tools/'];
croco_path=['~/croco/croco/'];
```
Note

You can use these env variables in matlab by using getenv('ENVVAR'), example: if you have a $tools environment variables for croco_tools, you can write in start.m: tools_path=[getenv('tools') '/'];

Then edit crocotools_param.m, which is the namelist file for Matlab pre-processing: crocotools_param.m is separated into several sections:

1 - Configuration parameters	used by make_grid.m (and others..)
2 - Generic file and directory names	need to match your work architecture
3 - Surface forcing parameters	used by make_forcing.m and by make_bulk.m
4 - Open boundaries and initial conditions parameters	used by make_clim.m, make_biol.m, make_bry.m make_OGCM.m and make_OGCM_frcst.m
5 - Parameters for tidal forcing	used by make_tides.m
6 - Reference date and simulation times	used for make_tides, make_CFSR (or make_NCEP), make_OGCM
7 - Parameters for Interannual forcing	SODA, ECCO, CFSR, NCEP, …
8 - Parameters for the forecast system	used by make_forecast.m
9 - Parameters for the diagnostic tools	used by scripts in `Diagnostic_tools`

The first section is already set for BENGUELA_LR configuration, so you just need to change the second section: directory names:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% 2 - Generic file and directory names
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%
%  CROCOTOOLS directory
%
CROCOTOOLS_dir = ['~/croco/croco_tools/'];
%
%  Run directory
%
RUN_dir=[pwd,'/'];
%
%  CROCO input netcdf files directory
%
CROCO_files_dir=[RUN_dir,'CROCO_FILES/'];
%
%  Global data directory (etopo, coads, datasets download from ftp, etc..)
%
DATADIR=['~/DATA/DATASETS_CROCOTOOLS/'];
%
%  Forcing data directory (ncep, quikscat, datasets download with opendap, etc..)
%
FORC_DATA_DIR = ['~/DATA/'];

Note

The crocotools_param.m is called at the beginning of all Preprocessing script. You do not have to launch it independently.

Now you are ready to launch pre-processing in Matlab: .. note:
```
All the pre-processing scripts used for climatological forcing are in the
``Preprocessing_tools`` directory
```
Launch Matlab, and set up paths:
```
matlab
start
```
Build the grid:
```
make_grid
```
During the grid generation process, the question “Do you want to use editmask ? y,[n]” is asked. The default answer is n (for no). If the answer is y (for yes), editmask, the graphic interface developed by A.Y.Shcherbina, will be launched to manually edit the mask. Otherwise the mask is generated from the unfiltered topography data. A procedure prevents the existence of isolated land (or sea) points.

Finally, a figure illustrates the obtained bottom topography. Note that at his low resolution (1/3°), the topography has been strongly smoothed.

Build the atmospheric forcing: 2 options are available:
- create a forcing file with wind stress (zonal and meridional components), surface net heat flux, surface freshwater flux (E-P), solar shortwave radiation, SST, SSS, surface net sensitivity to SST (used for heat flux correction dQdSST for nudging towards model SST and model SSS)
- or create a bulk file which will be read during the run to perform bulk parameterization of the fluxes using COAMPS or Fairall 2003 formulation. This bulk file contains: surface air temperature, relative humidity, precipitation rate, wind speed at 10m, net outgoing longwave radiation, downward longwave radiation, shortwave radiation, surface wind speed (zonal and meridional components). It also contains surface wind stress (zonal and meridional components), but it is not requested and used in the model (except for specific debugging work). The bulk formulation computes its own wind stress.
```
make_bulk
```
  or:
```
make_forcing
```
  The settings relative to surface forcing are in section 3 of crocotools_param.m. In the case of climatological forcing, the variables are cycled. You can see that here, for the sake of simplicity, we are running the model on a repeating climatological year of 360 days.
  
  A few figures illustrate the wind stress vectors and norm at 4 different periods of the year.
  
  Note
  
  make_bulk creates a forcing file that will be used with the cpp key BULK_FLUX, while make_forcing creates a forcing file containing wind stress directly and will be used when undefined BULK_FLUX. This second option is relevant if your atmospheric forcing comes from an atmospheric model with sufficient output frequency, or/and if your are comparing forced and coupled runs. Otherwise it is suggested to use make_bulk.
  
  Build the lateral boundary conditions: 2 options are available:
```
make_bry
```
  Note
  
  make_bry requests that you have previously run make_forcing to compute Ekman forcing at the surface.
  
  or:
```
make_clim
```
  The settings relative to boundary conditions are in section 4 of crocotools_param.m.
  
  A few figures illustrate vertical sections of temperature.
  
  Note
  
  make_clim interpolates the oceanic forcing fields over the whole domain: only boundary points + the 10 next points are actually used for sponge + nudging. Advantage: sponge + nudging layers at the boundaries, Disadvantage: large amount of unused data.
  
  make_bry interpolates the oceanic forcing fields at the boundary points only. Advantage: light files (useful for long simulations), Disadvantage: no nudging layers (only a sponge layer for smooth transition between the boundaries and the interior values).
  
  Build the initial conditions:
```
make_ini
```

You can look at your generated input files in CROCO_FILES directory: You should have:

croco_grd.nc
croco_ini.nc
croco_blk.nc # or croco_frc.nc
croco_bry.nc # or croco_clm.nc

Summary to create a simple configuration from climatology files: In Matlab, execute the following:

start
make_grid
make_forcing
make_bulk
make_bry       # or make_clim
make_ini

This will create:

croco_grd.nc
croco_frc.nc (or croco_blk.nc)
croco_bry.nc (or croco_clim.nc)
croco_ini.nc