3. Contents & Architecture#
3.1. Architecture#
A classical work architecture consists in:
croco/croco
croco/croco_tools
CONFIGS
To run a CROCO simulation, you need to follow these 3 steps:
complete the pre-processing (for realistic cases) => see Pre-processing tutorial
set-up the parameters and setting files (
param.h
andcppdefs.h
) and compiled the modelset-up the input file
croco.in
and run the model
CROCO contents, main inputs and setting files are described in the following:
3.2. Contents#
CROCO and its tools are distributed in separate directories croco
and
croco_tools
.
3.2.1. croco#
AGRIF |
Agrif library for nesting |
CVTK |
Regression test library |
MPI_NOLAND_preprocessing |
Fortran utility to determine the optimal MPI decomposition to supress land computation |
MUSTANG |
MUSTANG sediment model source files |
OBSTRUCTION |
OBSTRUCTION module source files |
OCEAN |
CROCO source files |
PISCES |
PISCES biogeochemical model source files |
|
Informations on CROCO version |
SCRIPTS |
Scripts for plurimonth runs, online analysis tools, and coupled simulations |
TEST_CASES |
Test cases namelists and useful files |
XIOS |
XIOS I/O server library |
|
Script to setup your configuration. It creates a configuration directory,
and copy useful files in it from croco and croco_tools sources
|
3.2.2. croco_tools#
CROCO preprocessing tools have been primarily developed under Matlab software by IRD researchers (former Roms_tools).
Note: These tools have been made to build easily regional configurations using climatological data. To use interannual data, some facilities are available (NCEP, CFSR, ERA5, ERA-Interim, QuickScat data for atmospheric forcing, SODA and CMEMS/Mercator for lateral boundaries). However, to use other data, you will need to adapt the scripts. All utilities/toolbox requested for matlab crocotools programs are provided within UTILITIES directory.
3.2.2.1. Scripts#
Aforc_CFSR |
Scripts for the recovery of surface forcing data (based on CFSR reanalysis) for
interannual simulations
|
Aforc_ECMWF |
Scripts for the recovery of surface forcing data (based on ECMWF-ERAinterim simulations) for
interannual simulations
|
Aforc_ERA5 |
Scripts for the recovery of surface forcing data (based on ECMWF-ERA5 simulations) for
interannual simulations
|
Aforc_NCEP |
Scripts for the recovery of surface forcing data (based on NCEP2 reanalysis) for
interannual simulations
|
Aforc_QuikSCAT |
Scripts for the recovery of wind stress from satellite scatterometer data (QuickSCAT) |
Coupling_tools |
Scripts for preparing coupled simulations |
Diagnostic_tools |
A few Matlab scripts for animations and basic statistical analysis |
Forecast_tools |
Scripts for the generation of an operational oceanic forecast system |
Nesting_tools |
Preprocessing tools used to prepare nested models |
Oforc_OGCM |
Scripts for the recovery of initial and lateral boundary conditions from global OGCMs
(SODA [Carton, 2005] or CMEMS/Mercator [Lellouche et al., 2021]) for inter-annual simulations
|
Opendap_tools |
LoadDAP mexcdf and several scripts to automatically download data over the Internet |
Preprocessing_tools |
Preprocessing Matlab scripts (make_grid.m, make_forcing, etc…) |
Rivers |
Scripts to prepare time-varying runoff forcing file and compute the runoff location |
Tides |
Matlab routines to prepare CROCO tidal simulations. Tidal data are derived from the
Oregon State University global models of ocean tides TPXO6 and TPXO7 [Egbert and Erofeeva, 2002]
|
Visualization_tools |
Matlab scripts for the CROCO visualization graphic user interface |
croco_pyvisu |
Python toolbox for CROCO visualization graphic user interface |
3.2.2.2. UTILITIES#
export_fig |
A MATLAB toolbox for exporting publication quality figures : altmany/export_fig |
mask |
Land mask edition toolbox developed by A.Y. Shcherbina. |
mex60 |
Matlab NetCDF interface for 32 & 64 bits Linux architectures and old matlab version: 6 and before |
mexcdf/mexnc |
Matlab NetCDF interface for 32 & 64 bits Linux architectures, MatlabR14sp1 until R2008a
(http://mexcdf.sourceforge.net/downloads/mexcdf-R2008a.r2691.zip). For next releases of Matlab,
R2008b, R2009a, it is more simpler, either use the native NetCDF toobox of matlab or use the
last release of mexcf at the same url for version after R2008a.
|
mexcdf/netcdf_toolbox |
The Matlab NetCDF toolbox available in the same mexcdf package. |
m_map |
The Matlab mapping toolbox (http://www2.ocgy.ubc.ca/rich/map.html). |
netcdf_x86_64 |
The NetCDF Fortran library for Linux, compiled with ifort on a 64 bits architecture. |
3.2.2.3. DATASETS#
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) |
GSHHS |
A Global Self-consistent, Hierarchical, High-resolution Geography Database
[Wessel and Smith, 1996]. Original data can be found at https://www.soest.hawaii.edu/pwessel/gshhg/
|
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.
|