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 and cppdefs.h) and compiled the model

  • set-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

DOC_SHINX

Model documentation

MPI_NOLAND_preprocessing

Fortran utility to determine the optimal MPI decomposition to supress land computation

MUSTANG

MUSTANG sediment model

OCEAN

CROCO source files

PISCES

PISCES biogeochemical model source files

README.md

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

create_config.bash

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
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

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

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.