ROMS_AGRIF / ROMSTOOLS


User's Guide



- ROMS_AGRIF v2.1 -
- ROMSTOOLS v2.1 -


Pierrick Penven, Gildas Cambon, Thi-Anh Tan,
Patrick Marchesiello and Laurent Debreu



Institut de Recherche pour le Développement (IRD)


44 Boulevard de Dunkerque
CS 90009
13572 Marseille cedex 02
France




\includegraphics[width=0.9\textwidth]{Figures/romsgui_vizu_pagegarde.eps}



July, 2010

2.2.1 Introduction

The Regional Ocean Modeling System (ROMS) is a new generation ocean circulation model (Shchepetkin and McWilliams, 2005) that has been specially designed for accurate simulations of regional oceanic systems. The reader is referred to Shchepetkin and McWilliams (2003) and to Shchepetkin and McWilliams (2005) for a complete description of the model. ROMS has been applied for the regional simulation of a variety of different regions of the world oceans (e.g. Marchesiello et al., 2003; Penven et al., 2001; MacCready et al., 2002; Haidvogel et al., 2000; Di Lorenzo et al., 2003; Blanke et al., 2002).

To perform a regional simulation using ROMS, the modeler needs to provide several data files in a specific format: horizontal grid, bottom topography, surface forcing, lateral boundary conditions... He also needs to analyze the model outputs. The tools which are described here have been designed to perform these tasks. The goal is to be able to build a standard regional model configuration in a minimum time.

In the first chapter, the system requirements and the installation process are exposed. A short note on ROMS model is presented in chapter 2. A tutorial on the use of ROMSTOOLS is shown in the third section. Tidal simulations, inter-annual simulations, nesting tools, biology and operational regional modeling are presented in section 4, 5, 6, 7 and 8.

In the second chapter, some details of the IRD version of ROMS new release, named Roms_Agrif v$2.1$, using the AGRIF nesting procedure are presented.
First, the new AGRIF 2-way nesting procedure implemented in the code is described, then new numerical and physical schemes and parametrization are exposed. Then a changelog section since the last Roms_Agrif v$1.1$ offical version is presented. Finally, the cpp-keys, parameters and input files are described in details to correctly configure the model options.

Contents

1. ROMSTOOLS matlab toolbox

1.1 Installation

1.1.1 System requirement

This toolbox has been designed for Matlab. It needs at least 2 Gbites of disk space. It has been tested on several Matlab versions ranging from Matlab6 to Matlab2006a. It has been mostly tested on Linux workstations, but it could be used on any platform if a NetCDF and a LoadDAP Matlab Mex files are provided. The NetCDF Matlab Mex file is needed to read and write into NetCDF files and it can be found at the web location: http://mexcdf.sourceforge.net/. The LoadDAP Matlab Mex file is used to download data from OpenDAP servers for inter-annual and forecast simulations. It can be found at the web location: http://www.opendap.org/download/ml-structs.html. The Matlab LoadDAP Mex file provides a way to read any OpenDAP-accessible data into Matlab. Note that the LibDAP library must be installed on your system before installing LoadDAP. Details can be found at the web location: http://www.opendap.org. MexCDF and LoadDAP mex files are provided for Linux (system FEDORA 32bits: mexcdf and Opendap_tools/FEDORA ; system CENTOS or FEDORA 64bits: mexnc and Opendap_tools/FEDORA_X64), but they are not working on all the plateforms.

All the other necessary Matlab toolboxes (i.e. air-sea, mask, netcdf or m_map...) are included in the ROMSTOOLS package. Global datasets, such as topography (Smith and Sandwell, 1997), hydrography (Conkright et al., 2002) or surface fluxes (Da Silva et al., 1994), are also included.

1.1.2 Getting the files

All the necessary compressed tar files (XXX.tar.gz) containing the Matlab programs, several datasets and other toolboxes and softwares needed by ROMSTOOLS are located at:

http://roms.mpl.ird.fr/Roms_tools/index.html
For the ROMS source code you should download ROMS_AGRIF version V2.1.





1.1.3 Extracting the files

Download all the compressed tar files. Uncompress and untar all the files (gunzip and tar -xvf). You should obtain the following directory tree :

Roms_tools

$\vert$- Aforc_NCEP

$\vert$- Aforc_QuikSCAT

$\vert$- air_sea

$\vert$- COADS05

$\vert$- Compile

$\vert$- Diagnostic_tools

$\vert$- Documentation

$\vert$ $\vert$- User_guide

$\vert$- Forecast_tools

$\vert$- mask

$\vert$- mex60

$\vert$- mexcdf

$\vert$ $\vert$- mexnc

$\vert$ $\vert$- private

$\vert$ $\vert$- src

$\vert$ $\vert$- tests

$\vert$ $\vert$- win32

$\vert$ $\vert$- win64

$\vert$ $\vert$- netcdf_toolbox

$\vert$ $\vert$- README

$\vert$ $\vert$- ChangeLog

$\vert$ $\vert$- netcdf

$\vert$ $\vert$- @listpick

$\vert$ $\vert$- @ncatt

$\vert$ $\vert$- @ncbrowser

$\vert$ $\vert$- @ncdim

$\vert$ $\vert$- @ncvar

$\vert$ $\vert$- @netcdf

$\vert$ $\vert$- @ncitem

$\vert$ $\vert$- @ncrec

$\vert$ $\vert$- nctype

$\vert$ $\vert$- ncutility

$\vert$ $\vert$- ncsources

$\vert$ $\vert$- snctools (unused yet)

$\vert$- m_map

$\vert$ $\vert$- private

$\vert$- Nesting_tools

$\vert$- netcdf_g77

$\vert$- netcdf_ifc

$\vert$- netcdf_x86_64

$\vert$- Oforc_OGCM

$\vert$- Opendap_tools

$\vert$ $\vert$- FEDORA

$\vert$ $\vert$- FEDORA_X64

$\vert$- Preprocessing_tools

$\vert$- Roms_Agrif

$\vert$ $\vert$- AGRIFZOOM

$\vert$ $\vert$ $\vert$- AGRIF_FILES

$\vert$ $\vert$ $\vert$- AGRIF_INC

$\vert$ $\vert$ $\vert$- AGRIF_OBJS

$\vert$ $\vert$ $\vert$- AGRIF_YOURFILES

$\vert$ $\vert$ $\vert$- LIB.clean

$\vert$- Run_v.2.1

$\vert$ $\vert$- DATA

$\vert$ $\vert$- FORECAST

$\vert$ $\vert$- ROMS_FILES

$\vert$ $\vert$- SCRATCH

$\vert$ $\vert$- TEST_CASES

$\vert$- Run

$\vert$ $\vert$- DATA

$\vert$ $\vert$- FORECAST

$\vert$ $\vert$- ROMS_FILES

$\vert$ $\vert$- SCRATCH

$\vert$ $\vert$- TEST_CASES

$\vert$- SeaWifs

$\vert$- SST_pathfinder

$\vert$- Tides

$\vert$- Topo

$\vert$ $\vert$- Matlab

$\vert$- TPX06

$\vert$- TPX07

$\vert$- Visualization_tools

$\vert$- WOA2001

$\vert$- WOA2005

Definition of the different directories :


1.2 LibDAP and LoadDAP

It is sometimes difficult to compile LoadDAP. LibDAP must be installed before installing LoadDAP. You have to declare the LibDAP binary and library in tour  /.bashrc with th command PATH and LD_LIBRARY_PATH. Once, compile and install LoadDAP.

Here are a few instructions for the installation of these libraries:

1.3 Future plans

1.4 Warnings

1.5 Tutorial : the Southern Benguela example

This section presents the essential steps for preparing and running a regional ROMS simulation. This is done following the example of a model of the Southern Benguela at low resolution and using climatological forcing at surface and boundaries.

1.5.1 Getting started : Processing input files

Once the installation has been successful, launch a Matlab session in the directory: $\sim$/Roms_tools/Run. Run the start.m script to set the Matlab paths for this session.

In this step of this installation, you have to know a few things concerning your matlab setup and tour computer environnmemnt:

In the Roms_tools, some NetCDF libraries for matlab are provided :

In the Roms_tools, some "Opendap" bins and librarys are also provided :

However, if your Linux distribution differs from Fedora, the best is to compile and install by your own the LibDAP and LoadDAP (section 1.2)

You are now ready to create a new configuration. It is important to respect the order of the following preprocessing steps: make_grid, make_forcing, make_clim. For all the preprocessing steps, there is only one file to edit : $\sim$/Roms_tools/Run/romstools_param.m . This file contains the necessary parameters for the generation of the ROMS input NetCDF files. The first section in romstools_param.m defines the general parameters, such as title, working directories or file names:

%%%%%%%%%%%%%%%%%%%%%%
%
% 1- General parameters
%
%%%%%%%%%%%%%%%%%%%%%%
%
% ROMS title names and directories
%
ROMS_title = 'Benguela Test Model';
ROMS_config = 'Benguela_LR';
%
ROMSTOOLS_dir = '../';
%
%
Run directory %
RUN_dir=[ROMSTOOLS_dir,'Run/'];
%
ROMS_files_dir=[RUN_dir,'ROMS_FILES/'];
%
% Global data directory (etopo, coads, datasets download from ftp, etc..)
%
DATADIR=ROMSTOOLS_dir; %
% Forcing data directory (ncep, quikscat, datasets download with opendap, etc..)
%
FORC_DATA_DIR = [RUN_dir,'DATA/'];
%
% ROMS file names (grid, forcing, bulk, climatology, initial)
%
eval(['!mkdir ',ROMS_files_dir])
%
bioname=[ROMS_files_dir,'roms_frcbio.nc']; %Iron Dust forcing file with PISCES
grdname=[ROMS_files_dir,'roms_grd.nc'];
frcname=[ROMS_files_dir,'roms_frc.nc'];
blkname=[ROMS_files_dir,'roms_blk.nc'];
clmname=[ROMS_files_dir,'roms_clm.nc'];
ininame=[ROMS_files_dir,'roms_ini.nc'];
oaname =[ROMS_files_dir,'roms_oa.nc']; % oa file : intermediate file not used
% in roms simulations
bryname=[ROMS_files_dir,'roms_bry.nc'];
Zbryname=[ROMS_files_dir,'roms_bry_Z.nc'];% Zbry file: intermediate file not used
% in roms simulations
%
frc_prefix=[ROMS_files_dir,'roms_frc']; % generic bulk forcing file name
% for inter-annual roms simulations (NCEP or GFS)
blk_prefix=[ROMS_files_dir,'roms_blk']; % generic forcing file name
% for inter-annual roms simulations (NCEP or GFS)
%
% Objective analysis decorrelation scale [m]
% (if Roa=0: simple extrapolation method; crude but much less costly)
%
%Roa=300e3;
Roa=0;
%
interp_method = 'linear'; % Interpolation method: 'linear' or 'cubic'
%
makeplot = 1; % 1: create a few graphics after each preprocessing step
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Variables description:

1.5.2 Building the grid

The part of the file romstools_param.m that you should be edit is :

%%%%%%%%%%%%%%%%%%%%%%
%
% 2-Grid parameters
% used by make_grid.m (and others..)
%
%%%%%%%%%%%%%%%%%%%%%%
%
% Grid dimensions:
%
lonmin = 8; % Minimum longitude [degree east]
lonmax = 22; % Maximum longitude [degree east]
latmin = -38; % Minimum latitude [degree north]
latmax = -26; % Maximum latitude [degree north]
%
% Grid resolution [degree]
%
dl = 1/3;
%
% Number of vertical Levels (! should be the same in param.h !)
%
N = 32;
%
% Vertical grid parameters (! should be the same in roms.in !)
%
theta_s = 8.;
theta_b = 0.;
hc =10.;
%
% Minimum depth at the shore [m] (depends on the resolution,
% rule of thumb: dl=1, hmin=300, dl=1/4, hmin=150, ...)
% This affect the filtering since it works on grad(h)/h.
%
hmin = 75;
%
% Maximum depth at the shore [m] (to prevent the generation
% of too big walls along the coast)
%
hmax_coast = 500;
%
% Topography netcdf file name (ETOPO 2 or any other netcdf file
% in the same format)
%
topofile = [DATADIR,'Topo/etopo2.nc'];
%
% Slope parameter (r=grad(h)/h) maximum value for topography smoothing
%
rtarget = 0.25;
%
% Number of pass of a selective filter to reduce the isolated
% seamounts on the deep ocean.
%
n_filter_deep_topo=4;
%
% Number of pass of a single hanning filter at the end of the
% smoothing procedure to ensure that there is no 2DX noise in the
% topography.
%
n_filter_final=2;
%
% GSHSS user defined coastline (see m_map)
% XXX_f.mat Full resolution data
% XXX_h.mat High resolution data
% XXX_i.mat Intermediate resolution data
% XXX_l.mat Low resolution data
% XXX_c.mat Crude resolution data
%
coastfileplot = 'coastline_l.mat';
coastfilemask = 'coastline_l_mask.mat';

Variables description:

Save romstools_param.m and run make_grid in the Matlab session :

$»$
$»$ make_grid

You should obtain in the Matlab session:
---------------------------------------------
Making the grid: ../Run/ROMS_FILES/roms_grd.nc

Title: Benguela Test Model

Resolution: 1/3 deg

Create the grid file...
LLm = 41
MMm = 42

Fill the grid file...

Compute the metrics...

Min dx=29.1913 km - Max dx=33.3244 km
Min dy=29.2434 km - Max dy=33.1967 km

Fill the grid file...

Add topography...
ROMS resolution : 31.3 km
Topography data resolution : 3.42 km
Topography resolution halved 4 times
New topography resolution : 54.6 km
Processing coastline_l.mat ...
Do you want to use editmask ? y,[n]
Apply a filter on the Deep Ocean to remove the isolated seamounts :
4 pass of a selective filter.
Apply a selective filter on log(h) to reduce grad(h)/h :
13 iterations - rmax = 0.24381
Smooth the topography a last time to prevent 2DX noise:
2 pass of a hanning smoother.
Write it down...
Do a plot...
$»$
---------------------------------------------

You should keep the values of LLm and MMm during the process. They will be necessary for the ROMS parameter file $\sim$/Roms_tools/Run/param.h. In this test case, LLm0 = 23 and MMm0 = 31.

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 (Note that, for the moment, editmask is not working with matlab7 and mexnc). Otherwise the mask is generated from the unfiltered topography data. A procedure prevents the existence of isolated land (or sea) points.

Figure (1.1) presents the bottom topography obtained with make_grid.m for the Southern Benguela example. Note that at this low resolution (1/3$^\circ$), the topography has been strongly smoothed.

Figure 1.1: Result of make_grid.m for the Benguela example
\begin{figure}\centerline{\psfig{figure=Figures/make_grid_benguela.eps,width=12cm}}\end{figure}

1.5.3 Getting the wind and other surface fluxes

The next step is to create the file containing the different surface fluxes. The part of the file romstools_param.m that you should edit is :

%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 3-Surface forcing parameters
% used by make_forcing.m and by make_bulk.m
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
% COADS directory (for climatology runs)
%
coads_dir=[ROMSTOOLS_dir,'COADS05/'];
%
% COADS time (for climatology runs)
%
coads_time=(15:30:345); % days: middle of each month
coads_cycle=360; % repetition of a typical year of 360 days
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% 3.1 Surface forcing parameters
% used by pathfinder_sst.m
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
pathfinder_sst_name=[ROMSTOOLS_dir,...
'SST_pathfinder/climato_pathfinder.nc'];

Variables description:

Save romstools_param.m and run make_forcing in the Matlab session :

$»$
$»$ make_forcing

You should obtain :
---------------------------------------------
Benguela Test Model

Read in the grid...

Create the forcing file...
Getting taux for time index 1
Getting tauy for time index 1
...
Make a few plots...
$»$
---------------------------------------------

This program can take a relatively long time to process all the forcing variables. Figure (1.2) presents the wind stress vectors and wind stress norm obtained from the global atlas of surface marine data at 1/2$^\circ$ resolution (Da Silva et al., 1994) at 4 different periods of the year. Da Silva et al. (1994) sea surface temperature (SST) is used for the restoring term (dQdSST) in the heat flux calculation. To improve the model solution it is possible to use a SST climatology at a finer resolution (9.28 km) (Casey and Cornillon, 1999). To do so, you can run pathfinder_sst.m in the Matlab session :

$»$
$»$ pathfinder_sst



You should obtain :
---------------------------------------------
... Month index: 1
... Month index: 2
...
$»$
---------------------------------------------

For the surface forcing, instead of directly prescribing the fluxes, it is possible to use a bulk formula to generate the surface fluxes from atmospheric variables during the model run. In this case, ROMS needs to be recompiled with the BULK_FLUX cpp key defined. To generate the bulk forcing file, you need to run make_bulk in the Matlab session :

$»$
$»$ make_bulk

You should obtain :
---------------------------------------------
Benguela Test Model

Read in the grid...

Create the bulk forcing file...
Getting sat for time index 1
Getting sat for time index 2
...
Make a few plots...
$»$
---------------------------------------------

Figure 1.2: Wind stress[N.m$^{-2}$] obtained using make_forcing.m for the Benguela example.
\begin{figure}\centerline{\psfig{figure=Figures/windspeed_make_forcing.eps,width=15cm}}\end{figure}

1.5.4 Getting the initial and the lateral boundary conditions

The last preprocessing step consists in generating the files containing the necessary informations for the ROMS initial and lateral open boundaries conditions. This script generates two files : the climatology file (XXX_clm.nc) which gives the lateral boundary conditions, and the initial conditions file (XXX_ini.nc).
The part which should be edited by the user in the file romstools_param.m is. Note that you can you can add the variables for the NPZD or PISCES biogeochemical models. For that, define makebio or makepisces flags in the romstools_param.m.


The part which should be edited by the user in the file romstools_param.m is:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% 4-Open boundaries and initial conditions parameters
% used by make_clim.m, make_biol.m, make_bry.m
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Open boundaries switches (! should be consistent with cppdefs.h !)
%
obc = [1 1 1 1]; % open boundaries (1=open , [S E N W])
%
% Level of reference for geostrophy calculation
%
zref = -1000;
%
% Switches for selecting what to process in make_clim (1=ON)
% (and also in make_OGCM.m and make_OGCM_frcst.m)
makeini=1; %1: process initial data
makeclim=1; %1: process lateral boundary data
makebry=0; %1: process boundary data
makebio=0; %1: process initial and boundary data for idealized NPZD type bio model makepisces=0; %1: process initial and boundary data for PISCES biogeochemical model %
makeoa=1; %1: process oa data (intermediate file)
makeZbry=0; %1: process data in Z coordinate
%
insitu2pot=1; %1: convert in-situ temperature into potential temperature
%
% Day of initialization for climatology experiments (=0 : 1st January 0h)
%
tini=0;
%
% World Ocean Atlas directory (WOA2001 or WOA2005)
%
woa_dir=[ROMSTOOLS_dir,'WOA2005/'];
%
% Surface chlorophyll seasonal climatology (WOA2001 or SeaWifs)
%
chla_dir=[ROMSTOOLS_dir,'SeaWifs/'];
%
% Set times and cycles for the boundary conditions:
% monthly climatology
%
woa_time=(15:30:345); % days: middle of each month
woa_cycle=360; % repetition of a typical year of 360 days
%

Variables description:

Save romstools_param.m and run make_clim in the Matlab session :

$»$
$»$ make_clim

You should obtain :
---------------------------------------------
Making the clim: ../Run/ROMS_FILES/roms_clm.nc

Title: Benguela Test Model

Read in the grid...
Create the climatology file...
Creating the file : ../Run/ROMS_FILES/roms_clm.nc
...
Make a few plots...
$»$
---------------------------------------------
This program can also take quite a long time to run. Figure (1.3) presents 4 different sections of temperature for the initial condition file for the Benguela example. The sections are in the X-direction (East-West), the first section is for the Southern part of the domain and the last one is for the Northern part of the domain.
Figure 1.3: Result of make_clim.m for the Benguela example
\begin{figure}\centerline{\psfig{figure=Figures/sectiontemp_make_clim_benguela.eps,width=14cm}}\end{figure}

An alternative of using a climatology file is to create a boundary file. In this case, only boundary values are stored. The cpp key FRC_BRY should be defined and ROMS recompiled. Run make_bry in the Matlab session :

$»$
$»$ make_bry

You should obtain :
---------------------------------------------
Making the file: ../Run/ROMS_FILES/roms_bry.nc

Title: Benguela Test Model

Read in the grid...
...
---------------------------------------------

1.5.5 Compiling the model

Once all the netcdf data files are ready (i.e. XXX_grd.nc, XXX_frc.nc, XXX_ini.nc, and XXX_clm.nc), we can prepare ROMS for compilation. All is done in the $\sim$/Roms_tools/Run/ directory.

1.5.5.1 Parameters of the configuration : param.h

Edit the file $\sim$/Roms_tools/Run/param.h. The line which needs to be changed is:

# elif defined BENGUELA_LR

parameter (LLm0=41, MMm0=42, N=32) ! $<-$ Southern Benguela Test Case
# else

These are the values of the model grid size: LLm0 points in the X direction, MMm0 points in the Y direction and N vertical levels. LLm0 and MMm0 are given by running make_grid.m, and N is defined in romstools_param.m. The param.h parameters are described in detail in section 2.4

1.5.5.2 Numerical and physical options : cppdefs.h

The second file to edit is $\sim$/Roms_tools/Run/cppdefs.h. This file defines the CPP keys that are used by the the C-preprocessor when compiling ROMS. The C-preprocessor selects the different parts of the Fortran code which needs to be compiled depending on the defined CPP options. These options are separated in two parts (the basic option keys and the advanced options keys) in cppdefs.h. All the keys and their organization are described in section 2.5.

1.5.5.3 Compilation script : jobcomp

ROMS can be compiled by running the UNIX tcsh script $\sim$/Roms_tools/Run/jobcomp. Jobcomp should be able to recognize your system. It has been tested on Linux, IBM, Sun and Compaq systems. On Linux PCs, the default compiler is the GNU g77, but it is possible to uncomment specific lines in jobcomp to use g95 or ifort. The latter is mandatory when using AGRIF and/or OPEN_MP. When changing the compiler you should provide a corresponding NetCDF library. Once the compilation is done, you should obtain a new executable (roms) in the $\sim$/Roms_tools/Run directory. ROMS should be recompiled each time param.h or cppdefs.h are changed. If you compile using MPI parallelization, the jobcomp scrip detect it and set the compiler to OpenMPI, so you need to have it installed (http://www.open-mpi.org)

1.5.6 Running the model

Edit the input parameter file: $\sim$/Roms_tools/Run/roms.in. The vertical grid parameters (THETA_S, THETA_B, HC) should be identical to the ones in romstools_param.m. Otherwise, the other default values should not be changed. The definition of all the input variables is given at the start of each ROMS simulation. To run the model, type in directory $\sim$/Roms_tools/Run/ : ./roms roms.in.
If you use paralelle computation, some more specific command are needed : in the case of OpenMP parallelization, set the environment variable OMP_NUM_THREADS to number_of_cpu_used (for example export OMP_NUM_THREADS=4 for 4 cpu parallel run) then ./roms roms.in. In the case of MPI parallelization, use the following command : mpirun -np number_of_processus_used ./roms roms.in.

The description of the namelist roms.in is descibed in details in section 2.6.

On the screen, you should check the Cu_max parameter: if it is greater than 1 you are violating the CFL criterion. In this case, you should reduce the time step.
Example of model run:

$>$ : ./roms roms.in

You should obtain :
---------------------------------------------
Southern Benguela
480 ntimes Total number of timesteps for 3D equations.
5400.00 dt Timestep [sec] for 3D equations
60 ndtfast Number of 2D timesteps within each 3D step.
1 ninfo Number of timesteps between runtime diagnostics.

6.000E+00 theta_s S-coordinate surface control parameter.
0.000E+00 theta_b S-coordinate bottom control parameter.
1.000E+01 Tcline S-coordinate surface/bottom layer width used in
vertical coordinate stretching, meters.
Grid File: ROMS_FILES/roms_grd.nc
Forcing Data File: ROMS_FILES/roms_frc.nc
Bulk Data File: ROMS_FILES/roms_blk.nc
Climatology File: ROMS_FILES/roms_clm.nc
Initial State File: ROMS_FILES/roms_ini.nc Record: 1
Restart File: ROMS_FILES/roms_rst.nc nrst = 480 rec/file: -1
History File: ROMS_FILES/roms_his.nc Create new: T nwrt = 480 rec/file = 0
1 ntsavg Starting timestep for the accumulation of output
time-averaged data.
48 navg Number of timesteps between writing of time-averaged
data into averages file.
Averages File: ROMS_FILES/roms_avg.nc rec/file = 0

Fields to be saved in history file: (T/F)
T write zeta free-surface.
F write UBAR 2D U-momentum component.
F write VBAR 2D V-momentum component.
F write U 3D U-momentum component.
F write V 3D V-momentum component.
F write T(1) Tracer of index 1.
F write T(2) Tracer of index 2.

F write RHO Density anomaly.
F write Omega Omega vertical velocity.
F write W True vertical velocity.
F write Akv Vertical viscosity.
F write Akt Vertical diffusivity for temperature.
F write Aks Vertical diffusivity for salinity.
F write Hbl Depth of KPP-model boundary layer.
F write Bostr Bottom Stress.

Fields to be saved in averages file: (T/F)
T write zeta free-surface.
T write UBAR 2D U-momentum component.
T write VBAR 2D V-momentum component.
T write U 3D U-momentum component.
T write V 3D V-momentum component.
T write T(1) Tracer of index 1.
T write T(2) Tracer of index 2.

F write RHO Density anomaly
T write Omega Omega vertical velocity.
T write W True vertical velocity.
F write Akv Vertical viscosity
T write Akt Vertical diffusivity for temperature.
F write Aks Vertical diffusivity for salinity.
T write Hbl Depth of KPP-model boundary layer
T write Bostr Bottom Stress.
1025.0000 rho0 Boussinesq approximation mean density, kg/m3.
0.000E+00 visc2 Horizontal Laplacian mixing coefficient [m2/s]
for momentum.
0.000E+00 tnu2(1) Horizontal Laplacian mixing coefficient (m2/s)
for tracer 1.
0.000E+00 tnu2(2) Horizontal Laplacian mixing coefficient (m2/s)
for tracer 2.
0.000E+00 rdrg Linear bottom drag coefficient (m/si).
0.000E+00 rdrg2 Quadratic bottom drag coefficient.
1.000E-02 Zob Bottom roughness for logarithmic law (m).
1.000E-04 Cdb_min Minimum bottom drag coefficient.
1.000E-01 Cdb_max Maximum bottom drag coefficient.

1.00 gamma2 Slipperiness parameter: free-slip +1, or no-slip -1.
1.00E+05 x_sponge Thickness of sponge and/or nudging layer (m)
800.00 v_sponge Viscosity in sponge layer (m2/s)
1.157E-05 tauT_in Nudging coefficients [sec-1]
3.215E-08 tauT_out Nudging coefficients [sec-1]
1.157E-06 tauM_in Nudging coefficients [sec-1]
3.215E-08 tauM_out Nudging coefficients [sec-1]

Activated C-preprocessing Options:

REGIONAL
BENGUELA_LR
OBC_EAST
OBC_WEST
OBC_NORTH
OBC_SOUTH
SOLVE3D
UV_COR
UV_ADV
CURVGRID
SPHERICAL
MASKING
UV_VIS2
MIX_GP_UV
MIX_GP_TS
TS_DIF2
LMD_MIXING
LMD_SKPP
LMD_BKPP
LMD_RIMIX
LMD_CONVEC
SALINITY
NONLIN_EOS
SPLIT_EOS
QCORRECTION
SFLX_CORR
DIURNAL_SRFLUX
SPONGE
CLIMATOLOGY
ZCLIMATOLOGY
M2CLIMATOLOGY
M3CLIMATOLOGY
TCLIMATOLOGY
ZNUDGING
M2NUDGING
M3NUDGING
TNUDGING
ANA_BSFLUX
ANA_BTFLUX
OBC_M2CHARACT
OBC_M3ORLANSKI
OBC_TORLANSKI
AVERAGES
AVERAGES_K
VAR_RHO_2D
M2FILTER_POWER
CLIMAT_UV_MIXH
VADV_SPLINES_UV
HADV_UPSTREAM_TS
CLIMAT_TS_MIXH
VADV_AKIMA_TS

$\rightarrow$ Non user defined cpp keys (in set_global_definitions.h)
DBLEPREC
Linux
QUAD
QuadZero
GLOBAL_2D_ARRAY
GLOBAL_1D_ARRAYXI
GLOBAL_1D_ARRAYETA
...
...
AGRIF_UPDATE_DECAL
AGRIF_SPONGE

Linux 2.6.9-42.0.3.ELsmp x86_64
NUMBER OF THREADS: 1 BLOCKING: 1 x 1.

Spherical grid detected.

hmin hmax grdmin grdmax Cu_min Cu_max
75.000000 4803.032721 .301836927E+05 .331215714E+05 0.12176008 0.91533005
volume=9.523986093261087500000E+14 open_cross=6.104836888312444686890E+09

Vertical S-coordinate System:

level S-coord Cs-curve at_hmin over_slope at_hmax

32 0.0000000 0.0000000 0.000 0.000 0.000
31 -0.0312500 -0.0009350 -0.373 -2.584 -4.794
30 -0.0625000 -0.0019030 -0.749 -5.247 -9.746
29 -0.0937500 -0.0029380 -1.128 -8.074 -15.019
28 -0.1250000 -0.0040767 -1.515 -11.152 -20.790
27 -0.1562500 -0.0053591 -1.911 -14.580 -27.249
26 -0.1875000 -0.0068304 -2.319 -18.466 -34.613
25 -0.2187500 -0.0085426 -2.743 -22.938 -43.132
24 -0.2500000 -0.0105560 -3.186 -28.141 -53.095
23 -0.2812500 -0.0129416 -3.654 -34.248 -64.842
22 -0.3125000 -0.0157835 -4.151 -41.463 -78.776
21 -0.3437500 -0.0191819 -4.684 -50.031 -95.377
20 -0.3750000 -0.0232566 -5.262 -60.241 -115.220
19 -0.4062500 -0.0281514 -5.892 -72.443 -138.993
18 -0.4375000 -0.0340388 -6.588 -87.056 -167.524
17 -0.4687500 -0.0411263 -7.361 -104.584 -201.807
16 -0.5000000 -0.0496640 -8.228 -125.635 -243.041
15 -0.5312500 -0.0599527 -9.209 -150.939 -292.668
14 -0.5625000 -0.0723554 -10.328 -181.377 -352.427
13 -0.5937500 -0.0873092 -11.613 -218.013 -424.414
12 -0.6250000 -0.1053416 -13.097 -262.126 -511.156
11 -0.6562500 -0.1270882 -14.823 -315.262 -615.700
10 -0.6875000 -0.1533158 -16.841 -379.282 -741.723
9 -0.7187500 -0.1849493 -19.209 -456.432 -893.656
8 -0.7500000 -0.2231040 -22.002 -549.423 -1076.845
7 -0.7812500 -0.2691252 -25.306 -661.522 -1297.738
6 -0.8125000 -0.3246355 -29.226 -796.670 -1564.114
5 -0.8437500 -0.3915923 -33.891 -959.622 -1885.352
4 -0.8750000 -0.4723564 -39.453 -1156.112 -2272.770
3 -0.9062500 -0.5697755 -46.098 -1393.057 -2740.015
2 -0.9375000 -0.6872846 -54.048 -1678.800 -3303.552
1 -0.9687500 -0.8290268 -63.574 -2023.407 -3983.240
0 -1.0000000 -1.0000000 -75.000 -2439.016 -4803.033

Time splitting: ndtfast = 60 nfast = 89
Maximum grid stiffness ratios: rx0 =0.2353349875 rx1 = 2.5672736953

GET_INITIAL - Processing data for time = 0.000 record = 1

GET_TCLIMA - Read climatology of tracer 1 for time = 345.0
GET_TCLIMA - Read climatology of tracer 1 for time = 15.00
GET_TCLIMA - Read climatology of tracer 2 for time = 345.0
GET_TCLIMA - Read climatology of tracer 2 for time = 15.00
GET_UCLIMA - Read momentum climatology for time = 345.0
GET_UCLIMA - Read momentum climatology for time = 15.00
GET_SSH - Read SSH climatology for time = 345.0
GET_SSH - Read SSH climatology for time = 15.00
GET_SMFLUX - Read surface momentum stresses for time = 345.0
GET_SMFLUX - Read surface momentum stresses for time = 15.00
GET_BULK - Read fields for bulk formula for time = 345.0
GET_BULK - Read fields for bulk formula for time = 15.00

DEF_HIS/AVG - Created new netCDF file 'ROMS_FILES/roms_his.nc'.
WRT_GRID - wrote grid data into file 'ROMS_FILES/roms_his.nc'.
WRT_HIS - wrote history fields into time record = 1 / 1

MAIN: started time-steping.

STEP time[DAYS] KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME trd
0 0.00000 0.000000000E+00 2.1475858E+01 2.1475858E+01 9.5239861E+14 0
1 0.06250 1.306369099E-04 2.1476230E+01 2.1476361E+01 9.5239208E+14 0
...
---------------------------------------------

1.5.7 Long simulations

In many studies, there is a need for long simulations: to reach the spin-up of the solution and/or to obtain statistical equilibriums. For regional models, 10 years appears to be a reasonable model simulation length. In this case, to prevent the generation of large output files, the strategy is to relaunch the model every simulated month. This is done by the UNIX csh script: run_roms.csh . Warning! the ROMS input file use for long simulations is roms_inter.in. It should be edited accordingly.

  1. It gets the grid, the forcing, the initial and the boundary files.
  2. It runs the model for 1 month.
  3. It stores the output files in a specific form: roms_avg_Y4M3.nc (for the ROMS averaged output of March of year 4).
  4. It replaces the initial file by the restart file (roms_rst.nc) which as been generated at the end of the month.
  5. It relaunch the model for next month.

Part to edit in run_roms.csh:

set MODEL=roms
set SCRATCHDIR=`pwd`/SCRATCH
set INPUTDIR=`pwd`
set MSSDIR=`pwd`/ROMS_FILES
set MSSOUT=`pwd`/ROMS_FILES
set CODFILE=roms
set AGRIF_FILE=AGRIF_FixedGrids.in
#
# Model time step [seconds]
#
set DT=5400
#
# Number of days per month
#
set NDAYS = 30
#
# number total of grid levels
#
set NLEVEL=1
#
# Time Schedule - TIME_SCHED=0 -$>$ yearly files
# TIME_SCHED=1 -$>$ monthly files
#
set TIME_SCHED=1
#
set NY_START=1
set NY_END=10
set NM_START=1
set NM_END=12

Variables definitions:

To run a ROMS long simulation in batch mode on a Linux workstation:

$>$ : nohup ./run_roms.csh $>$ exp1.out &

To check the execution of your model, type in the directory $\sim$/Roms_Tools/Run :
$>$: more exp1.out

1.5.8 Getting the results

1.5.8.1 roms_gui

Once the model has run, or during the simulation, it is possible to visualize the model outputs using a Matlab graphic user interface : roms_gui. Launch roms_gui in the Matlab session (in the $\sim$/Roms_tools/Run/ directory):

$»$
$»$ roms_gui

A window pops up, asking for a ROMS history NetCDF file (Figure 1.4). You should select roms_his.nc (history file) or roms_avg.nc (average file) and click "open".

Figure 1.4: Entrance window of roms_gui
\begin{figure}\centerline{\psfig{figure=Figures/roms_gui_entrance.eps,width=12cm}}\end{figure}

Figure 1.5: roms_gui
\begin{figure}\centerline{\psfig{figure=Figures/romsgui_vizuM2_2.eps,width=12cm}}\end{figure}

The main window appears, variables can be selected to obtain an image such as Figure (1.5). On the left side, the upper box gives the available ROMS variable names and the lower box presents the variables derived from the ROMS model outputs :

It is possible to add arrows for the horizontal currents by increasing the "Current vectors spatial step". It is also possible to obtain vertical sections, time series, vertical profiles and Hovmüller diagrams by clicking on the corresponding targets in roms_gui.

1.5.8.2 Diagnostics

To analyze the long simulations, a few scripts have been added in the directory:
$\sim$/Roms_tools/Diagnostic_tools:

Run these scripts in a Matlab session. The obtained mean or eddy files can be visualized with roms_gui.

If you need to create and play ".fli" animations, you should install ppm2fli and xanim on your system. If you have a Linux PC, you can follow these steps:

  1. log in as root
  2. go to the directory where the file is saved.
  3. type : rpm -Uvh ppm2fli-2.1-1.i386.rpm
  4. type : rpm -Uvh xanim-2.80.1-12.i386.rpm
  5. log out
If you are not using a Linux PC, you should ask your system administrator to install these programs.

1.6 Tides

Using the method described by Flather (1976), ROMS is able to propagate the different tidal constituents from its lateral boundaries. To do so, define the cpp keys TIDES, SSH_TIDES and UV_TIDES and recompile the model using jobcomp. To work correctly, the model should use the Flather (1976) open boundary radiation scheme (cpp key OBC_M2FLATHER defined).
The tidal components are added to the forcing file (XXX_frc.nc) by the Matlab program make_tides.m. Edit the file : $\sim$/Roms_tools/Run/romstools_param.m. The part of the file that you should change is :

%%%%%%%%%%%%%%%%%%%%%
%
% 5-Parameters for tidal forcing
%
%%%%%%%%%%%%%%%%%%%%%
%
% TPXO file name (TPXO6 or TPXO7)
%
tidename=[ROMSTOOLS_dir,'TPXO6/TPXO6.nc'];
%
% Number of tides component to process
%
Ntides=10;
%
% Chose order from the rank in the TPXO file :
% "M2 S2 N2 K2 K1 O1 P1 Q1 Mf Mm"
% " 1 2 3 4 5 6 7 8 9 10"
%
tidalrank=[1 2 3 4 5 6 7 8 9 10];
%
% Compare with tidegauge observations
%
lon0=18.37;
lat0=-33.91; % Cape Town location
Z0=1; % Mean depth of the tidegauge in Cape Town

Variables definitions : An important aspect is the definition of time and especially the choice of a time origin. This is defined in $\sim$/Roms_tools/Run/romstools_param.m:

%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% 6-Temporal parameters (used for make_tides, make_NCEP, make_OGCM)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
Yorig = 1900; % reference time for vector time
% in roms initial and forcing files
%
Ymin = 2000; % first forcing year
Ymax = 2000; % last forcing year
Mmin = 1; % first forcing month
Mmax = 3; % last forcing month
%
Dmin = 1; % Day of initialization
Hmin = 0; % Hour of initialization
Min_min = 0; % Minute of initialization
Smin = 0; % Second of initialization
%
SPIN_Long = 0; % SPIN-UP duration in Years

% The origin of time (Yorig: 1 january of year Yorig) should be kept the same for all the preprocessing and postprocessing steps. Save romstools_param.m and run make_tides in the Matlab session:
$»$
$»$ make_tides

You should obtain :
---------------------------------------------
Start date for nodal correction : 1-Jan-2000
Reading ROMS grid parameters ...
Tidal components : M2 S2 N2 K2 K1 O1 P1 Q1 Mf Mm
Processing tide : 1 of 10
...
---------------------------------------------

1.7 Biology

1.7.1 'Idealized' biogeochemical model : NChlPZD, N2ChlPZD2 or
N2P2Z2D2

ROMSTOOLS can help for the design of ROMS biogeochemical experiments. For the initial conditions and lateral boundary conditions, WOA provides a seasonal climatology for nitrateD concentration and WOA or SeaWifs can be used to obtain a seasonal climatology of surface chlorophyll concentration. Phytoplankton is estimated by a constant chlorophyll/phytoplankton ratio derived from previous simulations. Zooplankton is estimated in a similar way. The part which should be edited by the user in romstools_param.m is:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Open boundaries and initial conditions parameters
% used by make_clim.m, make_biol.m, make_bry.m
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
.....
makebio=1; %1: process initial and boundary data for idealized NPZD type bio model .....
%
% World Ocean Atlas directory (WOA2001 or WOA2005)
%
woa_dir=[DATADIR,'WOA2005/'];
%
% Pisces biogeochemical seasonal climatology (WOA2001 or WOA2005)
%
woapisces_dir=[DATADIR,'WOAPISCES/'];
%
% Surface chlorophyll seasonal climatology (WOA2001 or SeaWifs)
%
chla_dir=[DATADIR,'SeaWifs/']; %
....

Variables description :

Run make_biol (or if the flag makebio=1, make_clim.m will process make_biol.m ) in the Matlab session :
$»$
$»$ make_biol

You should obtain :
----------------------------------------
Add_no3: creating variables and attributes for the OA file
Add_no3: creating variables and attributes for the Climatology file

Ext tracers: Roa = 0 km - default value = NaN
Ext tracers: horizontal interpolation of the annual data
Ext tracers: horizontal interpolation of the seasonal data
time index: 1 of total: 4
time index: 2 of total: 4
time index: 3 of total: 4
time index: 4 of total: 4

Vertical interpolations

NO3...
Time index: 1 of total: 4
Time index: 2 of total: 4
Time index: 3 of total: 4
Time index: 4 of total: 4

CHla...
Add_chla: creating variable and attribute
...
Make a few plots...
----------------------------------------

The cpp keys related to these biology models are :

1.7.2 PISCES biogeochemical model

This latter is a more complex biogeochemical model, firstly coupled to OPA and now a beta version of the model can be coupled with ROMS_AGRIF. It is nicely described in (Aumont , 2005) provide in the documentation section of ROMS_TOOLS.

This part of ROMS_TOOLS use the World Ocean Atlas, called WOAPISCES. It provides the global data of Iron (Fe), Silicate (SiO3), Oxygen (O2), Phosphate (PO4), DIC (dissolved organic carbon), DOC (dissolved inorganic carbon) and Alkanility. The routines used to process these fields are : make_ini_pisces, make_clim_pisces, make_bry_pisces, make_bio_forcing.m as for the climatological experiments1.1.

The part which should be edited by the user in romstools_param.m is:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Open boundaries and initial conditions parameters
% used by make_clim.m, make_biol.m, make_bry.m
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
.....
makepisces %1: process initial and boundary data for PISCES biogeochemical model .....
%
% Pisces biogeochemical seasonal climatology (WOA2001 or WOA2005)
%
woapisces_dir=[DATADIR,'WOAPISCES/'];
%
....

Variables description :

To add boundary conditions of PISCES in the roms_clm.nc computed before, in a matlab session, run make_clim_pisces.
$»$
$»$ make_clim_pisces

You should obtain :
Add_no3: creating variables and attributes for the OA file
write no3time
Add_po4: creating variables and attributes for the OA file
Add_sio3: creating variables and attributes for the OA file
Add_o2: creating variables and attributes for the OA file
Add_dic: creating variables and attributes for the OA file
Add_talk: creating variables and attributes for the OA file
Add_doc: creating variables and attributes for the OA file
Add_fer: creating variables and attributes for the OA file

Ext tracers: Roa = 0 km - default value = NaN
Ext tracers: horizontal interpolation of the seasonal data
time index: 1 of total: 12
time index: 2 of total: 12
time index: 3 of total: 12
time index: 4 of total: 12
time index: 5 of total: 12
time index: 6 of total: 12
time index: 7 of total: 12
time index: 8 of total: 12
time index: 9 of total: 12
time index: 10 of total: 12
time index: 11 of total: 12
time index: 12 of total: 12

Similarly, to add initial condition for PISCES variables to roms_ini.nc file, in a matlab session, run make_ini_pisces.m
$»$
$»$ make_ini_pisces

Figure 1.6: Result of make_clim_pisces for the Benguela example : NO3 forcing fields [mMol N m-3].
[Surface map] \includegraphics[width=0.5\textwidth]{Figures/NO3_surf_t1.eps} [vertical sections along open boundaries] \includegraphics[width=0.5\textwidth]{Figures/NO3_profil_t1.eps}

Figure 1.7: Result of make_clim_pisces for the Benguela example : PO4 forcing fields [mMol P m-3].
[Surface map] \includegraphics[width=0.5\textwidth]{Figures/PO4_surf_t1.eps} [vertical sections along open boundaries] \includegraphics[width=0.5\textwidth]{Figures/PO4_profil_t1.eps}

Finally, to compute the Iron dust deposition forcing file roms_frcbio.nc file, in a matlab session, run make_dust.m :
$»$
$»$ make_dust

Figure 1.8: Result of make_clim_pisces for the Benguela example : Iron dust deposition forcing fields [nmol Fe m-3].
\includegraphics[width=1\textwidth]{Figures/dustdepo_surface.eps}

If the makepisces =1 in romstools_param.m, make_clim.m will process directly make_clim_pisces.m, make_dust.m and eventually make_ini_pisces.m. It is exactly the same procedure for the roms_bry.nc files.

The cpp keys related to this biogeochemical model are :

1.8 Inter-Annual simulations

ROMSTOOLS can help to realize inter-annual simulations. In this context, we rely on Ocean Global Circulations Models (OGCM) for the lateral boundary conditions and a global atmospheric reanalysis for the surface forcing (NCEP). To limit the volume of data which needs to be transfered over the Internet, we use Opendap to extract only the necessary subgrids.

1.8.1 Getting the surface forcing data from NCEP

The Matlab script make_NCEP.m is used to obtain the surface forcing data. It downloads the necessary NCEP surface forcing data (Sea Surface Temperature, Wind stress ...) over the Internet, and interpolates them on the model grid. Since make_NCEP.m works with the bulk parameterization (i.e. the BULK_FLUX and BULK_EP cpp keys should be defined in cppdefs.h), a surface forcing NetCDF file and a bulk NetCDF file are generated for each month of your simulation in the directory $\sim$/Roms_tools/Run/ROMSFILES/ . The part of the file romstools_param.m that you should change is:

%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% 7 Parameters for Interannual forcing (SODA, ECCO, NCEP, ...)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Download_data = 1; % Get data from the OPENDAP sites
level = 0; % AGRIF level; 0=parent grid
%
NCEP_version = 2; % NCEP version:
% 1: NCEP/NCAR Reanalysis, 1/1/1948 - present
% 2: NCEP-DOE Reanalysis, 1/1/1979 - present
%

% Path and option for using global datasets download from ftp
%
Get_My_Data = 0;
%

if NCEP_version == 1;
My_NCEP_dir = [DATADIR,'NCEP_REA1/'];
elseif NCEP_version == 2;
My_NCEP_dir = [DATADIR,'NCEP_REA2/'];
end

My_QSCAT_dir = [DATADIR,'QSCAT/'];
My_SODA_dir = [DATADIR,'SODA/'];
My_ECCO_dir = [DATADIR,'ECCO/'];

%======================================
%Options for make_NCEP and make_QSCAT_daily
%
NCEP_dir= [FORC_DATA_DIR,'NCEP_',ROMS_config,'/']; % NCEP data directory
makefrc = 1; % 1: Create forcing files
makeblk = 1; % 1: Create bulk files
QSCAT_blk = 1; % Correct NCEP frc/bulk file with the u,v,wspd fields from QSCAT daily data. Download u, v, wspd in the QSCAT frc file

add_tides = 0; % 1: Add the tides (To be done...)

%Overlap parameters :
itolap_qscat=11; %11 days if 1d time reso. QSCAT (should be <28 )
itolap_ncep=40; %10 days if 6h time res. NCEP (should be <4* 28 =112
% ...

Variables description :

Save romstools_param.m and run make_NCEP in the Matlab session.

1.8.1.1 Using OpenDAP : Get_My_Data = 0

You should obtain:

$»$ make_NCEP
Read in the grid ROMS_FILES/roms_grd.nc

$===========================================$
BEGIN DOWNLOAD STEP
$===========================================$
$===========================================$
Download NCEP data with OPENDAP or my FTP data
$===========================================$
$===========================================$
OPENDAP Procedure
$===========================================$

Get NCEP data from 2000 to 2000
From http://nomad1.ncep.noaa.gov:9090/dods/reanalyses/reanalysis-2/

Minimum Longitude: 8
Maximum Longitude: 22
Minimum Latitude: -38
Maximum Latitude: -25.8968 Making output data directory
......./Run/DATA/NCEP_Benguela_LR/
$=========================================$
VNAME IS landsfc
$=========================================$
$-$
Get time units and time: Get_My_Data is OFF
$-$
Reading: http://nomad1.ncep.noaa.gov:9090/dods/reanalyses/reanalysis-2/6hr/flx/flx
Constraint: time
Server version: dods/3.2
...

1.8.1.2 Using FTP global dataset : Get_My_Data $=$ 1

$»$ make_NCEP
Read in the grid ROMS_FILES/roms_grd.nc

$============================================$
Download NCEP data with OPENDAP or my FTP data
$============================================$
$============================================$
Direct FTP Procedure
$============================================$
Use my own ncep data NCEP$2$

Get NCEP data from $2000$ to $2000$
From path/NCEP_REA2/

Minimum Longitude: $8$
Maximum Longitude: $22$
Minimum Latitude: $-38$
Maximum Latitude: $-25.8968$

$============================================$
Get_My_Data = 1
Read subgrid from file/data1/gcambon/NCEP_REA2/land.sfc.gauss.nc
$============================================$
Get the Land Mask tindex = 1
In case of Get_My_Data ON

Get the Land Mask by using extract_NCEP_Mask_Mydata
Execute extract_NCEP_Mask_Mydata

Get land for year 2000 - month 1

Create path/Run/DATA/NCEP_Benguela_LR/land_Y2000M1.nc
$============================================$
VNAME IS air
$============================================$

$============================================$
Processing year: 2000
$============================================$

1.8.2 Getting the surface windstress data from QuickSCAT


1.8.2.1 QuikSCAT daily data from Ifremer OpenDap server

Similarly, The Matlab script make_QuickSCAT_daily.m is used to obtain the daily surface stress forcing provided by the OpenDAP server at Ifremer, France:
http://www.ifremer.fr/dodsG/CERSAT/quikscat_daily.
A surface forcing NetCDF file NetCDF file is generated for each month of your simulation in the directory $\sim$/Roms_tools/Run/ROMSFILES/.

You shoud edit this part of the file romstools_param.m:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% 7 Parameters for Interannual forcing (SODA, ECCO, NCEP, ...)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Path to Forcing data
.....
% Options for make_QSCAT_daily and make_QSCAT_clim
%
QSCAT_dir = [FORC_DATA_DIR,'QSCAT_',ROMS_config,'/'];% QSCAT data directory.
QSCAT_frc_prefix = [frc_prefix,'_QSCAT_']; % generic forcing file name for interannual roms simulations with QuickSCAT.
QSCAT_clim_file = [DATADIR,'QuikSCAT_clim/roms_QSCAT_month_clim_2000_2007.nc']; % QuikSCAT climatology file for make_QSCAT_clim.
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

In a Matlab session, run make_QSCAT_daily
$»$
$»$ make_QSCAT_daily

if you download data over the internet using OpenDAP, you should obtain that during the dowload step :

$»$
...
Reading: http://www.ifremer.fr/dodsG/CERSAT/quikscat_daily
Constraint: mwst[167:167][78:113][370:409]
Server version: apache-coyote/1.1
Processing day: 1

Reading: http://www.ifremer.fr/dodsG/CERSAT/quikscat_daily
Constraint: zwst[168:168][78:113][370:409]
Server version: apache-coyote/1.1

Reading: http://www.ifremer.fr/dodsG/CERSAT/quikscat_daily
Constraint: mwst[168:168][78:113][370:409]
Server version: apache-coyote/1.1
Processing day: 2
....
$»$


1.8.2.2 QuikSCAT monthly climatology data

If you want to use the QSCAT climatology, computed over $2000$-$2007$, based over these previous QSCAT data, in a Matlab session, run make_QSCAT_clim.

$»$
$»$ make_QSCAT_clim
$»$ ...

1.8.3 Getting the lateral boundary conditions

Initial conditions and lateral boundary conditions and can be obtained from several ocean global circulation models (OGCM) such as SODA (Carton et al., 2005) or ECCO (Stammer et al., 1999). The SODA reanalysis is available from 1958 to 2001 and ECCO is available from 1993 until now. The Matlab script make_OGCM.m is used to download data over the Internet, and to perform the interpolations on the model grid. A lateral boundary conditions NetCDF file is generated for each month of your simulation in the directory $\sim$/Roms_tools/Run/ROMSFILES/ .

The part of the file romstools_param.m that you should change is:

%%%%%%%%%%%%%%%%%%%
%
% Options for make_OGCM
%
%%%%%%%%%%%%%%%%%%%
OGCM = 'SODA'; % Select the OGCM: SODA(1958-2001), ECCO(1993-2005), ...
OGCM_dir = [FORC_DATA_DIR,OGCM,'_',ROMS_config,'/'];
bry_prefix = [ROMS_files_dir,'roms_bry_',OGCM,'_'];
clm_prefix = [ROMS_files_dir,'roms_clm_',OGCM,'_'];
ini_prefix = [ROMS_files_dir,'roms_ini_',OGCM,'_'];
OGCM_prefix = [OGCM,'_'];
rmdepth = 2;

%Overlap parameters : before (_a) and after (_p) the months.
itolap_a=2;   %Overlap parameter at the begining of the months.
itolap_p=2;   %Overlap parameter at the end of the months.
%

Variables description :

Save romstools_param.m and run make_OGCM in the Matlab session. You should obtain:

$»$ make_OGCM
Add the paths of the different toolboxes
Arch : x86_64 - Matlab version : 2006a
Use of mexnc and loaddap in 64 bits.
Download data...

Get data from Y2000M1 to Y2000M3
Minimum Longitude: 12.3
Maximum Longitude: 20.3
Minimum Latitude: -35.5
Maximum Latitude: -26.3815

Making output data directory ../Run/DATA/SODA_Benguela/
Process the dataset: http://iridl.ldeo.columbia.edu./SOURCES/.CARTON-GIESE/.SODA/.v1p4p3
Processing year: 2000
Processing month: 1
Download SODA for 2000 - 1
...SSH
...U
...

1.8.4 Running the model for interannual runs

Compile the model with jobcomp (and with the cpp keys BULK_FLUX and BULK_EP defined) and edit the input parameter file $\sim$/Roms_tools/Run/roms_inter.in as for the climatology experiments. As for the long simulations, a csh script (run_roms_inter.csh) manages the handling of input and output files. It also changes the number of time steps so each month has the correct length. This script takes care of leap years. For example Y1996M2 (February 1996) is 29 days long.

Part to edit in run_roms_inter.csh:

#
set MODEL=roms
set SCRATCHDIR=`pwd`/SCRATCH
set INPUTDIR=`pwd`
set MSSDIR=`pwd`/ROMS_FILES
set MSSOUT=`pwd`/ROMS_FILES
set CODFILE=roms
set AGRIF_FILE=AGRIF_FixedGrids.in
#
set BULK_FILES=1
set FORCING_FILES=1
set CLIMATOLOGY_FILES=0
set BOUNDARY_FILES=1
#
# Atmospheric surface forcing dataset (NCEP, GFS,...)
#
set ATMOS=NCEP
#
# Oceanic boundary and initial dataset (SODA, ECCO,...)
#
set OGCM=SODA
#
# Model time step [seconds]
#
set DT=5400
#
# number total of grid levels (1: No child grid)
#
set NLEVEL=1
#
set NY_START=2000
set NY_END=2000
set NM_START=1
set NM_END=3
#
# Restart file - RSTFLAG=0 -$>$ No Restart
# RSTFLAG=1 -$>$ Restart
#
set RSTFLAG=0
#
# Time Schedule - TIME_SCHED=0 -$>$ yearly files
# TIME_SCHED=1 -$>$ monthly files
#
set TIME_SCHED=1
#
########################################################

Variables definitions:

As for ROMS long climatology experiments, inter-annual experiments can be run in batch mode:
$>$: nohup ./run_roms_inter.csh $>$ exp1.out &

1.9 Embedding

1.9.1 Embedded (child) model preparation

To run an embedded model, the user must provide the grid, the surface forcing and the initial conditions. To name the different files, AGRIF employs a specific strategy: if the parent file names are of the form: XXX.nc, the first child names will be of the form: XXX.nc.1, the second: XXX.nc.2, etc... This convention is also applied for the "roms.in" input files.

A graphic user interface (NestGUI) facilitates the generation of the different NetCDF files. Launch nestgui in the Matlab session (in the $\sim$/Roms_tools/Run/ directory):

$»$
$»$ nestgui

A window pops up, asking for a "PARENT GRID" NetCDF file (Figure 1.9). In our Benguela test case, you should select $\sim$/Roms_tools/Run/ROMSFILES/roms_grd.nc (grid file) and click "open". The main window appears (Figure 1.10).

Figure 1.9: Entrance window of NestGUI
\includegraphics[width=12cm]{Figures/nestgui_entrance.eps}

Figure 1.10: The NestGUI main window
\includegraphics[width=1\textwidth]{Figures/nestgui_vizu.eps}

To generate the child model you should follow several steps:

  1. To define the child domain, click "Define child" and create the child domain on the main window. The size of the grid child (Lchild and Mchild) is now visible. This operation can be redone until you are satisfied with the size and the position of the child domain. The child domain can be finely tuned using the imin, imax, jmin and jmax boxes. Be aware that the mask interpolation from the parent grid to the child grid is not optimal close to corners. Parent/Child boundaries should be placed where the mask is showing a straight coastline. A warning will be given during the interpolation procedure if this is not the case.

  2. "Interp child" : It generates the child grid file. Before, you should select if you are using a new topography ("New child topo" button) for the child grid or if you are just interpolating the parent topography on the child grid. In the first case, you should defines what topography file will be used (e.g. $\sim$/Roms_tools/Topo/etopo2.nc or another dataset). You should also define if you want the volume of the child grid to match the volume of the parent close to the parent/child boundaries ("Match volume" button, it should be "on" by default). You should also define the 'r' factor (Beckmann and Haidvogel, 1993) for topography smoothing ("r-factor", 0.25 is safe) and the number of points to connect the child topography to the parent topography ("n-band", it follows the relation $h_{new}=\alpha.h_{child} + (1-\alpha).h_{parent}$, where $\alpha$ is going from 0 to 1 in "n-band" points from the parent/child boundaries). You should also select the child minimum depth ("Hmin", it should be lower or equal to the parent minimum depth), the maximum depth at the coast ("Hmax coast"), the number of selective hanning filter passes for the deep regions ("n filter deep") and the number of final hanning filter passes ("n filter final").

  3. "Interp forcing": It interpolates the parent surface forcing on the child grid. Select the parent forcing file to be interpolated (e.g. $\sim$/Roms_tools/Run/ROMSFILES/roms_frc.nc). The child forcing file roms_frc.nc.1 will be created. The parent surface fluxes are interpolated on the child grid. You can use "Interp bulk" if you are using a bulk formula. In this case, the parent bulk file (e.g. $\sim$/Roms_tools/Run/ROMSFILES/roms_blk.nc) will be interpolated on the child grid.

  4. "Interp initial": It interpolates parent initial conditions on the child grid. Select the parent initial file (e.g. $\sim$/Roms_tools/Run/ROMSFILES/roms_ini.nc). The child initial file (e.g. $\sim$/Roms_tools/Run/ROMSFILES/roms_ini.nc.1) will be created. If the topographies are different between the parent and the child grids, the child initial conditions are vertically re-interpolated. In this case you should check if the options "vertical corrections" and "extrapolations" are selected. It is preferable to always use these options.
    If there are parent biological fields in the initial files, they can be processed automatically, we have to define the type of biological models: either NPZD-type (NChlPZD, N2ChlPZD2 or N2P2Z2D2) then click on the 'Biol' button, either PISCES biogeochemical model, then click on the 'Pisces' button. The fields needed for the initialization of these biological model will be processed.
    For information, in the case of NPZD type model, there are 4 more fields and in the case of PISCES biogeochemical model, there is 8 more fields.

  5. "Interp dust": It interpolates parent Iron dust forcing file conditions on the child grid. This is needed only in case of PISCES biogeochemical experiments. Select the parent initial file (e.g. $\sim$/Roms_tools/Run/ROMSFILES/roms_frcbio.nc). The child initial file (e.g. $\sim$/Roms_tools/Run/ROMSFILES/roms_frcbio.nc.1) will be created.

  6. "Interp restart" generates a child restart file from a parent restart file
    (e.g. $\sim$/Roms_tools/Run/ROMSFILES/roms_rst.nc). This can be done to "hot start" a child model after the spin-up of the parent model. As in the case of initial files generation, there is the possibility to compute ans write in the nested restart file either the biological fields from NPZD-type biological model, either the PISCES biogeochemical fields. For this purpose, click either on the 'Biol' button, either on the the 'Pisces' button.

  7. You can click on "Create roms.in.*" to generate a child input file (roms.in.1) from the parent input file and click on "Create AGRIF_FixedGrids.in" to generate a AGRIF_FixedGrids.in file (the file which defines the child grid position in the parent grid).

  8. "River" can be used to locate the river on the coast.

  9. "Interp clim" can be useful to generate boundary conditions to test the child model alone. As in the case of restart an initial nested files generation, during the eventual phase of creation of a nested clim file, the fields related to the NPZD-type biological models or the PISCES one can be computed and written in the nested clim file. As usual, click either on the 'Biol' button or on the 'Pisces' button.

1.9.2 Compiling and running the model

The ROMS nesting procedure needs a Fortran 95 compiler. For Linux PCs, the Intel Fortran Compiler (ifort) is available at
http://www.intel.com/software/products/compilers/flin/noncom.htm. To be able to compile ROMS with ifort, you should change the corresponding comments in jobcomp.

To activate the AGRIF nesting procedure, define AGRIF in $\sim$/Roms_tools/Run/cppdefs.h. Moreover, to activate the AGRIF nesting with the $2$-way capability, define AGRIF and AGRIF_$2$WAYS.

It is possible to edit the file AGRIF_FixedGrids.in. This file contains the child grid positions (i.e. imin,imax,jmin,jmax) and coefficients of refinement. A first line gives the number of children grids per parent (if AGRIF_STORE_BAROT_CHILD is defined, only one child grid can be defined per parent grid). A second line gives the relative position of each grid and the coefficient of refinement for each dimension. Edit the input files roms.in.1, roms.in.2 , etc... to define correctly the file names and the time steps. To run the model, simply type at the prompt: roms roms.in.

To visualize the ROMS model outputs for different grid levels, change the value in the "child models" box in roms_gui.

1.10 Operational coastal modeling system

An operating coastal modeling system can be designed following the assumption that large scale offshore dynamics are slow in comparison to the coastal system. The lateral boundary conditions are interpolated from the last available ECCO model outputs and are kept constant during the ROMS simulation. ECCO model outputs are delayed by about two to four weeks, but we suppose that they are still relevant for the present large scale oceanic structure. The Global Forecast System (GFS) is used for the surface forcing. A first day of simulation is run in hindcast mode. This will provide the initial conditions for the next simulated day. Using GFS as surface forcing and ECCO for the lateral boundary conditions, a forecast of 7 days is conducted. A UNIX C-Shell script ( /Roms_tools/Run/run_roms_forecast.csh) manages data downloading, the hindcast and forecast simulations and datas storage. The script run_roms_forecast.csh starts Matlab in batch mode to download with OPENDAP the lateral boundary conditions from ECCO and the surface forcing from GFS. It interpolates the data on ROMS grid and launches the hindcast and the forecast runs.

The script run_roms_forecast.csh should be edited to change the directory pathways (HOME, RUNDIR, PATH, LD_LIBRAIRY_PATH, MATLAB,...).

The ROMS input files $\sim$/Roms_tools/Run/roms_hindcast.in and
$\sim$/Roms_tools/Run/roms_forecast.in should also be edited to change the length of the time step and the number of time steps. The ROMS input file roms_hindcast.in should be defined such as the hindcast run duration is 1 day and a restart file is generated at the end of the hindcast run.

The script run_roms_forecast.csh can be relaunched everyday in batch mode using crontab.

2. ROMS_AGRIF v2.1

2.1 The ROMS model

ROMS solves the primitive equations in an Earth-centered rotating environment, based on the Boussinesq approximation and hydrostatic vertical momentum balance. ROMS is discretized in coastline- and terrain-following curvilinear coordinates. ROMS is a split-explicit, free-surface ocean model, where short time steps are used to advance the surface elevation and barotropic momentum, with a much larger time step used for temperature, salinity, and baroclinic momentum. ROMS employs a special 2-way time-averaging procedure for the barotropic mode, which satisfies the 3D continuity equation (Shchepetkin and McWilliams, 2005). The specially designed predictor-corrector time step algorithm used in ROMS allows a substantial increase in the permissible time-step size.

ROMS has been designed to be optimized on shared memory parallel computer architectures such as the SGI/CRAY Origin 2000. Parallelization is done by two dimensional sub-domains partitioning. Multiple sub-domains can be assigned to each processor in order to optimize the use of processor cache memory. This allow super-linear scaling when performance growth even faster than the number of CPUs.

The third-order, upstream-biased advection scheme implemented in ROMS allows the generation of steep gradients, enhancing the effective resolution of the solution for a given grid size (Shchepetkin and McWilliams, 1998). Explicit lateral viscosity is null everywhere in the model domain except in sponge layers near the open boundaries where it increases smoothly close to the lateral open boundaries.

A non-local, K-profile planetary (KPP) boundary layer scheme (Large, 1994) parameterizes the unresolved physical vertical subgrid-scale processes. If a lateral boundary faces the open ocean, an active, implicit, upstream biased, radiation condition connects the model solution to the surroundings (Marchesiello et al., 2001).

More informations and model description can also be found in the SCRUM Manuel (Hedström, K. S. , 1997) and a more recent User Manual on ROMS (Rutgers version2.1), both written by Kate Hedström2.2 (Hedström, K. S. , 2009) 2.3. These documents are available on the ROMS_AGRIF web site : http://roms.mpl.ird.fr in the documentation section.

2.2 Nesting capabilities, 1-WAY and 2-WAY using the AGRIF procedure

2.2.1 Introduction

To address the challenge of bridging the gap between near-shore and offshore dynamics, a nesting capability has been added to ROMS and tested for the California Upwelling System (Penven et al., 2006). The method chosen for embedded griding takes advantage of the AGRIF (Adaptive Grid Refinement in Fortran) package (Debreu and Blayo, 2008; Blayo and Debreu, 1999; Debreu and Vouland, 2003; Debreu and Blayo, 2003; Debreu, 2000). AGRIF is a Fortran 95 package for the inclusion of adaptive mesh refinement features within a finite difference numerical model. One of the major advantages of AGRIF in static-grid embedding is the ability to manage an arbitrary number of fixed grids and an arbitrary number of embedding levels.

Figure 2.1: Temporal coupling between a parent and a child grid for a refinement factor of 3. The coupling is done at the baroclinic time step.
\begin{figure}\centerline{\psfig{figure=Figures/nesting_fig1.eps,width=15cm}}\end{figure}

A recursive integration procedure manages the time evolution for the child grids during the time step of the parent grids (Figure 2.1). In order to preserve the CFL criterion, for a typical coefficient of refinement (say, a factor of 3 for a 5 km resolution grid embedded in a 15 km grid), for each parent time step the child must be advanced using a time step divided by the coefficient of refinement as many time as necessary to reach the time of the parent (Figure (2.1)). For simple 2-level embedding, the procedure is as follows:

  1. Advance the parent grid by one parent time step.
  2. Interpolate the relevant parent variables in space and time to get the boundary conditions for the child grid.
  3. Advance the child grid by as much child time steps as necessary to reach the new parent model time.
  4. Update point by point the parent model by averaging the more accurate values of the child model (in the case of 2-way embedding).
The recursive approach used in AGRIF allows the specification of any number of embedding level. Other cpp keys are related to AGRIF, they are in set_global_definitions.h and set_obc_definitions.h files. These ones are the default conditions, are located in the ROMS_AGRIF code sources and should not be edit by standard user.


2.2.2 AGRIF nesting procedure

To have a better undersatnding of the nesting capabilties of ROMS using AGRIF, it can be useful to report to the homepage of the AGRIF project and papers related to its application to ROMS.
  1. AGRIF homepage : http://www-ljk.imag.fr/MOISE/AGRIF/
  2. ROMS - AGRIF 1 way nesting : Evaluation and application of the ROMS 1-way, embedding procedure to the central california upwelling system, (Penven et al., 2006)
  3. ROMS - AGRIF 2 way nesting: Two ways embedding algorithms for a split-explicit free surface model. (Debreu et al , 2010)


2.3 Changelog since ROMS_AGRIF 1.1


2.4 Parameters description : param.h

In this section, we present the more important parameters to configure your own run. These parameters are :


2.5 CPP-keys description : cppdefs.h

In this section, we present the differents cpp keys used to define the numerical or physical options in ROMS_AGRIF. These latters are ordered in differents sections and described in Table 2.1.

Table 2.1: Description of the CPP keys used in the cppdefs.h file
TYPE CPP KEYS NAME
   
TEST CASE  
  BASIN
  CANYON_A
  CANYON_B
  GRAV_ADJ
  INNERSHELF
  OVERFLOW
  SEAMOUNT
  SHELFRONT
  SOLITON
  UPWELLING
  INTERNAL
  VORTEX
  REGIONAL : realistric configuration
Basic options
Configuration Name  
  BENGUELA
Parallelization  
  OPENMP
  MPI
Embedding  
  AGRIF
  AGRIF_2WAY
Open Boundary Conditions  
  TIDES
  OBC_EAST
  OBC_WEST
  OBC_NORTH
  OBC_SOUTH
Tides  
  TIDES
  SSH_TIDES
  UV_TIDES
  TIDERAMP
Applications  
  BIOLOGY
  FLOATS
  STATIONS
  PASSIVE_TRACER
  SEDIMENT
  BBL
   
More advanced options
Parallelization  
  PARALLEL_FILES
  AUTOTILING
  ETALON_CHECK
Model dynamics  
  SOLVE3D
  UV_COR
  UV_ADV
Grid configuration  
  CURVGRID
  SPHERICAL
  MASKING
Lateral Momentum Mixing  
  MIX_GP_UV
  MIX_GP_UV
  UV_VIS2
  UV_VIS4
  VIS_SMAGO
Lateral Tracer Mixing  
  MIX_GP_TS
  MIX_S_TS
  MIX_EN_TS
  TS_DIF2
  TS_DIF4
  TS_SPLIT_UP3
Nudging  
  ZNUDGING
  M2NUDGING
  M3NUDGING
  TNUDGING
  ROBUST_DIAG
Vertical Mixing  
  BODYFORCE
  BVF_MIXING
  LMD_MIXING
  LMD_SKPP
  LMD_BKPP
  LMD_RIMIX
  LMD_CONVEC
  LMD_DDMIX
  LMD_NONLOCAL
Equation of State  
  SALINITY
  NONLIN_EOS
  SPLIT_EOS
Surface Forcing  
  QCORRECTION
  SFLX_CORR
  DIURNAL_SRFLUX
  BULK_FLUX
  BULK_FAIRALL
  BULK_LW
  BULK_EP
  BULK_SMFLUX
Sponge Layer  
  SPONGE
Lateral Forcing  
   
1-Climatology strategy : 3D fields covering the whole domain  
  CLIMATOLOGY
  ZCLIMATOLOGY
  M2CLIMATOLOGY
  M3CLIMATOLOGY
  TCLIMATOLOGY
   
2-Boundary strategy : 1D fields only on OBC points  
  FRC_BRY
  Z_FRC_BRY
  M2_FRC_BRY
  M3_FRC_BRY
  T_FRC_BRY
Bottom Forcing  
  ANA_BSFLUX
  ANA_BTFLUX
Point Sources - Rivers  
  PSOURCE
  ANA_PSOURCE
Open Boundary Conditions  
  OBC_M2SPECIFIED
  OBC_M2FLATHER
  OBC_M2CHARACT
  OBC_M2ORLANSKI
  OBC_VOLCONS
  OBC_M3ORLANSKI
  OBC_M3SPECIFIED
  OBC_TORLANSKI
  OBC_TSPECIFIED
Input/Output and Diagnostics  
  AVERAGES
  AVERAGES_K
  DIAGNOSTICS_TS
  DIAGNOSTICS_TS_ADV
  DIAGNOSTICS_TS_MLD
  DIAGNOSTICS_UV
BIOLOGY models  
  PISCES
  BIO_NChlPZD
  BIO_N2P2Z2D2
  BIO_N2ChlPZD2

 

Test Case

Table 2.2: Test Case related CPP keys
CPP KEYS NAME Description
BASIN Must be defined for running the Basin Example.
CANYON_A Must be defined for running the Canyon_A Example.
CANYON_B Must be defined for running the Canyon_B Example.
GRAV_ADJ Must be defined for running the Gravitational Adjustment Example.
INNERSHELF Must be defined for running the Inner Shelf Example.
OVERFLOW Must be defined for running the Gravitational/Overflow Example.
SEAMOUNT Must be defined for running the Seamount Example.
SHELFRONT Must be defined for running the Shelf Front Example.
SOLITON Must be defined for running the Equatorial Rossby Wave Example.
UPWELLING Must be defined for running the Upwelling Example.
INTERNAL Must be defined for running the Internal tides example.
VORTEX Must be defined for running the Baroclinic Vortex Example.
REGIONAL Must be defined if running realistic regional simulations.

 

Parallelization

Table 2.3: Parallelization related CPP keys
CPP KEYS NAME Description
OPENMP Activate the Open-MP parallelization protocol.
MPI Activate the MPI parallelization protocol.
PARALLEL_FILES Activate the I/O writing on multiprocessor.
AUTOTILING Activate the subdomains partitionning optimization.
 

2.5.0.0.1 Preselected options

 
# ifdef MPI
# $ $$ $undef PARALLEL_FILES
# endif
# undef AUTOTILING

Embedding

Table 2.4: Embedding related CPP keys
CPP KEY NAME Description
AGRIF Activate the (1-WAYS) nesting capabilities.
AGRIF_2WAY Add the the 2-WAYS nesting (update of the parent grid solution by the child grid solution) capabilities.
 

Open Boundary Conditions I

Table 2.5: Open Boundary Conditions (basic) related CPP keys
CPP KEY NAME Description
OBC_EAST Open eastern boundary.
OBC_WEST Open western boundary.
OBC_SOUTH Open southern boundary.
OBC_NORTH Open northern boundary.
 

Tides

Table 2.6: Tides forcing related CPP keys
CPP KEY NAME Description
TIDES Activate the forcing og tides at open-boundaries.
SSH_TIDES Define for processing sea surface elevation tidal data at the model boundaries.
UV_TIDES Define for processing ocean current tidal data at the model boundaries.
TIDERAMP Apply a ramping of the tidal current, (in general 2 days) at initialization. Warning! This should be off when restarting the model.
 

2.5.0.0.2 Preselected options

 
# ifdef TIDES
# define SSH_TIDES
# define UV_TIDES
# define TIDERAMP
# endif

Applications

Table 2.7: related CPP keys
CPP KEY NAME Description
BIOLOGY Activate the biogeochemical module.
FLOATS Activate floats.
STATIONS Store model outputs for each time step at different station locations.
PASSIVE_TRACER Add a passive tracer.
SEDIMENT Activate the sediment module.
BBL Activate the bottom boundary layer module.
 

2.5.0.0.3 Preselected options: 

 
# undef BIOLOGY
# undef FLOATS
# undef STATIONS
# undef PASSIVE_TRACER
# undef SEDIMENT
# undef BBL

Model dynamics

Table 2.8: Model dynamics related CPP keys
CPP KEY NAME Description
SOLVE3D Define if solving 3D primitive equations.
UV_COR Activate Coriolis terms.
UV_ADV Activate advection terms.
 

2.5.0.0.4 Preselected options: 

 
# define SOLVE3D
# define UV_COR
# define UV_ADV
# ifdef TIDES
# $  $ define SSH_TIDES
# $  $ define UV_TIDES
# $  $ define TIDERAMP
# endif

Grid configuration

Table 2.9: Model grid related CPP keys
CPP KEY NAME Description
CURVGRID Activate curvilinear coordinate grid option.
SPHERICAL Activate longitude/latitude grid positioning.
MASKING Activate land masking in the domain.
 

2.5.0.0.5 Preselected options: 

 
# define CURVGRID
# define SPHERICAL
# define MASKING

Lateral Momentum Mixing

Table 2.10: Lateral Momentum mixing related CPP keys
CPP KEY NAME Description
MIX_GP_UV Activate mixing on geopotential (constant Z) surfaces.
MIX_S_UV Activate mixing on iso-sigma (constant sigma) surfaces.
UV_VIS2 Activate Laplacian horizontal mixing of momentum.
UV_VIS4 Activate Bilaplacian horizontal mixing of momentum.
 

2.5.0.0.6 Preselected options: 

 
# define UV_VIS2
# define MIX_GP_UV

Lateral Tracer mixing

Table 2.11: Lateral Tracer mixing related CPP keys
CPP KEY NAME Description
MIX_GP_TS Activate mixing on geopotential (constant Z) surfaces.
MIX_S_TS Activate mixing on iso-sigma level surfaces.
MIX_EN_TS Activate mixing on isopygnal level surfaces.
TS_DIF2 Activate Laplacian horizontal mixing of tracer.
TS_DIF4 Activate Bilaplacian horizontal mixing of tracer.
TS_SPLIT_UP3 Activate the rotated split upstream advection-diffusion scheme for tracer equation. (Marchesiello et al , 2009)
 

2.5.0.0.7 Preselected options: 

 
# define MIX_GP_TS
# define TS_DIF2
# undef TS_SPLIT_UP3

Nudging

Table 2.12: Nudging related CPP keys
CPP KEY NAME Description
ZNUDGING Activate nudging layer for zeta.
M2NUDGING Activate nudging layer for barotropic velocities.
M3NUDGING Activate nudging layer for baroclinic velocities.
TNUDGING Activate nudging layer for tracer.
ROBUST_DIAG Activate strong tracer nudging in the interior for diagnostic simulations.
 

The nudging layer has the same location than sponge layer. In the sponge/nudging layer, the signal, tracers and momentum, is nudged towards climatology using a nudging coefficient $\tau_{out}$ expressed in $s{-1}$, equal to the inverse of the coefficient $TauM_{out}/TauT_{in}$ in the namelist roms.in

2.5.0.0.8 Preselected options: 

 
# define CLIMATOLOGY
# ifdef CLIMATOLOGY
.....
# $ $$ $define ZNUDGING
# $ $$ $define M2NUDGING
# $ $$ $define M3NUDGING
# $ $$ $define TNUDGING
# $ $$ $undef ROBUST_DIAG
# endif

Vertical Mixing

Table 2.13: Vertical mixing related CPP keys
CPP KEY NAME Description
BODYFORCE Define if applying surface and bottom stresses as bodyforces
BVF_MIXING Activate a simple mixing scheme based on the Brunt-Väisälä frequency
LMD_MIXING Activate Large/McWilliams/Doney mixing (LMD-KPP closure)
LMD_SKPP Activate surface boundary layer KPP mixing (LMD-KPP closure)
LMD_BKPP Activate bottom boundary layer KPP mixing (LMD-KPP closure)
LMD_RIMIX Activate shear instability interior mixing (LMD-KPP closure)
LMD_CONVEC Activate convection interior mixing (LMD-KPP closure)
LMD_DDMIX Activate double diffusion interior mixing (LMD-KPP closure)
LMD_NONLOCAL Activate nonlocal transport (LMD-KPP closure)
 

2.5.0.0.9 Preselected options: 

 
# undef BODYFORCE
# undef BVF_MIXING
# define LMD_MIXING
# ifdef LMD_MIXING
# $ $$ $ define LMD_SKPP
# $ $$ $ define LMD_BKPP
# $ $$ $ define LMD_RIMIX
# $ $$ $ define LMD_CONVEC
# $ $$ $ undef LMD_DDMIX
# $ $$ $ undef LMD_NONLOCAL
# endif

Equation of state

Table 2.14: Equation of state related CPP keys
CPP KEY NAME Description
SALINITY Define if using salinity.
NONLIN_EOS Activate the nonlinear equation of state.
SPLIT_EOS Activate the split of the nonlinear equation of state in a adiabatic part and a compressible part for the reduction of pressure gradient errors (Shchepetkin and McWilliams, 2003).
 

2.5.0.0.10 Preselected options: 

 
# define SALINITY
# define NONLIN_EOS
# define SPLIT_EOS

Surface Forcing

Table 2.15: Surface forcing related CPP keys
CPP KEY NAME Description
BULK_FLUX Activate the bulk parametrization.
BULK_EP Activate the bulk parametrization for salinity fluxes.
BULK_LW Activate online long-wave radiation calculation using model SST.
BULK_SMFLUX Activate the bulk parametrization for surface momentum stress.
QCORRECTION Activate net heat flux correction.
SFLX_CORR Activate freshwater flux correction.
DIURNAL_SRFLUX Activate diurnal modulation of the short wave radiation flux.
 

2.5.0.0.11 Preselected options: 

 
# define QCORRECTION
# define SFLX_CORR
# define DIURNAL_SRFLUX
# undef BULK_FLUX
# ifdef BULK_FLUX
# $ $$ $define LW_ONLINE
# $ $$ $define BULK_EP
# $ $$ $undef BULK_SMFLUX
# $ $$ $define DIURNAL_SRFLUX
# else
# $ $$ $define QCORRECTION
# $ $$ $define SFLX_CORR
# $ $$ $define DIURNAL_SRFLX
# endif

Sponge Layer

Table 2.16: Sponge layer related CPP keys
CPP KEY NAME Description
SPONGE Activate areas of enhanced viscosity/diffusion close to the lateral open boundaries.

 

Lateral forcing

Table 2.17: Lateral forcing related CPP keys
CPP KEY NAME Description
CLIMATOLOGY Activate processing of climatology data.
ZCLIMATOLOGY Activate processing of sea surface height climatology.
M2CLIMATOLOGY Activate processing of barotropic velocities climatology.
M3CLIMATOLOGY Activate processing of baroclinic velocities climatology.
TCLIMATOLOGY Activate processing of tracer climatology.
FRC_BRY Activate direct boundary forcing
Z_FRC_BRY Activate boundary forcing for zeta.
M2_FRC_BRY Activate boundary forcing for barotropic velocities.
M3_FRC_BRY Activate boundary forcing for baroclinic velocities
T_FRC_BRY Activate boundary forcing for tracers.
 

2.5.0.0.12 Preselected options: 

 
# define CLIMATOLOGY
# ifdef CLIMATOLOGY
# $ $ define ZCLIMATOLOGY
# $ $ define M2CLIMATOLOGY
# $ $ define M3CLIMATOLOGY
# $ $ define TCLIMATOLOGY
# $ $ ...
# endif

# undef FRC_BRY
# ifdef FRC_BRY
# $ $define Z_FRC_BRY
# $ $define M2_FRC_BRY
# $ $define M3_FRC_BRY
# $ $define T_FRC_BRY
# endif

Bottom forcing

Table 2.18: Bottom forcing related CPP keys
CPP KEY NAME Description
ANA_BSFLUX Define if using analytical bottom salinity flux
ANA_BTFLUX Define if using analytical bottom temperature flux.
 

2.5.0.0.13 Preselected options: 

 
# define ANA_BSFLUX
# define ANA_BTFLUX

Point Sources - Rivers

Table 2.19: Point Sources and Rivers related CPP keys
CPP KEY NAME Description
PSOURCES Define if using point sources (rivers)
ANA_PSOURCES Define if using analytical vertical profiles for the point sources (using fluxes defined in roms.in)

 

2.5.0.0.14 Preselected options: 

 
# undef PSOURCE
# undef ANA_PSOURCE

Open Boundary Conditions II

Table 2.20: Open Boundary Condition related CPP keys
CPP KEY NAME Description
OBC_VOLCONS Activate mass conservation enforcement at open boundaries.
OBC_M2SPECIFIED Activate specified open boundary conditions for ubar and vbar.
OBC_M2ORLANSKI Activate 2D radiation open boundary conditions for ubar and vbar.
OBC_M2FLATHER Activate Flather open boundary conditions for ubar and vbar.
OBC_M2CHARACT Activate open boundary conditions based on characteristic methods.
OBC_M3SPECIFIED Activate specified open boundary conditions for u and v.
OBC_M3ORLANSKI Activate 2D radiation open boundary conditions for u and v.
OBC_M3CHARACT Activate open boundary conditions based on characteristic methods for u and v.
OBC_TSPECIFIED Activate specified open boundary conditions for tracers.
OBC_TORLANSKI Activate 2D radiation open boundary conditions for tracers.
OBC_TUPWIND Activate upwind open boundary conditions for tracers.
 

2.5.0.0.15 Preselected options: 

 
# ifdef TIDES
#$ $ define OBC_M2FLATHER
# else
#$ $ undef OBC_M2SPECIFIED
#$ $ undef OBC_M2FLATHER
#$ $ define OBC_M2CHARACT
#$ $ undef OBC_M2ORLANSKI
#$ $ ifdef OBC_M2ORLANSKI
#$ $$ $ define OBC_VOLCONS
#$ $ endif
# endif
# define OBC_M3ORLANSKI
# define OBC_TORLANSKI
# undef OBC_M3SPECIFIED
# undef OBC_TSPECIFIED

Input - Output and Diagnostics

Table 2.21: I/O related CPP keys
CPP KEY NAME Description
AVERAGES Define if writing out time-averaged data.
AVERAGES_K Define if writing out time-averaged vertical mixing.
DIAGNOSTICS_TS Define if writing out tendency terms for the tracer equations.
DIAGNOSTICS_TS_ADV Activate advection formulation for tendency term for the tracer equations.
DIAGNOSTICS_TS_MLD Activate integration over the mixed-layer (MLD) for the tendency term for the tracer equation.
DIAGNOSTICS_UV Define if writing out tendency terms for the momentum equations.
 

2.5.0.0.16 Preselected options: 

 
# define AVERAGES
# define AVERAGES_K
# undef DIAGNOSTICS_TS
# undef DIAGNOSTICS_UV
# ifdef DIAGNOSTICS_TS
# $  $undef DIAGNOSTICS_TS_ADV
# $  $undef DIAGNOSTICS_TS_MLD
# endif

Biology models

Table 2.22: Biology model related CPP keys
CPP KEY NAME Description
PISCES Activate PISCES biogeochemical model
BIO_NChlPZD Activate idealized 4 compartiments NPZD type model
BIO_N2PZD2 Activate idealized 6 compartiments NPZD type model
BIO_N2ChlP2Z2D2 Activate idealized 8 compartiments NPZD type model
 

2.5.0.0.17 Preselected options: 

 
# ifdef BIOLOGY
# $  $ undef PISCES
# $  $ define BIO_NChlPZD
# $  $ undef BIO_N2P2Z2D2
# $  $ undef BIO_N2ChlPZD2
# endif


2.6 Namelist description : roms.in

2.6.1 Exemple of South Benguela Test Case

title:
South Benguela TEST MODEL
time_stepping: NTIMES dt[sec] NDTFAST NINFO
$720$ $3600$ $60$ $1$
S-coord: THETA_S, THETA_B, Hc (m)
$7.0d0$ $0.0d0$ $5.0d0$
grid: filename
roms_grd.nc
forcing: filename
roms_frc.nc
bulk_forcing: filename
roms_bulk.nc
climatology: filename
roms_clm.nc
boundary: filename
roms_bry.nc
initial: NRREC filename
$1$
roms_ini.nc
restart: NRST, NRPFRST / filename
$720$ $-1$
roms_rst.nc
history: LDEFHIS, NWRT, NRPFHIS / filename
$T$ $72$ $0$
roms_his.nc
averages: NTSAVG, NAVG, NRPFAVG / filename
$1$ $72$ $0$
roms_avg.nc
primary_history_fields: zeta UBAR VBAR U V wrtT(1:NT)
T T T T T $30$*T
auxiliary_history_fields: rho Omega W Akv Akt Aks HBL HBBL Bostr Wstr Ustr Vstr rsw rlw lat sen HEL
F F T F T F T T T T T T $10$*F
primary_averages: zeta UBAR VBAR U V wrtT(1:NT)
T T T T T $30$*T
auxiliary_averages: rho Omega W Akv Akt Aks HBL HBBL Bostr Wstr Ustr Vst rsw rlw lat sen HEL
F T T F T F T T T T T T $10$*F
rho0:
$1025.d0$
lateral_visc: VISC2, VISC4 [$m^{2}$/sec for all]
$0.$ $0.$
tracer_diff2: TNU2(1:NT) [$m^2$/sec for all]
$30*0.d0$
tracer_diff4: TNU4(1:NT) [$m^4$/sec for all]
$30*0.d11$
vertical_mixing: Akv_bak, Akt_bak [$m^2$/sec]
$0.$d$0$ $30*0.$d$0$
bottom_drag: RDRG [m/s], RDRG2, Zob [m], Cdb_min, Cdb_max
$3.0$d$-04$ $0.$d$-3$ $0$.d$-3$ $1$.d$-4$ $1$.d$-1$
gamma2:
$1.$d$0$
sponge: X_SPONGE [m], V_SPONGE [$m^2$ / sec]
$150.e3$ $100.$
nudg_cof: TauT_in, TauT_out, TauM_in, TauM_out [days for all]
$1.$ $360.$ $3.$ $360.$
diagnostics: ldefdia nwrtdia nrpfdia /filename
T $72$ $0$
roms_dia.nc
diag_avg: ldefdia_avg ntsdia_avg nwrtdia_avg nprfdia_avg /filename
T $1$ $72$ 0
roms_dia_avg.nc
diag$3$D_history_fields: diag_tracers$3$D(1:NT)
$30$*T
diag$2$D_history_fields: diag_tracers$2$D(1:NT)
$30$*T
diag$3$D_average_fields: diag_tracers$3$D_avg(1:NT)
$30$*T
diag$2$D_average_fields: diag_tracers$2$D_avg(1:NT)
$30$*T
diagnosticsM: ldefdiaM nwrtdiaM nrpfdiaM /filename
T $72$ $0$
roms_diaM.nc
diagM_avg: ldefdiaM_avg ntsdiaM_avg nwrtdiaM_avg nprfdiaM_avg /filename
T $1$ $72$ $0$
roms_diaM_avg.nc
diagM_history_fields: diagM_momentum(1:2)
T T
diagM_average_fields: diagM_momentum_avg(1:2)
T T
diagnostics_bio: ldefdiabio nwrtdiabio nrpfdiabio /filename
T $72$ $0$
roms_diabio.nc
diagbio_avg: ldefdiabio_avg ntsdiabio_avg nwrtdiabio_avg nprfdiabio_avg /filename
T $1$ $72$ $0$
roms_diabio_avg.nc
biology: forcing file
roms_frcbio.nc
sediments: input file
sediment.in
sediment_history_fields: bed_thick bed_poros be3d_fra(sand,silt)
T F T T
bbl_history_fields: Abed Hripple Lripple Zbnot Zbapp Bostrw
T F F T F T
floats: LDEFFLT, NFLT, NRPFFLT / inpname, hisname
T $6$ $0$
floats.in
floats.nc
float_fields: Grdvar Temp Salt Rho Vel
F F F F F
stations: LDEFSTA, NSTA, NRPFSTA / inpname, hisname
T $400$ $0$
stations.in
stations.nc
station_fields: Grdvar Temp Salt Rho Vel
T T T T T
psource: Nsrc Isrc Jsrc Dsrc Qbar [m3/s] Lsrc Tsrc
$2$
$3$ $54$ $1$ $200. $ T T $5. 0.$
$3$ $40$ 0 $200. $ T T $5. 0.$

2.6.2 Description

Table 2.23: Description of the roms.in file
KEYWORDS DESCRIPTIONS
title  
   
time_stepping  
  NTIMES : Number of time step for the run.
  dt : Baroclinic time step for the run [in s]
  NDTFAST : Number of bariotropic time step in one baroclinic time step.
  NINFO : frequency of output in time steps.
S-coord  
  THETA_S: $s$-coordinate surface control parameter, $0$ $<$ theta_s $<$ $20$
  THETA_B: $s$-coordinate bottom control parameter, $0$ $<$ theta_b $<$ $1$
  Hc(m): Width of the surface or bottom topography layer in which higher vertical resolution is required during stretching.
grid  
  /filename: Name of the grid file.
   
forcing  
  /filename: Name of the surface forcing file : wind stress, atmospheric fluxes (E-P, net heat fluxes) and nudging coefficients towards dQ/dSST.
   
bulk_forcing  
  /filename: Name of the bulk forcing file for atmospheric forcings.
climatology  
  /filename: Name of the open boundaries conditions (t, s, $\bar u$, $\bar v$, $u$, $v$). These files are 3d in space, covering the whole domain.
   
boundary  
  /filename: Name of the open boundaries conditions (T, S, $\bar u$, $\bar v$, $u$, $v$). These files are covering only the open-boundaries slices, inducing files much smaller than the ``climatology'' ones.
   
initial  
  NRREC: Record number of the restartfile to read as the initial conditions.
  /filename: Name of the file containing initial state.
   
restart  
  NRST: Frequency of writing
  NRPFRST 0: writing several records every NRST time steps. -1: overwriting record every NRST time steps
  /filename
   
history  
  LDEFHIS: flag (T/F) if writing history files
  NWRT: Frequency of writing
  NRPFHIS: 0: writing several records every NWRT time steps. -1: overwriting record every NRST time steps
  /filename: Name of the gistory file
   
averages  
  NTSAVG: Starting timestep for the accumulation of output time-averaged data. For instance, you might want to average over the last day of a thirty-day run.
  NAVG: frequency of writing
  NRPFAVG: 0: writing several records every NWRT time steps. -1: overwriting record every NAVG time steps
  /filename
   
primary_history _fields  
  Flags of written primary variables in history NetCDF file
   
auxiliary_history _fields  
  Flags of written auxiliary variables in history NetCDF file
   
primary_averages  
  Flags of written primary variables in history NetCDF file
   
auxiliary_averages  
  Flags of written variables in average NetCDF file
   
rho0 Mean density used in the Boussinesq equation.
   
lateral_visc  
  VISC2: Laplaplacian background viscosity
  VISC4: Bilaplacian background viscosity
   
tracer_diff2  
  TNU2(1:NT): Laplacian background diffusivity for each tracer.
   
tracer_diff4  
  TNU4(1:NT): Laplacian background diffusivity for each tracer.
   
vertical_mixing  
  Coefficient in case of use of analytical vertical mixing scheme.
   
bottom_drag  
  RDRG [m/s]: Drag coefficient in case of linear bottom stress formulation.
   
  RDRG2: Drag coefficient in case of constant quadratic bottom stress formulation.
   
  Zob [m]: Rugosity length in case of Von-Karman quadratic bottom stress formulation
  Cdb_min: Minimum value of the drag coefficient in case Von-Karman quadratic bottom stress formulation.
  Cdb_max: Maximum value of the drag coefficient in case Von-Karman quadratic bottom stress formulation.
   
gamma2  
  Free slip boundary condition. 1 mean free slip condition are ON.
   
sponge  
  X_SPONGE [m]: widthness of the sponge layers.
  V_SPONGE [$m^2/sec$]: Value of the viscosity and diffusity enhanced value at the boundary point in the nudging/sponge layer. These value are enhanced following a linear profil in the sponge/nudging layer, from the interior value to the max value V_SPONGE at boundary.
   
nudg_cof  
  TauT_in [days]: Nudging time scale for tracer signal going inward the domain. This coefficient is used at boundary point and impose a strong nudging towards climatology external data.
   
  TauT_out [days]: Nudging time scale for tracer signal going outward the domain. This coefficient is used at boundary point and impose a smooth nudging towards climatology external data. This coefficient is also used in the nudging/sponge layer to add a smooth nudging towards data. This is on only if the CLIMATOLOGY boundary stategy is used, not the BRY one.
   
  TauM_in [days]: Same as above, but concerning the momentum equations.
   
  TauM_out [days]: Same as above, but concerning the momentum equations.
   
diagnostics  
  ldefdia: Boolean flag to activate the tracer equation "snap-shot" diagnostic file writing
  nwrtdia: Frequency of writing
  nrpfdia: nrpfdia: 0: writing several records every nwrtdia time steps. -1: overwriting record every nwrtdia time steps
  /filename: Name of the file tracer equation diagnostic file.
diag_avg  
  ldefdia_avg: Boolean flag to activate the tracer equation average diagnostic file writing
  ntsdia_avg: Starting timestep for the accumulation of output time-averaged data. For instance, you might want to average over the last day of a thirty-day run.
  nwrtdia_avg: Frequency of writing and average time.
  nprfdia_avg: nrpfdia_avg: 0: writing several records every nwrtdia_avg time steps. -1: overwriting record every nwrtdia_avg time steps
  /filename: Name of the file tracer equation average diagnostic file.
   
diag3D_history _fields  
  Boolean flag to choose which tracer equation (temp, salt, etc ...) is computed in diagnostics and saved in NetCDF file. Terms are 3D
   
diag2D_history _fields  
  Boolean flags to choose which tracer equation, after mixed layer depth integration (cf DIAGNOSTICS_TS_MLD) is computed in diagnostics and saved in NetCDF file. Terms are 2D
   
diag3D_average _fields  
  Boolean flag to choose which tracer equation (temp, salt, etc ...) is computed in diagnostics and saved in NetCDF file. Terms are 3D and are averaged over the diagnostic TS period defined as above, as nwrtdia
   
diag2D_average _fields  
  Boolean flags to choose which tracer equation, after mixed layer depth integration (cf DIAGNOSTICS_TS_MLD) is computed in diagnostics and saved in NetCDF file. Terms are 2D and are averaged over the diagnostic period defined as above, as nwrtdia
   
diagnosticsM Same format as diagnostics but for the momentum equation.
  ldefdiaM:
  nwrtdiaM:
  nrpfdiaM:
  /filename:
   
diagM_avg Same format as diag_avg but for the momentum equation.
  ldefdiaM_avg:
  ntsdiaM_avg:
  nwrtdiaM_avg:
  nprfdiaM_avg:
  /filename
   
diagM_history _fields  
  Boolean flag to choose which momentum equations are diagnosed and saved in NetCDF file. The diagnostics terms are 3D.
   
diagM_average _fields  
  Boolean flag to choose which momentum equation are diagnosed and saved in NetCDF file. The diagnostics terms are 3D and are averaged over the diagnostic period defined above, as nwrtdiaM_avg.
   
diagnosticsM_bio Same format as diagnostics
  ldefdiabio
  nwrtdiabio
  nrpfdiabio
  / filename
   
diagbio_avg Same format as diag_avg
  ldefdiabio_avg
  ntsdiabio_avg
  nwrtdiabio_avg
  nprfdiabio_avg
  / filename
   
biology  
  Name of the file containing the Iron dust forcing if using PISCES biogeochemical mode.
   
sediments  
   
sediment_history _fields  
  bed_thick
  bed_poros
  bed_fra(sand,silt)
   
bbl_history_fields  
  Abed
  Hripple
  Lripple
  Zbnot
  Zbapp
  Bostrw
   
floats Lagrangian floats application
  Same format as diagnostics
  LDEFFLT
  NFLT
  NRPFFLT
  / inpname, hisname
   
floats_fields  
  Type of fields computed for each lagrangian floats.
   
station_fields Fixed station application.
  Same format as diagnostics
  LDEFSTA
  NSTA
  NRPFSTA
  / inpname, hisname
   
psource  
  Nsrc
  Isrc
  Jsrc
  Dsrc
  Qbar [m3/s]
  Lsrc
  Tsrc
   
 

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The translation was initiated by Gildas Cambon on 2010-07-20

Footnotes

... experiments1.1
These routines use add_dic.m, add_doc.m, add_fer.m, add_o2.m, add_talk.m, add_sio3.m, add_ini_dic.m, add_ini_doc.m, add_ini_fer.m, add_ini_o2.m, add_ini_talk.m, add_ini_po4.m, add_ini_sio3.m
... version2.1
http://myroms.org
... Hedström2.2
Kate Hedström, University of Alaska Fairbanks, Center for Arctic Region Supercomputing Center, University of Alaska Fairbanks,
...hedstroem2009 2.3
Many thanks to Kate Hedstroëm for this work.

Gildas Cambon 2010-07-20