Regional Coastal Ocean
Modeling: Tutorial
Roms_tools
Patrick Marchesiello IRD 2005
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System requirements
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F95 (ifort), Matlab
Netcdf library for Fortran and Matlab
(MexCDF)
2 Gbites of disk space
ROMS_AGRIF sources
Matlab toolbox for ROMS: ROMS_tools
Data: bathymetry, hydrography, surface
fluxes global climatological datasets are
included
Patrick Marchesiello IRD 2005
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Package
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Pre-processing data
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% cd ~/Roms_tools/Run
% matlab
>> start adds the path of different toolboxes
>> make_grid
>> make_forcing
>> make_clim
>> make_tides
>> make_biol
>> nestgui
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make_grid.m
%
% Title
%
title='Peru Test Model';
%
% Grid file name
%
lon, lat, dx,
grdname='roms_grd.nc';
dy, h
%
% Grid dimensions:
%
lonmin=-85;
lonmax=-75;
latmin=-15;
latmax=-7;
L=31 M=26
%
% Grid resolution [degree]
%
dl=1/3;
%
% Minimum depth [m]
%
hmin=10;
%
% Topography netcdf file name (ETOPO 2)
%
topofile='../Topo/etopo2.nc';
%
% Slope parameter (r=grad(h)/h) maximum value for
topography smoothing
%
rtarget=0.2;
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Smoothing methods
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r = Δh / h is the slope of the logarithm of h
One method (ROMS): smoothing ln(h) until r < rmax
Res: 1 km
r < 0.25
Res: 5 km
r < 0.25
Senegal Bathymetry Profil
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Smoothing method and resolution
Standard Deviation [m]
Bathymetry Smoothing Error off Senegal
Convergence at
~ 4 km resolution
Grid Resolution [deg]
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Errors in Bathymetry data compilations
Gebco1 compilation
Etopo2: Satellite observations
Shelf errors
(noise)
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Refine the mask
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>> editmask
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Interactive
matlab tool to
modify masking
according to
high resolution
coastline data
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Getting the wind forcing
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>> make_forcing
%
% Title - Grid file name - Forcing file name
%
title='Forcing (COADS)';
Default COADS
grdname='roms_grd.nc';
climatological surface forcing
frcname='roms_frc.nc';
of Da Silva et al., 1994
%
%
% Set times and cycles: monthly climatology for all data
%
time=[15:30:345]; % time
cycle=360;
% cycle
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Patrick Marchesiello IRD 2005
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Modified Julian dates
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MJD is a modification of the Julian Date that is routinely used by
astronomers, geodesists, and even some historians.
This dating convention, designed to facilitate chronological
calculations, numbers all days in consecutive fashion, beginning
so as to precede the historical period.
Julian Day Number 0 is noon 1 January 4713 B.C.
MJD modifies this Julian Date in two ways.
 The MJD begins at midnight rather than noon, in keeping with
more standard conventions.
 Secondly, for simplicity, the first two digits of the Julian Date are
removed. This is because, for some three centuries following 17
November 1858, the Julian day lies between 2400000 and
2500000. The MJD drops those first "24" digits. Thus, we have
MJD = JD - 2400000.5
To convert Julian Dates to Gregorian dates (month/day/year) we
can use various converters
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Getting the lateral boundary conditions
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>> make_clim
OA (objective analysis) files
are intermediate files where
hydrographic data are
interpolated (extrapolated
under bathymetry) and
stored on a horizontal grid
but on z vertical grid. The
transformation to Scoordinate is done after.
%
% Title
%
title='Climatology';
%
% Switches for selecting what to process (1=ON)
%
makeclim=1; %1: process boundary data
makeoa=1; %1: process oa data
makeini=1; %1: process initial data
%
% Grid file name - Climatology file name
% Initial file name - OA file name
%
grdname ='roms_grd.nc';
frcname ='roms_frc.nc';
clmname ='roms_clm.nc';
ininame ='roms_ini.nc';
oaname ='roms_oa.nc';
%
% Vertical grid parameters
%
theta_s=7.;
theta_b=0.;
hc=5.;
N=20; % number of vertical levels (rho)
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obc=[1 0 1 1]; % open boundaries (1=open , [S E N W])
%
% Level of reference for geostrophy calculation
%
zref=-500;
%
% Day of initialization
%
tini=15;
%
% Set times and cycles: monthly climatology for all data
%
time=[15:30:345]; % time
cycle=360; % cycle
%
% Data climatologies file names:
%
temp_month_data ='../WOA2001/temp_month.cdf';
temp_ann_data ='../WOA2001/temp_ann.cdf';
insitu2pot=1;
% transform in-situ temperature to potential temperature
salt_month_data ='../WOA2001/salt_month.cdf';
salt_ann_data
='../WOA2001/salt_ann.cdf';
%
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Getting the tides boundary conditions
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>> make_tides
This is where tidal
information is
added
This is the starting time of
simulation. A procedure correct
phases and amplitudes (nodal
corrections) for real time runs.
It employs parts of a postprocessing code from Egbert
and Erofeeva (2002) TPXO
model. Running Real-time tides
requires using modified julian
dates as initial time
(roms_ini.nc).
%
% TPXO file name
%
tidename='../Tides/TPXO6.nc';
%
% ROMS file names
%
gname = 'roms_grd.nc';
fname = 'roms_frc.nc';
%
% Number of tides component to process
%
Ntides=10;
%
% Set start time of simulation
%
year
= 2000;
month = 1;
day
= 15;
hr
= 0.;
minute = 0.;
second = 0.;
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Getting child grids for nesting
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>> nestgui
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Preparing the model
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% vi param.h
parameter (LLm0=29, MMm0=24, N=20) !
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Peru Test Case
% vi cppdefs.h
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Define CPP keys that used by the C-preprocessor
when compiling the model
Reduce code to its minimal size: fast compilation
Avoid fortran logical statements: efficient coding
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•PERU : Configuration Name, this is used in param.h.
•OPENMP : Activate Open-MP parallelization protocol.
•MPI : Activate MPI parallelization protocol.
•AGRIF : Activate the nesting capabilities
•SOLVE3D : Define if solving 3D primitive equations
•UV_COR : Activate Coriolis terms.
•UV_ADV : Activate advection terms.
•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.
•VAR_RHO_2D : Activate nonuniform density in barotropic mode pressure- gradient terms.
•FLAT_WEIGHTS : Use a more dissipative averaging for the baroclinic/barotropic coupling.
•CURVGRID : Activate curvilinear coordinate grid option.
•SPHERICAL : Activate longitude/latitude grid positioning.
•MASKING : Activate land masking in the domain.
•AVERAGES : Define if writing out time-averaged data.
•SALINITY : Define if using salinity.
•NONLIN_EOS : Activate the nonlinear equation of state.
•SPLIT_EOS : Activate to split the nonlinear equation of state in a adiabatic part and a
compressible part.
•ZCLIMATOLOGY : Activate processing of sea surface height climatology.
•UCLIMATOLOGY : Activate processing of momentum climatology.
•ZNUDGING : Activate open boundary passive/active term + nudging layer for zeta.
•M2NUDGING : Activate open boundary passive/active term + nudging layer for ubar and vbar.
•SPONGE : Activate areas of enhanced viscosity/diffusion.
•…
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Input parameter file
title:
PERU TEST MODEL
time_stepping: NTIMES dt[sec] NDTFAST NINFO
720
1800
45
1
S-coord: THETA_S, THETA_B,
7.0d0
0.0d0
5.0d0
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grid: filename
% vi roms.in
rho0:
1025.d0
lateral_visc: VISC2,
0.
VISC4
0.
tracer_diff2: TNU2(1:NT)
10*0.d0
bottom_drag:
[m^2/sec for all]
[m^2/sec for all]
RDRG [m/s], RDRG2, Zob [m], Cdb_min, Cdb_max
3.0d-04
0.d-3
0.d-3
1.d-4
1.d-1
gamma2:
1.d0
sponge:
nudg_cof:
X_SPONGE [m],
150.e3
Hc (m)
V_SPONGE [m^2/sec]
500.
TauT_in, TauT_out, TauM_in, TauM_out [days for all]
1.
360.
3.
360.
roms_grd.nc
forcing: filename
roms_frc.nc
climatology: filename
roms_clm.nc
initial: NRREC filename
1
roms_ini.nc
restart:
NRST, NRPFRST / filename
720 -1
roms_rst.nc
history: LDEFHIS, NWRT, NRPFHIS / filename
T
144
0
roms_his.nc
averages: NTSAVG, NAVG, NRPFAVG / filename
1
144
0
roms_avg.nc
primary_history_fields: zeta UBAR VBAR U V wrtT(1:NT)
T
F
F
T T 10*T
auxiliary_history_fields: rho Omega W Akv Akt Aks HBL Bostr
F F
F F T F
T
F
primary_averages: zeta UBAR VBAR U V wrtT(1:NT)
T
T
T
T T 10*T
auxiliary_averages: rho Omega W Akv Akt Aks HBL
F
T
F F T F
T
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Compiling the model
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% jobcomp
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Automatic selection of compilation options
according to the plateform
Set library path
Use Makefile:
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C-preprocessing: file.F  file.f
Compiling: file.f  file.o
Links with libraries  executable roms
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Preparing AGRIF
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% vi AGRIF_FixedGrids.in
2
1
20 45 34 59 3 3 3
20 33 34 44 3 3 3
30 55 70 89 3 3 2
0
PERU test case
1
10 30 20 40 5 3 5
0
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Running
the model
% roms roms.in
MAIN: started time-steping.
STEP time[DAYS] KIN_EN
POT_EN
TOTAL_EN NET_VOLUME trd
0 15.00000 0.000000000E+00 2.5311945E+01 2.5311945E+01 2.2335422E+15 0
1 15.02083 3.332338732E-06 2.5312150E+01 2.5312154E+01 2.2335431E+15 0
2 15.04167 1.062963402E-05 2.5312316E+01 2.5312327E+01 2.2335455E+15 0
3 15.06250 2.075678260E-05 2.5312446E+01 2.5312466E+01 2.2335461E+15 0
4 15.08333 3.186463589E-05 2.5312543E+01 2.5312575E+01 2.2335469E+15 0
5 15.10417 4.285427484E-05 2.5312627E+01 2.5312670E+01 2.2335480E+15 0
6 15.12500 5.333102059E-05 2.5312691E+01 2.5312744E+01 2.2335479E+15 0
7 15.14583 6.354045596E-05 2.5312719E+01 2.5312782E+01 2.2335465E+15 0
8 15.16667 7.411816854E-05 2.5312701E+01 2.5312775E+01 2.2335457E+15 0
9 15.18750 8.562138804E-05 2.5312650E+01 2.5312735E+01 2.2335467E+15 0
10 15.20833 9.828165268E-05 2.5312569E+01 2.5312667E+01 2.2335473E+15 0
11 15.22917 1.117146701E-04 2.5312465E+01 2.5312577E+01 2.2335475E+15 0
12 15.25000 1.255576462E-04 2.5312345E+01 2.5312471E+01 2.2335475E+15 0
13 15.27083 1.393087941E-04 2.5312135E+01 2.5312275E+01 2.2335470E+15 0
14 15.29167 1.525558114E-04 2.5311800E+01 2.5311952E+01 2.2335463E+15 0
15 15.31250 1.653985076E-04 2.5311350E+01 2.5311515E+01 2.2335465E+15 0
16 15.33333 1.779958127E-04 2.5310792E+01 2.5310970E+01 2.2335468E+15 0
17 15.35417 1.905668926E-04 2.5310134E+01 2.5310325E+01 2.2335470E+15 0
18 15.37500 2.034591092E-04 2.5309385E+01 2.5309588E+01 2.2335470E+15 0
19 15.39583 2.165195050E-04 2.5308554E+01 2.5308771E+01 2.2335469E+15 0
20 15.41667 2.294900067E-04 2.5307653E+01 2.5307882E+01 2.2335465E+15 0
21 15.43750 2.422211112E-04 2.5306695E+01 2.5306937E+01 2.2335463E+15 0
22 15.45833 2.545401621E-04 2.5305693E+01 2.5305948E+01 2.2335463E+15 0
23 15.47917 2.664383353E-04 2.5304665E+01 2.5304932E+01 2.2335464E+15 0
24 15.50000 2.780681955E-04 2.5303629E+01 2.5303907E+01 2.2335465E+15 0
25 15.52083 2.896947197E-04 2.5302600E+01 2.5302890E+01 2.2335465E+15 0
26 15.54167 3.013595537E-04 2.5301595E+01 2.5301897E+01 2.2335462E+15 0
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Visualizing the results
>> roms_gui
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Analysing the results
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Make statistics (mean, variance, …)
Use tracers, compute residence times and
Lagrangian transport
Make budgets (energy, heat, vorticity,
momentum, …)
Comparison with available data
…
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