patrick marchesiello ird 20051 regional coastal ocean modeling: tutorial roms_tools

Patrick Marchesiello IRD 2005 1

Regional Coastal Ocean Modeling: Tutorial

Roms_tools


System requirements

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


Package


Pre-processing data

% cd ~/Roms_tools/Run % matlab >> start adds the path of different toolboxes >> make_grid >> make_forcing >> make_clim >> make_tides >> make_biol >> nestgui


% % Title % title='Peru Test Model'; % % Grid file name % grdname='roms_grd.nc'; % % Grid dimensions: % lonmin=-85; lonmax=-75; latmin=-15; latmax=-7; % % 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;

make_grid.m

L=31 M=26

lon, lat, dx, dy, h

h


Smoothing methods

r = Δh / h is the slope of the logarithm of h One method (ROMS): smoothing ln(h) until r < rmax

Res: 5 kmr < 0.25

Res: 1 kmr < 0.25

Senegal Bathymetry Profil


Smoothing method and resolution

Grid Resolution [deg]

Bathymetry Smoothing Error off Senegal

Convergence at ~ 4 km resolution

Sta

ndar

d D

evia

tion

[m]


Errors in Bathymetry data compilations

Shelf errors(noise)

Etopo2: Satellite observationsGebco1 compilation


Refine the mask

>> editmask Interactive

matlab tool to modify masking according to high resolution coastline data


Getting the wind forcing

>> make_forcing

% % Title - Grid file name - Forcing file name % title='Forcing (COADS)'; grdname='roms_grd.nc'; frcname='roms_frc.nc'; % % % Set times and cycles: monthly climatology for all data % time=[15:30:345]; % time cycle=360; % cycle

Default COADS climatological surface forcing of Da Silva et al., 1994


Modified Julian dates 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


Getting the lateral boundary conditions >> make_clim

% % 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)

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 S-coordinate is done after.


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'; %


Getting the tides boundary conditions >> make_tides %

% 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.;

This is the starting time of simulation. A procedure correct phases and amplitudes (nodal corrections) for real time runs. It employs parts of a post-processing code from Egbert and Erofeeva (2002) TPXO model. Running Real-time tides requires using modified julian dates as initial time (roms_ini.nc).

This is where tidal information is added


Getting child grids for nesting >> nestgui


Preparing the model

% vi param.h

% vi cppdefs.h 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

parameter (LLm0=29, MMm0=24, N=20) ! Peru Test Case


•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. • …


Input parameter file

% vi roms.in

title: PERU TEST MODEL

time_stepping: NTIMES dt[sec] NDTFAST NINFO 720 1800 45 1

S-coord: THETA_S, THETA_B, Hc (m) 7.0d0 0.0d0 5.0d0

grid: filename roms_grd.ncforcing: filename roms_frc.ncclimatology: filename roms_clm.ncinitial: NRREC filename 1 roms_ini.ncrestart: NRST, NRPFRST / filename 720 -1 roms_rst.nchistory: LDEFHIS, NWRT, NRPFHIS / filename T 144 0 roms_his.ncaverages: 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*Tauxiliary_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

rho0: 1025.d0

lateral_visc: VISC2, VISC4 [m^2/sec for all] 0. 0.

tracer_diff2: TNU2(1:NT) [m^2/sec for all] 10*0.d0

bottom_drag: 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: X_SPONGE [m], V_SPONGE [m^2/sec] 150.e3 500.

nudg_cof: TauT_in, TauT_out, TauM_in, TauM_out [days for all] 1. 360. 3. 360.


Compiling the model

% jobcomp Automatic selection of compilation options

according to the plateform Set library path Use Makefile:

C-preprocessing: file.F file.f Compiling: file.f file.o Links with libraries executable roms


Preparing AGRIF

% vi AGRIF_FixedGrids.in

2

20 45 34 59 3 3 3

30 55 70 89 3 3 2

0

1

10 30 20 40 5 3 5

0

1

20 33 34 44 3 3 3

PERU test case


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


Visualizing the results

>> roms_gui


Analysing the results

Make statistics (mean, variance, …) Use tracers, compute residence times and

Lagrangian transport Make budgets (energy, heat, vorticity,

momentum, …) Comparison with available data …

patrick marchesiello ird 20051 regional coastal ocean modeling: tutorial roms_tools

Documents

patrick marchesiello

h h slide

tools slide

package slide

title grid file

biol nestgui slide

grid resolution degree

method roms