%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % crocotools_param: common parameter file for the preprocessing % of CROCO simulations using CROCOTOOLS % % This file is used by oct_make_grid.m, oct_make_forcing.m, % oct_make_clim.m, oct_make_biol.m, oct_make_bry.m, oct_make_tides.m, % oct_make_NCEP.m, make_OGCM_*.m, make_... % % Further Information: % http://www.croco-ocean.org % % This file is part of CROCOTOOLS % % CROCOTOOLS is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published % by the Free Software Foundation; either version 2 of the License, % or (at your option) any later version. % % CROCOTOOLS is distributed in the hope that it will be useful, but % WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License for more details. % % You should have received a copy of the GNU General Public License % along with this program; if not, write to the Free Software % Foundation, Inc., 59 Temple Place, Suite 330, Boston, % MA 02111-1307 USA % % Copyright (c) 2005-2006 by Patrick Marchesiello and Pierrick Penven % e-mail:Pierrick.Penven@ird.fr % % Updated 6-Sep-2006 by Pierrick Penven % Updated 2006/10/05 by Pierrick Penven (add tidegauge observations) % Updated 24-Oct-2006 by Pierrick Penven (diagnostics, chla etc...) % Updated 08-Apr-2009 by Gildas Cambon % Updated 23-Oct-2009 by Gildas Cambon % Updated 17-Nov-2011 by Pierrick Penven (CFSR) % Updated 07-Nov-2012 by Patrick Marchesiello (cleaning) % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % 1 - Configuration parameters % used by oct_make_grid.m (and others..) % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% isoctave=exist('octave_config_info'); % % CROCO title names and directories % CROCO_title = 'Benguela Model'; CROCO_config = 'Benguela_LR'; % % 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 croco.in !) % theta_s = 7.; theta_b = 2.; hc = 200.; vtransform = 2.; % s-coordinate type (1: old- ; 2: new- coordinates) % ! take care to define NEW_S_COORD cpp-key in cppdefs.h % % Topography: choice of filter % topo_smooth = 1; % 1: old ; 2: new filter (better but slower) % % 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; % % Maximum depth [m] (cut the topography to prevent % extrapolations below WOA data) % hmax = 6000; % % 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 oct_hanning filter at the end of the % smooting 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'; % % Objective analysis decorrelation scale [m] % (if Roa=0: nearest extrapolation method; crude but much cheaper) % %Roa=300e3; Roa=0; % interp_method = 'spline'; % Interpolation method: 'linear' or 'spline' % makeplot = 0; % 1: create graphics after each preprocessing step % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % 2 - Generic file and directory names % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % CROCOTOOLS directory % CROCOTOOLS_dir = '../'; % % Run directory % RUN_dir=[pwd,'/']; % % CROCO input oct_netcdf files directory % CROCO_files_dir=[RUN_dir,'CROCO_FILES/']; % % Global data directory (etopo, coads, datasets download from ftp, etc..) % DATADIR='../../croco_tools/'; % % Forcing data directory (ncep, quikscat, datasets download with opendap, etc..) % FORC_DATA_DIR = [RUN_dir,'DATA/']; % if (isoctave == 0) eval(['!mkdir ',CROCO_files_dir]) else system(['mkdir ',CROCO_files_dir]) end % % CROCO file names (grid, forcing, bulk, climatology, initial) % grdname = [CROCO_files_dir,'croco_grd.nc']; frcname = [CROCO_files_dir,'croco_frc.nc']; blkname = [CROCO_files_dir,'croco_blk.nc']; clmname = [CROCO_files_dir,'croco_clm.nc']; bryname = [CROCO_files_dir,'croco_bry.nc']; ininame = [CROCO_files_dir,'croco_ini.nc']; bioname = [CROCO_files_dir,'croco_frcbio.nc']; % Iron Dust forcing for PISCES rivname = [CROCO_files_dir,'croco_runoff.nc']; % % intermediate z-level data files (not used in simulations) % oaname = [CROCO_files_dir,'croco_oa.nc']; % for climatology data processing Zbryname = [CROCO_files_dir,'croco_bry_Z.nc']; % for boundary data processing % % Generic forcing file root names for interannual simulations (NCEP/GFS) % frc_prefix=[CROCO_files_dir,'croco_frc']; % forcing file name blk_prefix=[CROCO_files_dir,'croco_blk']; % bulk file name % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % % Topography oct_netcdf file name (ETOPO 2 or any other oct_netcdf file % in the same format) % topofile = [DATADIR,'Topo/etopo2.nc']; % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % % GSHHS coastline user : add path to gshhs native private data) % COASTFILE_DIR = [DATADIR,'gshhs/']; % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % 3 - Surface forcing parameters % used by oct_make_forcing.m and by oct_make_bulk.m % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % COADS directory (for climatology runs) % coads_dir=[DATADIR,'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 % %coads_time=(15.2188:30.4375:350.0313); % year of 365.25 days in case %coads_cycle=365.25; % interannual QSCAT winds % % are used with clim. heat flux % % Pathfinder SST data used by oct_pathfinder_sst.m % pathfinder_sst_name=[DATADIR,... 'SST_pathfinder/climato_pathfinder.nc']; % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % 4 - Open boundaries and initial conditions parameters % used by oct_make_clim.m, oct_make_biol.m, oct_make_bry.m % make_OGCM_*.m and make_OGCM_frcst.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 oct_geostrophy calculation % zref = -1000; % % initial/boundary data options (1 = process) % (used in oct_make_clim, oct_make_biol, oct_make_bry, % make_OGCM_*.m and make_OGCM_*frcst.m) % makeini = 1; % initial data makeclim = 1; % climatological data (for boundaries and nudging layers) makebry = 1; % lateral boundary data makenpzd = 0; % initial and boundary data for NChlPZD and N2ChlPZD2 models makebioebus= 0; % initial and boundary data for BioEBUS model makepisces = 0; % initial and boundary data for PISCES model makequota = 0; % initial and boundary data for quota version of PISCES model % % makeoa = 1; % oa data (intermediate file) makeZbry = 1; % boundary data in Z coordinate (intermediate file) insitu2pot = 1; % transform in-situ temperature to potential temperature % % Day of initialisation for climatology experiments (=0 : 1st january 0h) % tini=0; % % Select Climatology Atlas (temp, salt and biological variables) from: % - World Ocean Atlas directory (WOA2009) OR ... % - CARS2009 climatology directory (CARS2009) % woa_dir = [DATADIR,'WOA2009/']; cars2009_dir = [DATADIR,'CARS2009/']; climato_dir = woa_dir; % % Pisces biogeochemical seasonal climatology % woapisces_dir = [DATADIR,'WOAPISCES/']; % only compatible with woa_dir % % Surface chlorophyll seasonal climatology (SeaWifs) % chla_dir=[DATADIR,'SeaWifs/']; % % Runoff monthly seasonal climatology (Dai and Trenberth) % global_clim_riverdir=[DATADIR,'RUNOFF_DAI/']; global_clim_rivername=[global_clim_riverdir,'Dai_Trenberth_runoff_global_clim.nc']; % % 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 % %woa_time=(15.2188:30.4375:350.0313); % year of 365.25 days in case %woa_cycle=365.25; % interannual QSCAT winds are used % % with clim. boundary conditions % % For rivers setup : go in the routine Rivers/oct_make_runoff.m to % setup your options % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % 5 - Parameters for tidal forcing % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % TPXO file name (TPXO6 or TPXO7) % tidename=[DATADIR,'TPXO7/TPXO7.nc']; % % Self-Attraction and Loading GOT99.2 file name % sal_tides=1; salname=[DATADIR,'GOT99.2/GOT99_SAL.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; % Example: lat0 = -33.91; % Cape Town location Z0 = 1; % Mean depth of tide gauge % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % 6 - Reference date and simulation times % (used for oct_make_tides, oct_make_CFSR (or oct_make_NCEP), make_OGCM_*) % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Yorig = 2000; % reference time for vector time % in croco initial and forcing files % Ymin = 2005; % first forcing year Ymax = 2005; % 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 % Mth_format = '%02d'; % Number of digit for month on input files % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % 7 - Parameters for Interannual forcing (SODA, mercator, CFSR, ERA5 ...) % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Download_data = 1; % Get data from OPENDAP sites level = 0; % AGRIF level; 0 = oct_parent grid % NCEP_version = 3; % NCEP version: % [ CFSR up-to-date product are recommended ] % 1: NCEP/NCAR Reanalysis, 1/1/1948 - present % 2: NCEP-DOE Reanalysis, 1/1/1979 - present % 3: CFSR (Climate Forecast System Reanalysis), % 1/1/1979 - 31/3/2011 % %-------------------------------------------- % Options for oct_make_NCEP and oct_make_QSCAT_daily %-------------------------------------------- % % NCEP data directory for files downloaded via opendap % if NCEP_version == 1; NCEP_dir= [FORC_DATA_DIR,'NCEP1_',CROCO_config,'/']; elseif NCEP_version == 2; NCEP_dir= [FORC_DATA_DIR,'NCEP2_',CROCO_config,'/']; elseif NCEP_version == 3; NCEP_dir= [FORC_DATA_DIR,'CFSR_',CROCO_config,'/']; % CFSR data dir. [croco format] end makefrc = 0; % 1: create forcing files makeblk = 1; % 1: create bulk files QSCAT_blk = 0; % 1: a) correct NCEP frc/bulk files with % u,v,wspd fields from daily QSCAT data % b) download u,v,wspd in QSCAT frc file add_tides = 0; % 1: add tides add_waves = 0; % 1: add waves % % Overlap parameters % itolap_qscat = 2; % 2 records for daily QSCAT itolap_ncep = 8; % 8 records for 4-daily NCEP % %-------------------------------------------------- % Options for oct_make_QSCAT_daily and oct_make_QSCAT_clim %-------------------------------------------------- % QSCAT_dir = [FORC_DATA_DIR,'QSCAT_',CROCO_config,'/']; % QSCAT data dir. [croco format] QSCAT_frc_prefix = [frc_prefix,'_QSCAT_']; % QSCAT Generic file name for % interannual simulations QSCAT_clim_file = [DATADIR,'QuikSCAT_clim/',... % QSCAT climatology file 'roms_SCOW_month_clim_1999_2009.nc']; % for oct_make_QSCAT_clim. % %-------------------------------------------------- % Options for oct_make_ECMWF and oct_make_ECMWF_daily %-------------------------------------------------- % Reformat_ECMWF = 1; ECMWF_dir = [FORC_DATA_DIR,'ECMWF_',CROCO_config,'/']; % ERA-I data dir. [croco format] My_ECMWF_dir = [FORC_DATA_DIR,'ERAI/']; % ERA-I native data downloaded % with python script itolap_ecmwf = 3; % 3 records for daily ECMWF % %-------------------------------------------------- % Options for oct_make_ERA5 %-------------------------------------------------- % ERA5_dir = [FORC_DATA_DIR,'ERA5_',CROCO_config,'/']; % ERA5 data dir. [croco format] My_ERA5_dir = [FORC_DATA_DIR,'ERA5_native_',CROCO_config,'/']; % ERA5 native data downloaded % with python script itolap_era5 = 2; % 2 records = 2 hours % % %-------------------------------------------- % Options for oct_make_OGCM_SODA or oct_make_OGCM_mercator %-------------------------------------------- % OGCM = 'SODA'; % Select OGCM: SODA or mercator % OGCM_dir = [FORC_DATA_DIR,OGCM,'_',CROCO_config,'/']; % OGCM data dir. [croco format] % bry_prefix = [CROCO_files_dir,'croco_bry_',OGCM,'_']; % generic boundary file name clm_prefix = [CROCO_files_dir,'croco_clm_',OGCM,'_']; % generic climatology file name ini_prefix = [CROCO_files_dir,'croco_ini_',OGCM,'_']; % generic initial file name OGCM_prefix = [OGCM,'_']; % generic OGCM file name mercator_type=1; % 1 --> 1/12 deg Mercator global reanalysis % 2 --> 1/12 deg Mercator global analysis % 3 --> 1/12 deg Mercator global forecast (See Section 8.) % 4 --> 1/24 deg Mercator Mediterranean analysis/forecast (See Section 8.) % 5 --> the same than 4 but with detiding postprocessing on current and ssh % ============= % To download CMEMS data: set login/password (http://marine.copernicus.eu) % and path to copernicusmarine executable % see Oforc_OGCM/Copernicus_Marine_Toolbox_installation.md % % Various sets of data are proposed in the Copernicus web site % if strcmp(OGCM,'mercator') % pathCMC='/path/to/home/copernicusmarine'; % copernicusmarine client % user = 'XXXX'; password = 'XXXX'; % if mercator_type==1 % ======================== % For GLORYS 12 reanalysis extraction % ======================== kdata='MONTHLY' ; % DAILY or MONTHLY if strcmp(kdata,'DAILY') product_id='cmems_mod_glo_phy_my_0.083deg_P1D-m'; elseif strcmp(kdata,'MONTHLY') product_id='cmems_mod_glo_phy_my_0.083deg_P1M-m'; else disp('Please specify what kind of data you want (DAILY or MONTHLY)') end % elseif mercator_type==2 % ======================== % 2 -> For analysis PSY4 % ======================== product_id={'cmems_mod_glo_phy_anfc_0.083deg_P1D-m' ... 'cmems_mod_glo_phy-cur_anfc_0.083deg_P1D-m', ... 'cmems_mod_glo_phy-thetao_anfc_0.083deg_P1D-m', ... 'cmems_mod_glo_phy-so_anfc_0.083deg_P1D-m'}; % else end % end % % Number of OGCM bottom levels to remove % (usefull if CROCO depth is shallower than OGCM depth) % rmdepth = 2; % % Overlap parameters : nb of records around each sequence % => for SODA put itolap_a = itolap_p = 1 % => for mercator daily put itolap_a = itolap_p = 2 % (due to date of the month first day of month) % itolap_a = 1; % before itolap_p = 1; % after % %---------------------------------------------------- % Options for make_bry_WKB_ECMWF or make_bry_WKB_ERA5 %---------------------------------------------------- % wkb_prefix=[CROCO_files_dir,'croco_wkb']; wkb_obc= [1 1 1 1]; % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % 8 - Parameters for the forecast system % % --> select OGCM name above (mercator ...) % --> select Aforc name (GFS) % --> don't forget to define in cppdefs.h: % - ROBUST_DIAG % - CLIMATOLOGY % - BULK_FLUX % - TIDES if you choose so, but without TIDERAMP % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % FRCST_dir = [FORC_DATA_DIR,'Forecast/']; % path to local OGCM data directory % % Number of hindcast / forecast days % hdays=1; fdays=3; % % Local time= UTC + timezone % timezone = +2; % % Add tides % add_tides_fcst = 1; % 1: add tides % % MERCATOR cases (See Section 7): % ============= % if strcmp(OGCM,'mercator') if mercator_type==3 % ======================== % 3 -> For Global Forecast PSY4 % ======================== product_id={'cmems_mod_glo_phy_anfc_0.083deg_P1D-m' ... 'cmems_mod_glo_phy-cur_anfc_0.083deg_P1D-m', ... 'cmems_mod_glo_phy-thetao_anfc_0.083deg_P1D-m', ... 'cmems_mod_glo_phy-so_anfc_0.083deg_P1D-m'}; % elseif mercator_type==4 % ======================== % 4 -> For Mediterannean Forecast PSY4 4.2km % ======================== product_id={'cmems_mod_med_phy-ssh_anfc_4.2km_P1D-m', ... 'cmems_mod_med_phy-cur_anfc_4.2km_P1D-m', ... 'cmems_mod_med_phy-tem_anfc_4.2km_P1D-m', ... 'cmems_mod_med_phy-sal_anfc_4.2km_P1D-m'}; % elseif mercator_type==5 % ======================== % 5 -> For Mediterannean Forecast PSY4 4.2km (ssh detided) % ======================== product_id={'cmems_mod_med_phy-ssh_anfc_detided_4.2km_P1D-m', ... 'cmems_mod_med_phy-cur_anfc_4.2km_P1D-m', ... 'cmems_mod_med_phy-tem_anfc_4.2km_P1D-m', ... 'cmems_mod_med_phy-sal_anfc_4.2km_P1D-m'}; % else end end % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % 9 Parameters for the diagnostic tools % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % DIAG_dir = [CROCOTOOLS_dir,'Diagnostic_tools/']; % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % 10 Change default netCDF file format for writing % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % netcdf.setDefaultFormat('FORMAT_NETCDF4'); %