From eadaad41ae84f5a0d2cc6c1063b5d5f2e9e6b3ba Mon Sep 17 00:00:00 2001 From: jpolton Date: Thu, 2 Sep 2021 16:51:11 +0100 Subject: [PATCH 01/12] updates for ERA5 forcing: extract and weights files --- BUILD_CFG/SURFACE_FORCING/create_LCM.py | 43 +++ .../namelist_reshape_bicubic_atmos | 62 ++-- .../namelist_reshape_bilin_atmos | 64 ++-- .../OFFICIAL_Generate_NEMO_Forcing_NEWERA.py | 296 ++++++++++++++++++ SCRIPTS/make_paths.sh | 2 + 5 files changed, 404 insertions(+), 63 deletions(-) create mode 100644 BUILD_CFG/SURFACE_FORCING/create_LCM.py create mode 100755 SCRIPTS/OFFICIAL_Generate_NEMO_Forcing_NEWERA.py diff --git a/BUILD_CFG/SURFACE_FORCING/create_LCM.py b/BUILD_CFG/SURFACE_FORCING/create_LCM.py new file mode 100644 index 0000000..66dd3d8 --- /dev/null +++ b/BUILD_CFG/SURFACE_FORCING/create_LCM.py @@ -0,0 +1,43 @@ + +from netCDF4 import Dataset +import numpy as np + +coorfile = 'ERA5_MSL_y2013.nc' ## One ERA forcing file generated previously +maskfile = 'my_era5_LSM.nc' ## Land Sea Mask from ncks +outfile = 'ERA5_LSM.nc' ## Output file + +#---------------------------------------------------------------------------- + +## READ SRC BATHYMETRY +#nc_c = Dataset( coorfile, 'r' ) +#lon_src = nc_c.variables[ 'lon' ][:] +#lat_src = nc_c.variables[ 'lat' ][:] +#nc_c.close() +#print(coorfile, "loaded", lon_src.shape) + +## READ SRC BATHYMETRY +nc_src = Dataset( maskfile, 'r' ) +msk_src = nc_src.variables[ 'lsm' ][0,::-1] ## lat to be reverse as it was done in the generation of the forcing files +lat_src = nc_src.variables['latitude'][::-1] +lon_src = nc_src.variables['longitude'][:] +print(maskfile, "loaded", msk_src.shape) +#msk_src[(msk_src==0.)] = -1 +#msk_src[(msk_src<1)] = -1 +seas = msk_src < 0.5 +land = msk_src >= 0.5 +msk_src[seas] = -1 +msk_src[land] = 1 +nlat = msk_src.shape[0] +nlon = msk_src.shape[1] + +## NETCDF OUTPUT +ncout = Dataset( outfile, 'w', format='NETCDF3_CLASSIC' ) +ncout.createDimension( 'nlat', nlat ) +ncout.createDimension( 'nlon', nlon ) +lon = ncout.createVariable( 'lon', 'f4', ('nlat', 'nlon',), zlib='True' ) +lat = ncout.createVariable( 'lat', 'f4', ('nlat', 'nlon',), zlib='True' ) +lon[:] = np.broadcast_to(lon_src.reshape(1,nlon), (nlat,nlon)) +lat[:] = np.broadcast_to(lat_src.reshape(nlat,1), (nlat,nlon)) +bout = ncout.createVariable( "LSM", 'f4', ('nlat','nlon',), zlib='True', fill_value=-999. ) +bout[:] = msk_src +ncout.close() diff --git a/BUILD_CFG/SURFACE_FORCING/namelist_reshape_bicubic_atmos b/BUILD_CFG/SURFACE_FORCING/namelist_reshape_bicubic_atmos index 71b438c..e321856 100755 --- a/BUILD_CFG/SURFACE_FORCING/namelist_reshape_bicubic_atmos +++ b/BUILD_CFG/SURFACE_FORCING/namelist_reshape_bicubic_atmos @@ -12,18 +12,18 @@ nemo_lat: name of latitude variable in the coordinates.nc / &grid_inputs - input_file = '/work/n01/n01/acc/DFS/DFS5.2/1960/drowned_precip_DFS5.2_y1960.nc' - nemo_file = 'coordinates.nc' + input_file = './ERA5_MSL_y2013.nc' + nemo_file = './coordinates.nc' datagrid_file = 'remap_data_grid_atmos.nc' nemogrid_file = 'remap_nemo_grid_atmos.nc' - method = 'regular' - input_lon = 'lon0' - input_lat = 'lat0' - nemo_lon = 'glamt' - nemo_lat = 'gphit' - nemo_mask = 'none' - nemo_mask_value = 0 - input_mask = 'none' + method = 'regular' + input_lon = 'lon' + input_lat = 'lat' + nemo_lon = 'glamt' + nemo_lat = 'gphit' + nemo_mask = 'none' + nemo_mask_value = 0 + input_mask = 'none' input_mask_value = 0 / &comments @@ -45,38 +45,38 @@ - output_opt may be supplied and set to either 'scrip' or 'ncar-csm' / &remap_inputs - num_maps = 1 - grid1_file = 'remap_data_grid_atmos.nc' - grid2_file = 'remap_nemo_grid_atmos.nc' - interp_file1 = 'data_nemo_bicubic_atmos.nc' - interp_file2 = 'nemo_data_bicubic_atmos.nc' - map1_name = 'atmos to nemo bicubic Mapping' - map2_name = 'nemo to atmos bicubic Mapping' - map_method = 'bicubic' + num_maps = 1 + grid1_file = 'remap_data_grid_atmos.nc' + grid2_file = 'remap_nemo_grid_atmos.nc' + interp_file1 = 'data_nemo_bicubic_atmos.nc' + interp_file2 = 'nemo_data_bicubic_atmos.nc' + map1_name = 'atmos to nemo bicubic Mapping' + map2_name = 'nemo to atmos bicubic Mapping' + map_method = 'bicubic' normalize_opt = 'frac' - output_opt = 'scrip' + output_opt = 'scrip' restrict_type = 'latitude' num_srch_bins = 90 luse_grid1_area = .false. luse_grid2_area = .false. / &interp_inputs - input_file = "nothing.nc" - interp_file = "data_nemo_bicubic_atmos.nc" - input_name = "nothing" - input_start = 1,1 + input_file = "nothing.nc" + interp_file = "data_nemo_bicubic_atmos.nc" + input_name = "nothing" + input_start = 1,1 input_stride = 1,1 - input_stop = 0,0 + input_stop = 0,0 / &interp_outputs - output_file = "nothing.nc" - output_mode = "create" - output_dims = 'x', 'y' + output_file = "nothing.nc" + output_mode = "create" + output_dims = 'x', 'y' output_scaling = "topo|1.0" - output_name = 'topo' - output_lon = 'x' - output_lat = 'y' + output_name = 'topo' + output_lon = 'x' + output_lat = 'y' / &comments @@ -86,6 +86,6 @@ / &shape_inputs interp_file = 'data_nemo_bicubic_atmos.nc' - output_file = 'weights_bicubic_atmos.nc' + output_file = 'weights_era5_SEVERN_bicubic.nc' ew_wrap = -1 / diff --git a/BUILD_CFG/SURFACE_FORCING/namelist_reshape_bilin_atmos b/BUILD_CFG/SURFACE_FORCING/namelist_reshape_bilin_atmos index 867206f..e321856 100755 --- a/BUILD_CFG/SURFACE_FORCING/namelist_reshape_bilin_atmos +++ b/BUILD_CFG/SURFACE_FORCING/namelist_reshape_bilin_atmos @@ -12,18 +12,18 @@ nemo_lat: name of latitude variable in the coordinates.nc / &grid_inputs - input_file = '/work/n01/n01/acc/DFS/DFS5.2/1960/drowned_precip_DFS5.2_y1960.nc' - nemo_file = 'coordinates.nc' + input_file = './ERA5_MSL_y2013.nc' + nemo_file = './coordinates.nc' datagrid_file = 'remap_data_grid_atmos.nc' nemogrid_file = 'remap_nemo_grid_atmos.nc' - method = 'regular' - input_lon = 'lon0' - input_lat = 'lat0' - nemo_lon = 'glamt' - nemo_lat = 'gphit' - nemo_mask = 'none' - nemo_mask_value = 0 - input_mask = 'none' + method = 'regular' + input_lon = 'lon' + input_lat = 'lat' + nemo_lon = 'glamt' + nemo_lat = 'gphit' + nemo_mask = 'none' + nemo_mask_value = 0 + input_mask = 'none' input_mask_value = 0 / &comments @@ -45,38 +45,38 @@ - output_opt may be supplied and set to either 'scrip' or 'ncar-csm' / &remap_inputs - num_maps = 1 - grid1_file = 'remap_data_grid_atmos.nc' - grid2_file = 'remap_nemo_grid_atmos.nc' - interp_file1 = 'data_nemo_bilin_atmos.nc' - interp_file2 = 'nemo_data_bilin_atmos.nc' - map1_name = 'atmos to nemo bilin Mapping' - map2_name = 'nemo to atmos bilin Mapping' - map_method = 'bilinear' + num_maps = 1 + grid1_file = 'remap_data_grid_atmos.nc' + grid2_file = 'remap_nemo_grid_atmos.nc' + interp_file1 = 'data_nemo_bicubic_atmos.nc' + interp_file2 = 'nemo_data_bicubic_atmos.nc' + map1_name = 'atmos to nemo bicubic Mapping' + map2_name = 'nemo to atmos bicubic Mapping' + map_method = 'bicubic' normalize_opt = 'frac' - output_opt = 'scrip' + output_opt = 'scrip' restrict_type = 'latitude' num_srch_bins = 90 luse_grid1_area = .false. luse_grid2_area = .false. / &interp_inputs - input_file = "nothing.nc" - interp_file = "data_nemo_bilin_atmos.nc" - input_name = "nothing" - input_start = 1,1 + input_file = "nothing.nc" + interp_file = "data_nemo_bicubic_atmos.nc" + input_name = "nothing" + input_start = 1,1 input_stride = 1,1 - input_stop = 0,0 + input_stop = 0,0 / &interp_outputs - output_file = "nothing.nc" - output_mode = "create" - output_dims = 'x', 'y' + output_file = "nothing.nc" + output_mode = "create" + output_dims = 'x', 'y' output_scaling = "topo|1.0" - output_name = 'topo' - output_lon = 'x' - output_lat = 'y' + output_name = 'topo' + output_lon = 'x' + output_lat = 'y' / &comments @@ -85,7 +85,7 @@ into the form needed by the nemo on the fly interpolation code. / &shape_inputs - interp_file = 'data_nemo_bilin_atmos.nc' - output_file = 'weights_bilinear_atmos.nc' + interp_file = 'data_nemo_bicubic_atmos.nc' + output_file = 'weights_era5_SEVERN_bicubic.nc' ew_wrap = -1 / diff --git a/SCRIPTS/OFFICIAL_Generate_NEMO_Forcing_NEWERA.py b/SCRIPTS/OFFICIAL_Generate_NEMO_Forcing_NEWERA.py new file mode 100755 index 0000000..f2272e7 --- /dev/null +++ b/SCRIPTS/OFFICIAL_Generate_NEMO_Forcing_NEWERA.py @@ -0,0 +1,296 @@ +# +#====================== DOCSTRING ============================ +""" +Generate ERA5 atmospheric forcing for NEMO +So far to prduce a year by a year - need to be automated +-------------------------------------------------------------- +""" +__author__ = "Nicolas Bruneau" +__copyright__ = "Copyright 2018, NOC" +__email__ = "nibrun@noc.ac.uk" +__date__ = "2018-05" + +#====================== USR PARAMS =========================== + +Year_init = 2013 ## First year to process +Year_end = 2014 ## Last one [included] +East = 0 ## East Border +West = -10 ## West Border +North = 55 ## North Border +South = 45 ## South Border +path_ERA5 = '/projectsa/NEMO/Forcing/ERA5/SURFACE_FORCING/' ## ROOT PATH OD ERA5 DATA +path_EXTRACT = './BUILD_CFG/SURFACE_FORCING/EXTRACTION/' ## WHERE TO EXTRACT YOUR REGION +path_FORCING = './BUILD_CFG/SURFACE_FORCING/' ## NEMO FORCING TARGET DIR +clean = False ## Clean extraction (longest bit) +sph_ON = True ## Compute specific humidity or not + +#================== NEMO DOCUMENTATION ======================= + +""" +See the manual in section SBC for more details on the way data +are used in NEMO +The time variable from the netcdf is not used +""" + +#====================== LOAD MODULES ========================= + +import os, sys, glob +import subprocess +import numpy as np +import datetime +from netCDF4 import Dataset, MFDataset +import netcdftime +import matplotlib.pyplot as plt +from matplotlib.mlab import griddata +import scipy.spatial.qhull as qhull + +#====================== VARIABLE DEF ========================= + +var_path = { "10m_u_component_of_wind" : "u10", \ + "10m_v_component_of_wind" : "v10", \ + "2m_temperature" : "t2m", \ + "mean_sea_level_pressure" : "msl", \ + "mean_snowfall_rate" : "msr" , \ + "mean_surface_downward_long_wave_radiation_flux" : "msdwlwrf", \ + "mean_surface_downward_short_wave_radiation_flux" : "msdwswrf", \ + "mean_total_precipitation_rate" : "mtpr" } + +if sph_ON : + var_path[ "surface_pressure" ] = 'sp' + var_path[ "2m_dewpoint_temperature" ] = 'd2m' + +#===================== INTERNAL FCTNS ======================== + +help_tosec = np.vectorize( lambda x : x.total_seconds() ) + +def Read_NetCDF_Concatenate( fname, KeyVar ) : + 'Read NetCDF file' + lfiles = sorted( glob.glob( fname ) ) + for iF, myfile in enumerate(lfiles) : + nc = Dataset( myfile, 'r' ) + ## Get time using the time variable + Time_Var = nc.variables[ 'time'] + dt = Time_Var[:][1] - Time_Var[:][0] + Time_H = np.arange( Time_Var[:][0], Time_Var[:][0]+dt*Time_Var[:].size, dt ) + try : Tref = netcdftime.utime( Time_Var.units, calendar = Time_Var.calendar ) + except : Tref = netcdftime.utime( Time_Var.units, calendar = "gregorian" ) + Time = Tref.num2date( Time_H ) + ## Get Coordinates + if iF == 0: + try : + Lon = nc.variables[ 'longitude' ][:] + Lat = nc.variables[ 'latitude' ][:] + LON, LAT = np.meshgrid( Lon, Lat ) + except : + LON = nc.variables[ 'lon' ][:] + LAT = nc.variables[ 'lat' ][:] + ## Get Variable + dum = nc.variables[ KeyVar ] + Var = dum[:]; ind = ( Var == dum._FillValue ); Var[ind] = np.nan + ## save + if iF == 0 : out = Var; tout = Time + else : out = np.concatenate( [out,Var], axis=0 ); tout = np.concatenate( [tout,Time], axis=0 ) + print tout[0], tout[-1], tout.shape, out.shape, LON.shape + try : return tout, LON, LAT, out, dum.units, dum.long_name + except : return tout, LON, LAT, out, dum.units, dum.standard_name + + +def Read_NetCDF( fname, KeyVar ) : + 'Read NetCDF file' + if "*" in fname : nc = MFDataset( fname, 'r' ) + else : nc = Dataset( fname, 'r' ) + ## Get time using the time variable + Time_Var = nc.variables[ 'time'] + dt = Time_Var[:][1] - Time_Var[:][0] + Time_H = np.arange( Time_Var[:][0], Time_Var[:][0]+dt*Time_Var[:].size, dt ) + try : Tref = netcdftime.utime( Time_Var.units, calendar = Time_Var.calendar ) + except : Tref = netcdftime.utime( Time_Var.units, calendar = "gregorian" ) + Time = Tref.num2date( Time_H ) + print "====================++++" + ## Get Coordinates + try : + Lon = nc.variables[ 'longitude' ][:] + Lat = nc.variables[ 'latitude' ][:] + LON, LAT = np.meshgrid( Lon, Lat ) + except : + LON = nc.variables[ 'lon' ][:] + LAT = nc.variables[ 'lat' ][:] + + ## Get Variable + dum = nc.variables[ KeyVar ] + Var = dum[:] + ind = ( Var == dum._FillValue ) + Var[ind] = np.nan + #Var = Var / dum.scale_factor + dum.add_offset + ind = (np.isnan(Var)) + Var[ind] = -9999999 + + print Time[0], Time[-1], Var.shape, Time.shape, np.sum(ind) + try : return Time, LON, LAT, Var, dum.units, dum.long_name + except : return Time, LON, LAT, Var, dum.units, dum.standard_name + +#=================== MANIPULATE NetCDF ======================= + +def compute_scale_and_offset( Var, n ): + 'http://james.hiebert.name/blog/work/2015/04/18/NetCDF-Scale-Factors/' + Vmin = np.nanmin( Var ) + Vmax = np.nanmax( Var ) + print "scaleoffset", Vmin, Vmax + # stretch/compress data to the available packed range + scale_factor = (Vmax - Vmin) / (2 ** n - 1) + # translate the range to be symmetric about zero + add_offset = Vmin + 2 ** (n - 1) * scale_factor + return scale_factor, add_offset + +def Add_Variable( nc, vName, vDim, vVal, long_name=None, units=None, standard_name=None, fill_value=None) : + "Add a variable with its attributes in a netcdf file" + if vName not in ['time','lon','lat',] : fprec = 'i' + else : fprec = 'f8' + + if fill_value != None : nc.createVariable( vName, fprec, vDim, fill_value=fill_value, zlib=True, complevel=5 ) + else : nc.createVariable( vName, fprec, vDim, zlib=True, complevel=5 ) + if long_name != None : nc.variables[ vName ].long_name = long_name + if units != None : nc.variables[ vName ].units = units + if standard_name != None : nc.variables[ vName ].standard_name = standard_name + if vName not in ['time','lon','lat',] : + sc, off = compute_scale_and_offset( vVal, 16 ) + nc.variables[ vName ].scale_factor = sc + nc.variables[ vName ].add_offset = off + + nc.variables[ vName ][:] = vVal # np.floor((vVal-off)/sc) + +def Create_Dimensions( nc, lon_name, nLon, lat_name, nLat ) : + "Create NetCDF dimensions time, nx, ny" + nc.createDimension( lon_name , nLon ) + nc.createDimension( lat_name , nLat ) + nc.createDimension( 'time' , None ) + +def Create_NetCDF_core( nc, tDim, tRef, tVal, sDim, sVal_lon, sVal_lat ) : + "Create Lon, Lat and Time variables" + # WRITE TIME INFO + tUnit = "days since {0} UTC".format( tRef.strftime( "%Y-%m-%d %H:%M:%S" ) ); tCal = "standard" + Tref = netcdftime.utime( tUnit, calendar = tCal ) + Add_Variable( nc, 'time', ('time'), Tref.date2num( tVal ), \ + long_name = "time since {0}".format(tUnit) , \ + units = tUnit ) + nc.variables['time'].calendar = tCal + #nc.variables['time'].base_date = np.array( [ tRef.year, tRef.month, tRef.day, tRef.hour ] ) + + # WRITE LON INFO + Add_Variable( nc, 'lon', sDim, sVal_lon, long_name = 'Longitude', \ + units = 'degree_east', standard_name = 'longitude' ) + + # WRITE L INFOT + Add_Variable( nc, 'lat', sDim, sVal_lat, long_name = 'Latitude', \ + units = 'degree_north', standard_name = 'latitude' ) + +def Create_Attributes( nc ) : + "Add some info - I do it at the end as I had issue with not properly readable netcdf if not" + nc.Description = 'ERA5 Atmospheric conditions for AMM15 NEMO3.6' + nc.Author = 'Prepare_ERA5.py' + nc.Created = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S") + nc.Conventions = "CF-1.0" + nc.close() + +#======================= EXTRACTION ========================== + +def Extract( fin, fout, clean=True ) : + if clean : os.system( "rm {0}".format( fout ) ) + if not os.path.exists( fout ) : + command = "ncks -d latitude,{0},{1} -d longitude,{2},{3} {4} {5}".format( np.float(South), np.float(North),\ + np.float(West), np.float(East), fin, fout ) + print command + os.system( command ) + +def datetime_range(start, end, delta): + current = [start, ] + while current[-1] < end: + current.append( current[-1]+delta ) + return np.array(current) + +#======================= CORE PROGR ========================== + +## load NCO +os.system( "module load nco/gcc/4.4.2.ncwa" ) +os.system( "mkdir {0} {1}".format( path_EXTRACT, path_FORCING ) ) +if West < 0 : West = 360.+West +if East < 0 : East = 360.+East + +## Loop over each variable +for dirVar, nameVar in var_path.iteritems() : + + print "================== {0} - {1} ==================".format( dirVar, nameVar ) + + ##---------- EXTRACT ALL DATA FOR DOMAIN ---------------- + for iY in range( Year_init, Year_end+1 ) : + ## Files + finput = "{0}/{1}/{2}_{1}.nc".format( path_ERA5, dirVar, iY ) + foutput = "./{2}/{0}_{1}.nc".format( nameVar, iY, path_EXTRACT ) + ## Extract the subdomain + Extract( finput, foutput, clean=clean ) + + ##---------- LOAD FULLL TIME SERIES IN MEMORY ----------- + Time, Lon, Lat, dum, Units, Name = Read_NetCDF_Concatenate( "./{1}/{0}_*.nc".format( nameVar, path_EXTRACT ), nameVar ) + print "Time" , Time + + dt = Time[1] - Time[0] ## assume to be constant in time + dt2 = datetime.timedelta( seconds=dt.total_seconds() / 2. ) + print "dt", dt, dt2 + + ##---------- SOME PREPROCESSING ------------------------- + ## Add time step for last hour - copy the last input + dumA = np.concatenate( [ dum, dum[-1][np.newaxis,...] ], axis = 0 ) + TimeA = np.array( Time.tolist() + [Time[-1],] ) + + print "Time" , Time + print "TimeA", TimeA + ## instantaneous field every hour. we center it in mid-time step (00:30) as it + ## is what NEMO assumes according to documentation + dumC = ( dumA[0:-1] + dumA[1::] ) / 2.0 + TimeC = TimeA[0:-1] + dt2 ## shift half time step positively due to averaging + suffix = '' + + print "TimeC", TimeC + + ##---------- OUTPUT A FILE PER YEAR --------------------- + for iY in range( Year_init, Year_end+1 ) : + + print datetime.datetime( iY ,1,1 ), datetime.datetime( iY+1,1,1 ) + indT = ( np.array(TimeC) >= datetime.datetime( iY ,1,1,0,0,0 ) ) \ + * ( np.array(TimeC) < datetime.datetime( iY+1,1,1,0,0,0 ) ) + print "indT",np.sum(indT) + + if nameVar in [ "d2m", "sp" ] : + Fout = "./{2}/forSPH_ERA5_{0}_y{1}.nc".format( nameVar.upper(), iY, path_FORCING ) + else : Fout = "./{2}/ERA5_{0}_y{1}.nc".format( nameVar.upper(), iY, path_FORCING ) + nc = Dataset( Fout, 'w', format='NETCDF4_CLASSIC') + Create_Dimensions ( nc, 'nLon', Lon.shape[1], 'nLat' , Lat.shape[0] ) + Create_NetCDF_core( nc, ('time'), TimeC[indT][0], TimeC[indT], ('nLat', 'nLon'), Lon[::-1,:], Lat[::-1,:] ) + Add_Variable( nc, nameVar.upper(), ( 'time', 'nLat', 'nLon'), dumC[indT,::-1,:], units=Units+suffix, standard_name=Name, fill_value=-999999 ) + Create_Attributes( nc ) + + +##---------- PROCESS SPECIFIC HUMIDITY ---------------------- +## Compute Specific Humidity according to ECMWF documentation + +if sph_ON : + + for iY in range( Year_init, Year_end+1 ) : + Time, Lon, Lat, d2m, dUnits, dName = Read_NetCDF( "./{1}/forSPH_ERA5_D2M_y{0}.nc".format( iY, path_FORCING ), 'D2M' ) + Time, Lon, Lat, sp , dUnits, dName = Read_NetCDF( "./{1}/forSPH_ERA5_SP_y{0}.nc" .format( iY, path_FORCING ), 'SP' ) + esat = 611.21 * np.exp( 17.502 * (d2m-273.16) / (d2m-32.19) ) + dyrvap = 287.0597 / 461.5250 + dVar = dyrvap * esat / ( sp - (1-dyrvap) * esat) + Units = "1"; Name = "Specific Humidity" + + indT = ( Time >= datetime.datetime( iY ,1,1 ) ) \ + * ( Time < datetime.datetime( iY+1,1,1 ) ) + + Fout = "./{1}/ERA5_SPH_y{0}.nc".format( iY, path_FORCING ) + nc = Dataset( Fout, 'w', format='NETCDF4_CLASSIC') + Create_Dimensions ( nc, 'nLon', Lon.shape[1], 'nLat' , Lat.shape[0] ) + Create_NetCDF_core( nc, ('time'), Time[indT][0], Time[indT], ('nLat', 'nLon'), Lon[:,:], Lat[:,:] ) + Add_Variable( nc, "SPH", ( 'time', 'nLat', 'nLon'), dVar[indT,:,:], units=Units, standard_name=Name, fill_value=-999999 ) + Create_Attributes( nc ) + + diff --git a/SCRIPTS/make_paths.sh b/SCRIPTS/make_paths.sh index 5a9a767..5d16020 100644 --- a/SCRIPTS/make_paths.sh +++ b/SCRIPTS/make_paths.sh @@ -37,3 +37,5 @@ export TDIR=$NEMO/tools # base tools source and build directory export DOMAIN=$WDIR/BUILD_CFG/DOMAIN # base directory for building domain configuration file export DOWNLOADS=$WDIR/DOWNLOADS + +export SBC = $WDIR/BUILD_CFG/SURFACE_FORCING From 8c7c7cfb29be0058de7f922a5778cb410dd2c07f Mon Sep 17 00:00:00 2001 From: not populated Date: Thu, 2 Sep 2021 17:43:21 +0100 Subject: [PATCH 02/12] start EXP for tides + met --- .../namelist_reshape_bilin_atmos | 16 +- .../EXP_barotropicTide_ERA5/context_nemo.xml | 35 + .../file_def_nemo-oce.xml | 76 +++ .../EXP_barotropicTide_ERA5/iodef.xml | 26 + .../EXP_barotropicTide_ERA5/namelist_cfg | 644 ++++++++++++++++++ .../EXP_barotropicTide_ERA5/submit.slurm | 33 + SCRIPTS/make_paths.sh | 2 +- SCRIPTS/run_barotropicTide_ERA5.sh | 53 ++ 8 files changed, 876 insertions(+), 9 deletions(-) create mode 100755 RUN_DIRECTORIES/EXP_barotropicTide_ERA5/context_nemo.xml create mode 100755 RUN_DIRECTORIES/EXP_barotropicTide_ERA5/file_def_nemo-oce.xml create mode 100755 RUN_DIRECTORIES/EXP_barotropicTide_ERA5/iodef.xml create mode 100755 RUN_DIRECTORIES/EXP_barotropicTide_ERA5/namelist_cfg create mode 100644 RUN_DIRECTORIES/EXP_barotropicTide_ERA5/submit.slurm create mode 100644 SCRIPTS/run_barotropicTide_ERA5.sh diff --git a/BUILD_CFG/SURFACE_FORCING/namelist_reshape_bilin_atmos b/BUILD_CFG/SURFACE_FORCING/namelist_reshape_bilin_atmos index e321856..2b037a4 100755 --- a/BUILD_CFG/SURFACE_FORCING/namelist_reshape_bilin_atmos +++ b/BUILD_CFG/SURFACE_FORCING/namelist_reshape_bilin_atmos @@ -48,11 +48,11 @@ num_maps = 1 grid1_file = 'remap_data_grid_atmos.nc' grid2_file = 'remap_nemo_grid_atmos.nc' - interp_file1 = 'data_nemo_bicubic_atmos.nc' - interp_file2 = 'nemo_data_bicubic_atmos.nc' - map1_name = 'atmos to nemo bicubic Mapping' - map2_name = 'nemo to atmos bicubic Mapping' - map_method = 'bicubic' + interp_file1 = 'data_nemo_bilin_atmos.nc' + interp_file2 = 'nemo_data_bilin_atmos.nc' + map1_name = 'atmos to nemo bilin Mapping' + map2_name = 'nemo to atmos bilin Mapping' + map_method = 'bilinear' normalize_opt = 'frac' output_opt = 'scrip' restrict_type = 'latitude' @@ -62,7 +62,7 @@ / &interp_inputs input_file = "nothing.nc" - interp_file = "data_nemo_bicubic_atmos.nc" + interp_file = "data_nemo_bilin_atmos.nc" input_name = "nothing" input_start = 1,1 input_stride = 1,1 @@ -85,7 +85,7 @@ into the form needed by the nemo on the fly interpolation code. / &shape_inputs - interp_file = 'data_nemo_bicubic_atmos.nc' - output_file = 'weights_era5_SEVERN_bicubic.nc' + interp_file = 'data_nemo_bilin_atmos.nc' + output_file = 'weights_era5_SEVERN_bilin.nc' ew_wrap = -1 / diff --git a/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/context_nemo.xml b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/context_nemo.xml new file mode 100755 index 0000000..d5df832 --- /dev/null +++ b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/context_nemo.xml @@ -0,0 +1,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/file_def_nemo-oce.xml b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/file_def_nemo-oce.xml new file mode 100755 index 0000000..1cbd7fa --- /dev/null +++ b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/file_def_nemo-oce.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/iodef.xml b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/iodef.xml new file mode 100755 index 0000000..b49154c --- /dev/null +++ b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/iodef.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + 10 + true + false + oceanx + + + + + + + + + + + diff --git a/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/namelist_cfg b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/namelist_cfg new file mode 100755 index 0000000..7fdab9a --- /dev/null +++ b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/namelist_cfg @@ -0,0 +1,644 @@ +!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +!! NEMO/OCE Configuration namelist : overwrite default values defined in SHARED/namelist_ref +!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +!! NEMO/OCE : 1 - Domain & run manager (namrun, namcfg, namdom, namtsd, namcrs, namc1d, namc1d_uvd) +!! namelists 2 - Surface boundary (namsbc, namsbc_flx, namsbc_blk, namsbc_cpl, +!! namsbc_sas, namtra_qsr, namsbc_rnf, +!! namsbc_isf, namsbc_iscpl, namsbc_apr, +!! namsbc_ssr, namsbc_wave, namberg) +!! 3 - lateral boundary (namlbc, namagrif, nambdy, nambdy_tide) +!! 4 - top/bot boundary (namdrg, namdrg_top, namdrg_bot, nambbc, nambbl) +!! 5 - Tracer (nameos, namtra_adv, namtra_ldf, namtra_eiv, namtra_dmp) +!! 6 - dynamics (namdyn_adv, namdyn_vor, namdyn_hpg, namdyn_spg, namdyn_ldf) +!! 7 - Vertical physics (namzdf, namzdf_ric, namzdf_tke, namzdf_gls, namzdf_iwm) +!! 8 - diagnostics (namnc4, namtrd, namspr, namflo, namhsb) +!! 9 - Obs & Assim (namobs, nam_asminc) +!! 10 - miscellaneous (nammpp, namctl, namsto) +!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + +!!====================================================================== +!! *** Domain & Run management namelists *** !! +!! !! +!! namrun parameters of the run +!! namdom space and time domain +!! namcfg parameters of the configuration (default: user defined GYRE) +!! namwad Wetting and drying (default: OFF) +!! namtsd data: temperature & salinity (default: OFF) +!! namcrs coarsened grid (for outputs and/or TOP) (ln_crs =T) +!! namc1d 1D configuration options ("key_c1d") +!! namc1d_dyndmp 1D newtonian damping applied on currents ("key_c1d") +!! namc1d_uvd 1D data (currents) ("key_c1d") +!!====================================================================== +! +!----------------------------------------------------------------------- +&namrun ! parameters of the run +!----------------------------------------------------------------------- + nn_no = 0 ! Assimilation cycle index + cn_exp = "SEVERN_Tid_met" + nn_it000 = 1 ! 8641 ! 1 ! first time step + nn_itend = 600 ! ! 4320 per 24hr ! last time step + nn_date0 = 20130101 ! date at nit_0000 (format yyyymmdd) used if ln_rstart=F or (ln_rstart=T and nn_rstctl=0 or 1) + nn_time0 = 0 ! initial time of day in hhmm + nn_leapy = 1 ! Leap year calendar (1) or not (0) + ln_rstart = .false. ! start from rest (F) or from a restart file (T) + nn_euler = 1 ! = 0 : start with forward time step if ln_rstart=T + nn_rstctl = 0 ! restart control ==> activated only if ln_rstart=T + ! ! = 0 nn_date0 read in namelist ; nn_it000 : read in namelist + ! ! = 1 nn_date0 read in namelist ; nn_it000 : check consistancy between namelist and restart + ! ! = 2 nn_date0 read in restart ; nn_it000 : check consistancy between namelist and restart + cn_ocerst_in = "" ! suffix of ocean restart name (input) + cn_ocerst_indir = "" ! directory from which to read input ocean restarts + cn_ocerst_out = "restart" ! suffix of ocean restart name (output) + cn_ocerst_outdir = "./RESTART" ! directory in which to write output ocean restarts + ln_iscpl = .false. ! cavity evolution forcing or coupling to ice sheet model + nn_istate = 0 ! output the initial state (1) or not (0) + ln_rst_list = .false. ! output restarts at list of times using nn_stocklist (T) or at set frequency with nn_stock (F) + nn_stock = 600 ! used only if ln_rst_list = F: output restart freqeuncy (modulo referenced to 1) + ! ! = 0 force to write restart files only at the end of the run + ! ! = -1 do not do any restart + nn_stocklist = 600 ! 0,0,0,0,0,0,0,0,0,0 ! List of timesteps when a restart file is to be written + nn_write = 0 ! used only if key_iomput is not defined: output frequency (modulo referenced to nn_it000) + ! ! = 0 force to write output files only at the end of the run + ! ! = -1 do not do any output file + ln_mskland = .false. ! mask land points in NetCDF outputs + ln_cfmeta = .false. ! output additional data to netCDF files required for compliance with the CF metadata standard + ln_clobber = .true. ! clobber (overwrite) an existing file + nn_chunksz = 0 ! chunksize (bytes) for NetCDF file (works only with iom_nf90 routines) + ln_xios_read = .TRUE. ! use XIOS to read restart file (only for a single file restart) + nn_wxios = 1 ! use XIOS to write restart file 0 - no, 1 - single file output, 2 - multiple file output +/ +!----------------------------------------------------------------------- +&namdom ! time and space domain +!----------------------------------------------------------------------- + ln_linssh = .false. ! .false. ! =T linear free surface ==>> model level are fixed in time + rn_isfhmin = 1.00 ! treshold [m] to discriminate grounding ice from floating ice + ! + rn_rdt = 20. ! time step for the dynamics and tracer + rn_atfp = 0.1 ! asselin time filter parameter + ! + ln_crs = .false. ! Logical switch for coarsening module (T => fill namcrs) + ! + ln_meshmask = .false. ! =T create a mesh file +/ +!----------------------------------------------------------------------- +&namcfg ! parameters of the configuration (default: use namusr_def in namelist_cfg) +!----------------------------------------------------------------------- + ln_read_cfg = .true. ! (=T) read the domain configuration file + ! ! (=F) user defined configuration (F => create/check namusr_def) + cn_domcfg = "domain_cfg" !"domain_cfg" ! domain configuration filename + ! + ln_closea = .false. ! T => keep closed seas (defined by closea_mask field) in the + ! ! domain and apply special treatment of freshwater fluxes. + ! ! F => suppress closed seas (defined by closea_mask field) + ! ! from the bathymetry at runtime. + ! ! If closea_mask field doesn't exist in the domain_cfg file + ! ! then this logical does nothing. + ln_write_cfg = .false. ! (=T) create the domain configuration file + cn_domcfg_out = "domain_cfg_out" ! newly created domain configuration filename + ! + ln_use_jattr = .false. ! use (T) the file attribute: open_ocean_jstart, if present + ! ! in netcdf input files, as the start j-row for reading +/ +!----------------------------------------------------------------------- +&namzgr ! vertical coordinate (default: NO selection) +!----------------------------------------------------------------------- + ln_zco = .false. ! z-coordinate - full steps + ln_zps = .false. ! z-coordinate - partial steps + ln_sco = .true. ! s- or hybrid z-s-coordinate + ln_isfcav = .false. ! ice shelf cavity +! ln_linssh = .false. ! linear free surface +/ +!----------------------------------------------------------------------- +&namzgr_sco +!----------------------------------------------------------------------- + ln_s_sf12=.false., + ln_s_sh94=.true., + ln_sigcrit=.false., + rn_alpha=4.4, + rn_bb=0.8, + rn_efold=0.0, + rn_hc=39.0, + rn_rmax=0.05, + rn_sbot_max=6000.0, + rn_sbot_min=10., + rn_theta=6.0, + rn_thetb=1.0, + rn_zb_a=0.024, + rn_zb_b=-0.2, + rn_zs=1.0, +/ +!----------------------------------------------------------------------- +&namtsd ! Temperature & Salinity Data (init/dmp) (default: OFF) +!----------------------------------------------------------------------- + ! ! =T read T-S fields for: + ln_tsd_init = .false. ! ocean initialisation + ln_tsd_interp = .false. ! Interpolation of T & S in the verticalinput data (T) or not (F) + ln_tsd_dmp = .false. ! T-S restoring (see namtra_dmp) + +/ +!!====================================================================== +!! *** Surface Boundary Condition namelists *** !! +!! !! +!! namsbc surface boundary condition manager (default: NO selection) +!! namsbc_flx flux formulation (ln_flx =T) +!! namsbc_blk Bulk formulae formulation (ln_blk =T) +!! namsbc_cpl CouPLed formulation ("key_oasis3" ) +!! namsbc_sas Stand-Alone Surface module (SAS_SRC only) +!! namsbc_iif Ice-IF: use observed ice cover (nn_ice = 1 ) +!! namtra_qsr penetrative solar radiation (ln_traqsr =T) +!! namsbc_ssr sea surface restoring term (for T and/or S) (ln_ssr =T) +!! namsbc_rnf river runoffs (ln_rnf =T) +!! namsbc_apr Atmospheric Pressure (ln_apr_dyn =T) +!! namsbc_isf ice shelf melting/freezing (ln_isfcav =T : read (ln_read_cfg=T) or set or usr_def_zgr ) +!! namsbc_iscpl coupling option between land ice model and ocean (ln_isfcav =T) +!! namsbc_wave external fields from wave model (ln_wave =T) +!! namberg iceberg floats (ln_icebergs=T) +!!====================================================================== +! +!----------------------------------------------------------------------- +&namsbc ! Surface Boundary Condition manager (default: NO selection) +!----------------------------------------------------------------------- + nn_fsbc = 1 ! frequency of SBC module call + ! ! (control sea-ice & iceberg model call) + ! Type of air-sea fluxes + ln_usr = .false. ! user defined formulation (T => check usrdef_sbc) + ln_flx = .false. ! flux formulation (T => fill namsbc_flx ) + ln_blk = .true. ! Bulk formulation (T => fill namsbc_blk ) + ! ! Type of coupling (Ocean/Ice/Atmosphere) : + ln_cpl = .false. ! atmosphere coupled formulation ( requires key_oasis3 ) + ln_mixcpl = .false. ! forced-coupled mixed formulation ( requires key_oasis3 ) + nn_components = 0 ! configuration of the opa-sas OASIS coupling + ! ! =0 no opa-sas OASIS coupling: default single executable config. + ! ! =1 opa-sas OASIS coupling: multi executable config., OPA component + ! ! =2 opa-sas OASIS coupling: multi executable config., SAS component + ! Sea-ice : + nn_ice = 0 ! =0 no ice boundary condition + ! ! =1 use observed ice-cover ( => fill namsbc_iif ) + ! ! =2 or 3 automatically for SI3 or CICE ("key_si3" or "key_cice") + ! ! except in AGRIF zoom where it has to be specified + ln_ice_embd = .false. ! =T embedded sea-ice (pressure + mass and salt exchanges) + ! ! =F levitating ice (no pressure, mass and salt exchanges) + ! Misc. options of sbc : + ln_traqsr = .false. ! Light penetration in the ocean (T => fill namtra_qsr) + ln_dm2dc = .false. ! daily mean to diurnal cycle on short wave + ln_ssr = .false. ! Sea Surface Restoring on T and/or S (T => fill namsbc_ssr) + nn_fwb = 0 ! FreshWater Budget: =0 unchecked + ! ! =1 global mean of e-p-r set to zero at each time step + ! ! =2 annual global mean of e-p-r set to zero + ln_rnf = .false. ! runoffs (T => fill namsbc_rnf) + ln_apr_dyn = .false. ! Patm gradient added in ocean & ice Eqs. (T => fill namsbc_apr ) + ln_isf = .false. ! ice shelf (T => fill namsbc_isf & namsbc_iscpl) + ln_wave = .false. ! Activate coupling with wave (T => fill namsbc_wave) + ln_cdgw = .false. ! Neutral drag coefficient read from wave model (T => ln_wave=.true. & fill namsbc_wave) + ln_sdw = .false. ! Read 2D Surf Stokes Drift & Computation of 3D stokes drift (T => ln_wave=.true. & fill namsbc_wave) + nn_sdrift = 0 ! Parameterization for the calculation of 3D-Stokes drift from the surface Stokes drift + ! ! = 0 Breivik 2015 parameterization: v_z=v_0*[exp(2*k*z)/(1-8*k*z)] + ! ! = 1 Phillips: v_z=v_o*[exp(2*k*z)-beta*sqrt(-2*k*pi*z)*erfc(sqrt(-2*k*z))] + ! ! = 2 Phillips as (1) but using the wave frequency from a wave model + ln_tauwoc = .false. ! Activate ocean stress modified by external wave induced stress (T => ln_wave=.true. & fill namsbc_wave) + ln_tauw = .false. ! Activate ocean stress components from wave model + ln_stcor = .false. ! Activate Stokes Coriolis term (T => ln_wave=.true. & ln_sdw=.true. & fill namsbc_wave) + nn_lsm = 0 ! =0 land/sea mask for input fields is not applied (keep empty land/sea mask filename field) , + ! =1:n number of iterations of land/sea mask application for input fields (fill land/sea mask filename field) +/ +!----------------------------------------------------------------------- +&namsbc_blk ! namsbc_blk generic Bulk formula (ln_blk = T) +!----------------------------------------------------------------------- +! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! +! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! + sn_wndi = 'ERA5_U10' , 1 , 'U10', .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bicubic.nc' , 'Uwnd' , 'ERA5_LSM' + sn_wndj = 'ERA5_V10' , 1 , 'V10', .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bicubic.nc' , 'Vwnd' , 'ERA5_LSM' + sn_qsr = 'ERA5_MSDWSWRF' , 1 , 'MSDWSWRF', .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bilin.nc' , '' , 'ERA5_LSM' + sn_qlw = 'ERA5_MSDWLWRF' , 1 , 'MSDWLWRF', .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bilin.nc' , '' , 'ERA5_LSM' + sn_tair = 'ERA5_T2M' , 1 , 'T2M', .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bilin.nc' , '' , 'ERA5_LSM' + sn_humi = 'ERA5_SPH' , 1 , 'SPH', .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bilin.nc' , '' , 'ERA5_LSM' + sn_prec = 'ERA5_MTPR' , 1 , 'MTPR', .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bilin.nc' , '' , 'ERA5_LSM' + sn_snow = 'ERA5_MSR' , 1 , 'MSR' , .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bilin.nc' , '' , 'ERA5_LSM' + sn_slp = 'ERA5_MSL' , 1 , 'MSL', .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bilin.nc' , '' , '' ! DUMMY variable. Fill with T +! sn_slp = 'slp.15JUNE2009_fill' , 6 , 'SLP' , .true. , .true. , 'yearly' , 'weights_core_orca2_bilinear_noc.nc' , '' , '' +! sn_tdif = 'taudif_core' , 24 , 'taudif' , .true. , .true. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' + ! ! bulk algorithm : + ln_NCAR = .false. ! "NCAR" algorithm (Large and Yeager 2008) + ln_COARE_3p0= .false. ! "COARE 3.0" algorithm (Fairall et al. 2003) + ln_COARE_3p5= .false. ! "COARE 3.5" algorithm (Edson et al. 2013) + ln_ECMWF = .true. ! "ECMWF" algorithm (IFS cycle 31) + ! + cn_dir = '/work/n01/n01/jelt/SEVERN-SWOT/BUILD_CFG/SURFACE_FORCING/' ! root directory for the location of the bulk files + ln_taudif = .false. ! HF tau contribution: use "mean of stress module - module of the mean stress" data + rn_zqt = 2. ! Air temperature and humidity reference height (m) + rn_zu = 10. ! Wind vector reference height (m) + rn_pfac = 1. ! multiplicative factor for precipitation (total & snow) + rn_efac = 1. ! multiplicative factor for evaporation (0. or 1.) + rn_vfac = 0. ! multiplicative factor for ocean/ice velocity + ! in the calculation of the wind stress (0.=absolute winds or 1.=relative winds) + ln_Cd_L12 = .false. ! Modify the drag ice-atm and oce-atm depending on ice concentration + ! This parameterization is from Lupkes et al. (JGR 2012) +/ +!!====================================================================== +!! *** Lateral boundary condition *** !! +!! !! +!! namlbc lateral momentum boundary condition (default: NO selection) +!! namagrif agrif nested grid (read by child model only) ("key_agrif") +!! nam_tide Tidal forcing (default: OFF) +!! nambdy Unstructured open boundaries (default: OFF) +!! nambdy_dta Unstructured open boundaries - external data (see nambdy) +!! nambdy_tide tidal forcing at open boundaries (default: OFF) +!!====================================================================== +! +!----------------------------------------------------------------------- +&namlbc ! lateral momentum boundary condition (default: NO selection) +!----------------------------------------------------------------------- + ! ! free slip ! partial slip ! no slip ! strong slip + rn_shlat = 0 ! shlat = 0 ! 0 < shlat < 2 ! shlat = 2 ! 2 < shlat + ln_vorlat = .false. ! consistency of vorticity boundary condition with analytical Eqs. +/ +!----------------------------------------------------------------------- +&nam_tide ! tide parameters (default: OFF) +!----------------------------------------------------------------------- + ln_tide = .true. ! Activate tides + ln_tide_pot = .false. ! use tidal potential forcing + ln_scal_load = .false. ! Use scalar approximation for + rn_scal_load = 0.094 ! load potential + ln_read_load = .false. ! Or read load potential from file + cn_tide_load = 'tide_LOAD_grid_T.nc' ! filename for load potential + ! + ln_tide_ramp = .false. ! Use linear ramp for tides at startup + rdttideramp = 0. ! ramp duration in days + dn_love_number = 0.69 ! + clname(1)='M2' + clname(2)='S2' +! clname(3)='K1' +! clname(1) ='2N2' +! clname(2)='EPS2' +! clname(3)='J1' +! clname(4)='K1' +! clname(5)='K2' +! clname(6)='L2' +! clname(7)='LA2' +! clname(8)='M2' +! clname(9)='M3' +! clname(10)='M4' +! clname(11)='M6' +! clname(12)='M8' +! clname(13)='MF' +! clname(14)='MKS2' +! clname(15)='MM' +! clname(16)='MN4' +! clname(17)='MS4' +! clname(18)='MSF' +! clname(19)='MSQM' +! clname(20)='MTM' +! clname(21)='MU2' +! clname(22)='N2' +! clname(23)='N4' +! clname(24)='NU2' +! clname(25)='O1' +! clname(26)='P1' +! clname(27)='Q1' +! clname(28)='R2' +! clname(29)='S1' +! clname(30)='S2' +! clname(31)='S4' +! clname(32)='SA' +! clname(33)='SSA' +! clname(34)='T2' +/ +!----------------------------------------------------------------------- +&nambdy ! unstructured open boundaries (default: OFF) +!----------------------------------------------------------------------- + ln_bdy = .true. ! Use unstructured open boundaries + nb_bdy = 1 ! number of open boundary sets + ! + ln_coords_file = .true. ! =T : read bdy coordinates from file + cn_coords_file = 'coordinates.bdy.nc' ! bdy coordinates files + ln_mask_file = .false. ! =T : read mask from file + cn_mask_file = '' ! name of mask file (if ln_mask_file=.TRUE.) + cn_dyn2d = 'flather' ! + nn_dyn2d_dta = 2 ! = 0, bdy data are equal to the initial state + ! = 1, bdy data are read in 'bdydata .nc' files + ! = 2, use tidal harmonic forcing data from files + ! = 3, use external data AND tidal harmonic forcing + cn_dyn3d = 'specified' ! 'zerograd','none' ! + nn_dyn3d_dta = 0 ! = 0, bdy data are equal to the initial state + ! = 1, bdy data are read in 'bdydata .nc' files + cn_tra = 'frs' + nn_tra_dta = 0 ! = 0, bdy data are equal to the initial state + ! = 1, bdy data are read in 'bdydata .nc' files + + ln_tra_dmp =.false. ! open boudaries conditions for tracers + ln_dyn3d_dmp =.false. ! open boundary condition for baroclinic velocities + rn_time_dmp = 8. ! Damping time scale in days + rn_time_dmp_out = 64. ! Outflow damping time scale + nn_rimwidth = 9 ! width of the relaxation zone + ln_vol = .false. ! total volume correction (see nn_volctl parameter) + nn_volctl = 1 ! = 0, the total water flux across open boundaries is zero +/ +!!----------------------------------------------------------------------- +!&nambdy_index ! open boundaries - definition ("key_bdy") +!!----------------------------------------------------------------------- +! ctypebdy = 'S' +! nbdyind = -1 +!/ +!!----------------------------------------------------------------------- +!&nambdy_index ! open boundaries - definition ("key_bdy") +!!----------------------------------------------------------------------- +! ctypebdy = 'W' +! nbdyind = -1 +!/ +!----------------------------------------------------------------------- +!&nambdy_ssh +!----------------------------------------------------------------------- + ln_ssh_bdy = .false. + rn_ssh_shift = 0. +!/ +!----------------------------------------------------------------------- +&nambdy_dta ! open boundaries - external data +!----------------------------------------------------------------------- + ln_zinterp = .true. ! T if a vertical interpolation is required. Variables gdep[tuv] and e3[tuv] must exist in the file + ! ! automatically defined to T if the number of vertical levels in bdy dta /= jpk + ln_full_vel = .true. ! T if [uv]3d are "full" velocities and not only its baroclinic components + ! + cn_dir = './OBC/' + !___________!_________________________!___________________!___________!_____________!________!___________!__________________!__________!_______________! + ! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! + ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! ! pairing ! filename ! + bn_ssh = 'SEAsia_R36_bt_bdyT' , 24 , 'sossheig' , .true. , .false. , 'monthly' , '' , '' , ' ' + bn_u2d = 'SEAsia_R36_bdyU' , 24 , 'vobtcrtx', .true. , .false. , 'monthly' , '' , '' , '' + bn_v2d = 'SEAsia_R36_bdyV' , 24 , 'vobtcrty', .true. , .false. , 'monthly' , '' , '' , '' + bn_u3d = 'SEAsia_R36_bdyU' , 24 , 'vozocrtx', .true. , .false. , 'monthly' , '' , '' , '' + bn_v3d = 'SEAsia_R36_bdyV' , 24 , 'vomecrty', .true. , .false. , 'monthly' , '' , '' , '' + bn_tem = 'SEAsia_R36_bdyT' , 24 , 'votemper', .true. , .false. , 'monthly' , '' , '' , '' + bn_sal = 'SEAsia_R36_bdyT' , 24 , 'vosaline', .true. , .false. , 'monthly' , '' , '' , '' +/ +!----------------------------------------------------------------------- +&nambdy_tide ! tidal forcing at open boundaries +!----------------------------------------------------------------------- + filtide = 'TIDES/SEVERN_FES14_bdytide_' ! file name root of tidal forcing files +/ +!!====================================================================== +!! *** Top/Bottom boundary condition *** !! +!! !! +!! namdrg top/bottom drag coefficient (default: NO selection) +!! namdrg_top top friction (ln_OFF =F & ln_isfcav=T) +!! namdrg_bot bottom friction (ln_OFF =F) +!! nambbc bottom temperature boundary condition (default: OFF) +!! nambbl bottom boundary layer scheme (default: OFF) +!!====================================================================== +! +!----------------------------------------------------------------------- +&namdrg ! top/bottom drag coefficient (default: NO selection) +!----------------------------------------------------------------------- + ln_drg_OFF = .false. ! free-slip : Cd = 0 (F => fill namdrg_bot + ln_lin = .false. ! linear drag: Cd = Cd0 Uc0 & namdrg_top) + ln_non_lin = .true. ! non-linear drag: Cd = Cd0 |U| + ln_loglayer = .false. ! logarithmic drag: Cd = vkarmn/log(z/z0) |U| + ! + ln_drgimp = .true. ! implicit top/bottom friction flag + ln_drgice_imp = .false. ! implicit ice-ocean drag +/ +!----------------------------------------------------------------------- +&namdrg_top ! TOP friction (ln_drg_OFF =F & ln_isfcav=T) +!----------------------------------------------------------------------- + rn_Cd0 = 1.e-3 ! drag coefficient [-] + rn_Uc0 = 0.4 ! ref. velocity [m/s] (linear drag=Cd0*Uc0) + rn_Cdmax = 0.1 ! drag value maximum [-] (logarithmic drag) + rn_ke0 = 2.5e-3 ! background kinetic energy [m2/s2] (non-linear cases) + rn_z0 = 3.0e-3 ! roughness [m] (ln_loglayer=T) + ln_boost = .false. ! =T regional boost of Cd0 ; =F constant + rn_boost = 50. ! local boost factor [-] +/ +!----------------------------------------------------------------------- +&namdrg_bot ! BOTTOM friction (ln_drg_OFF =F) +!----------------------------------------------------------------------- + rn_Cd0 = 2.5e-3 !1.e-3 ! drag coefficient [-] + rn_Uc0 = 0.4 ! ref. velocity [m/s] (linear drag=Cd0*Uc0) + rn_Cdmax = 1.e-1 ! drag value maximum [-] (logarithmic drag) + rn_ke0 = 0.0e-3 !2.5e-3 ! background kinetic energy [m2/s2] (non-linear cases) + rn_z0 = 3.e-3 ! roughness [m] (ln_loglayer=T) + ln_boost = .false. ! =T regional boost of Cd0 ; =F constant + rn_boost = 50. ! local boost factor [-] +/ +!!====================================================================== +!! Tracer (T & S) namelists !! +!! !! +!! nameos equation of state (default: NO selection) +!! namtra_adv advection scheme (default: NO selection) +!! namtra_ldf lateral diffusion scheme (default: NO selection) +!! namtra_mle mixed layer eddy param. (Fox-Kemper param.) (default: OFF) +!! namtra_eiv eddy induced velocity param. (default: OFF) +!! namtra_dmp T & S newtonian damping (default: OFF) +!!====================================================================== +! +!----------------------------------------------------------------------- +&nameos ! ocean Equation Of Seawater (default: NO selection) +!----------------------------------------------------------------------- + ln_teos10 = .true. ! = Use TEOS-10 equation of state + ln_eos80 = .false. + ! rn_lambda2=5.4914e-4 +/ +!----------------------------------------------------------------------- +&namtra_adv ! advection scheme for tracer (default: NO selection) +!----------------------------------------------------------------------- + ln_traadv_OFF = .false. + ln_traadv_fct = .true. !.true.! FCT scheme + nn_fct_h = 2 ! =2/4, horizontal 2nd / 4th order + nn_fct_v = 2 ! =2/4, vertical 2nd / COMPACT 4th order +/ +!----------------------------------------------------------------------- +&namtra_ldf ! lateral diffusion scheme for tracers (default: NO selection) +!----------------------------------------------------------------------- + ln_traldf_lap = .true. ! T laplacian operator + ln_traldf_hor = .true. ! T horizontal (geopotential) + ln_traldf_OFF = .false. ! + + ! ! Coefficients: + nn_aht_ijk_t = 0 ! = 0 constant = 1/2 Ud*Ld (lap case) + rn_Ud = 0.01 ! lateral diffusive velocity [m/s] (nn_aht_ijk_t= 0, 10, 20, 30) + rn_Ld = 5.e+3 ! lateral diffusive length [m] (nn_aht_ijk_t= 0, 10) +/ +!!====================================================================== +!! *** Dynamics namelists *** !! +!! !! +!! nam_vvl vertical coordinate options (default: z-star) +!! namdyn_adv formulation of the momentum advection (default: NO selection) +!! namdyn_vor advection scheme (default: NO selection) +!! namdyn_hpg hydrostatic pressure gradient (default: NO selection) +!! namdyn_spg surface pressure gradient (default: NO selection) +!! namdyn_ldf lateral diffusion scheme (default: NO selection) +!! namdta_dyn offline TOP: dynamics read in files (OFF_SRC only) +!!====================================================================== +! +!----------------------------------------------------------------------- +&nam_vvl ! vertical coordinate options (default: z-star) +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namdyn_adv ! formulation of the momentum advection (default: NO selection) +!----------------------------------------------------------------------- + ln_dynadv_OFF = .false. + ln_dynadv_vec = .true. !.true. ! vector form - 2nd centered scheme + nn_dynkeg = 0 ! grad(KE) scheme: =0 C2 ; =1 Hollingsworth correction +/ +!----------------------------------------------------------------------- +&namdyn_vor ! Vorticity / Coriolis scheme (default: NO selection) +!----------------------------------------------------------------------- + ln_dynvor_een = .true. ! energy & enstrophy scheme + nn_een_e3f = 1 ! e3f = masked averaging of e3t divided by 4 (=0) or by the sum of mask (=1) +/ +!----------------------------------------------------------------------- +&namdyn_hpg ! Hydrostatic pressure gradient option (default: NO selection) +!----------------------------------------------------------------------- + ln_hpg_prj = .true. ! s-coordinate (Pressure Jacobian scheme) + ln_hpg_sco = .false. ! +/ +!----------------------------------------------------------------------- +&namdyn_spg ! surface pressure gradient (default: NO selection) +!----------------------------------------------------------------------- + ln_dynspg_exp = .false. ! explicit free surface + ln_dynspg_ts = .true. ! split-explicit free surface + ln_bt_auto = .true. ! Number of sub-step defined from: + nn_baro = 30 ! =F : the number of sub-step in rn_rdt seconds + rn_bt_cmax = 0.5 ! =T : the Maximum Courant Number allowed + ln_bt_fw = .true. ! Forward integration of barotropic Eqs. + ln_bt_av = .true. ! Time filtering of barotropic variables + nn_bt_flt = 1 ! Time filter choice = 0 None + ! ! = 1 Boxcar over nn_baro sub-steps + ! ! = 2 Boxcar over 2*nn_baro " " +/ +!----------------------------------------------------------------------- +&namdyn_ldf ! lateral diffusion on momentum (default: NO selection) +!----------------------------------------------------------------------- + ln_dynldf_OFF = .false. + ln_dynldf_blp = .true. !.true. ! bilaplacian operator + ln_dynldf_lap = .false. + ln_dynldf_lev = .true. ! .true. ! iso-level + ln_dynldf_iso = .false. + ln_dynldf_hor = .false. + + nn_ahm_ijk_t = 0 ! =0 constant = 1/12 Uv*Lv^3 (blp case) + rn_Uv = 0.01 !0.02 ! lateral viscous velocity [m/s] + rn_Lv = 200 ! lateral viscous length [m] + rn_csmc = 3.5 !2 !3.5 ! Smagorinsky constant of proportionality + rn_minfac = 1.0 ! multiplier of theorectical lower limit + rn_maxfac = 1.0 ! multiplier of theorectical upper limit +/ +!!====================================================================== +!! vertical physics namelists !! +!! !! +!! namzdf vertical physics manager (default: NO selection) +!! namzdf_ric richardson number vertical mixing (ln_zdfric=T) +!! namzdf_tke TKE vertical mixing (ln_zdftke=T) +!! namzdf_gls GLS vertical mixing (ln_zdfgls=T) +!! namzdf_osm OSM vertical diffusion (ln_zdfosm=T) +!! namzdf_iwm tidal mixing parameterization (ln_zdfiwm=T) +!!====================================================================== +! +!----------------------------------------------------------------------- +&namzdf ! vertical physics (default: NO selection) +!----------------------------------------------------------------------- + ln_zdfcst = .false. ! + ln_zdfgls = .true. ! Generic Length Scale closure (T => fill namzdf_gls) ! coefficients + ln_zdfevd = .false. ! enhanced vertical diffusion + nn_evdm = 1 ! apply on tracer (=0) or on tracer and momentum (=1) + rn_evd = 100. ! mixing coefficient [m2/s] + ln_zdfnpc = .false. ! Non-Penetrative Convective algorithm + nn_npc = 1 ! frequency of application of npc + nn_npcp = 365 ! npc control print frequency + rn_avm0 = 1.2e-6 ! vertical eddy viscosity [m2/s] (background Kz if ln_zdfcst=F) + rn_avt0 = 1.2e-6 ! vertical eddy diffusivity [m2/s] (background Kz if ln_zdfcst=F) + nn_avb = 0 ! profile for background avt & avm (=1) or not (=0) + nn_havtb = 0 ! horizontal shape for avtb (=1) or not (=0) +/ +!----------------------------------------------------------------------- +&namzdf_gls ! GLS vertical diffusion (ln_zdfgls =T) +!----------------------------------------------------------------------- + rn_emin = 1.e-6 ! minimum value of e [m2/s2] + rn_epsmin = 1.e-12 ! minimum value of eps [m2/s3] + ln_length_lim = .true. ! limit on the dissipation rate under stable stratification (Galperin et al., 1988) + rn_clim_galp = 0.267 ! galperin limit + ln_sigpsi = .true. ! Activate or not Burchard 2001 mods on psi schmidt number in the wb case + rn_crban = 100. ! Craig and Banner 1994 constant for wb tke flux + rn_charn = 70000. ! Charnock constant for wb induced roughness length + rn_hsro = 0.02 ! Minimum surface roughness + rn_frac_hs = 1.3 ! Fraction of wave height as roughness (if nn_z0_met=2) + nn_z0_met = 2 ! Method for surface roughness computation (0/1/2) + nn_bc_surf = 1 ! surface condition (0/1=Dir/Neum) + nn_bc_bot = 1 ! bottom condition (0/1=Dir/Neum) + nn_stab_func = 2 ! stability function (0=Galp, 1= KC94, 2=CanutoA, 3=CanutoB) + nn_clos = 1 ! predefined closure type (0=MY82, 1=k-eps, 2=k-w, 3=Gen) +/ +!!====================================================================== +!! *** Diagnostics namelists *** !! +!! !! +!! namtrd dynamics and/or tracer trends (default: OFF) +!! namptr Poleward Transport Diagnostics (default: OFF) +!! namhsb Heat and salt budgets (default: OFF) +!! namdiu Cool skin and warm layer models (default: OFF) +!! namdiu Cool skin and warm layer models (default: OFF) +!! namflo float parameters ("key_float") +!! nam_diaharm Harmonic analysis of tidal constituents ("key_diaharm") +!! nam_diaharm_fast Harmonic analysis of tidal constituents (fast) ("key_diaharm_fast") +!! namdct transports through some sections ("key_diadct") +!! nam_diatmb Top Middle Bottom Output (default: OFF) +!! nam_dia25h 25h Mean Output (default: OFF) +!! namnc4 netcdf4 chunking and compression settings ("key_netcdf4") +!!====================================================================== +!----------------------------------------------------------------------- +&nam_diatmb ! Top Middle Bottom Output (default F) +!----------------------------------------------------------------------- + ln_diatmb = .false. ! Choose Top Middle and Bottom output or not +/ +!----------------------------------------------------------------------- +&nam_dia25h ! 25h Mean Output (default F) +!----------------------------------------------------------------------- + ln_dia25h = .false. ! Choose 25h mean output or not +/ +!!====================================================================== +!! *** Observation & Assimilation *** !! +!! !! +!! namobs observation and model comparison (default: OFF) +!! nam_asminc assimilation increments ('key_asminc') +!!====================================================================== +! +!!====================================================================== +!! *** Miscellaneous namelists *** !! +!! !! +!! nammpp Massively Parallel Processing ("key_mpp_mpi") +!! namctl Control prints (default: OFF) +!! namsto Stochastic parametrization of EOS (default: OFF) +!!====================================================================== +! +!----------------------------------------------------------------------- +&nammpp ! Massively Parallel Processing ("key_mpp_mpi") +!----------------------------------------------------------------------- + ln_listonly = .false. ! do nothing else than listing the best domain decompositions (with land domains suppression) + ! ! if T: the largest number of cores tested is defined by max(mppsize, jpni*jpnj) + ln_nnogather = .true. ! activate code to avoid mpi_allgather use at the northfold + jpni = 2 ! jpni number of processors following i (set automatically if < 1) + jpnj = 1 ! jpnj number of processors following j (set automatically if < 1) +/ +!----------------------------------------------------------------------- +&namctl ! Control prints (default: OFF) +!----------------------------------------------------------------------- + ln_ctl = .FALSE. ! Toggle all report printing on/off (T/F); Ignored if sn_cfctl%l_config is T + sn_cfctl%l_config = .TRUE. ! IF .true. then control which reports are written with the following + sn_cfctl%l_runstat = .TRUE. ! switches and which areas produce reports with the proc integer settings. + sn_cfctl%l_trcstat = .FALSE. ! The default settings for the proc integers should ensure + sn_cfctl%l_oceout = .FALSE. ! that all areas report. + sn_cfctl%l_layout = .FALSE. ! + sn_cfctl%l_mppout = .FALSE. ! + sn_cfctl%l_mpptop = .FALSE. ! + sn_cfctl%procmin = 0 ! Minimum area number for reporting [default:0] + sn_cfctl%procmax = 1000000 ! Maximum area number for reporting [default:1000000] + sn_cfctl%procincr = 1 ! Increment for optional subsetting of areas [default:1] + sn_cfctl%ptimincr = 24 ! Timestep increment for writing time step progress info + nn_print = 0 ! level of print (0 no extra print) + nn_ictls = 0 ! start i indice of control sum (use to compare mono versus + nn_ictle = 0 ! end i indice of control sum multi processor runs + nn_jctls = 0 ! start j indice of control over a subdomain) + nn_jctle = 0 ! end j indice of control + nn_isplt = 1 ! number of processors in i-direction + nn_jsplt = 1 ! number of processors in j-direction + ln_timing = .true. ! timing by routine write out in timing.output file + ln_diacfl = .true. ! CFL diagnostics write out in cfl_diagnostics.ascii +/ diff --git a/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/submit.slurm b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/submit.slurm new file mode 100644 index 0000000..10d84a0 --- /dev/null +++ b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/submit.slurm @@ -0,0 +1,33 @@ +#!/bin/bash +#SBATCH --job-name=nemo_test +#SBATCH --time=00:10:00 +#SBATCH --nodes=1 +#SBATCH --ntasks=3 +#SBATCH --account=n01-ACCORD +#SBATCH --partition=standard +#SBATCH --qos=standard +##BATCH --reservation=shortqos +##BATCH --qos=short +# Created by: mkslurm -S 1 -s 16 -m 1 -C 2 -c 2 -t 00:10:00 -a n01-ACCORD -j nemo_test + +# Setup the job environment (this module needs to be loaded before any other modules) +module -s restore /work/n01/shared/acc/n01_modules/ucx_env +#module load cpe/21.03 +#module load cray-hdf5-parallel +#module load cray-netcdf-hdf5parallel +#export LD_LIBRARY_PATH=$CRAY_LD_LIBRARY_PATH:$LD_LIBRARY_PATH + +export OMP_NUM_THREADS=1 +# +cat > myscript_wrapper2.sh << EOFB +#!/bin/ksh +# +set -A map /work/n01/n01/jelt/SEVERN-SWOT/BUILD_EXE/XIOS/xios-2.5/bin/xios_server.exe /work/n01/n01/jelt/SEVERN-SWOT/BUILD_EXE/NEMO/4.0.6/cfgs/NEMOconstTS/BLD/bin/nemo.exe +exec_map=( 0 1 1 ) +# +exec \${map[\${exec_map[\$SLURM_PROCID]}]} +## +EOFB +chmod u+x ./myscript_wrapper2.sh +# +srun --mem-bind=local --cpu-bind=v,map_cpu:00,0x10,0x12, ./myscript_wrapper2.sh diff --git a/SCRIPTS/make_paths.sh b/SCRIPTS/make_paths.sh index 5d16020..0a19b0b 100644 --- a/SCRIPTS/make_paths.sh +++ b/SCRIPTS/make_paths.sh @@ -38,4 +38,4 @@ export DOMAIN=$WDIR/BUILD_CFG/DOMAIN # base directory for building domain config export DOWNLOADS=$WDIR/DOWNLOADS -export SBC = $WDIR/BUILD_CFG/SURFACE_FORCING +export SBC=$WDIR/BUILD_CFG/SURFACE_FORCING diff --git a/SCRIPTS/run_barotropicTide_ERA5.sh b/SCRIPTS/run_barotropicTide_ERA5.sh new file mode 100644 index 0000000..a520861 --- /dev/null +++ b/SCRIPTS/run_barotropicTide_ERA5.sh @@ -0,0 +1,53 @@ + +#!/bin/bash + +#:' +# +#****************************** +#run_EXP_barotropicTide_ERA5.sh +#****************************** +#' + +# Run the experiment with contant T,S initial condition with tides-only. +# and ERA5 SLP + 10m winds +#:: + +export CONFIG=NEMOconstTS +export EXP=$WDIR/RUN_DIRECTORIES/EXP_barotropicTide_ERA5 + +# Choose an appropriate directory for your EXP installation +if [ ! -d "$EXP/RESTART" ]; then + #mkdir $EXP + mkdir $EXP/RESTART +fi + +rsync -av --ignore-existing $NEMO/cfgs/SHARED/*namelist* $EXP/. # only get the files not already in the repo. +rsync -av --ignore-existing $NEMO/cfgs/SHARED/*.xml $EXP/. + +# Copy in NEMO/XIOS executables +ln -s $NEMO/cfgs/$CONFIG/BLD/bin/nemo.exe $EXP/nemo.exe +ln -s $XIOS_DIR/bin/xios_server.exe $EXP/xios_server.exe + +# Link in domain_cfg file +ln -s $DOMAIN/domain_cfg_$REPO.nc $EXP/domain_cfg.nc + +# Link in tidal bondary forcing +#ln -s /work/n01/n01/annkat/SEAsia_HadGEM_R12/TIDES $EXP/. +ln -s $WDIR/INPUTS/TIDES $EXP/. + +# Link in boundary files (just coordinates.bdy.nc) +ln -s $WDIR/INPUTS/OBC/coordinates.bdy.nc $EXP/. + +# namelist_cfg +# nambdy: Except for tides, freeze the boundary conditions. Set to initial state +# ln_usr = true. User defined initial state and surface forcing. Here we use +# homogenous initial conditions and no met forcing. +# with the expression being compiled into the executable. (In +# ``usrdef_sbc.F90`` and ``usrdef_istate.F90``). + +# Submit job +cd $EXP +sbatch submit.slurm + +## Check on queue +# squeue -u $USER From 9118e4f978e33389f982172553a6303726a0b1c9 Mon Sep 17 00:00:00 2001 From: not populated Date: Thu, 2 Sep 2021 21:52:54 +0100 Subject: [PATCH 03/12] mods to inspect hydrolic jump issue --- .../EXP_barotropicTide_ERA5/file_def_nemo-oce.xml | 13 ++++++++----- .../EXP_barotropicTide_ERA5/namelist_cfg | 4 ++-- 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/file_def_nemo-oce.xml b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/file_def_nemo-oce.xml index 1cbd7fa..4352eb7 100755 --- a/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/file_def_nemo-oce.xml +++ b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/file_def_nemo-oce.xml @@ -10,9 +10,10 @@ - - + + @@ -21,7 +22,7 @@ ---> + - + @@ -43,7 +44,8 @@ - + diff --git a/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/namelist_cfg b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/namelist_cfg index 7fdab9a..a29cb78 100755 --- a/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/namelist_cfg +++ b/RUN_DIRECTORIES/EXP_barotropicTide_ERA5/namelist_cfg @@ -36,7 +36,7 @@ nn_no = 0 ! Assimilation cycle index cn_exp = "SEVERN_Tid_met" nn_it000 = 1 ! 8641 ! 1 ! first time step - nn_itend = 600 ! ! 4320 per 24hr ! last time step + nn_itend = 295 !600 ! ! 4320 per 24hr ! last time step nn_date0 = 20130101 ! date at nit_0000 (format yyyymmdd) used if ln_rstart=F or (ln_rstart=T and nn_rstctl=0 or 1) nn_time0 = 0 ! initial time of day in hhmm nn_leapy = 1 ! Leap year calendar (1) or not (0) @@ -214,7 +214,7 @@ sn_humi = 'ERA5_SPH' , 1 , 'SPH', .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bilin.nc' , '' , 'ERA5_LSM' sn_prec = 'ERA5_MTPR' , 1 , 'MTPR', .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bilin.nc' , '' , 'ERA5_LSM' sn_snow = 'ERA5_MSR' , 1 , 'MSR' , .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bilin.nc' , '' , 'ERA5_LSM' - sn_slp = 'ERA5_MSL' , 1 , 'MSL', .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bilin.nc' , '' , '' ! DUMMY variable. Fill with T + sn_slp = 'ERA5_MSL' , 1 , 'MSL', .true. , .false. , 'yearly' , 'weights_era5_SEVERN_bilin.nc' , '' , 'ERA5_LSM' ! DUMMY variable. Fill with T ! sn_slp = 'slp.15JUNE2009_fill' , 6 , 'SLP' , .true. , .true. , 'yearly' , 'weights_core_orca2_bilinear_noc.nc' , '' , '' ! sn_tdif = 'taudif_core' , 24 , 'taudif' , .true. , .true. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' ! ! bulk algorithm : From 91a4e8ebe106c119cd4cff80f64eb63d8432ca63 Mon Sep 17 00:00:00 2001 From: jpolton Date: Fri, 3 Sep 2021 18:03:01 +0100 Subject: [PATCH 04/12] typo: rename to create_LSM.py --- BUILD_CFG/SURFACE_FORCING/{create_LCM.py => create_LSM.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename BUILD_CFG/SURFACE_FORCING/{create_LCM.py => create_LSM.py} (100%) diff --git a/BUILD_CFG/SURFACE_FORCING/create_LCM.py b/BUILD_CFG/SURFACE_FORCING/create_LSM.py similarity index 100% rename from BUILD_CFG/SURFACE_FORCING/create_LCM.py rename to BUILD_CFG/SURFACE_FORCING/create_LSM.py From 7557fbee6dfdfcd7340d20b2d41c2be19d2e69ee Mon Sep 17 00:00:00 2001 From: jpolton Date: Fri, 3 Sep 2021 18:28:54 +0100 Subject: [PATCH 05/12] add mask fix at coastal point (land --> sea) --- BUILD_CFG/SURFACE_FORCING/create_LSM.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/BUILD_CFG/SURFACE_FORCING/create_LSM.py b/BUILD_CFG/SURFACE_FORCING/create_LSM.py index 66dd3d8..f41d37e 100644 --- a/BUILD_CFG/SURFACE_FORCING/create_LSM.py +++ b/BUILD_CFG/SURFACE_FORCING/create_LSM.py @@ -30,6 +30,10 @@ nlat = msk_src.shape[0] nlon = msk_src.shape[1] + +# FIX AN COASTAL POINT TO MAKE IT OCEAN. +msk_src[20,19] = -1 + ## NETCDF OUTPUT ncout = Dataset( outfile, 'w', format='NETCDF3_CLASSIC' ) ncout.createDimension( 'nlat', nlat ) From 7b72c3c589eb316fe4cd35d388efbe8682b5bfba Mon Sep 17 00:00:00 2001 From: jpolton Date: Fri, 3 Sep 2021 19:25:31 +0100 Subject: [PATCH 06/12] change LSM edit to a comment --- BUILD_CFG/SURFACE_FORCING/create_LSM.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/BUILD_CFG/SURFACE_FORCING/create_LSM.py b/BUILD_CFG/SURFACE_FORCING/create_LSM.py index f41d37e..02b2bff 100644 --- a/BUILD_CFG/SURFACE_FORCING/create_LSM.py +++ b/BUILD_CFG/SURFACE_FORCING/create_LSM.py @@ -30,9 +30,9 @@ nlat = msk_src.shape[0] nlon = msk_src.shape[1] - -# FIX AN COASTAL POINT TO MAKE IT OCEAN. -msk_src[20,19] = -1 +## Edit the LSM as required +# E.g. FIX AN COASTAL POINT TO MAKE IT OCEAN. +# msk_src[20,19] = -1 ## NETCDF OUTPUT ncout = Dataset( outfile, 'w', format='NETCDF3_CLASSIC' ) From cd6943de3efd73a9d3592982d55f337103d28f1c Mon Sep 17 00:00:00 2001 From: jpolton Date: Wed, 8 Sep 2021 13:27:42 +0100 Subject: [PATCH 07/12] Delete RUN_DIRECTORIES/EXP_fullforcing directory --- .../EXP_fullforcing/1_namelist_cfg | 247 --- .../EXP_fullforcing/1_namelist_ice_cfg | 49 - .../EXP_fullforcing/1_namelist_ice_ref | 1 - .../EXP_fullforcing/1_namelist_ref | 1 - .../EXP_fullforcing/context_nemo.xml | 122 -- .../EXP_fullforcing/domain_def_nemo.xml | 1 - .../EXP_fullforcing/field_def_nemo-lim.xml | 1 - .../EXP_fullforcing/field_def_nemo-opa.xml | 1 - .../EXP_fullforcing/field_def_nemo-pisces.xml | 1 - .../EXP_fullforcing/file_def_nemo.xml | 132 -- RUN_DIRECTORIES/EXP_fullforcing/iodef.xml | 26 - RUN_DIRECTORIES/EXP_fullforcing/namelist_cfg | 1319 ----------------- .../EXP_fullforcing/namelist_ice_cfg | 48 - .../EXP_fullforcing/namelist_ice_ref | 1 - .../EXP_fullforcing/namelist_pisces_cfg | 63 - .../EXP_fullforcing/namelist_pisces_ref | 1 - RUN_DIRECTORIES/EXP_fullforcing/namelist_ref | 1 - .../EXP_fullforcing/namelist_top_cfg | 109 -- .../EXP_fullforcing/namelist_top_ref | 1 - RUN_DIRECTORIES/EXP_fullforcing/runscript | 30 - .../EXP_fullforcing/runscript_short | 33 - 21 files changed, 2188 deletions(-) delete mode 100755 RUN_DIRECTORIES/EXP_fullforcing/1_namelist_cfg delete mode 100755 RUN_DIRECTORIES/EXP_fullforcing/1_namelist_ice_cfg delete mode 120000 RUN_DIRECTORIES/EXP_fullforcing/1_namelist_ice_ref delete mode 120000 RUN_DIRECTORIES/EXP_fullforcing/1_namelist_ref delete mode 100755 RUN_DIRECTORIES/EXP_fullforcing/context_nemo.xml delete mode 120000 RUN_DIRECTORIES/EXP_fullforcing/domain_def_nemo.xml delete mode 120000 RUN_DIRECTORIES/EXP_fullforcing/field_def_nemo-lim.xml delete mode 120000 RUN_DIRECTORIES/EXP_fullforcing/field_def_nemo-opa.xml delete mode 120000 RUN_DIRECTORIES/EXP_fullforcing/field_def_nemo-pisces.xml delete mode 100755 RUN_DIRECTORIES/EXP_fullforcing/file_def_nemo.xml delete mode 100755 RUN_DIRECTORIES/EXP_fullforcing/iodef.xml delete mode 100755 RUN_DIRECTORIES/EXP_fullforcing/namelist_cfg delete mode 100755 RUN_DIRECTORIES/EXP_fullforcing/namelist_ice_cfg delete mode 120000 RUN_DIRECTORIES/EXP_fullforcing/namelist_ice_ref delete mode 100755 RUN_DIRECTORIES/EXP_fullforcing/namelist_pisces_cfg delete mode 120000 RUN_DIRECTORIES/EXP_fullforcing/namelist_pisces_ref delete mode 120000 RUN_DIRECTORIES/EXP_fullforcing/namelist_ref delete mode 100755 RUN_DIRECTORIES/EXP_fullforcing/namelist_top_cfg delete mode 120000 RUN_DIRECTORIES/EXP_fullforcing/namelist_top_ref delete mode 100755 RUN_DIRECTORIES/EXP_fullforcing/runscript delete mode 100755 RUN_DIRECTORIES/EXP_fullforcing/runscript_short diff --git a/RUN_DIRECTORIES/EXP_fullforcing/1_namelist_cfg b/RUN_DIRECTORIES/EXP_fullforcing/1_namelist_cfg deleted file mode 100755 index b49add1..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/1_namelist_cfg +++ /dev/null @@ -1,247 +0,0 @@ -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! NEMO/OPA : Configuration namelist used to overwrite SHARED/1_namelist_ref -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!----------------------------------------------------------------------- -&namrun ! parameters of the run -!----------------------------------------------------------------------- - cn_exp = "Agulhas" ! experience name - nn_it000 = 1 ! first time step - nn_itend = 10950 ! last time step - nn_stock = 10950 ! frequency of creation of a restart file (modulo referenced to 1) - nn_write = 10950 ! frequency of write in the output file (modulo referenced to nn_it000) - ln_clobber = .true. ! clobber (overwrite) an existing file -/ -!----------------------------------------------------------------------- -&namcfg ! parameters of the configuration -!----------------------------------------------------------------------- - ln_read_cfg = .true. ! (=T) read the domain configuration file - ! ! (=F) user defined configuration ==>>> see usrdef(_...) modules - cn_domcfg = "AGRIF_AGULHAS_domain_cfg" ! domain configuration filename -/ -!----------------------------------------------------------------------- -&namdom ! space and time domain (bathymetry, mesh, timestep) -!----------------------------------------------------------------------- - ln_linssh = .true. ! =T linear free surface ==>> model level are fixed in time - nn_closea = 0 ! remove (=0) or keep (=1) closed seas and lakes (ORCA) - ! - rn_rdt = 2880. ! time step for the dynamics (and tracer if nn_acc=0) - ! -/ -!----------------------------------------------------------------------- -&namcrs ! Grid coarsening for dynamics output and/or -! ! passive tracer coarsened online simulations -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namtsd ! data : Temperature & Salinity -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namsbc ! Surface Boundary Condition (surface module) -!----------------------------------------------------------------------- - ln_blk = .true. ! CORE bulk formulation (T => fill namsbc_core) - nn_ice = 3 ! =0 no ice boundary condition , - ! =1 use observed ice-cover , - ! =2 ice-model used ("key_lim3" or "key_lim2) - ln_rnf = .false. ! runoffs (T => fill namsbc_rnf) - ln_ssr = .false. ! Sea Surface Restoring on T and/or S (T => fill namsbc_ssr) - nn_fwb = 0 ! FreshWater Budget: =0 unchecked - ! =1 global mean of e-p-r set to zero at each time step - ! =2 annual global mean of e-p-r set to zero - ! =3 global emp set to zero and spread out over erp area -/ -!----------------------------------------------------------------------- -&namsbc_blk ! namsbc_blk generic Bulk formula (ln_blk = T) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_wndi = 'u_10.15JUNE2009_fill' , 6 , 'U_10_MOD', .false. , .true. , 'yearly' , 'weights_core2_agrif_bicubic.nc' , 'Uwnd' , '' - sn_wndj = 'v_10.15JUNE2009_fill' , 6 , 'V_10_MOD', .false. , .true. , 'yearly' , 'weights_core2_agrif_bicubic.nc' , 'Vwnd' , '' - sn_qsr = 'ncar_rad.15JUNE2009_fill' , 24 , 'SWDN_MOD', .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_qlw = 'ncar_rad.15JUNE2009_fill' , 24 , 'LWDN_MOD', .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_tair = 't_10.15JUNE2009_fill' , 6 , 'T_10_MOD', .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_humi = 'q_10.15JUNE2009_fill' , 6 , 'Q_10_MOD', .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_prec = 'ncar_precip.15JUNE2009_fill', -1 , 'PRC_MOD1', .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_snow = 'ncar_precip.15JUNE2009_fill', -1 , 'SNOW' , .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_slp = 'slp.15JUNE2009_fill' , 6 , 'SLP' , .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_tdif = 'taudif_core' , 24 , 'taudif' , .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - ! - ! ! bulk algorithm : - ln_NCAR = .true. ! "NCAR" algorithm (Large and Yeager 2008) - ! -/ -!----------------------------------------------------------------------- -&namtra_qsr ! penetrative solar radiation -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! - sn_chl ='chlorophyll', -1 , 'CHLA' , .true. , .true. , 'yearly' , 'weights_bilin.nc' , '' -/ -!----------------------------------------------------------------------- -&namlbc ! lateral momentum boundary condition -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namagrif ! AGRIF zoom ("key_agrif") -!----------------------------------------------------------------------- - nn_cln_update = 1 ! baroclinic update frequency -/ -!----------------------------------------------------------------------- -&nambfr ! bottom friction -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&nambbc ! bottom temperature boundary condition -!----------------------------------------------------------------------- - ln_trabbc = .true. ! Apply a geothermal heating at the ocean bottom -/ -!----------------------------------------------------------------------- -&nambbl ! bottom boundary layer scheme -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&nameos ! ocean physical parameters -!----------------------------------------------------------------------- - ln_teos10 = .true. ! = Use TEOS-10 equation of state -/ -!----------------------------------------------------------------------- -&namtra_dmp ! tracer: T & S newtonian damping -!----------------------------------------------------------------------- - ln_tradmp = .false. ! add a damping termn (T) or not (F) -/ -!----------------------------------------------------------------------- -&namtra_adv ! advection scheme for tracer -!----------------------------------------------------------------------- - ln_traadv_fct = .true. ! FCT scheme - nn_fct_h = 2 ! =2/4, horizontal 2nd / 4th order - nn_fct_v = 2 ! =2/4, vertical 2nd / COMPACT 4th order - nn_fct_zts = 0 ! >=1, 2nd order FCT scheme with vertical sub-timestepping - ! ! (number of sub-timestep = nn_fct_zts) -/ -!----------------------------------------------------------------------- -&namtra_ldf ! lateral diffusion scheme for tracers -!---------------------------------------------------------------------------------- - ! ! Operator type: - ln_traldf_lap = .true. ! laplacian operator - ln_traldf_blp = .false. ! bilaplacian operator - ! ! Direction of action: - ln_traldf_lev = .false. ! iso-level - ln_traldf_hor = .false. ! horizontal (geopotential) - ln_traldf_iso = .true. ! iso-neutral (Standard operator) - ln_traldf_triad = .false. ! iso-neutral (Triads operator) - ! - ! ! iso-neutral options: - ln_traldf_msc = .true. ! Method of Stabilizing Correction (both operators) - rn_slpmax = 0.01 ! slope limit (both operators) - ln_triad_iso = .false. ! pure horizontal mixing in ML (triad only) - rn_sw_triad = 1 ! =1 switching triad ; =0 all 4 triads used (triad only) - ln_botmix_triad = .false. ! lateral mixing on bottom (triad only) - ! - ! ! Coefficients: - nn_aht_ijk_t = 20 ! space/time variation of eddy coef - ! ! =-20 (=-30) read in eddy_diffusivity_2D.nc (..._3D.nc) file - ! ! = 0 constant - ! ! = 10 F(k) =ldf_c1d - ! ! = 20 F(i,j) =ldf_c2d - ! ! = 21 F(i,j,t) =Treguier et al. JPO 1997 formulation - ! ! = 30 F(i,j,k) =ldf_c2d + ldf_c1d - ! ! = 31 F(i,j,k,t)=F(local velocity) - rn_aht_0 = 1000. ! lateral eddy diffusivity (lap. operator) [m2/s] - rn_bht_0 = 1.e+12 ! lateral eddy diffusivity (bilap. operator) [m4/s] -/ -!---------------------------------------------------------------------------------- -&namtra_ldfeiv ! eddy induced velocity param. -!---------------------------------------------------------------------------------- - ln_ldfeiv =.false. ! use eddy induced velocity parameterization -/ -!----------------------------------------------------------------------- -&namdyn_adv ! formulation of the momentum advection -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namdyn_vor ! option of physics/algorithm (not control by CPP keys) -!----------------------------------------------------------------------- - ln_dynvor_ene = .false. ! enstrophy conserving scheme - ln_dynvor_ens = .false. ! energy conserving scheme - ln_dynvor_mix = .false. ! mixed scheme - ln_dynvor_een = .true. ! energy & enstrophy scheme - nn_een_e3f = 0 ! e3f = masked averaging of e3t divided by 4 (=0) or by the sum of mask (=1) -/ -!----------------------------------------------------------------------- -&namdyn_hpg ! Hydrostatic pressure gradient option -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namdyn_spg ! surface pressure gradient -!----------------------------------------------------------------------- - ln_dynspg_ts = .true. ! split-explicit free surface -/ -!----------------------------------------------------------------------- -&namdyn_ldf ! lateral diffusion on momentum -!----------------------------------------------------------------------- - ! ! Type of the operator : - ! ! no diffusion: set ln_dynldf_lap=..._blp=F - ln_dynldf_lap = .false. ! laplacian operator - ln_dynldf_blp = .true. ! bilaplacian operator - ! ! Direction of action : - ln_dynldf_lev = .true. ! iso-level - ln_dynldf_hor = .false. ! horizontal (geopotential) - ln_dynldf_iso = .false. ! iso-neutral - ! ! Coefficient - nn_ahm_ijk_t = 0 ! space/time variation of eddy coef - ! ! =-30 read in eddy_viscosity_3D.nc file - ! ! =-20 read in eddy_viscosity_2D.nc file - ! ! = 0 constant - ! ! = 10 F(k)=c1d - ! ! = 20 F(i,j)=F(grid spacing)=c2d - ! ! = 30 F(i,j,k)=c2d*c1d - ! ! = 31 F(i,j,k)=F(grid spacing and local velocity) - rn_ahm_0 = 40000. ! horizontal laplacian eddy viscosity [m2/s] - rn_ahm_b = 0. ! background eddy viscosity for ldf_iso [m2/s] - rn_bhm_0 = 8.5e+11 ! horizontal bilaplacian eddy viscosity [m4/s] -/ -!----------------------------------------------------------------------- -&namzdf ! vertical physics -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namzdf_tke ! turbulent eddy kinetic dependent vertical diffusion ("key_zdftke") -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namzdf_ddm ! double diffusive mixing parameterization ("key_zdfddm") -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namzdf_tmx ! tidal mixing parameterization ("key_zdftmx") -!----------------------------------------------------------------------- - ln_tmx_itf = .false. ! ITF specific parameterisation -/ -!----------------------------------------------------------------------- -&nammpp ! Massively Parallel Processing ("key_mpp_mpi) -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&nammpp_dyndist ! Massively Parallel Distribution for AGRIF zoom ("key_agrif" && "key_mpp_dyndist") -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namctl ! Control prints & Benchmark -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namptr ! Poleward Transport Diagnostic -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namhsb ! Heat and salt budgets -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namobs ! observation usage ('key_diaobs') -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&nam_asminc ! assimilation increments ('key_asminc') -!----------------------------------------------------------------------- -/ diff --git a/RUN_DIRECTORIES/EXP_fullforcing/1_namelist_ice_cfg b/RUN_DIRECTORIES/EXP_fullforcing/1_namelist_ice_cfg deleted file mode 100755 index 8a2e1fd..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/1_namelist_ice_cfg +++ /dev/null @@ -1,49 +0,0 @@ -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! NEMO/LIM3 configuration namelist: Overwrites 1_namelist_ice_ref -!! 1 - Generic parameters (namicerun) -!! 2 - Diagnostics (namicediag) -!! 3 - Ice initialization (namiceini) -!! 4 - Ice discretization (namiceitd) -!! 5 - Ice dynamics and transport (namicedyn) -!! 6 - Ice diffusion (namicehdf) -!! 7 - Ice thermodynamics (namicethd) -!! 8 - Ice salinity (namicesal) -!! 9 - Ice mechanical redistribution (namiceitdme) -!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!------------------------------------------------------------------------------ -&namicerun ! Generic parameters -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicediag ! Diagnostics -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namiceini ! Ice initialization -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namiceitd ! Ice discretization -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicedyn ! Ice dynamics and transport -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicehdf ! Ice horizontal diffusion -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicethd ! Ice thermodynamics -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicesal ! Ice salinity -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namiceitdme ! Ice mechanical redistribution (ridging and rafting) -!------------------------------------------------------------------------------ -/ diff --git a/RUN_DIRECTORIES/EXP_fullforcing/1_namelist_ice_ref b/RUN_DIRECTORIES/EXP_fullforcing/1_namelist_ice_ref deleted file mode 120000 index f945af9..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/1_namelist_ice_ref +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/1_namelist_ice_ref \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_fullforcing/1_namelist_ref b/RUN_DIRECTORIES/EXP_fullforcing/1_namelist_ref deleted file mode 120000 index 9c9608b..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/1_namelist_ref +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/1_namelist_ref \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_fullforcing/context_nemo.xml b/RUN_DIRECTORIES/EXP_fullforcing/context_nemo.xml deleted file mode 100755 index e25fc9d..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/context_nemo.xml +++ /dev/null @@ -1,122 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/RUN_DIRECTORIES/EXP_fullforcing/domain_def_nemo.xml b/RUN_DIRECTORIES/EXP_fullforcing/domain_def_nemo.xml deleted file mode 120000 index 59f94cc..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/domain_def_nemo.xml +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/domain_def_nemo.xml \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_fullforcing/field_def_nemo-lim.xml b/RUN_DIRECTORIES/EXP_fullforcing/field_def_nemo-lim.xml deleted file mode 120000 index 9d4fc40..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/field_def_nemo-lim.xml +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/field_def_nemo-lim.xml \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_fullforcing/field_def_nemo-opa.xml b/RUN_DIRECTORIES/EXP_fullforcing/field_def_nemo-opa.xml deleted file mode 120000 index c3ab102..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/field_def_nemo-opa.xml +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/field_def_nemo-opa.xml \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_fullforcing/field_def_nemo-pisces.xml b/RUN_DIRECTORIES/EXP_fullforcing/field_def_nemo-pisces.xml deleted file mode 120000 index 0c986f0..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/field_def_nemo-pisces.xml +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/field_def_nemo-pisces.xml \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_fullforcing/file_def_nemo.xml b/RUN_DIRECTORIES/EXP_fullforcing/file_def_nemo.xml deleted file mode 100755 index fbe3beb..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/file_def_nemo.xml +++ /dev/null @@ -1,132 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/RUN_DIRECTORIES/EXP_fullforcing/iodef.xml b/RUN_DIRECTORIES/EXP_fullforcing/iodef.xml deleted file mode 100755 index b49154c..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/iodef.xml +++ /dev/null @@ -1,26 +0,0 @@ - - - - - - - - - - - - 10 - true - false - oceanx - - - - - - - - - - - diff --git a/RUN_DIRECTORIES/EXP_fullforcing/namelist_cfg b/RUN_DIRECTORIES/EXP_fullforcing/namelist_cfg deleted file mode 100755 index c443a2d..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/namelist_cfg +++ /dev/null @@ -1,1319 +0,0 @@ -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! namelist_ref -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! NEMO/OPA : 1 - run manager (namrun) -!! namelists 2 - Domain (namcfg, namzgr, namdom, namtsd, namcrs, namc1d, namc1d_uvd) -!! 3 - Surface boundary (namsbc, namsbc_flx, namsbc_blk, namsbc_sas) -!! namsbc_cpl, namtra_qsr, namsbc_rnf, -!! namsbc_apr, namsbc_ssr, namsbc_alb, namsbc_wave) -!! 4 - lateral boundary (namlbc, namagrif, nambdy, nambdy_tide) -!! 5 - bottom boundary (nambfr, nambbc, nambbl) -!! 6 - Tracer (nameos, namtra_adv, namtra_ldf, namtra_ldfeiv, namtra_dmp) -!! 7 - dynamics (namdyn_adv, namdyn_vor, namdyn_hpg, namdyn_spg, namdyn_ldf) -!! 8 - Verical physics (namzdf, namzdf_ric, namzdf_tke, namzdf_ddm, namzdf_tmx, namzdf_tmx_new) -!! 9 - diagnostics (namnc4, namtrd, namspr, namflo, namhsb, namsto) -!! 10 - miscellaneous (nammpp, namctl) -!! 11 - Obs & Assim (namobs, nam_asminc) -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - -!!====================================================================== -!! *** Run management namelists *** -!!====================================================================== -!! namrun parameters of the run -!!====================================================================== -! -!----------------------------------------------------------------------- -&namrun ! parameters of the run -!----------------------------------------------------------------------- - cn_exp = "SEAsia" ! experience name - nn_it000 = 86401 ! first time step - nn_itend = 115200 ! 1200 ! 960 ! 1920 ! 7200 ! 1 days. 10day=14400 ! last time step (std 5475) - nn_date0 = 19600101 ! date at nit_0000 (format yyyymmdd) used if ln_rstart=F or (ln_rstart=T and nn_rstctl=0 or 1) - nn_time0 = 0 ! initial time of day in hhmm - nn_leapy = 1 ! Leap year calendar (1) or not (0) - ln_rstart = .true. ! start from rest (F) or from a restart file (T) - nn_euler = 1 ! = 0 : start with forward time step if ln_rstart=T - nn_rstctl = 2 ! restart control ==> activated only if ln_rstart=T - ! ! = 0 nn_date0 read in namelist ; nn_it000 : read in namelist - ! ! = 1 nn_date0 read in namelist ; nn_it000 : check consistancy between namelist and restart - ! ! = 2 nn_date0 read in restart ; nn_it000 : check consistancy between namelist and restart - cn_ocerst_in = "SEAsia_00086400_restart" ! suffix of ocean restart name (input) - cn_ocerst_indir = "./restarts" ! directory from which to read input ocean restarts - cn_ocerst_out = "restart" ! suffix of ocean restart name (output) - cn_ocerst_outdir= "./restarts" ! directory in which to write output ocean restarts - ln_iscpl = .false. ! cavity evolution forcing or coupling to ice sheet model - nn_istate = 0 ! output the initial state (1) or not (0) - ln_rst_list = .false. ! output restarts at list of times using nn_stocklist (T) or at set frequency with nn_stock (F) - nn_stock = 7200 ! 960 ! 7200 ! 14400 ! frequency of creation of a restart file (modulo referenced to 1) - nn_stocklist = 0,0,0,0,0,0,0,0,0,0 ! List of timesteps when a restart file is to be written - nn_write = 7200! 960 ! 7200 ! 1440 ! frequency of write in the output file (modulo referenced to nn_it000) - ln_mskland = .false. ! mask land points in NetCDF outputs (costly: + ~15%) - ln_cfmeta = .false. ! output additional data to netCDF files required for compliance with the CF metadata standard - ln_clobber = .true. ! clobber (overwrite) an existing file - nn_chunksz = 0 ! chunksize (bytes) for NetCDF file (works only with iom_nf90 routines) -/ -! -!!====================================================================== -!! *** Domain namelists *** -!!====================================================================== -!! namcfg parameters of the configuration -!! namzgr vertical coordinate (default: NO selection) -!! namdom space and time domain (bathymetry, mesh, timestep) -!! namwad Wetting and drying (default F) -!! namtsd data: temperature & salinity -!! namcrs coarsened grid (for outputs and/or TOP) ("key_crs") -!! namc1d 1D configuration options ("key_c1d") -!! namc1d_dyndmp 1D newtonian damping applied on currents ("key_c1d") -!! namc1d_uvd 1D data (currents) ("key_c1d") -!!====================================================================== -! -!----------------------------------------------------------------------- -&namcfg ! parameters of the configuration -!----------------------------------------------------------------------- - ln_read_cfg = .true. ! (=T) read the domain configuration file - ! ! (=F) user defined configuration ==>>> see usrdef(_...) modules - cn_domcfg = "../INPUTS/domain_cfg_gebco.nc" ! domain configuration filename - ! - ln_write_cfg= .false. ! (=T) create the domain configuration file - cn_domcfg_out = "domain_cfg_out" ! newly created domain configuration filename - ! - ln_use_jattr = .false. ! use (T) the file attribute: open_ocean_jstart, if present - ! ! in netcdf input files, as the start j-row for reading -/ -!----------------------------------------------------------------------- -&namzgr ! vertical coordinate (default: NO selection) -!----------------------------------------------------------------------- - ln_zco = .false. ! z-coordinate - full steps - ln_zps = .false. ! z-coordinate - partial steps - ln_sco = .true. ! s- or hybrid z-s-coordinate - ln_isfcav = .false. ! ice shelf cavity -! ln_linssh = .false. ! linear free surface -/ -!----------------------------------------------------------------------- -&namzgr_sco -!----------------------------------------------------------------------- - ln_s_sf12=.false., - ln_s_sh94=.true., - ln_sigcrit=.false., - rn_alpha=4.4, - rn_bb=0.8, - rn_efold=0.0, - rn_hc=39.0, - rn_rmax=0.05, - rn_sbot_max=6000.0, - rn_sbot_min=10., - rn_theta=6.0, - rn_thetb=1.0, - rn_zb_a=0.024, - rn_zb_b=-0.2, - rn_zs=1.0, -/ -!----------------------------------------------------------------------- -&namdom ! space and time domain (bathymetry, mesh, timestep) -!----------------------------------------------------------------------- - - ln_linssh = .false. ! =T linear free surface ==>> model level are fixed in time - nn_closea = 0 ! remove (=0) or keep (=1) closed seas and lakes (ORCA) - ! - nn_msh = 0 ! create (>0) a mesh file or not (=0) - rn_isfhmin = 1.00 ! treshold (m) to discriminate grounding ice to floating ice - ! - rn_rdt = 360 ! 360. ! time step for the dynamics (and tracer if nn_acc=0) - rn_atfp = 0.1 ! asselin time filter parameter - ! - ln_crs = .false. ! Logical switch for coarsening module -! ldbletanh = .false. ! Use/do not use double tanf function for vertical coordinates -/ -!----------------------------------------------------------------------- -&namtsd ! data : Temperature & Salinity -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_tem = 'votemper_ORCA0083-N06-SEAsia_1960.nc', -12 ,'votemper' , .false. , .true. , 'yearly' , '' , '' , '' - sn_sal = 'vosaline_ORCA0083-N06-SEAsia_1960.nc', -12 ,'vosaline' , .false. , .true. , 'yearly' , '' , '' , '' - sn_dep = 'initcd_depth.nc' , -12 ,'gdept_4D', .false. , .true. , 'yearly' , '' , '' , '' - sn_msk = 'initcd_mask.nc' , -12 ,'mask', .false. , .true. , 'yearly' , '' , '' , '' - - ! - cn_dir = '../INPUTS/ICS/' ! root directory for the location of the runoff files - ln_tsd_init = .true. ! Initialisation of ocean T & S with T &S input data (T) or not (F) - ln_tsd_interp = .true. ! Interpolation of T & S in the verticalinput data (T) or not (F) - ln_tsd_tradmp = .false. ! damping of ocean T & S toward T &S input data (T) or not (F) -/ -!----------------------------------------------------------------------- -&namwad ! Wetting and drying (default F) -!----------------------------------------------------------------------- - ln_wd = .false. ! T/F activation of wetting and drying - rn_wdmin1 = 0.1 ! Minimum wet depth on dried cells - rn_wdmin2 = 0.01 ! Tolerance of min wet depth on dried cells - rn_wdld = 20.0 ! Land elevation below which wetting/drying is allowed - nn_wdit = 10 ! Max iterations for W/D limiter -/ -!----------------------------------------------------------------------- -&namcrs ! coarsened grid (for outputs and/or TOP) ("key_crs") -!----------------------------------------------------------------------- - nn_factx = 3 ! Reduction factor of x-direction - nn_facty = 3 ! Reduction factor of y-direction - nn_binref = 0 ! Bin centering preference: NORTH or EQUAT - ! 0, coarse grid is binned with preferential treatment of the north fold - ! 1, coarse grid is binned with centering at the equator - ! Symmetry with nn_facty being odd-numbered. Asymmetry with even-numbered nn_facty. - nn_msh_crs = 1 ! create (=1) a mesh file or not (=0) - nn_crs_kz = 0 ! 0, MEAN of volume boxes - ! 1, MAX of boxes - ! 2, MIN of boxes - ln_crs_wn = .true. ! wn coarsened (T) or computed using horizontal divergence ( F ) -/ -!----------------------------------------------------------------------- -&namc1d ! 1D configuration options ("key_c1d") -!----------------------------------------------------------------------- - rn_lat1d = 50 ! Column latitude (default at PAPA station) - rn_lon1d = -145 ! Column longitude (default at PAPA station) - ln_c1d_locpt= .true. ! Localization of 1D config in a grid (T) or independant point (F) -/ -!----------------------------------------------------------------------- -&namc1d_dyndmp ! U & V newtonian damping ("key_c1d") -!----------------------------------------------------------------------- - ln_dyndmp = .false. ! add a damping term (T) or not (F) -/ -!----------------------------------------------------------------------- -&namc1d_uvd ! data: U & V currents ("key_c1d") -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_ucur = 'ucurrent' , -1 ,'u_current', .false. , .true. , 'monthly' , '' , 'Ume' , '' - sn_vcur = 'vcurrent' , -1 ,'v_current', .false. , .true. , 'monthly' , '' , 'Vme' , '' -! - cn_dir = './' ! root directory for the location of the files - ln_uvd_init = .false. ! Initialisation of ocean U & V with U & V input data (T) or not (F) - ln_uvd_dyndmp = .false. ! damping of ocean U & V toward U & V input data (T) or not (F) -/ - -!!====================================================================== -!! *** Surface Boundary Condition namelists *** -!!====================================================================== -!! namsbc surface boundary condition -!! namsbc_flx flux formulation (ln_flx =T) -!! namsbc_blk Bulk formulae formulation (ln_blk =T) -!! namsbc_cpl CouPLed formulation ("key_oasis3" ) -!! namsbc_sas Stand-Alone Surface module -!! namtra_qsr penetrative solar radiation (ln_traqsr =T) -!! namsbc_rnf river runoffs (ln_rnf =T) -!! namsbc_isf ice shelf melting/freezing (nn_isf >0) -!! namsbc_iscpl coupling option between land ice model and ocean -!! namsbc_apr Atmospheric Pressure (ln_apr_dyn =T) -!! namsbc_ssr sea surface restoring term (for T and/or S) (ln_ssr =T) -!! namsbc_alb albedo parameters -!! namsbc_wave external fields from wave model (ln_wave =T) -!! namberg iceberg floats (ln_icebergs=T) -!!====================================================================== -! -!----------------------------------------------------------------------- -&namsbc ! Surface Boundary Condition (surface module) -!----------------------------------------------------------------------- - nn_fsbc = 1 ! frequency of surface boundary condition computation - ! (also = the frequency of sea-ice & iceberg model call) - ! Type of air-sea fluxes - ln_usr = .false. ! user defined formulation (T => check usrdef_sbc) - ln_flx = .false. ! flux formulation (T => fill namsbc_flx ) - ln_blk = .true. ! Bulk formulation (T => fill namsbc_blk ) - ! Type of coupling (Ocean/Ice/Atmosphere) : - ln_cpl = .false. ! atmosphere coupled formulation ( requires key_oasis3 ) - ln_mixcpl = .false. ! forced-coupled mixed formulation ( requires key_oasis3 ) - nn_components = 0 ! configuration of the opa-sas OASIS coupling - ! =0 no opa-sas OASIS coupling: default single executable configuration - ! =1 opa-sas OASIS coupling: multi executable configuration, OPA component - ! =2 opa-sas OASIS coupling: multi executable configuration, SAS component - nn_limflx = -1 ! LIM3 Multi-category heat flux formulation (use -1 if LIM3 is not used) - ! =-1 Use per-category fluxes, bypass redistributor, forced mode only, not yet implemented coupled - ! = 0 Average per-category fluxes (forced and coupled mode) - ! = 1 Average and redistribute per-category fluxes, forced mode only, not yet implemented coupled - ! = 2 Redistribute a single flux over categories (coupled mode only) - ! Sea-ice : - nn_ice = 0 ! =0 no ice boundary condition , - ! =1 use observed ice-cover , - ! =2 to 4 : ice-model used (LIM2, LIM3 or CICE) ("key_lim3", "key_lim2", or "key_cice") - nn_ice_embd = 1 ! =0 levitating ice (no mass exchange, concentration/dilution effect) - ! =1 levitating ice with mass and salt exchange but no presure effect - ! =2 embedded sea-ice (full salt and mass exchanges and pressure) - ! Misc. options of sbc : - ln_traqsr = .false. ! Light penetration in the ocean (T => fill namtra_qsr) - ln_dm2dc = .false. ! daily mean to diurnal cycle on short wave - ln_rnf = .true. ! runoffs (T => fill namsbc_rnf) - ln_ssr = .false. ! Sea Surface Restoring on T and/or S (T => fill namsbc_ssr) - nn_fwb = 0 ! FreshWater Budget: =0 unchecked - ! =1 global mean of e-p-r set to zero at each time step - ! =2 annual global mean of e-p-r set to zero - ln_apr_dyn = .false. ! Patm gradient added in ocean & ice Eqs. (T => fill namsbc_apr ) - ln_isf = .false. ! ice shelf (T => fill namsbc_isf) - ln_wave = .false. ! Activate coupling with wave (T => fill namsbc_wave) - ln_cdgw = .false. ! Neutral drag coefficient read from wave model (T => ln_wave=.true. & fill namsbc_wave) - ln_sdw = .false. ! Read 2D Surf Stokes Drift & Computation of 3D stokes drift (T => ln_wave=.true. & fill namsbc_wave) - ln_tauoc = .false. ! Activate ocean stress modified by external wave induced stress (T => ln_wave=.true. & fill namsbc_wave) - ln_stcor = .false. ! Activate Stokes Coriolis term (T => ln_wave=.true. & ln_sdw=.true. & fill namsbc_wave) - nn_lsm = 0 ! =0 land/sea mask for input fields is not applied (keep empty land/sea mask filename field) , - ! =1:n number of iterations of land/sea mask application for input fields (fill land/sea mask filename field) -/ -!----------------------------------------------------------------------- -&namsbc_flx ! surface boundary condition : flux formulation -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_utau = 'utau' , 24 , 'utau' , .false. , .false., 'yearly' , '' , '' , '' - sn_vtau = 'vtau' , 24 , 'vtau' , .false. , .false., 'yearly' , '' , '' , '' - sn_qtot = 'qtot' , 24 , 'qtot' , .false. , .false., 'yearly' , '' , '' , '' - sn_qsr = 'qsr' , 24 , 'qsr' , .false. , .false., 'yearly' , '' , '' , '' - sn_emp = 'emp' , 24 , 'emp' , .false. , .false., 'yearly' , '' , '' , '' - - cn_dir = './' ! root directory for the location of the flux files -/ -!----------------------------------------------------------------------- -&namsbc_blk ! namsbc_blk generic Bulk formula (ln_blk = T) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_wndi = 'drowned_u10_DFS5.2' , 3 , 'u10', .false. , .false. , 'yearly' , 'weights_bicubic_atmos.nc' , 'Uwnd' , '' - sn_wndj = 'drowned_v10_DFS5.2' , 3 , 'v10', .false. , .false. , 'yearly' , 'weights_bicubic_atmos.nc' , 'Vwnd' , '' - sn_qsr = 'drowned_radsw_DFS5.2' , 24 , 'radsw', .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - sn_qlw = 'drowned_radlw_DFS5.2' , 24 , 'radlw', .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - sn_tair = 'drowned_t2_DFS5.2' , 3 , 't2', .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - sn_humi = 'drowned_q2_DFS5.2' , 3 , 'q2', .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - sn_prec = 'drowned_precip_DFS5.2' , 24 , 'precip', .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - sn_snow = 'drowned_snow_DFS5.2' , 24 , 'snow' , .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - sn_slp = 'drowned_t2_DFS5.2' , 3 , 't2', .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' ! DUMMY variable. Fill with T -! sn_slp = 'slp.15JUNE2009_fill' , 6 , 'SLP' , .false. , .true. , 'yearly' , 'weights_core_orca2_bilinear_noc.nc' , '' , '' -! sn_tdif = 'taudif_core' , 24 , 'taudif' , .false. , .true. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - ! ! bulk algorithm : - ln_NCAR = .true. ! "NCAR" algorithm (Large and Yeager 2008) - ln_COARE_3p0= .false. ! "COARE 3.0" algorithm (Fairall et al. 2003) - ln_COARE_3p5= .false. ! "COARE 3.5" algorithm (Edson et al. 2013) - ln_ECMWF = .false. ! "ECMWF" algorithm (IFS cycle 31) - ! - cn_dir = '../INPUTS/SBC/' ! root directory for the location of the bulk files - ln_taudif = .false. ! HF tau contribution: use "mean of stress module - module of the mean stress" data - rn_zqt = 2. ! Air temperature and humidity reference height (m) - rn_zu = 10. ! Wind vector reference height (m) - rn_pfac = 1. ! multiplicative factor for precipitation (total & snow) - rn_efac = 1. ! multiplicative factor for evaporation (0. or 1.) - rn_vfac = 0. ! multiplicative factor for ocean/ice velocity - ! in the calculation of the wind stress (0.=absolute winds or 1.=relative winds) - ln_Cd_L12 = .false. ! Modify the drag ice-atm and oce-atm depending on ice concentration - ! This parameterization is from Lupkes et al. (JGR 2012) -/ -!----------------------------------------------------------------------- -&namsbc_cpl ! coupled ocean/atmosphere model ("key_oasis3") -!----------------------------------------------------------------------- -! ! description ! multiple ! vector ! vector ! vector ! -! ! ! categories ! reference ! orientation ! grids ! -! send - sn_snd_temp = 'weighted oce and ice' , 'no' , '' , '' , '' - sn_snd_alb = 'weighted ice' , 'no' , '' , '' , '' - sn_snd_thick = 'none' , 'no' , '' , '' , '' - sn_snd_crt = 'none' , 'no' , 'spherical' , 'eastward-northward' , 'T' - sn_snd_co2 = 'coupled' , 'no' , '' , '' , '' - sn_snd_crtw = 'none' , 'no' , '' , '' , 'U,V' - sn_snd_ifrac = 'none' , 'no' , '' , '' , '' - sn_snd_wlev = 'coupled' , 'no' , '' , '' , '' -! receive - sn_rcv_w10m = 'none' , 'no' , '' , '' , '' - sn_rcv_taumod = 'coupled' , 'no' , '' , '' , '' - sn_rcv_tau = 'oce only' , 'no' , 'cartesian' , 'eastward-northward', 'U,V' - sn_rcv_dqnsdt = 'coupled' , 'no' , '' , '' , '' - sn_rcv_qsr = 'oce and ice' , 'no' , '' , '' , '' - sn_rcv_qns = 'oce and ice' , 'no' , '' , '' , '' - sn_rcv_emp = 'conservative' , 'no' , '' , '' , '' - sn_rcv_rnf = 'coupled' , 'no' , '' , '' , '' - sn_rcv_cal = 'coupled' , 'no' , '' , '' , '' - sn_rcv_co2 = 'coupled' , 'no' , '' , '' , '' - sn_rcv_hsig = 'none' , 'no' , '' , '' , '' - sn_rcv_iceflx = 'none' , 'no' , '' , '' , '' - sn_rcv_mslp = 'none' , 'no' , '' , '' , '' - sn_rcv_phioc = 'none' , 'no' , '' , '' , '' - sn_rcv_sdrfx = 'none' , 'no' , '' , '' , '' - sn_rcv_sdrfy = 'none' , 'no' , '' , '' , '' - sn_rcv_wper = 'none' , 'no' , '' , '' , '' - sn_rcv_wnum = 'none' , 'no' , '' , '' , '' - sn_rcv_wstrf = 'none' , 'no' , '' , '' , '' - sn_rcv_wdrag = 'none' , 'no' , '' , '' , '' -! - nn_cplmodel = 1 ! Maximum number of models to/from which NEMO is potentialy sending/receiving data - ln_usecplmask = .false. ! use a coupling mask file to merge data received from several models - ! ! -> file cplmask.nc with the float variable called cplmask (jpi,jpj,nn_cplmodel) -/ -!----------------------------------------------------------------------- -&namsbc_sas ! Stand Alone Surface boundary condition -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - l_sasread = .TRUE. ! Read fields in a file if .TRUE. , or initialize to 0. in sbcssm.F90 if .FALSE. - sn_usp = 'sas_grid_U', 120 , 'vozocrtx', .true. , .true. , 'yearly' , '' , '' , '' - sn_vsp = 'sas_grid_V', 120 , 'vomecrty', .true. , .true. , 'yearly' , '' , '' , '' - sn_tem = 'sas_grid_T', 120 , 'sosstsst', .true. , .true. , 'yearly' , '' , '' , '' - sn_sal = 'sas_grid_T', 120 , 'sosaline', .true. , .true. , 'yearly' , '' , '' , '' - sn_ssh = 'sas_grid_T', 120 , 'sossheig', .true. , .true. , 'yearly' , '' , '' , '' - sn_e3t = 'sas_grid_T', 120 , 'e3t_m' , .true. , .true. , 'yearly' , '' , '' , '' - sn_frq = 'sas_grid_T', 120 , 'frq_m' , .true. , .true. , 'yearly' , '' , '' , '' - - ln_3d_uve = .true. ! specify whether we are supplying a 3D u,v and e3 field - ln_read_frq = .false. ! specify whether we must read frq or not - cn_dir = './' ! root directory for the location of the bulk files are -/ -!----------------------------------------------------------------------- -&namtra_qsr ! penetrative solar radiation (ln_traqsr=T) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_chl ='chlorophyll', -1 , 'CHLA' , .true. , .true. , 'yearly' , '' , '' , '' - - cn_dir = './' ! root directory for the location of the runoff files - ln_qsr_rgb = .false. ! RGB (Red-Green-Blue) light penetration - ln_qsr_2bd = .true. ! 2 bands light penetration - ln_qsr_bio = .false. ! bio-model light penetration - nn_chldta = 0 ! RGB : Chl data (=1) or cst value (=0) - rn_abs = 0.58 ! RGB & 2 bands: fraction of light (rn_si1) - rn_si0 = 0.35 ! RGB & 2 bands: shortess depth of extinction - rn_si1 = 23.0 ! 2 bands: longest depth of extinction - ln_qsr_ice = .false. ! light penetration for ice-model LIM3 -/ -!----------------------------------------------------------------------- -&namsbc_rnf ! runoffs namelist surface boundary condition (ln_rnf=T) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_rnf = 'SEAsia_rivers', -1 , 'sorunoff', .true. , .true. , 'yearly' , '' , '' , '' - sn_cnf = 'SEAsia_rivers', 0 , 'socoefr', .false. , .true. , 'yearly' , '' , '' , '' - - cn_dir = '../INPUTS/RIVERS/' ! root directory for the location of the runoff files - ln_rnf_mouth= .false. ! specific treatment at rivers mouths - rn_hrnf = 15.e0 ! depth over which enhanced vertical mixing is used (ln_rnf_mouth=T) - rn_avt_rnf = 1.e-3 ! value of the additional vertical mixing coef. [m2/s] (ln_rnf_mouth=T) - rn_rfact = 1.e0 ! multiplicative factor for runoff - ln_rnf_depth= .false. ! read in depth information for runoff - ln_rnf_tem = .false. ! read in temperature information for runoff - ln_rnf_sal = .false. ! read in salinity information for runoff - ln_rnf_depth_ini = .false. ! compute depth at initialisation from runoff file - rn_rnf_max = 1.6224 ! 5.735e-4 ! max value of the runoff climatologie over global domain ( ln_rnf_depth_ini = .true ) - rn_dep_max = 50. ! depth over which runoffs is spread ( ln_rnf_depth_ini = .true ) - nn_rnf_depth_file = 0 ! create (=1) a runoff depth file or not (=0) -/ -!----------------------------------------------------------------------- -&namsbc_isf ! Top boundary layer (ISF) (nn_isf >0) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! -! nn_isf == 4 - sn_fwfisf = 'rnfisf' , -12 ,'sowflisf', .false. , .true. , 'yearly' , '' , '' , '' -! nn_isf == 3 - sn_rnfisf = 'rnfisf' , -12 ,'sofwfisf', .false. , .true. , 'yearly' , '' , '' , '' -! nn_isf == 2 and 3 - sn_depmax_isf='rnfisf' , -12 ,'sozisfmax', .false. , .true. , 'yearly' , '' , '' , '' - sn_depmin_isf='rnfisf' , -12 ,'sozisfmin', .false. , .true. , 'yearly' , '' , '' , '' -! nn_isf == 2 - sn_Leff_isf = 'rnfisf' , -12 ,'Leff' , .false. , .true. , 'yearly' , '' , '' , '' -! -! for all case - nn_isf = 0 ! ice shelf melting/freezing - ! 1 = presence of ISF 2 = bg03 parametrisation - ! 3 = rnf file for isf 4 = ISF fwf specified - ! option 1 and 4 need ln_isfcav = .true. (domzgr) -! only for nn_isf = 1 or 2 - rn_gammat0 = 1.e-4 ! gammat coefficient used in blk formula - rn_gammas0 = 1.e-4 ! gammas coefficient used in blk formula -! only for nn_isf = 1 or 4 - rn_hisf_tbl = 30. ! thickness of the top boundary layer (Losh et al. 2008) - ! ! 0 => thickness of the tbl = thickness of the first wet cell -! only for nn_isf = 1 - nn_isfblk = 1 ! 1 ISOMIP like: 2 equations formulation (Hunter et al., 2006) - ! ! 2 ISOMIP+ like: 3 equations formulation (Asay-Davis et al., 2015) - nn_gammablk = 1 ! 0 = cst Gammat (= gammat/s) - ! ! 1 = velocity dependend Gamma (u* * gammat/s) (Jenkins et al. 2010) - ! ! 2 = velocity and stability dependent Gamma (Holland et al. 1999) -/ -!----------------------------------------------------------------------- -&namsbc_iscpl ! land ice / ocean coupling option -!----------------------------------------------------------------------- - nn_drown = 10 ! number of iteration of the extrapolation loop (fill the new wet cells) - ln_hsb = .false. ! activate conservation module (conservation exact after a time of rn_fiscpl) - nn_fiscpl = 43800 ! (number of time step) conservation period (maybe should be fix to the coupling frequencey of restart frequency) -/ -!----------------------------------------------------------------------- -&namsbc_apr ! Atmospheric pressure used as ocean forcing (ln_apr_dyn =T) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_apr = 'patm' , -1 ,'somslpre', .true. , .true. , 'yearly' , '' , '' , '' - - cn_dir = './' ! root directory for the location of the bulk files - rn_pref = 101000. ! reference atmospheric pressure [N/m2]/ - ln_ref_apr = .false. ! ref. pressure: global mean Patm (T) or a constant (F) - ln_apr_obc = .false. ! inverse barometer added to OBC ssh data -/ -!----------------------------------------------------------------------- -&namsbc_ssr ! surface boundary condition : sea surface restoring (ln_ssr=T) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_sst = 'sst_data', 24 , 'sst' , .false. , .false., 'yearly' , '' , '' , '' - sn_sss = 'sss_data', -1 , 'sss' , .true. , .true. , 'yearly' , '' , '' , '' - - cn_dir = './' ! root directory for the location of the runoff files - nn_sstr = 0 ! add a retroaction term in the surface heat flux (=1) or not (=0) - nn_sssr = 0 ! add a damping term in the surface freshwater flux (=2) - ! or to SSS only (=1) or no damping term (=0) - rn_dqdt = -40. ! magnitude of the retroaction on temperature [W/m2/K] - rn_deds = -166.67 ! magnitude of the damping on salinity [mm/day] - ln_sssr_bnd = .true. ! flag to bound erp term (associated with nn_sssr=2) - rn_sssr_bnd = 4.e0 ! ABS(Max/Min) value of the damping erp term [mm/day] -/ -!----------------------------------------------------------------------- -&namsbc_alb ! albedo parameters -!----------------------------------------------------------------------- - nn_ice_alb = 0 ! parameterization of ice/snow albedo - ! 0: Shine & Henderson-Sellers (JGR 1985) - ! 1: "home made" based on Brandt et al. (J. Climate 2005) - ! and Grenfell & Perovich (JGR 2004) - rn_albice = 0.53 ! albedo of bare puddled ice (values from 0.49 to 0.58) - ! 0.53 (default) => if nn_ice_alb=0 - ! 0.50 (default) => if nn_ice_alb=1 -/ -!----------------------------------------------------------------------- -&namsbc_wave ! External fields from wave model -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_cdg = 'sdw_wave' , 1 , 'drag_coeff' , .true. , .false. , 'daily' , '' , '' , '' - sn_usd = 'sdw_wave' , 1 , 'u_sd2d' , .true. , .false. , 'daily' , '' , '' , '' - sn_vsd = 'sdw_wave' , 1 , 'v_sd2d' , .true. , .false. , 'daily' , '' , '' , '' - sn_swh = 'sdw_wave' , 1 , 'hs' , .true. , .false. , 'daily' , '' , '' , '' - sn_wmp = 'sdw_wave' , 1 , 'wmp' , .true. , .false. , 'daily' , '' , '' , '' - sn_wnum = 'sdw_wave' , 1 , 'wave_num' , .true. , .false. , 'daily' , '' , '' , '' - sn_tauoc = 'sdw_wave' , 1 , 'wave_stress', .true. , .false. , 'daily' , '' , '' , '' -! - cn_dir = './' ! root directory for the location of drag coefficient files -/ -!----------------------------------------------------------------------- -&namberg ! iceberg parameters (default: No iceberg) -!----------------------------------------------------------------------- - ln_icebergs = .false. ! iceberg floats or not - ln_bergdia = .true. ! Calculate budgets - nn_verbose_level = 1 ! Turn on more verbose output if level > 0 - nn_verbose_write = 15 ! Timesteps between verbose messages - nn_sample_rate = 1 ! Timesteps between sampling for trajectory storage - ! Initial mass required for an iceberg of each class - rn_initial_mass = 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 - ! Proportion of calving mass to apportion to each class - rn_distribution = 0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02 - ! Ratio between effective and real iceberg mass (non-dim) - ! i.e. number of icebergs represented at a point - rn_mass_scaling = 2000, 200, 50, 20, 10, 5, 2, 1, 1, 1 - ! thickness of newly calved bergs (m) - rn_initial_thickness = 40., 67., 133., 175., 250., 250., 250., 250., 250., 250. - rn_rho_bergs = 850. ! Density of icebergs - rn_LoW_ratio = 1.5 ! Initial ratio L/W for newly calved icebergs - ln_operator_splitting = .true. ! Use first order operator splitting for thermodynamics - rn_bits_erosion_fraction = 0. ! Fraction of erosion melt flux to divert to bergy bits - rn_sicn_shift = 0. ! Shift of sea-ice concn in erosion flux (0=1, 2nd order FCT scheme with vertical sub-timestepping - ! ! (number of sub-timestep = nn_fct_zts) - ln_traadv_mus = .false. ! MUSCL scheme - ln_mus_ups = .false. ! use upstream scheme near river mouths - ln_traadv_ubs = .false. ! UBS scheme - nn_ubs_v = 2 ! =2 , vertical 2nd order FCT / COMPACT 4th order - ln_traadv_qck = .false. ! QUICKEST scheme -/ -!----------------------------------------------------------------------- -&namtra_adv_mle ! mixed layer eddy parametrisation (Fox-Kemper param) (default: NO) -!----------------------------------------------------------------------- - ln_mle = .false. ! (T) use the Mixed Layer Eddy (MLE) parameterisation - rn_ce = 0.06 ! magnitude of the MLE (typical value: 0.06 to 0.08) - nn_mle = 1 ! MLE type: =0 standard Fox-Kemper ; =1 new formulation - rn_lf = 5.e+3 ! typical scale of mixed layer front (meters) (case rn_mle=0) - rn_time = 172800. ! time scale for mixing momentum across the mixed layer (seconds) (case rn_mle=0) - rn_lat = 20. ! reference latitude (degrees) of MLE coef. (case rn_mle=1) - nn_mld_uv = 0 ! space interpolation of MLD at u- & v-pts (0=min,1=averaged,2=max) - nn_conv = 0 ! =1 no MLE in case of convection ; =0 always MLE - rn_rho_c_mle= 0.01 ! delta rho criterion used to calculate MLD for FK -/ -!----------------------------------------------------------------------- -&namtra_ldf ! lateral diffusion scheme for tracers (default: NO diffusion) -!----------------------------------------------------------------------- - ! ! Operator type: - ! ! no diffusion: set ln_traldf_lap=..._blp=F - ln_traldf_lap = .true. ! laplacian operator - ln_traldf_blp = .false. ! bilaplacian operator - ! - ! ! Direction of action: - ln_traldf_lev = .false. ! iso-level - ln_traldf_hor = .true. ! horizontal (geopotential) - ln_traldf_iso = .false. ! iso-neutral (standard operator) - ln_traldf_triad = .false. ! iso-neutral (triad operator) - ! - ! ! iso-neutral options: - ln_traldf_msc = .false. ! Method of Stabilizing Correction (both operators) - rn_slpmax = 0.01 ! slope limit (both operators) - ln_triad_iso = .false. ! pure horizontal mixing in ML (triad only) - rn_sw_triad = 1 ! =1 switching triad ; =0 all 4 triads used (triad only) - ln_botmix_triad = .false. ! lateral mixing on bottom (triad only) - ! - ! ! Coefficients: - nn_aht_ijk_t = 0 ! space/time variation of eddy coef - ! ! =-20 (=-30) read in eddy_diffusivity_2D.nc (..._3D.nc) file - ! ! = 0 constant - ! ! = 10 F(k) =ldf_c1d - ! ! = 20 F(i,j) =ldf_c2d - ! ! = 21 F(i,j,t) =Treguier et al. JPO 1997 formulation - ! ! = 30 F(i,j,k) =ldf_c2d * ldf_c1d - ! ! = 31 F(i,j,k,t)=F(local velocity and grid-spacing) - rn_aht_0 = 125. ! lateral eddy diffusivity (lap. operator) [m2/s] - rn_bht_0 = 1.e+12 ! lateral eddy diffusivity (bilap. operator) [m4/s] -/ -!----------------------------------------------------------------------- -&namtra_ldfeiv ! eddy induced velocity param. (default: NO) -!----------------------------------------------------------------------- - ln_ldfeiv =.false. ! use eddy induced velocity parameterization - ln_ldfeiv_dia =.false. ! diagnose eiv stream function and velocities - rn_aeiv_0 = 2000. ! eddy induced velocity coefficient [m2/s] - nn_aei_ijk_t = 21 ! space/time variation of the eiv coeficient - ! ! =-20 (=-30) read in eddy_induced_velocity_2D.nc (..._3D.nc) file - ! ! = 0 constant - ! ! = 10 F(k) =ldf_c1d - ! ! = 20 F(i,j) =ldf_c2d - ! ! = 21 F(i,j,t) =Treguier et al. JPO 1997 formulation - ! ! = 30 F(i,j,k) =ldf_c2d + ldf_c1d -/ -!----------------------------------------------------------------------- -&namtra_dmp ! tracer: T & S newtonian damping (default: NO) -!----------------------------------------------------------------------- - ln_tradmp = .false. ! add a damping termn (T) or not (F) - nn_zdmp = 0 ! vertical shape =0 damping throughout the water column - ! =1 no damping in the mixing layer (kz criteria) - ! =2 no damping in the mixed layer (rho crieria) - cn_resto ='resto.nc' ! Name of file containing restoration coeff. field (use dmp_tools to create this) -/ - -!!====================================================================== -!! *** Dynamics namelists *** -!!====================================================================== -!! namdyn_adv formulation of the momentum advection -!! namdyn_vor advection scheme -!! namdyn_hpg hydrostatic pressure gradient -!! namdyn_spg surface pressure gradient -!! namdyn_ldf lateral diffusion scheme -!!====================================================================== -! -!----------------------------------------------------------------------- -&namdyn_adv ! formulation of the momentum advection (default: vector form) -!----------------------------------------------------------------------- - ln_dynadv_vec = .true. ! vector form (T) or flux form (F) - nn_dynkeg = 0 ! scheme for grad(KE): =0 C2 ; =1 Hollingsworth correction - ln_dynadv_cen2= .false. ! flux form - 2nd order centered scheme - ln_dynadv_ubs = .false. ! flux form - 3rd order UBS scheme - ln_dynzad_zts = .false. ! Use (T) sub timestepping for vertical momentum advection -/ -!----------------------------------------------------------------------- -&nam_vvl ! vertical coordinate options (default: zstar) -!----------------------------------------------------------------------- - ln_vvl_zstar = .true. ! zstar vertical coordinate - ln_vvl_ztilde = .false. ! ztilde vertical coordinate: only high frequency variations - ln_vvl_layer = .false. ! full layer vertical coordinate - ln_vvl_ztilde_as_zstar = .false. ! ztilde vertical coordinate emulating zstar - ln_vvl_zstar_at_eqtor = .false. ! ztilde near the equator - rn_ahe3 = 0.0e0 ! thickness diffusion coefficient - rn_rst_e3t = 30.e0 ! ztilde to zstar restoration timescale [days] - rn_lf_cutoff = 5.0e0 ! cutoff frequency for low-pass filter [days] - rn_zdef_max = 0.9e0 ! maximum fractional e3t deformation - ln_vvl_dbg = .true. ! debug prints (T/F) -/ -!----------------------------------------------------------------------- -&namdyn_vor ! Vorticity / Coriolis scheme (default: NO) -!----------------------------------------------------------------------- - ln_dynvor_ene = .false. ! enstrophy conserving scheme - ln_dynvor_ens = .false. ! energy conserving scheme - ln_dynvor_mix = .false. ! mixed scheme - ln_dynvor_een = .true. ! energy & enstrophy scheme - nn_een_e3f = 1 ! e3f = masked averaging of e3t divided by 4 (=0) or by the sum of mask (=1) - ln_dynvor_msk = .false. ! vorticity multiplied by fmask (=T) or not (=F) (all vorticity schemes) ! PLEASE DO NOT ACTIVATE -/ -!----------------------------------------------------------------------- -&namdyn_hpg ! Hydrostatic pressure gradient option (default: zps) -!----------------------------------------------------------------------- - ln_hpg_zco = .false. ! z-coordinate - full steps - ln_hpg_zps = .false. ! z-coordinate - partial steps (interpolation) - ln_hpg_sco = .false. ! s-coordinate (standard jacobian formulation) - ln_hpg_isf = .false. ! s-coordinate (sco ) adapted to isf - ln_hpg_djc = .false. ! s-coordinate (Density Jacobian with Cubic polynomial) - ln_hpg_prj = .true. ! s-coordinate (Pressure Jacobian scheme) -/ -!----------------------------------------------------------------------- -&namdyn_spg ! surface pressure gradient (default: NO) -!----------------------------------------------------------------------- - ln_dynspg_exp = .false. ! explicit free surface - ln_dynspg_ts = .true. ! split-explicit free surface - ln_bt_fw = .true. ! Forward integration of barotropic Eqs. - ln_bt_av = .true. ! Time filtering of barotropic variables - nn_bt_flt = 1 ! Time filter choice = 0 None - ! ! = 1 Boxcar over nn_baro sub-steps - ! ! = 2 Boxcar over 2*nn_baro " " - ln_bt_auto = .true. ! Number of sub-step defined from: - rn_bt_cmax = 0.5 ! =T : the Maximum Courant Number allowed - nn_baro = 30 ! =F : the number of sub-step in rn_rdt seconds - ln_ulimit = .true. - cn_ulimit = 0.9 ! maximum velocity inverse courant number - cnn_ulimit = 0.54 ! how much to reduce cn by in divergen flow -/ -!----------------------------------------------------------------------- -&namdyn_ldf ! lateral diffusion on momentum (default: NO) -!----------------------------------------------------------------------- - ! ! Type of the operator : - ! ! no diffusion: set ln_dynldf_lap=..._blp=F - ln_dynldf_lap = .false. ! laplacian operator - ln_dynldf_blp = .true. ! bilaplacian operator - ! ! Direction of action : - ln_dynldf_lev = .true. ! iso-level - ln_dynldf_hor = .false. ! horizontal (geopotential) - ln_dynldf_iso = .false. ! iso-neutral - ! ! Coefficient - nn_ahm_ijk_t = 0 ! space/time variation of eddy coef - ! ! =-30 read in eddy_viscosity_3D.nc file - ! ! =-20 read in eddy_viscosity_2D.nc file - ! ! = 0 constant - ! ! = 10 F(k)=c1d - ! ! = 20 F(i,j)=F(grid spacing)=c2d - ! ! = 30 F(i,j,k)=c2d*c1d - ! ! = 31 F(i,j,k)=F(grid spacing and local velocity) - ! ! = 32 F(i,j,k)=F(local gridscale and deformation rate) - ! Caution in 20 and 30 cases the coefficient have to be given for a 1 degree grid (~111km) - rn_ahm_0 = 60. ! horizontal laplacian eddy viscosity [m2/s] - rn_ahm_b = 0. ! background eddy viscosity for ldf_iso [m2/s] - rn_bhm_0 = -1.25e+10 ! horizontal bilaplacian eddy viscosity [m4/s] - ! ! Smagorinsky settings (nn_ahm_ijk_t = 32) : - rn_csmc = 3.5 ! Smagorinsky constant of proportionality - rn_minfac = 1.0 ! multiplier of theorectical lower limit - rn_maxfac = 1.0 ! multiplier of theorectical upper limit -/ - -!!====================================================================== -!! Tracers & Dynamics vertical physics namelists -!!====================================================================== -!! namzdf vertical physics -!! namzdf_ric richardson number dependent vertical mixing ("key_zdfric") -!! namzdf_tke TKE dependent vertical mixing ("key_zdftke") -!! namzdf_gls GLS vertical mixing ("key_zdfgls") -!! namzdf_ddm double diffusive mixing parameterization ("key_zdfddm") -!! namzdf_tmx tidal mixing parameterization ("key_zdftmx") -!!====================================================================== -! -!----------------------------------------------------------------------- -&namzdf ! vertical physics -!----------------------------------------------------------------------- - rn_avm0 = 1.2e-6 ! vertical eddy viscosity [m2/s] (background Kz if not "key_zdfcst") - rn_avt0 = 1.2e-6 ! vertical eddy diffusivity [m2/s] (background Kz if not "key_zdfcst") - nn_avb = 0 ! profile for background avt & avm (=1) or not (=0) - nn_havtb = 0 ! horizontal shape for avtb (=1) or not (=0) - ln_zdfevd = .false. ! enhanced vertical diffusion (evd) (T) or not (F) - nn_evdm = 1 ! evd apply on tracer (=0) or on tracer and momentum (=1) - rn_avevd = 100. ! evd mixing coefficient [m2/s] - ln_zdfnpc = .true. ! Non-Penetrative Convective algorithm (T) or not (F) - nn_npc = 1 ! frequency of application of npc - nn_npcp = 365 ! npc control print frequency - ln_zdfexp = .false. ! time-stepping: split-explicit (T) or implicit (F) time stepping - nn_zdfexp = 3 ! number of sub-timestep for ln_zdfexp=T - ln_zdfqiao = .false. ! Enhanced wave vertical mixing Qiao (2010) (T => ln_wave=.true. & ln_sdw=.true. & fill namsbc_wave) -/ -!----------------------------------------------------------------------- -&namzdf_ric ! richardson number dependent vertical diffusion ("key_zdfric" ) -!----------------------------------------------------------------------- - rn_avmri = 100.e-4 ! maximum value of the vertical viscosity - rn_alp = 5. ! coefficient of the parameterization - nn_ric = 2 ! coefficient of the parameterization - rn_ekmfc = 0.7 ! Factor in the Ekman depth Equation - rn_mldmin = 1.0 ! minimum allowable mixed-layer depth estimate (m) - rn_mldmax = 1000.0 ! maximum allowable mixed-layer depth estimate (m) - rn_wtmix = 10.0 ! vertical eddy viscosity coeff [m2/s] in the mixed-layer - rn_wvmix = 10.0 ! vertical eddy diffusion coeff [m2/s] in the mixed-layer - ln_mldw = .true. ! Flag to use or not the mixed layer depth param. -/ -!----------------------------------------------------------------------- -&namzdf_tke ! turbulent eddy kinetic dependent vertical diffusion ("key_zdftke") -!----------------------------------------------------------------------- - rn_ediff = 0.1 ! coef. for vertical eddy coef. (avt=rn_ediff*mxl*sqrt(e) ) - rn_ediss = 0.7 ! coef. of the Kolmogoroff dissipation - rn_ebb = 67.83 ! coef. of the surface input of tke (=67.83 suggested when ln_mxl0=T) - rn_emin = 1.e-6 ! minimum value of tke [m2/s2] - rn_emin0 = 1.e-4 ! surface minimum value of tke [m2/s2] - rn_bshear = 1.e-20 ! background shear (>0) currently a numerical threshold (do not change it) - nn_mxl = 3 ! mixing length: = 0 bounded by the distance to surface and bottom - ! = 1 bounded by the local vertical scale factor - ! = 2 first vertical derivative of mixing length bounded by 1 - ! = 3 as =2 with distinct disspipative an mixing length scale - nn_pdl = 1 ! Prandtl number function of richarson number (=1, avt=pdl(Ri)*avm) or not (=0, avt=avm) - ln_mxl0 = .true. ! surface mixing length scale = F(wind stress) (T) or not (F) - rn_mxl0 = 0.01 ! surface buoyancy lenght scale minimum value - ln_lc = .true. ! Langmuir cell parameterisation (Axell 2002) - rn_lc = 0.15 ! coef. associated to Langmuir cells - nn_etau = 1 ! penetration of tke below the mixed layer (ML) due to near intertial waves - ! = 0 no penetration - ! = 1 add a tke source below the ML - ! = 2 add a tke source just at the base of the ML - ! = 3 as = 1 applied on HF part of the stress (ln_cpl=T) - rn_efr = 0.05 ! fraction of surface tke value which penetrates below the ML (nn_etau=1 or 2) - nn_htau = 1 ! type of exponential decrease of tke penetration below the ML - ! = 0 constant 10 m length scale - ! = 1 0.5m at the equator to 30m poleward of 40 degrees -/ -!----------------------------------------------------------------------- -&namzdf_gls ! GLS vertical diffusion ("key_zdfgls") -!----------------------------------------------------------------------- - rn_emin = 1.e-6 ! minimum value of e [m2/s2] - rn_epsmin = 1.e-12 ! minimum value of eps [m2/s3] - ln_length_lim = .true. ! limit on the dissipation rate under stable stratification (Galperin et al., 1988) - rn_clim_galp = 0.267 ! galperin limit - ln_sigpsi = .true. ! Activate or not Burchard 2001 mods on psi schmidt number in the wb case - rn_crban = 100. ! Craig and Banner 1994 constant for wb tke flux - rn_charn = 70000. ! Charnock constant for wb induced roughness length - rn_hsro = 0.02 ! Minimum surface roughness - rn_frac_hs = 1.3 ! Fraction of wave height as roughness (if nn_z0_met=2) - nn_z0_met = 2 ! Method for surface roughness computation (0/1/2) - nn_bc_surf = 1 ! surface condition (0/1=Dir/Neum) - nn_bc_bot = 1 ! bottom condition (0/1=Dir/Neum) - nn_stab_func = 2 ! stability function (0=Galp, 1= KC94, 2=CanutoA, 3=CanutoB) - nn_clos = 1 ! predefined closure type (0=MY82, 1=k-eps, 2=k-w, 3=Gen) -/ -!----------------------------------------------------------------------- -&namzdf_ddm ! double diffusive mixing parameterization ("key_zdfddm") -!----------------------------------------------------------------------- - rn_avts = 1.e-4 ! maximum avs (vertical mixing on salinity) - rn_hsbfr = 1.6 ! heat/salt buoyancy flux ratio -/ -!----------------------------------------------------------------------- -&namzdf_tmx ! tidal mixing parameterization ("key_zdftmx") -!----------------------------------------------------------------------- - rn_htmx = 500. ! vertical decay scale for turbulence (meters) - rn_n2min = 1.e-8 ! threshold of the Brunt-Vaisala frequency (s-1) - rn_tfe = 0.333 ! tidal dissipation efficiency - rn_me = 0.2 ! mixing efficiency - ln_tmx_itf = .false. ! ITF specific parameterisation - rn_tfe_itf = 1. ! ITF tidal dissipation efficiency -/ -!----------------------------------------------------------------------- -&namzdf_tmx_new ! internal wave-driven mixing parameterization ("key_zdftmx_new" & "key_zdfddm") -!----------------------------------------------------------------------- - nn_zpyc = 1 ! pycnocline-intensified dissipation scales as N (=1) or N^2 (=2) - ln_mevar = .true. ! variable (T) or constant (F) mixing efficiency - ln_tsdiff = .true. ! account for differential T/S mixing (T) or not (F) -/ -!!====================================================================== -!! *** Miscellaneous namelists *** -!!====================================================================== -!! nammpp Massively Parallel Processing ("key_mpp_mpi) -!! namctl Control prints -!! namsto Stochastic parametrization of EOS -!!====================================================================== -! -!----------------------------------------------------------------------- -&nammpp ! Massively Parallel Processing ("key_mpp_mpi) -!----------------------------------------------------------------------- - cn_mpi_send = 'I' ! mpi send/recieve type ='S', 'B', or 'I' for standard send, - ! buffer blocking send or immediate non-blocking sends, resp. - nn_buffer = 0 ! size in bytes of exported buffer ('B' case), 0 no exportation - ln_nnogather= .false. ! activate code to avoid mpi_allgather use at the northfold - jpni = 30 ! standardqueue:30 ! shortqueue:11 ! jpni number of processors following i (set automatically if < 1) - jpnj = 16 ! standardqueue:16 ! shortqueue: 8 ! jpnj number of processors following j (set automatically if < 1) - jpnij = 480 ! standardqueue:480 ! shortqueue:88 ! jpnij number of local domains (set automatically if < 1) -/ -!----------------------------------------------------------------------- -&namctl ! Control prints -!----------------------------------------------------------------------- - ln_ctl = .false. ! trends control print (expensive!) - nn_print = 0 ! level of print (0 no extra print) - nn_ictls = 0 ! start i indice of control sum (use to compare mono versus - nn_ictle = 0 ! end i indice of control sum multi processor runs - nn_jctls = 0 ! start j indice of control over a subdomain) - nn_jctle = 0 ! end j indice of control - nn_isplt = 1 ! number of processors in i-direction - nn_jsplt = 1 ! number of processors in j-direction - nn_timing = 1 ! timing by routine activated (=1) creates timing.output file, or not (=0) - nn_diacfl = 0 ! Write out CFL diagnostics (=1) in cfl_diagnostics.ascii, or not (=0) -/ -!----------------------------------------------------------------------- -&namsto ! Stochastic parametrization of EOS (default: NO) -!----------------------------------------------------------------------- - ln_sto_eos = .false. ! stochastic equation of state - nn_sto_eos = 1 ! number of independent random walks - rn_eos_stdxy= 1.4 ! random walk horz. standard deviation (in grid points) - rn_eos_stdz = 0.7 ! random walk vert. standard deviation (in grid points) - rn_eos_tcor = 1440. ! random walk time correlation (in timesteps) - nn_eos_ord = 1 ! order of autoregressive processes - nn_eos_flt = 0 ! passes of Laplacian filter - rn_eos_lim = 2.0 ! limitation factor (default = 3.0) - ln_rststo = .false. ! start from mean parameter (F) or from restart file (T) - ln_rstseed = .true. ! read seed of RNG from restart file - cn_storst_in = "restart_sto" ! suffix of stochastic parameter restart file (input) - cn_storst_out = "restart_sto" ! suffix of stochastic parameter restart file (output) -/ - -!!====================================================================== -!! *** Diagnostics namelists *** -!!====================================================================== -!! namtrd dynamics and/or tracer trends (default F) -!! namptr Poleward Transport Diagnostics (default F) -!! namhsb Heat and salt budgets (default F) -!! namdiu Cool skin and warm layer models (default F) -!! namdiu Cool skin and warm layer models (default F) -!! namflo float parameters ("key_float") -!! nam_diaharm Harmonic analysis of tidal constituents ("key_diaharm") -!! namdct transports through some sections ("key_diadct") -!! nam_diatmb Top Middle Bottom Output (default F) -!! nam_dia25h 25h Mean Output (default F) -!! namnc4 netcdf4 chunking and compression settings ("key_netcdf4") -!!====================================================================== -! -!----------------------------------------------------------------------- -&namtrd ! trend diagnostics (default F) -!----------------------------------------------------------------------- - ln_glo_trd = .false. ! (T) global domain averaged diag for T, T^2, KE, and PE - ln_dyn_trd = .false. ! (T) 3D momentum trend output - ln_dyn_mxl = .false. ! (T) 2D momentum trends averaged over the mixed layer (not coded yet) - ln_vor_trd = .false. ! (T) 2D barotropic vorticity trends (not coded yet) - ln_KE_trd = .false. ! (T) 3D Kinetic Energy trends - ln_PE_trd = .false. ! (T) 3D Potential Energy trends - ln_tra_trd = .false. ! (T) 3D tracer trend output - ln_tra_mxl = .false. ! (T) 2D tracer trends averaged over the mixed layer (not coded yet) - nn_trd = 365 ! print frequency (ln_glo_trd=T) (unit=time step) -/ -!!gm nn_ctls = 0 ! control surface type in mixed-layer trends (0,1 or n /seconds ; =86400. -> /day) -!!gm cn_trdrst_in = "restart_mld" ! suffix of ocean restart name (input) -!!gm cn_trdrst_out = "restart_mld" ! suffix of ocean restart name (output) -!!gm ln_trdmld_restart = .false. ! restart for ML diagnostics -!!gm ln_trdmld_instant = .false. ! flag to diagnose trends of instantantaneous or mean ML T/S -!!gm -!----------------------------------------------------------------------- -&namptr ! Poleward Transport Diagnostic (default F) -!----------------------------------------------------------------------- - ln_diaptr = .false. ! Poleward heat and salt transport (T) or not (F) - ln_subbas = .false. ! Atlantic/Pacific/Indian basins computation (T) or not -/ -!----------------------------------------------------------------------- -&namhsb ! Heat and salt budgets (default F) -!----------------------------------------------------------------------- - ln_diahsb = .false. ! check the heat and salt budgets (T) or not (F) -/ -!----------------------------------------------------------------------- -&namdiu ! Cool skin and warm layer models (default F) -!----------------------------------------------------------------------- - ln_diurnal = .false. ! - ln_diurnal_only = .false. ! -/ -!----------------------------------------------------------------------- -&namflo ! float parameters ("key_float") -!----------------------------------------------------------------------- - jpnfl = 1 ! total number of floats during the run - jpnnewflo = 0 ! number of floats for the restart - ln_rstflo = .false. ! float restart (T) or not (F) - nn_writefl = 75 ! frequency of writing in float output file - nn_stockfl = 5475 ! frequency of creation of the float restart file - ln_argo = .false. ! Argo type floats (stay at the surface each 10 days) - ln_flork4 = .false. ! trajectories computed with a 4th order Runge-Kutta (T) - ! ! or computed with Blanke' scheme (F) - ln_ariane = .true. ! Input with Ariane tool convention(T) - ln_flo_ascii= .true. ! Output with Ariane tool netcdf convention(F) or ascii file (T) -/ -!----------------------------------------------------------------------- -&nam_diaharm ! Harmonic analysis of tidal constituents ("key_diaharm") -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&nam_diaharm_fast ! Harmonic analysis of tidal constituents ("key_diaharm_fast") -!----------------------------------------------------------------------- - ln_diaharm_store = .false. - ln_diaharm_compute = .true. - ln_diaharm_read_restart = .false. - ln_ana_ssh = .true. - ln_ana_uvbar = .false. - ln_ana_bfric = .false. - ln_ana_rho = .false. - ln_ana_uv3d = .false. - ln_ana_w3d = .false. - tname(1)='K1' - tname(2)='K2' - tname(3)='M2' - tname(4)='M4' - tname(5)='N2' - tname(6)='O1' - tname(7)='P1' - tname(8)='Q1' - tname(9)='S2' -!! FES2014 full list -! tname(1) ='2N2' -! tname(2)='EPS2' -! tname(3)='J1' -! tname(4)='K1' -! tname(5)='K2' -! tname(6)='L2' -! tname(7)='LA2' -! tname(8)='M2' -! tname(9)='M3' -! tname(10)='M4' -! tname(11)='M6' -! tname(12)='M8' -! tname(13)='MF' -! tname(14)='MKS2' -! tname(15)='MM' -! tname(16)='MN4' -! tname(17)='MS4' -! tname(18)='MSF' -! tname(19)='MSQM' -! tname(20)='MTM' -! tname(21)='MU2' -! tname(22)='N2' -! tname(23)='N4' -! tname(24)='NU2' -! tname(25)='O1' -! tname(26)='P1' -! tname(27)='Q1' -! tname(28)='R2' -! tname(29)='S1' -! tname(30)='S2' -! tname(31)='S4' -! tname(32)='SA' -! tname(33)='SSA' -! tname(34)='T2' -/ -!----------------------------------------------------------------------- -&namdct ! transports through some sections ("key_diadct") -!----------------------------------------------------------------------- - nn_dct = 15 ! time step frequency for transports computing - nn_dctwri = 15 ! time step frequency for transports writing - nn_secdebug= 112 ! 0 : no section to debug - ! ! -1 : debug all section - ! ! 0 < n : debug section number n -/ -!----------------------------------------------------------------------- -&nam_diatmb ! Top Middle Bottom Output (default F) -!----------------------------------------------------------------------- - ln_diatmb = .false. ! Choose Top Middle and Bottom output or not -/ -!----------------------------------------------------------------------- -&nam_dia25h ! 25h Mean Output (default F) -!----------------------------------------------------------------------- - ln_dia25h = .false. ! Choose 25h mean output or not -/ -!----------------------------------------------------------------------- -&namnc4 ! netcdf4 chunking and compression settings ("key_netcdf4") -!----------------------------------------------------------------------- - ln_diatmb = .false. ! Choose Top Middle and Bottom output or not -/ -!----------------------------------------------------------------------- -&nam_dia25h ! 25h Mean Output (default F) -!----------------------------------------------------------------------- - ln_dia25h = .false. ! Choose 25h mean output or not -/ -!----------------------------------------------------------------------- -&namnc4 ! netcdf4 chunking and compression settings ("key_netcdf4") -!----------------------------------------------------------------------- - nn_nchunks_i= 4 ! number of chunks in i-dimension - nn_nchunks_j= 4 ! number of chunks in j-dimension - nn_nchunks_k= 31 ! number of chunks in k-dimension - ! ! setting nn_nchunks_k = jpk will give a chunk size of 1 in the vertical which - ! ! is optimal for postprocessing which works exclusively with horizontal slabs - ln_nc4zip = .true. ! (T) use netcdf4 chunking and compression - ! ! (F) ignore chunking information and produce netcdf3-compatible files -/ - -!!====================================================================== -!! *** Observation & Assimilation *** -!!====================================================================== -!! namobs observation and model comparison -!! nam_asminc assimilation increments ('key_asminc') -!!====================================================================== -! -!----------------------------------------------------------------------- -&namobs ! observation usage switch -!----------------------------------------------------------------------- - ln_diaobs = .false. ! Logical switch for the observation operator - ln_t3d = .false. ! Logical switch for T profile observations - ln_s3d = .false. ! Logical switch for S profile observations - ln_sla = .false. ! Logical switch for SLA observations - ln_sst = .false. ! Logical switch for SST observations - ln_sic = .false. ! Logical switch for Sea Ice observations - ln_vel3d = .false. ! Logical switch for velocity observations - ln_altbias = .false. ! Logical switch for altimeter bias correction - ln_nea = .false. ! Logical switch for rejection of observations near land - ln_grid_global = .true. ! Logical switch for global distribution of observations - ln_grid_search_lookup = .false. ! Logical switch for obs grid search w/lookup table - ln_ignmis = .true. ! Logical switch for ignoring missing files - ln_s_at_t = .false. ! Logical switch for computing model S at T obs if not there - ln_sstnight = .false. ! Logical switch for calculating night-time average for SST obs -! All of the *files* variables below are arrays. Use namelist_cfg to add more files - cn_profbfiles = 'profiles_01.nc' ! Profile feedback input observation file names - cn_slafbfiles = 'sla_01.nc' ! SLA feedback input observation file names - cn_sstfbfiles = 'sst_01.nc' ! SST feedback input observation file names - cn_sicfbfiles = 'sic_01.nc' ! SIC feedback input observation file names - cn_velfbfiles = 'vel_01.nc' ! Velocity feedback input observation file names - cn_altbiasfile = 'altbias.nc' ! Altimeter bias input file name - cn_gridsearchfile='gridsearch.nc' ! Grid search file name - rn_gridsearchres = 0.5 ! Grid search resolution - rn_dobsini = 00010101.000000 ! Initial date in window YYYYMMDD.HHMMSS - rn_dobsend = 00010102.000000 ! Final date in window YYYYMMDD.HHMMSS - nn_1dint = 0 ! Type of vertical interpolation method - nn_2dint = 0 ! Type of horizontal interpolation method - nn_msshc = 0 ! MSSH correction scheme - rn_mdtcorr = 1.61 ! MDT correction - rn_mdtcutoff = 65.0 ! MDT cutoff for computed correction - nn_profdavtypes = -1 ! Profile daily average types - array - ln_sstbias = .false. ! - cn_sstbias_files = 'sstbias.nc' ! -/ -!----------------------------------------------------------------------- -&nam_asminc ! assimilation increments ('key_asminc') -!----------------------------------------------------------------------- - ln_bkgwri = .false. ! Logical switch for writing out background state - ln_trainc = .false. ! Logical switch for applying tracer increments - ln_dyninc = .false. ! Logical switch for applying velocity increments - ln_sshinc = .false. ! Logical switch for applying SSH increments - ln_asmdin = .false. ! Logical switch for Direct Initialization (DI) - ln_asmiau = .false. ! Logical switch for Incremental Analysis Updating (IAU) - nitbkg = 0 ! Timestep of background in [0,nitend-nit000-1] - nitdin = 0 ! Timestep of background for DI in [0,nitend-nit000-1] - nitiaustr = 1 ! Timestep of start of IAU interval in [0,nitend-nit000-1] - nitiaufin = 15 ! Timestep of end of IAU interval in [0,nitend-nit000-1] - niaufn = 0 ! Type of IAU weighting function - ln_salfix = .false. ! Logical switch for ensuring that the sa > salfixmin - salfixmin = -9999 ! Minimum salinity after applying the increments - nn_divdmp = 0 ! Number of iterations of divergence damping operator -/ diff --git a/RUN_DIRECTORIES/EXP_fullforcing/namelist_ice_cfg b/RUN_DIRECTORIES/EXP_fullforcing/namelist_ice_cfg deleted file mode 100755 index 784d2d7..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/namelist_ice_cfg +++ /dev/null @@ -1,48 +0,0 @@ -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! LIM3 configuration namelist: Overwrites SHARED/namelist_ice_lim3_ref -!! 1 - Generic parameters (namicerun) -!! 2 - Diagnostics (namicediag) -!! 3 - Ice initialization (namiceini) -!! 4 - Ice discretization (namiceitd) -!! 5 - Ice dynamics and transport (namicedyn) -!! 6 - Ice diffusion (namicehdf) -!! 7 - Ice thermodynamics (namicethd) -!! 8 - Ice salinity (namicesal) -!! 9 - Ice mechanical redistribution (namiceitdme) -!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!------------------------------------------------------------------------------ -&namicerun ! Generic parameters -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicediag ! Diagnostics -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namiceini ! Ice initialization -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namiceitd ! Ice discretization -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicedyn ! Ice dynamics and transport -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicehdf ! Ice horizontal diffusion -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicethd ! Ice thermodynamics -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicesal ! Ice salinity -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namiceitdme ! Ice mechanical redistribution (ridging and rafting) -!------------------------------------------------------------------------------ -/ diff --git a/RUN_DIRECTORIES/EXP_fullforcing/namelist_ice_ref b/RUN_DIRECTORIES/EXP_fullforcing/namelist_ice_ref deleted file mode 120000 index d298c6e..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/namelist_ice_ref +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/namelist_ice_lim3_ref \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_fullforcing/namelist_pisces_cfg b/RUN_DIRECTORIES/EXP_fullforcing/namelist_pisces_cfg deleted file mode 100755 index 9c24e03..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/namelist_pisces_cfg +++ /dev/null @@ -1,63 +0,0 @@ -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! PISCES : Configuration namelist : used to overwrite defaults values defined in SHARED/namelist_pis_ref -!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisext ! air-sea exchange -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisatm ! Atmospheric prrssure -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisbio ! biological parameters -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampislim ! parameters for nutrient limitations -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisopt ! parameters for optics -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisprod ! parameters for phytoplankton growth -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampismort ! parameters for phytoplankton sinks -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampismes ! parameters for mesozooplankton -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampiszoo ! parameters for microzooplankton -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisfer ! parameters for iron chemistry -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisrem ! parameters for remineralization -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampiscal ! parameters for Calcite chemistry -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampissbc ! parameters for inputs deposition -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisdmp ! Damping -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampismass ! Mass conservation -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ diff --git a/RUN_DIRECTORIES/EXP_fullforcing/namelist_pisces_ref b/RUN_DIRECTORIES/EXP_fullforcing/namelist_pisces_ref deleted file mode 120000 index e4b4056..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/namelist_pisces_ref +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/namelist_pisces_ref \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_fullforcing/namelist_ref b/RUN_DIRECTORIES/EXP_fullforcing/namelist_ref deleted file mode 120000 index a1435a3..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/namelist_ref +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/namelist_ref \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_fullforcing/namelist_top_cfg b/RUN_DIRECTORIES/EXP_fullforcing/namelist_top_cfg deleted file mode 100755 index 82732c6..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/namelist_top_cfg +++ /dev/null @@ -1,109 +0,0 @@ -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! NEMO/TOP1 : Configuration namelist : used to overwrite defaults values defined in SHARED/namelist_top_ref -!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!----------------------------------------------------------------------- -&namtrc_run ! run information -!----------------------------------------------------------------------- - ln_top_euler = .true. -/ -!----------------------------------------------------------------------- -&namtrc ! tracers definition -!----------------------------------------------------------------------- - jp_bgc = 24 -! - ln_pisces = .true. - ln_my_trc = .false. - ln_age = .false. - ln_cfc11 = .false. - ln_cfc12 = .false. - ln_c14 = .false. -! - ln_trcdta = .true. ! Initialisation from data input file (T) or not (F) -! ! ! ! ! -! ! name ! title of the field ! units ! initial data from file or not ! -! ! ! ! ! - sn_tracer(1) = 'DIC ' , 'Dissolved inorganic Concentration ', 'mol-C/L' , .true. - sn_tracer(2) = 'Alkalini' , 'Total Alkalinity Concentration ', 'eq/L ' , .true. - sn_tracer(3) = 'O2 ' , 'Dissolved Oxygen Concentration ', 'mol-C/L' , .true. - sn_tracer(4) = 'CaCO3 ' , 'Calcite Concentration ', 'mol-C/L' , .false. - sn_tracer(5) = 'PO4 ' , 'Phosphate Concentration ', 'mol-C/L' , .true. - sn_tracer(6) = 'POC ' , 'Small organic carbon Concentration ', 'mol-C/L' , .false. - sn_tracer(7) = 'Si ' , 'Silicate Concentration ', 'mol-C/L' , .true. - sn_tracer(8) = 'PHY ' , 'Nanophytoplankton Concentration ', 'mol-C/L' , .false. - sn_tracer(9) = 'ZOO ' , 'Microzooplankton Concentration ', 'mol-C/L' , .false. - sn_tracer(10) = 'DOC ' , 'Dissolved organic Concentration ', 'mol-C/L' , .true. - sn_tracer(11) = 'PHY2 ' , 'Diatoms Concentration ', 'mol-C/L' , .false. - sn_tracer(12) = 'ZOO2 ' , 'Mesozooplankton Concentration ', 'mol-C/L' , .false. - sn_tracer(13) = 'DSi ' , 'Diatoms Silicate Concentration ', 'mol-C/L' , .false. - sn_tracer(14) = 'Fer ' , 'Dissolved Iron Concentration ', 'mol-C/L' , .true. - sn_tracer(15) = 'BFe ' , 'Big iron particles Concentration ', 'mol-C/L' , .false. - sn_tracer(16) = 'GOC ' , 'Big organic carbon Concentration ', 'mol-C/L' , .false. - sn_tracer(17) = 'SFe ' , 'Small iron particles Concentration ', 'mol-C/L' , .false. - sn_tracer(18) = 'DFe ' , 'Diatoms iron Concentration ', 'mol-C/L' , .false. - sn_tracer(19) = 'GSi ' , 'Sinking biogenic Silicate Concentration', 'mol-C/L' , .false. - sn_tracer(20) = 'NFe ' , 'Nano iron Concentration ', 'mol-C/L' , .false. - sn_tracer(21) = 'NCHL ' , 'Nano chlorophyl Concentration ', 'mol-C/L' , .false. - sn_tracer(22) = 'DCHL ' , 'Diatoms chlorophyl Concentration ', 'mol-C/L' , .false. - sn_tracer(23) = 'NO3 ' , 'Nitrates Concentration ', 'mol-C/L' , .true. - sn_tracer(24) = 'NH4 ' , 'Ammonium Concentration ', 'mol-C/L' , .false. -/ -!----------------------------------------------------------------------- -&namtrc_dta ! Initialisation from data input file -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_trcdta(1) = 'data_DIC_nomask' , -12 , 'DIC' , .false. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(2) = 'data_Alkalini_nomask' , -12 , 'Alkalini', .false. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(3) = 'data_O2_nomask' , -1 , 'O2' , .true. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(5) = 'data_PO4_nomask' , -1 , 'PO4' , .true. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(7) = 'data_Si_nomask' , -1 , 'Si' , .true. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(10) = 'data_DOC_nomask' , -12 , 'DOC' , .false. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(14) = 'data_Fer_nomask' , -12 , 'Fer' , .false. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(23) = 'data_NO3_nomask' , -1 , 'NO3' , .true. , .true. , 'yearly' , '' , '' , '' - rn_trfac(1) = 1.0e-06 ! multiplicative factor - rn_trfac(2) = 1.0e-06 ! - - - - - rn_trfac(3) = 44.6e-06 ! - - - - - rn_trfac(5) = 122.0e-06 ! - - - - - rn_trfac(7) = 1.0e-06 ! - - - - - rn_trfac(10) = 1.0 ! - - - - - rn_trfac(14) = 1.0 ! - - - - - rn_trfac(23) = 7.6e-06 ! - - - - -/ -!----------------------------------------------------------------------- -&namtrc_adv ! advection scheme for passive tracer -!----------------------------------------------------------------------- - ln_trcadv_mus = .true. ! MUSCL scheme - ln_mus_ups = .false. ! use upstream scheme near river mouths -/ -!----------------------------------------------------------------------- -&namtrc_ldf ! lateral diffusion scheme for passive tracer -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namtrc_zdf ! vertical physics -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namtrc_rad ! treatment of negative concentrations -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namtrc_dmp ! passive tracer newtonian damping -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namtrc_ice ! Representation of sea ice growth & melt effects -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namtrc_trd ! diagnostics on tracer trends ('key_trdtrc') -! or mixed-layer trends ('key_trdmld_trc') -!---------------------------------------------------------------------- -/ -!---------------------------------------------------------------------- -&namtrc_bc ! data for boundary conditions -!----------------------------------------------------------------------- -/ -!---------------------------------------------------------------------- -&namtrc_bdy ! Setup of tracer boundary conditions -!----------------------------------------------------------------------- diff --git a/RUN_DIRECTORIES/EXP_fullforcing/namelist_top_ref b/RUN_DIRECTORIES/EXP_fullforcing/namelist_top_ref deleted file mode 120000 index 49690ad..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/namelist_top_ref +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/namelist_top_ref \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_fullforcing/runscript b/RUN_DIRECTORIES/EXP_fullforcing/runscript deleted file mode 100755 index 4c43693..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/runscript +++ /dev/null @@ -1,30 +0,0 @@ -#!/bin/bash -#PBS -N SEAsia -#PBS -l select=21 -#PBS -l walltime=02:00:00 -#PBS -A n01-ACCORD -# mail alert at (b)eginning, (e)nd and (a)bortion of execution -#PBS -m bea -#PBS -M jelt@noc.ac.uk - -module swap PrgEnv-cray PrgEnv-intel -module load cray-netcdf-hdf5parallel -module load cray-hdf5-parallel - -export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR) -# echo $(readlink -f $PBS_O_WORKDIR) -# export OMP_NUM_THREADS=1 - -cd $PBS_O_WORKDIR -# - echo " "; - OCEANCORES=480 #92 - XIOSCORES=4 -ulimit -c unlimited -ulimit -s unlimited - -rm -f core - -aprun -b -n $XIOSCORES -N 4 ./xios_server.exe : -n $OCEANCORES -N 24 ./opa - -exit diff --git a/RUN_DIRECTORIES/EXP_fullforcing/runscript_short b/RUN_DIRECTORIES/EXP_fullforcing/runscript_short deleted file mode 100755 index d531813..0000000 --- a/RUN_DIRECTORIES/EXP_fullforcing/runscript_short +++ /dev/null @@ -1,33 +0,0 @@ -#!/bin/bash -#PBS -N SEAsia -#PBS -l select=5 -#PBS -l walltime=00:20:00 -#PBS -A n01-ACCORD -# mail alert at (b)eginning, (e)nd and (a)bortion of execution -#PBS -m bea -#PBS -M jelt@noc.ac.uk -#PBS -q short - -module swap PrgEnv-cray PrgEnv-intel -module load cray-netcdf-hdf5parallel -module load cray-hdf5-parallel - -export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR) -# echo $(readlink -f $PBS_O_WORKDIR) -# export OMP_NUM_THREADS=1 - -cd $PBS_O_WORKDIR -# - echo " "; - OCEANCORES=88 - XIOSCORES=4 -ulimit -c unlimited -ulimit -s unlimited - -rm -f core - -#aprun -n $OCEANCORES -N 24 ./opa -aprun -b -n $XIOSCORES -N 4 ./xios_server.exe : -n $OCEANCORES -N 24 ./opa -#aprun -b -n $XIOCORES -N 1 ./xios_server.exe : -n $OCEANCORES -N 24 ./opa - -exit From 200db69570db931fc8733451ac581023b67f0064 Mon Sep 17 00:00:00 2001 From: jpolton Date: Wed, 8 Sep 2021 13:27:56 +0100 Subject: [PATCH 08/12] Delete RUN_DIRECTORIES/EXP_eORCAR12 directory --- RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_cfg | 247 --- .../EXP_eORCAR12/1_namelist_ice_cfg | 49 - .../EXP_eORCAR12/1_namelist_ice_ref | 1 - RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ref | 1 - RUN_DIRECTORIES/EXP_eORCAR12/context_nemo.xml | 122 -- .../EXP_eORCAR12/domain_def_nemo.xml | 1 - .../EXP_eORCAR12/field_def_nemo-lim.xml | 1 - .../EXP_eORCAR12/field_def_nemo-opa.xml | 1 - .../EXP_eORCAR12/field_def_nemo-pisces.xml | 1 - .../EXP_eORCAR12/file_def_nemo.xml | 132 -- RUN_DIRECTORIES/EXP_eORCAR12/iodef.xml | 26 - RUN_DIRECTORIES/EXP_eORCAR12/namelist_cfg | 1319 ----------------- RUN_DIRECTORIES/EXP_eORCAR12/namelist_ice_cfg | 48 - RUN_DIRECTORIES/EXP_eORCAR12/namelist_ice_ref | 1 - .../EXP_eORCAR12/namelist_pisces_cfg | 63 - .../EXP_eORCAR12/namelist_pisces_ref | 1 - RUN_DIRECTORIES/EXP_eORCAR12/namelist_ref | 1 - RUN_DIRECTORIES/EXP_eORCAR12/namelist_top_cfg | 109 -- RUN_DIRECTORIES/EXP_eORCAR12/namelist_top_ref | 1 - RUN_DIRECTORIES/EXP_eORCAR12/runscript | 30 - RUN_DIRECTORIES/EXP_eORCAR12/runscript_short | 33 - 21 files changed, 2188 deletions(-) delete mode 100755 RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_cfg delete mode 100755 RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ice_cfg delete mode 120000 RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ice_ref delete mode 120000 RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ref delete mode 100755 RUN_DIRECTORIES/EXP_eORCAR12/context_nemo.xml delete mode 120000 RUN_DIRECTORIES/EXP_eORCAR12/domain_def_nemo.xml delete mode 120000 RUN_DIRECTORIES/EXP_eORCAR12/field_def_nemo-lim.xml delete mode 120000 RUN_DIRECTORIES/EXP_eORCAR12/field_def_nemo-opa.xml delete mode 120000 RUN_DIRECTORIES/EXP_eORCAR12/field_def_nemo-pisces.xml delete mode 100755 RUN_DIRECTORIES/EXP_eORCAR12/file_def_nemo.xml delete mode 100755 RUN_DIRECTORIES/EXP_eORCAR12/iodef.xml delete mode 100755 RUN_DIRECTORIES/EXP_eORCAR12/namelist_cfg delete mode 100755 RUN_DIRECTORIES/EXP_eORCAR12/namelist_ice_cfg delete mode 120000 RUN_DIRECTORIES/EXP_eORCAR12/namelist_ice_ref delete mode 100755 RUN_DIRECTORIES/EXP_eORCAR12/namelist_pisces_cfg delete mode 120000 RUN_DIRECTORIES/EXP_eORCAR12/namelist_pisces_ref delete mode 120000 RUN_DIRECTORIES/EXP_eORCAR12/namelist_ref delete mode 100755 RUN_DIRECTORIES/EXP_eORCAR12/namelist_top_cfg delete mode 120000 RUN_DIRECTORIES/EXP_eORCAR12/namelist_top_ref delete mode 100755 RUN_DIRECTORIES/EXP_eORCAR12/runscript delete mode 100755 RUN_DIRECTORIES/EXP_eORCAR12/runscript_short diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_cfg b/RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_cfg deleted file mode 100755 index b49add1..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_cfg +++ /dev/null @@ -1,247 +0,0 @@ -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! NEMO/OPA : Configuration namelist used to overwrite SHARED/1_namelist_ref -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!----------------------------------------------------------------------- -&namrun ! parameters of the run -!----------------------------------------------------------------------- - cn_exp = "Agulhas" ! experience name - nn_it000 = 1 ! first time step - nn_itend = 10950 ! last time step - nn_stock = 10950 ! frequency of creation of a restart file (modulo referenced to 1) - nn_write = 10950 ! frequency of write in the output file (modulo referenced to nn_it000) - ln_clobber = .true. ! clobber (overwrite) an existing file -/ -!----------------------------------------------------------------------- -&namcfg ! parameters of the configuration -!----------------------------------------------------------------------- - ln_read_cfg = .true. ! (=T) read the domain configuration file - ! ! (=F) user defined configuration ==>>> see usrdef(_...) modules - cn_domcfg = "AGRIF_AGULHAS_domain_cfg" ! domain configuration filename -/ -!----------------------------------------------------------------------- -&namdom ! space and time domain (bathymetry, mesh, timestep) -!----------------------------------------------------------------------- - ln_linssh = .true. ! =T linear free surface ==>> model level are fixed in time - nn_closea = 0 ! remove (=0) or keep (=1) closed seas and lakes (ORCA) - ! - rn_rdt = 2880. ! time step for the dynamics (and tracer if nn_acc=0) - ! -/ -!----------------------------------------------------------------------- -&namcrs ! Grid coarsening for dynamics output and/or -! ! passive tracer coarsened online simulations -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namtsd ! data : Temperature & Salinity -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namsbc ! Surface Boundary Condition (surface module) -!----------------------------------------------------------------------- - ln_blk = .true. ! CORE bulk formulation (T => fill namsbc_core) - nn_ice = 3 ! =0 no ice boundary condition , - ! =1 use observed ice-cover , - ! =2 ice-model used ("key_lim3" or "key_lim2) - ln_rnf = .false. ! runoffs (T => fill namsbc_rnf) - ln_ssr = .false. ! Sea Surface Restoring on T and/or S (T => fill namsbc_ssr) - nn_fwb = 0 ! FreshWater Budget: =0 unchecked - ! =1 global mean of e-p-r set to zero at each time step - ! =2 annual global mean of e-p-r set to zero - ! =3 global emp set to zero and spread out over erp area -/ -!----------------------------------------------------------------------- -&namsbc_blk ! namsbc_blk generic Bulk formula (ln_blk = T) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_wndi = 'u_10.15JUNE2009_fill' , 6 , 'U_10_MOD', .false. , .true. , 'yearly' , 'weights_core2_agrif_bicubic.nc' , 'Uwnd' , '' - sn_wndj = 'v_10.15JUNE2009_fill' , 6 , 'V_10_MOD', .false. , .true. , 'yearly' , 'weights_core2_agrif_bicubic.nc' , 'Vwnd' , '' - sn_qsr = 'ncar_rad.15JUNE2009_fill' , 24 , 'SWDN_MOD', .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_qlw = 'ncar_rad.15JUNE2009_fill' , 24 , 'LWDN_MOD', .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_tair = 't_10.15JUNE2009_fill' , 6 , 'T_10_MOD', .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_humi = 'q_10.15JUNE2009_fill' , 6 , 'Q_10_MOD', .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_prec = 'ncar_precip.15JUNE2009_fill', -1 , 'PRC_MOD1', .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_snow = 'ncar_precip.15JUNE2009_fill', -1 , 'SNOW' , .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_slp = 'slp.15JUNE2009_fill' , 6 , 'SLP' , .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - sn_tdif = 'taudif_core' , 24 , 'taudif' , .false. , .true. , 'yearly' , 'weights_core2_agrif_bilinear.nc' , '' , '' - ! - ! ! bulk algorithm : - ln_NCAR = .true. ! "NCAR" algorithm (Large and Yeager 2008) - ! -/ -!----------------------------------------------------------------------- -&namtra_qsr ! penetrative solar radiation -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! - sn_chl ='chlorophyll', -1 , 'CHLA' , .true. , .true. , 'yearly' , 'weights_bilin.nc' , '' -/ -!----------------------------------------------------------------------- -&namlbc ! lateral momentum boundary condition -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namagrif ! AGRIF zoom ("key_agrif") -!----------------------------------------------------------------------- - nn_cln_update = 1 ! baroclinic update frequency -/ -!----------------------------------------------------------------------- -&nambfr ! bottom friction -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&nambbc ! bottom temperature boundary condition -!----------------------------------------------------------------------- - ln_trabbc = .true. ! Apply a geothermal heating at the ocean bottom -/ -!----------------------------------------------------------------------- -&nambbl ! bottom boundary layer scheme -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&nameos ! ocean physical parameters -!----------------------------------------------------------------------- - ln_teos10 = .true. ! = Use TEOS-10 equation of state -/ -!----------------------------------------------------------------------- -&namtra_dmp ! tracer: T & S newtonian damping -!----------------------------------------------------------------------- - ln_tradmp = .false. ! add a damping termn (T) or not (F) -/ -!----------------------------------------------------------------------- -&namtra_adv ! advection scheme for tracer -!----------------------------------------------------------------------- - ln_traadv_fct = .true. ! FCT scheme - nn_fct_h = 2 ! =2/4, horizontal 2nd / 4th order - nn_fct_v = 2 ! =2/4, vertical 2nd / COMPACT 4th order - nn_fct_zts = 0 ! >=1, 2nd order FCT scheme with vertical sub-timestepping - ! ! (number of sub-timestep = nn_fct_zts) -/ -!----------------------------------------------------------------------- -&namtra_ldf ! lateral diffusion scheme for tracers -!---------------------------------------------------------------------------------- - ! ! Operator type: - ln_traldf_lap = .true. ! laplacian operator - ln_traldf_blp = .false. ! bilaplacian operator - ! ! Direction of action: - ln_traldf_lev = .false. ! iso-level - ln_traldf_hor = .false. ! horizontal (geopotential) - ln_traldf_iso = .true. ! iso-neutral (Standard operator) - ln_traldf_triad = .false. ! iso-neutral (Triads operator) - ! - ! ! iso-neutral options: - ln_traldf_msc = .true. ! Method of Stabilizing Correction (both operators) - rn_slpmax = 0.01 ! slope limit (both operators) - ln_triad_iso = .false. ! pure horizontal mixing in ML (triad only) - rn_sw_triad = 1 ! =1 switching triad ; =0 all 4 triads used (triad only) - ln_botmix_triad = .false. ! lateral mixing on bottom (triad only) - ! - ! ! Coefficients: - nn_aht_ijk_t = 20 ! space/time variation of eddy coef - ! ! =-20 (=-30) read in eddy_diffusivity_2D.nc (..._3D.nc) file - ! ! = 0 constant - ! ! = 10 F(k) =ldf_c1d - ! ! = 20 F(i,j) =ldf_c2d - ! ! = 21 F(i,j,t) =Treguier et al. JPO 1997 formulation - ! ! = 30 F(i,j,k) =ldf_c2d + ldf_c1d - ! ! = 31 F(i,j,k,t)=F(local velocity) - rn_aht_0 = 1000. ! lateral eddy diffusivity (lap. operator) [m2/s] - rn_bht_0 = 1.e+12 ! lateral eddy diffusivity (bilap. operator) [m4/s] -/ -!---------------------------------------------------------------------------------- -&namtra_ldfeiv ! eddy induced velocity param. -!---------------------------------------------------------------------------------- - ln_ldfeiv =.false. ! use eddy induced velocity parameterization -/ -!----------------------------------------------------------------------- -&namdyn_adv ! formulation of the momentum advection -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namdyn_vor ! option of physics/algorithm (not control by CPP keys) -!----------------------------------------------------------------------- - ln_dynvor_ene = .false. ! enstrophy conserving scheme - ln_dynvor_ens = .false. ! energy conserving scheme - ln_dynvor_mix = .false. ! mixed scheme - ln_dynvor_een = .true. ! energy & enstrophy scheme - nn_een_e3f = 0 ! e3f = masked averaging of e3t divided by 4 (=0) or by the sum of mask (=1) -/ -!----------------------------------------------------------------------- -&namdyn_hpg ! Hydrostatic pressure gradient option -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namdyn_spg ! surface pressure gradient -!----------------------------------------------------------------------- - ln_dynspg_ts = .true. ! split-explicit free surface -/ -!----------------------------------------------------------------------- -&namdyn_ldf ! lateral diffusion on momentum -!----------------------------------------------------------------------- - ! ! Type of the operator : - ! ! no diffusion: set ln_dynldf_lap=..._blp=F - ln_dynldf_lap = .false. ! laplacian operator - ln_dynldf_blp = .true. ! bilaplacian operator - ! ! Direction of action : - ln_dynldf_lev = .true. ! iso-level - ln_dynldf_hor = .false. ! horizontal (geopotential) - ln_dynldf_iso = .false. ! iso-neutral - ! ! Coefficient - nn_ahm_ijk_t = 0 ! space/time variation of eddy coef - ! ! =-30 read in eddy_viscosity_3D.nc file - ! ! =-20 read in eddy_viscosity_2D.nc file - ! ! = 0 constant - ! ! = 10 F(k)=c1d - ! ! = 20 F(i,j)=F(grid spacing)=c2d - ! ! = 30 F(i,j,k)=c2d*c1d - ! ! = 31 F(i,j,k)=F(grid spacing and local velocity) - rn_ahm_0 = 40000. ! horizontal laplacian eddy viscosity [m2/s] - rn_ahm_b = 0. ! background eddy viscosity for ldf_iso [m2/s] - rn_bhm_0 = 8.5e+11 ! horizontal bilaplacian eddy viscosity [m4/s] -/ -!----------------------------------------------------------------------- -&namzdf ! vertical physics -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namzdf_tke ! turbulent eddy kinetic dependent vertical diffusion ("key_zdftke") -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namzdf_ddm ! double diffusive mixing parameterization ("key_zdfddm") -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namzdf_tmx ! tidal mixing parameterization ("key_zdftmx") -!----------------------------------------------------------------------- - ln_tmx_itf = .false. ! ITF specific parameterisation -/ -!----------------------------------------------------------------------- -&nammpp ! Massively Parallel Processing ("key_mpp_mpi) -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&nammpp_dyndist ! Massively Parallel Distribution for AGRIF zoom ("key_agrif" && "key_mpp_dyndist") -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namctl ! Control prints & Benchmark -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namptr ! Poleward Transport Diagnostic -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namhsb ! Heat and salt budgets -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namobs ! observation usage ('key_diaobs') -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&nam_asminc ! assimilation increments ('key_asminc') -!----------------------------------------------------------------------- -/ diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ice_cfg b/RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ice_cfg deleted file mode 100755 index 8a2e1fd..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ice_cfg +++ /dev/null @@ -1,49 +0,0 @@ -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! NEMO/LIM3 configuration namelist: Overwrites 1_namelist_ice_ref -!! 1 - Generic parameters (namicerun) -!! 2 - Diagnostics (namicediag) -!! 3 - Ice initialization (namiceini) -!! 4 - Ice discretization (namiceitd) -!! 5 - Ice dynamics and transport (namicedyn) -!! 6 - Ice diffusion (namicehdf) -!! 7 - Ice thermodynamics (namicethd) -!! 8 - Ice salinity (namicesal) -!! 9 - Ice mechanical redistribution (namiceitdme) -!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!------------------------------------------------------------------------------ -&namicerun ! Generic parameters -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicediag ! Diagnostics -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namiceini ! Ice initialization -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namiceitd ! Ice discretization -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicedyn ! Ice dynamics and transport -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicehdf ! Ice horizontal diffusion -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicethd ! Ice thermodynamics -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicesal ! Ice salinity -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namiceitdme ! Ice mechanical redistribution (ridging and rafting) -!------------------------------------------------------------------------------ -/ diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ice_ref b/RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ice_ref deleted file mode 120000 index f945af9..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ice_ref +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/1_namelist_ice_ref \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ref b/RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ref deleted file mode 120000 index 9c9608b..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/1_namelist_ref +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/1_namelist_ref \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/context_nemo.xml b/RUN_DIRECTORIES/EXP_eORCAR12/context_nemo.xml deleted file mode 100755 index e25fc9d..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/context_nemo.xml +++ /dev/null @@ -1,122 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/domain_def_nemo.xml b/RUN_DIRECTORIES/EXP_eORCAR12/domain_def_nemo.xml deleted file mode 120000 index 59f94cc..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/domain_def_nemo.xml +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/domain_def_nemo.xml \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/field_def_nemo-lim.xml b/RUN_DIRECTORIES/EXP_eORCAR12/field_def_nemo-lim.xml deleted file mode 120000 index 9d4fc40..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/field_def_nemo-lim.xml +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/field_def_nemo-lim.xml \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/field_def_nemo-opa.xml b/RUN_DIRECTORIES/EXP_eORCAR12/field_def_nemo-opa.xml deleted file mode 120000 index c3ab102..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/field_def_nemo-opa.xml +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/field_def_nemo-opa.xml \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/field_def_nemo-pisces.xml b/RUN_DIRECTORIES/EXP_eORCAR12/field_def_nemo-pisces.xml deleted file mode 120000 index 0c986f0..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/field_def_nemo-pisces.xml +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/field_def_nemo-pisces.xml \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/file_def_nemo.xml b/RUN_DIRECTORIES/EXP_eORCAR12/file_def_nemo.xml deleted file mode 100755 index 91705ba..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/file_def_nemo.xml +++ /dev/null @@ -1,132 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/iodef.xml b/RUN_DIRECTORIES/EXP_eORCAR12/iodef.xml deleted file mode 100755 index b49154c..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/iodef.xml +++ /dev/null @@ -1,26 +0,0 @@ - - - - - - - - - - - - 10 - true - false - oceanx - - - - - - - - - - - diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_cfg b/RUN_DIRECTORIES/EXP_eORCAR12/namelist_cfg deleted file mode 100755 index ee0cbb8..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_cfg +++ /dev/null @@ -1,1319 +0,0 @@ -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! namelist_ref -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! NEMO/OPA : 1 - run manager (namrun) -!! namelists 2 - Domain (namcfg, namzgr, namdom, namtsd, namcrs, namc1d, namc1d_uvd) -!! 3 - Surface boundary (namsbc, namsbc_flx, namsbc_blk, namsbc_sas) -!! namsbc_cpl, namtra_qsr, namsbc_rnf, -!! namsbc_apr, namsbc_ssr, namsbc_alb, namsbc_wave) -!! 4 - lateral boundary (namlbc, namagrif, nambdy, nambdy_tide) -!! 5 - bottom boundary (nambfr, nambbc, nambbl) -!! 6 - Tracer (nameos, namtra_adv, namtra_ldf, namtra_ldfeiv, namtra_dmp) -!! 7 - dynamics (namdyn_adv, namdyn_vor, namdyn_hpg, namdyn_spg, namdyn_ldf) -!! 8 - Verical physics (namzdf, namzdf_ric, namzdf_tke, namzdf_ddm, namzdf_tmx, namzdf_tmx_new) -!! 9 - diagnostics (namnc4, namtrd, namspr, namflo, namhsb, namsto) -!! 10 - miscellaneous (nammpp, namctl) -!! 11 - Obs & Assim (namobs, nam_asminc) -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - -!!====================================================================== -!! *** Run management namelists *** -!!====================================================================== -!! namrun parameters of the run -!!====================================================================== -! -!----------------------------------------------------------------------- -&namrun ! parameters of the run -!----------------------------------------------------------------------- - cn_exp = "SEAsia" ! experience name - nn_it000 = 172561 ! 86401 ! first time step - nn_itend = 263040 ! 1200 ! 960 ! 1920 ! 7200 ! 1 days. 10day=14400 ! last time step (std 5475) - nn_date0 = 19600101 ! date at nit_0000 (format yyyymmdd) used if ln_rstart=F or (ln_rstart=T and nn_rstctl=0 or 1) - nn_time0 = 0 ! initial time of day in hhmm - nn_leapy = 1 ! Leap year calendar (1) or not (0) - ln_rstart = .true. ! start from rest (F) or from a restart file (T) - nn_euler = 1 ! = 0 : start with forward time step if ln_rstart=T - nn_rstctl = 2 ! restart control ==> activated only if ln_rstart=T - ! ! = 0 nn_date0 read in namelist ; nn_it000 : read in namelist - ! ! = 1 nn_date0 read in namelist ; nn_it000 : check consistancy between namelist and restart - ! ! = 2 nn_date0 read in restart ; nn_it000 : check consistancy between namelist and restart - cn_ocerst_in = "SEAsia_00172560_restart" ! suffix of ocean restart name (input) - cn_ocerst_indir = "./restarts" ! directory from which to read input ocean restarts - cn_ocerst_out = "restart" ! suffix of ocean restart name (output) - cn_ocerst_outdir= "./restarts" ! directory in which to write output ocean restarts - ln_iscpl = .false. ! cavity evolution forcing or coupling to ice sheet model - nn_istate = 0 ! output the initial state (1) or not (0) - ln_rst_list = .false. ! output restarts at list of times using nn_stocklist (T) or at set frequency with nn_stock (F) - nn_stock = 7200 ! 960 ! 7200 ! 14400 ! frequency of creation of a restart file (modulo referenced to 1) - nn_stocklist = 0,0,0,0,0,0,0,0,0,0 ! List of timesteps when a restart file is to be written - nn_write = 7200! 960 ! 7200 ! 1440 ! frequency of write in the output file (modulo referenced to nn_it000) - ln_mskland = .false. ! mask land points in NetCDF outputs (costly: + ~15%) - ln_cfmeta = .false. ! output additional data to netCDF files required for compliance with the CF metadata standard - ln_clobber = .true. ! clobber (overwrite) an existing file - nn_chunksz = 0 ! chunksize (bytes) for NetCDF file (works only with iom_nf90 routines) -/ -! -!!====================================================================== -!! *** Domain namelists *** -!!====================================================================== -!! namcfg parameters of the configuration -!! namzgr vertical coordinate (default: NO selection) -!! namdom space and time domain (bathymetry, mesh, timestep) -!! namwad Wetting and drying (default F) -!! namtsd data: temperature & salinity -!! namcrs coarsened grid (for outputs and/or TOP) ("key_crs") -!! namc1d 1D configuration options ("key_c1d") -!! namc1d_dyndmp 1D newtonian damping applied on currents ("key_c1d") -!! namc1d_uvd 1D data (currents) ("key_c1d") -!!====================================================================== -! -!----------------------------------------------------------------------- -&namcfg ! parameters of the configuration -!----------------------------------------------------------------------- - ln_read_cfg = .true. ! (=T) read the domain configuration file - ! ! (=F) user defined configuration ==>>> see usrdef(_...) modules - cn_domcfg = "../INPUTS/domain_cfg_eORCAR12.nc" ! domain configuration filename - ! - ln_write_cfg= .false. ! (=T) create the domain configuration file - cn_domcfg_out = "domain_cfg_out" ! newly created domain configuration filename - ! - ln_use_jattr = .false. ! use (T) the file attribute: open_ocean_jstart, if present - ! ! in netcdf input files, as the start j-row for reading -/ -!----------------------------------------------------------------------- -&namzgr ! vertical coordinate (default: NO selection) -!----------------------------------------------------------------------- - ln_zco = .false. ! z-coordinate - full steps - ln_zps = .false. ! z-coordinate - partial steps - ln_sco = .true. ! s- or hybrid z-s-coordinate - ln_isfcav = .false. ! ice shelf cavity -! ln_linssh = .false. ! linear free surface -/ -!----------------------------------------------------------------------- -&namzgr_sco -!----------------------------------------------------------------------- - ln_s_sf12=.false., - ln_s_sh94=.true., - ln_sigcrit=.false., - rn_alpha=4.4, - rn_bb=0.8, - rn_efold=0.0, - rn_hc=39.0, - rn_rmax=0.05, - rn_sbot_max=6000.0, - rn_sbot_min=10., - rn_theta=6.0, - rn_thetb=1.0, - rn_zb_a=0.024, - rn_zb_b=-0.2, - rn_zs=1.0, -/ -!----------------------------------------------------------------------- -&namdom ! space and time domain (bathymetry, mesh, timestep) -!----------------------------------------------------------------------- - - ln_linssh = .false. ! =T linear free surface ==>> model level are fixed in time - nn_closea = 0 ! remove (=0) or keep (=1) closed seas and lakes (ORCA) - ! - nn_msh = 0 ! create (>0) a mesh file or not (=0) - rn_isfhmin = 1.00 ! treshold (m) to discriminate grounding ice to floating ice - ! - rn_rdt = 360 ! 360. ! time step for the dynamics (and tracer if nn_acc=0) - rn_atfp = 0.1 ! asselin time filter parameter - ! - ln_crs = .false. ! Logical switch for coarsening module -! ldbletanh = .false. ! Use/do not use double tanf function for vertical coordinates -/ -!----------------------------------------------------------------------- -&namtsd ! data : Temperature & Salinity -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_tem = 'votemper_ORCA0083-N06-SEAsia_1960.nc', -12 ,'votemper' , .false. , .true. , 'yearly' , '' , '' , '' - sn_sal = 'vosaline_ORCA0083-N06-SEAsia_1960.nc', -12 ,'vosaline' , .false. , .true. , 'yearly' , '' , '' , '' - sn_dep = 'initcd_depth.nc' , -12 ,'gdept_4D', .false. , .true. , 'yearly' , '' , '' , '' - sn_msk = 'initcd_mask.nc' , -12 ,'mask', .false. , .true. , 'yearly' , '' , '' , '' - - ! - cn_dir = '../INPUTS/ICS/' ! root directory for the location of the runoff files - ln_tsd_init = .true. ! Initialisation of ocean T & S with T &S input data (T) or not (F) - ln_tsd_interp = .true. ! Interpolation of T & S in the verticalinput data (T) or not (F) - ln_tsd_tradmp = .false. ! damping of ocean T & S toward T &S input data (T) or not (F) -/ -!----------------------------------------------------------------------- -&namwad ! Wetting and drying (default F) -!----------------------------------------------------------------------- - ln_wd = .false. ! T/F activation of wetting and drying - rn_wdmin1 = 0.1 ! Minimum wet depth on dried cells - rn_wdmin2 = 0.01 ! Tolerance of min wet depth on dried cells - rn_wdld = 20.0 ! Land elevation below which wetting/drying is allowed - nn_wdit = 10 ! Max iterations for W/D limiter -/ -!----------------------------------------------------------------------- -&namcrs ! coarsened grid (for outputs and/or TOP) ("key_crs") -!----------------------------------------------------------------------- - nn_factx = 3 ! Reduction factor of x-direction - nn_facty = 3 ! Reduction factor of y-direction - nn_binref = 0 ! Bin centering preference: NORTH or EQUAT - ! 0, coarse grid is binned with preferential treatment of the north fold - ! 1, coarse grid is binned with centering at the equator - ! Symmetry with nn_facty being odd-numbered. Asymmetry with even-numbered nn_facty. - nn_msh_crs = 1 ! create (=1) a mesh file or not (=0) - nn_crs_kz = 0 ! 0, MEAN of volume boxes - ! 1, MAX of boxes - ! 2, MIN of boxes - ln_crs_wn = .true. ! wn coarsened (T) or computed using horizontal divergence ( F ) -/ -!----------------------------------------------------------------------- -&namc1d ! 1D configuration options ("key_c1d") -!----------------------------------------------------------------------- - rn_lat1d = 50 ! Column latitude (default at PAPA station) - rn_lon1d = -145 ! Column longitude (default at PAPA station) - ln_c1d_locpt= .true. ! Localization of 1D config in a grid (T) or independant point (F) -/ -!----------------------------------------------------------------------- -&namc1d_dyndmp ! U & V newtonian damping ("key_c1d") -!----------------------------------------------------------------------- - ln_dyndmp = .false. ! add a damping term (T) or not (F) -/ -!----------------------------------------------------------------------- -&namc1d_uvd ! data: U & V currents ("key_c1d") -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_ucur = 'ucurrent' , -1 ,'u_current', .false. , .true. , 'monthly' , '' , 'Ume' , '' - sn_vcur = 'vcurrent' , -1 ,'v_current', .false. , .true. , 'monthly' , '' , 'Vme' , '' -! - cn_dir = './' ! root directory for the location of the files - ln_uvd_init = .false. ! Initialisation of ocean U & V with U & V input data (T) or not (F) - ln_uvd_dyndmp = .false. ! damping of ocean U & V toward U & V input data (T) or not (F) -/ - -!!====================================================================== -!! *** Surface Boundary Condition namelists *** -!!====================================================================== -!! namsbc surface boundary condition -!! namsbc_flx flux formulation (ln_flx =T) -!! namsbc_blk Bulk formulae formulation (ln_blk =T) -!! namsbc_cpl CouPLed formulation ("key_oasis3" ) -!! namsbc_sas Stand-Alone Surface module -!! namtra_qsr penetrative solar radiation (ln_traqsr =T) -!! namsbc_rnf river runoffs (ln_rnf =T) -!! namsbc_isf ice shelf melting/freezing (nn_isf >0) -!! namsbc_iscpl coupling option between land ice model and ocean -!! namsbc_apr Atmospheric Pressure (ln_apr_dyn =T) -!! namsbc_ssr sea surface restoring term (for T and/or S) (ln_ssr =T) -!! namsbc_alb albedo parameters -!! namsbc_wave external fields from wave model (ln_wave =T) -!! namberg iceberg floats (ln_icebergs=T) -!!====================================================================== -! -!----------------------------------------------------------------------- -&namsbc ! Surface Boundary Condition (surface module) -!----------------------------------------------------------------------- - nn_fsbc = 1 ! frequency of surface boundary condition computation - ! (also = the frequency of sea-ice & iceberg model call) - ! Type of air-sea fluxes - ln_usr = .false. ! user defined formulation (T => check usrdef_sbc) - ln_flx = .false. ! flux formulation (T => fill namsbc_flx ) - ln_blk = .true. ! Bulk formulation (T => fill namsbc_blk ) - ! Type of coupling (Ocean/Ice/Atmosphere) : - ln_cpl = .false. ! atmosphere coupled formulation ( requires key_oasis3 ) - ln_mixcpl = .false. ! forced-coupled mixed formulation ( requires key_oasis3 ) - nn_components = 0 ! configuration of the opa-sas OASIS coupling - ! =0 no opa-sas OASIS coupling: default single executable configuration - ! =1 opa-sas OASIS coupling: multi executable configuration, OPA component - ! =2 opa-sas OASIS coupling: multi executable configuration, SAS component - nn_limflx = -1 ! LIM3 Multi-category heat flux formulation (use -1 if LIM3 is not used) - ! =-1 Use per-category fluxes, bypass redistributor, forced mode only, not yet implemented coupled - ! = 0 Average per-category fluxes (forced and coupled mode) - ! = 1 Average and redistribute per-category fluxes, forced mode only, not yet implemented coupled - ! = 2 Redistribute a single flux over categories (coupled mode only) - ! Sea-ice : - nn_ice = 0 ! =0 no ice boundary condition , - ! =1 use observed ice-cover , - ! =2 to 4 : ice-model used (LIM2, LIM3 or CICE) ("key_lim3", "key_lim2", or "key_cice") - nn_ice_embd = 1 ! =0 levitating ice (no mass exchange, concentration/dilution effect) - ! =1 levitating ice with mass and salt exchange but no presure effect - ! =2 embedded sea-ice (full salt and mass exchanges and pressure) - ! Misc. options of sbc : - ln_traqsr = .false. ! Light penetration in the ocean (T => fill namtra_qsr) - ln_dm2dc = .false. ! daily mean to diurnal cycle on short wave - ln_rnf = .true. ! runoffs (T => fill namsbc_rnf) - ln_ssr = .false. ! Sea Surface Restoring on T and/or S (T => fill namsbc_ssr) - nn_fwb = 0 ! FreshWater Budget: =0 unchecked - ! =1 global mean of e-p-r set to zero at each time step - ! =2 annual global mean of e-p-r set to zero - ln_apr_dyn = .false. ! Patm gradient added in ocean & ice Eqs. (T => fill namsbc_apr ) - ln_isf = .false. ! ice shelf (T => fill namsbc_isf) - ln_wave = .false. ! Activate coupling with wave (T => fill namsbc_wave) - ln_cdgw = .false. ! Neutral drag coefficient read from wave model (T => ln_wave=.true. & fill namsbc_wave) - ln_sdw = .false. ! Read 2D Surf Stokes Drift & Computation of 3D stokes drift (T => ln_wave=.true. & fill namsbc_wave) - ln_tauoc = .false. ! Activate ocean stress modified by external wave induced stress (T => ln_wave=.true. & fill namsbc_wave) - ln_stcor = .false. ! Activate Stokes Coriolis term (T => ln_wave=.true. & ln_sdw=.true. & fill namsbc_wave) - nn_lsm = 0 ! =0 land/sea mask for input fields is not applied (keep empty land/sea mask filename field) , - ! =1:n number of iterations of land/sea mask application for input fields (fill land/sea mask filename field) -/ -!----------------------------------------------------------------------- -&namsbc_flx ! surface boundary condition : flux formulation -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_utau = 'utau' , 24 , 'utau' , .false. , .false., 'yearly' , '' , '' , '' - sn_vtau = 'vtau' , 24 , 'vtau' , .false. , .false., 'yearly' , '' , '' , '' - sn_qtot = 'qtot' , 24 , 'qtot' , .false. , .false., 'yearly' , '' , '' , '' - sn_qsr = 'qsr' , 24 , 'qsr' , .false. , .false., 'yearly' , '' , '' , '' - sn_emp = 'emp' , 24 , 'emp' , .false. , .false., 'yearly' , '' , '' , '' - - cn_dir = './' ! root directory for the location of the flux files -/ -!----------------------------------------------------------------------- -&namsbc_blk ! namsbc_blk generic Bulk formula (ln_blk = T) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_wndi = 'drowned_u10_DFS5.2' , 3 , 'u10', .false. , .false. , 'yearly' , 'weights_bicubic_atmos.nc' , 'Uwnd' , '' - sn_wndj = 'drowned_v10_DFS5.2' , 3 , 'v10', .false. , .false. , 'yearly' , 'weights_bicubic_atmos.nc' , 'Vwnd' , '' - sn_qsr = 'drowned_radsw_DFS5.2' , 24 , 'radsw', .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - sn_qlw = 'drowned_radlw_DFS5.2' , 24 , 'radlw', .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - sn_tair = 'drowned_t2_DFS5.2' , 3 , 't2', .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - sn_humi = 'drowned_q2_DFS5.2' , 3 , 'q2', .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - sn_prec = 'drowned_precip_DFS5.2' , 24 , 'precip', .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - sn_snow = 'drowned_snow_DFS5.2' , 24 , 'snow' , .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - sn_slp = 'drowned_t2_DFS5.2' , 3 , 't2', .false. , .false. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' ! DUMMY variable. Fill with T -! sn_slp = 'slp.15JUNE2009_fill' , 6 , 'SLP' , .false. , .true. , 'yearly' , 'weights_core_orca2_bilinear_noc.nc' , '' , '' -! sn_tdif = 'taudif_core' , 24 , 'taudif' , .false. , .true. , 'yearly' , 'weights_bilinear_atmos.nc' , '' , '' - ! ! bulk algorithm : - ln_NCAR = .true. ! "NCAR" algorithm (Large and Yeager 2008) - ln_COARE_3p0= .false. ! "COARE 3.0" algorithm (Fairall et al. 2003) - ln_COARE_3p5= .false. ! "COARE 3.5" algorithm (Edson et al. 2013) - ln_ECMWF = .false. ! "ECMWF" algorithm (IFS cycle 31) - ! - cn_dir = '../INPUTS/SBC/' ! root directory for the location of the bulk files - ln_taudif = .false. ! HF tau contribution: use "mean of stress module - module of the mean stress" data - rn_zqt = 2. ! Air temperature and humidity reference height (m) - rn_zu = 10. ! Wind vector reference height (m) - rn_pfac = 1. ! multiplicative factor for precipitation (total & snow) - rn_efac = 1. ! multiplicative factor for evaporation (0. or 1.) - rn_vfac = 0. ! multiplicative factor for ocean/ice velocity - ! in the calculation of the wind stress (0.=absolute winds or 1.=relative winds) - ln_Cd_L12 = .false. ! Modify the drag ice-atm and oce-atm depending on ice concentration - ! This parameterization is from Lupkes et al. (JGR 2012) -/ -!----------------------------------------------------------------------- -&namsbc_cpl ! coupled ocean/atmosphere model ("key_oasis3") -!----------------------------------------------------------------------- -! ! description ! multiple ! vector ! vector ! vector ! -! ! ! categories ! reference ! orientation ! grids ! -! send - sn_snd_temp = 'weighted oce and ice' , 'no' , '' , '' , '' - sn_snd_alb = 'weighted ice' , 'no' , '' , '' , '' - sn_snd_thick = 'none' , 'no' , '' , '' , '' - sn_snd_crt = 'none' , 'no' , 'spherical' , 'eastward-northward' , 'T' - sn_snd_co2 = 'coupled' , 'no' , '' , '' , '' - sn_snd_crtw = 'none' , 'no' , '' , '' , 'U,V' - sn_snd_ifrac = 'none' , 'no' , '' , '' , '' - sn_snd_wlev = 'coupled' , 'no' , '' , '' , '' -! receive - sn_rcv_w10m = 'none' , 'no' , '' , '' , '' - sn_rcv_taumod = 'coupled' , 'no' , '' , '' , '' - sn_rcv_tau = 'oce only' , 'no' , 'cartesian' , 'eastward-northward', 'U,V' - sn_rcv_dqnsdt = 'coupled' , 'no' , '' , '' , '' - sn_rcv_qsr = 'oce and ice' , 'no' , '' , '' , '' - sn_rcv_qns = 'oce and ice' , 'no' , '' , '' , '' - sn_rcv_emp = 'conservative' , 'no' , '' , '' , '' - sn_rcv_rnf = 'coupled' , 'no' , '' , '' , '' - sn_rcv_cal = 'coupled' , 'no' , '' , '' , '' - sn_rcv_co2 = 'coupled' , 'no' , '' , '' , '' - sn_rcv_hsig = 'none' , 'no' , '' , '' , '' - sn_rcv_iceflx = 'none' , 'no' , '' , '' , '' - sn_rcv_mslp = 'none' , 'no' , '' , '' , '' - sn_rcv_phioc = 'none' , 'no' , '' , '' , '' - sn_rcv_sdrfx = 'none' , 'no' , '' , '' , '' - sn_rcv_sdrfy = 'none' , 'no' , '' , '' , '' - sn_rcv_wper = 'none' , 'no' , '' , '' , '' - sn_rcv_wnum = 'none' , 'no' , '' , '' , '' - sn_rcv_wstrf = 'none' , 'no' , '' , '' , '' - sn_rcv_wdrag = 'none' , 'no' , '' , '' , '' -! - nn_cplmodel = 1 ! Maximum number of models to/from which NEMO is potentialy sending/receiving data - ln_usecplmask = .false. ! use a coupling mask file to merge data received from several models - ! ! -> file cplmask.nc with the float variable called cplmask (jpi,jpj,nn_cplmodel) -/ -!----------------------------------------------------------------------- -&namsbc_sas ! Stand Alone Surface boundary condition -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - l_sasread = .TRUE. ! Read fields in a file if .TRUE. , or initialize to 0. in sbcssm.F90 if .FALSE. - sn_usp = 'sas_grid_U', 120 , 'vozocrtx', .true. , .true. , 'yearly' , '' , '' , '' - sn_vsp = 'sas_grid_V', 120 , 'vomecrty', .true. , .true. , 'yearly' , '' , '' , '' - sn_tem = 'sas_grid_T', 120 , 'sosstsst', .true. , .true. , 'yearly' , '' , '' , '' - sn_sal = 'sas_grid_T', 120 , 'sosaline', .true. , .true. , 'yearly' , '' , '' , '' - sn_ssh = 'sas_grid_T', 120 , 'sossheig', .true. , .true. , 'yearly' , '' , '' , '' - sn_e3t = 'sas_grid_T', 120 , 'e3t_m' , .true. , .true. , 'yearly' , '' , '' , '' - sn_frq = 'sas_grid_T', 120 , 'frq_m' , .true. , .true. , 'yearly' , '' , '' , '' - - ln_3d_uve = .true. ! specify whether we are supplying a 3D u,v and e3 field - ln_read_frq = .false. ! specify whether we must read frq or not - cn_dir = './' ! root directory for the location of the bulk files are -/ -!----------------------------------------------------------------------- -&namtra_qsr ! penetrative solar radiation (ln_traqsr=T) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_chl ='chlorophyll', -1 , 'CHLA' , .true. , .true. , 'yearly' , '' , '' , '' - - cn_dir = './' ! root directory for the location of the runoff files - ln_qsr_rgb = .false. ! RGB (Red-Green-Blue) light penetration - ln_qsr_2bd = .true. ! 2 bands light penetration - ln_qsr_bio = .false. ! bio-model light penetration - nn_chldta = 0 ! RGB : Chl data (=1) or cst value (=0) - rn_abs = 0.58 ! RGB & 2 bands: fraction of light (rn_si1) - rn_si0 = 0.35 ! RGB & 2 bands: shortess depth of extinction - rn_si1 = 23.0 ! 2 bands: longest depth of extinction - ln_qsr_ice = .false. ! light penetration for ice-model LIM3 -/ -!----------------------------------------------------------------------- -&namsbc_rnf ! runoffs namelist surface boundary condition (ln_rnf=T) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_rnf = 'SEAsia_rivers', -1 , 'sorunoff', .true. , .true. , 'yearly' , '' , '' , '' - sn_cnf = 'SEAsia_rivers', 0 , 'socoefr', .false. , .true. , 'yearly' , '' , '' , '' - - cn_dir = '../INPUTS/RIVERS/' ! root directory for the location of the runoff files - ln_rnf_mouth= .false. ! specific treatment at rivers mouths - rn_hrnf = 15.e0 ! depth over which enhanced vertical mixing is used (ln_rnf_mouth=T) - rn_avt_rnf = 1.e-3 ! value of the additional vertical mixing coef. [m2/s] (ln_rnf_mouth=T) - rn_rfact = 1.e0 ! multiplicative factor for runoff - ln_rnf_depth= .false. ! read in depth information for runoff - ln_rnf_tem = .false. ! read in temperature information for runoff - ln_rnf_sal = .false. ! read in salinity information for runoff - ln_rnf_depth_ini = .false. ! compute depth at initialisation from runoff file - rn_rnf_max = 1.6224 ! 5.735e-4 ! max value of the runoff climatologie over global domain ( ln_rnf_depth_ini = .true ) - rn_dep_max = 50. ! depth over which runoffs is spread ( ln_rnf_depth_ini = .true ) - nn_rnf_depth_file = 0 ! create (=1) a runoff depth file or not (=0) -/ -!----------------------------------------------------------------------- -&namsbc_isf ! Top boundary layer (ISF) (nn_isf >0) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! -! nn_isf == 4 - sn_fwfisf = 'rnfisf' , -12 ,'sowflisf', .false. , .true. , 'yearly' , '' , '' , '' -! nn_isf == 3 - sn_rnfisf = 'rnfisf' , -12 ,'sofwfisf', .false. , .true. , 'yearly' , '' , '' , '' -! nn_isf == 2 and 3 - sn_depmax_isf='rnfisf' , -12 ,'sozisfmax', .false. , .true. , 'yearly' , '' , '' , '' - sn_depmin_isf='rnfisf' , -12 ,'sozisfmin', .false. , .true. , 'yearly' , '' , '' , '' -! nn_isf == 2 - sn_Leff_isf = 'rnfisf' , -12 ,'Leff' , .false. , .true. , 'yearly' , '' , '' , '' -! -! for all case - nn_isf = 0 ! ice shelf melting/freezing - ! 1 = presence of ISF 2 = bg03 parametrisation - ! 3 = rnf file for isf 4 = ISF fwf specified - ! option 1 and 4 need ln_isfcav = .true. (domzgr) -! only for nn_isf = 1 or 2 - rn_gammat0 = 1.e-4 ! gammat coefficient used in blk formula - rn_gammas0 = 1.e-4 ! gammas coefficient used in blk formula -! only for nn_isf = 1 or 4 - rn_hisf_tbl = 30. ! thickness of the top boundary layer (Losh et al. 2008) - ! ! 0 => thickness of the tbl = thickness of the first wet cell -! only for nn_isf = 1 - nn_isfblk = 1 ! 1 ISOMIP like: 2 equations formulation (Hunter et al., 2006) - ! ! 2 ISOMIP+ like: 3 equations formulation (Asay-Davis et al., 2015) - nn_gammablk = 1 ! 0 = cst Gammat (= gammat/s) - ! ! 1 = velocity dependend Gamma (u* * gammat/s) (Jenkins et al. 2010) - ! ! 2 = velocity and stability dependent Gamma (Holland et al. 1999) -/ -!----------------------------------------------------------------------- -&namsbc_iscpl ! land ice / ocean coupling option -!----------------------------------------------------------------------- - nn_drown = 10 ! number of iteration of the extrapolation loop (fill the new wet cells) - ln_hsb = .false. ! activate conservation module (conservation exact after a time of rn_fiscpl) - nn_fiscpl = 43800 ! (number of time step) conservation period (maybe should be fix to the coupling frequencey of restart frequency) -/ -!----------------------------------------------------------------------- -&namsbc_apr ! Atmospheric pressure used as ocean forcing (ln_apr_dyn =T) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_apr = 'patm' , -1 ,'somslpre', .true. , .true. , 'yearly' , '' , '' , '' - - cn_dir = './' ! root directory for the location of the bulk files - rn_pref = 101000. ! reference atmospheric pressure [N/m2]/ - ln_ref_apr = .false. ! ref. pressure: global mean Patm (T) or a constant (F) - ln_apr_obc = .false. ! inverse barometer added to OBC ssh data -/ -!----------------------------------------------------------------------- -&namsbc_ssr ! surface boundary condition : sea surface restoring (ln_ssr=T) -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_sst = 'sst_data', 24 , 'sst' , .false. , .false., 'yearly' , '' , '' , '' - sn_sss = 'sss_data', -1 , 'sss' , .true. , .true. , 'yearly' , '' , '' , '' - - cn_dir = './' ! root directory for the location of the runoff files - nn_sstr = 0 ! add a retroaction term in the surface heat flux (=1) or not (=0) - nn_sssr = 0 ! add a damping term in the surface freshwater flux (=2) - ! or to SSS only (=1) or no damping term (=0) - rn_dqdt = -40. ! magnitude of the retroaction on temperature [W/m2/K] - rn_deds = -166.67 ! magnitude of the damping on salinity [mm/day] - ln_sssr_bnd = .true. ! flag to bound erp term (associated with nn_sssr=2) - rn_sssr_bnd = 4.e0 ! ABS(Max/Min) value of the damping erp term [mm/day] -/ -!----------------------------------------------------------------------- -&namsbc_alb ! albedo parameters -!----------------------------------------------------------------------- - nn_ice_alb = 0 ! parameterization of ice/snow albedo - ! 0: Shine & Henderson-Sellers (JGR 1985) - ! 1: "home made" based on Brandt et al. (J. Climate 2005) - ! and Grenfell & Perovich (JGR 2004) - rn_albice = 0.53 ! albedo of bare puddled ice (values from 0.49 to 0.58) - ! 0.53 (default) => if nn_ice_alb=0 - ! 0.50 (default) => if nn_ice_alb=1 -/ -!----------------------------------------------------------------------- -&namsbc_wave ! External fields from wave model -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_cdg = 'sdw_wave' , 1 , 'drag_coeff' , .true. , .false. , 'daily' , '' , '' , '' - sn_usd = 'sdw_wave' , 1 , 'u_sd2d' , .true. , .false. , 'daily' , '' , '' , '' - sn_vsd = 'sdw_wave' , 1 , 'v_sd2d' , .true. , .false. , 'daily' , '' , '' , '' - sn_swh = 'sdw_wave' , 1 , 'hs' , .true. , .false. , 'daily' , '' , '' , '' - sn_wmp = 'sdw_wave' , 1 , 'wmp' , .true. , .false. , 'daily' , '' , '' , '' - sn_wnum = 'sdw_wave' , 1 , 'wave_num' , .true. , .false. , 'daily' , '' , '' , '' - sn_tauoc = 'sdw_wave' , 1 , 'wave_stress', .true. , .false. , 'daily' , '' , '' , '' -! - cn_dir = './' ! root directory for the location of drag coefficient files -/ -!----------------------------------------------------------------------- -&namberg ! iceberg parameters (default: No iceberg) -!----------------------------------------------------------------------- - ln_icebergs = .false. ! iceberg floats or not - ln_bergdia = .true. ! Calculate budgets - nn_verbose_level = 1 ! Turn on more verbose output if level > 0 - nn_verbose_write = 15 ! Timesteps between verbose messages - nn_sample_rate = 1 ! Timesteps between sampling for trajectory storage - ! Initial mass required for an iceberg of each class - rn_initial_mass = 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 - ! Proportion of calving mass to apportion to each class - rn_distribution = 0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02 - ! Ratio between effective and real iceberg mass (non-dim) - ! i.e. number of icebergs represented at a point - rn_mass_scaling = 2000, 200, 50, 20, 10, 5, 2, 1, 1, 1 - ! thickness of newly calved bergs (m) - rn_initial_thickness = 40., 67., 133., 175., 250., 250., 250., 250., 250., 250. - rn_rho_bergs = 850. ! Density of icebergs - rn_LoW_ratio = 1.5 ! Initial ratio L/W for newly calved icebergs - ln_operator_splitting = .true. ! Use first order operator splitting for thermodynamics - rn_bits_erosion_fraction = 0. ! Fraction of erosion melt flux to divert to bergy bits - rn_sicn_shift = 0. ! Shift of sea-ice concn in erosion flux (0=1, 2nd order FCT scheme with vertical sub-timestepping - ! ! (number of sub-timestep = nn_fct_zts) - ln_traadv_mus = .false. ! MUSCL scheme - ln_mus_ups = .false. ! use upstream scheme near river mouths - ln_traadv_ubs = .false. ! UBS scheme - nn_ubs_v = 2 ! =2 , vertical 2nd order FCT / COMPACT 4th order - ln_traadv_qck = .false. ! QUICKEST scheme -/ -!----------------------------------------------------------------------- -&namtra_adv_mle ! mixed layer eddy parametrisation (Fox-Kemper param) (default: NO) -!----------------------------------------------------------------------- - ln_mle = .false. ! (T) use the Mixed Layer Eddy (MLE) parameterisation - rn_ce = 0.06 ! magnitude of the MLE (typical value: 0.06 to 0.08) - nn_mle = 1 ! MLE type: =0 standard Fox-Kemper ; =1 new formulation - rn_lf = 5.e+3 ! typical scale of mixed layer front (meters) (case rn_mle=0) - rn_time = 172800. ! time scale for mixing momentum across the mixed layer (seconds) (case rn_mle=0) - rn_lat = 20. ! reference latitude (degrees) of MLE coef. (case rn_mle=1) - nn_mld_uv = 0 ! space interpolation of MLD at u- & v-pts (0=min,1=averaged,2=max) - nn_conv = 0 ! =1 no MLE in case of convection ; =0 always MLE - rn_rho_c_mle= 0.01 ! delta rho criterion used to calculate MLD for FK -/ -!----------------------------------------------------------------------- -&namtra_ldf ! lateral diffusion scheme for tracers (default: NO diffusion) -!----------------------------------------------------------------------- - ! ! Operator type: - ! ! no diffusion: set ln_traldf_lap=..._blp=F - ln_traldf_lap = .true. ! laplacian operator - ln_traldf_blp = .false. ! bilaplacian operator - ! - ! ! Direction of action: - ln_traldf_lev = .false. ! iso-level - ln_traldf_hor = .true. ! horizontal (geopotential) - ln_traldf_iso = .false. ! iso-neutral (standard operator) - ln_traldf_triad = .false. ! iso-neutral (triad operator) - ! - ! ! iso-neutral options: - ln_traldf_msc = .false. ! Method of Stabilizing Correction (both operators) - rn_slpmax = 0.01 ! slope limit (both operators) - ln_triad_iso = .false. ! pure horizontal mixing in ML (triad only) - rn_sw_triad = 1 ! =1 switching triad ; =0 all 4 triads used (triad only) - ln_botmix_triad = .false. ! lateral mixing on bottom (triad only) - ! - ! ! Coefficients: - nn_aht_ijk_t = 0 ! space/time variation of eddy coef - ! ! =-20 (=-30) read in eddy_diffusivity_2D.nc (..._3D.nc) file - ! ! = 0 constant - ! ! = 10 F(k) =ldf_c1d - ! ! = 20 F(i,j) =ldf_c2d - ! ! = 21 F(i,j,t) =Treguier et al. JPO 1997 formulation - ! ! = 30 F(i,j,k) =ldf_c2d * ldf_c1d - ! ! = 31 F(i,j,k,t)=F(local velocity and grid-spacing) - rn_aht_0 = 125. ! lateral eddy diffusivity (lap. operator) [m2/s] - rn_bht_0 = 1.e+12 ! lateral eddy diffusivity (bilap. operator) [m4/s] -/ -!----------------------------------------------------------------------- -&namtra_ldfeiv ! eddy induced velocity param. (default: NO) -!----------------------------------------------------------------------- - ln_ldfeiv =.false. ! use eddy induced velocity parameterization - ln_ldfeiv_dia =.false. ! diagnose eiv stream function and velocities - rn_aeiv_0 = 2000. ! eddy induced velocity coefficient [m2/s] - nn_aei_ijk_t = 21 ! space/time variation of the eiv coeficient - ! ! =-20 (=-30) read in eddy_induced_velocity_2D.nc (..._3D.nc) file - ! ! = 0 constant - ! ! = 10 F(k) =ldf_c1d - ! ! = 20 F(i,j) =ldf_c2d - ! ! = 21 F(i,j,t) =Treguier et al. JPO 1997 formulation - ! ! = 30 F(i,j,k) =ldf_c2d + ldf_c1d -/ -!----------------------------------------------------------------------- -&namtra_dmp ! tracer: T & S newtonian damping (default: NO) -!----------------------------------------------------------------------- - ln_tradmp = .false. ! add a damping termn (T) or not (F) - nn_zdmp = 0 ! vertical shape =0 damping throughout the water column - ! =1 no damping in the mixing layer (kz criteria) - ! =2 no damping in the mixed layer (rho crieria) - cn_resto ='resto.nc' ! Name of file containing restoration coeff. field (use dmp_tools to create this) -/ - -!!====================================================================== -!! *** Dynamics namelists *** -!!====================================================================== -!! namdyn_adv formulation of the momentum advection -!! namdyn_vor advection scheme -!! namdyn_hpg hydrostatic pressure gradient -!! namdyn_spg surface pressure gradient -!! namdyn_ldf lateral diffusion scheme -!!====================================================================== -! -!----------------------------------------------------------------------- -&namdyn_adv ! formulation of the momentum advection (default: vector form) -!----------------------------------------------------------------------- - ln_dynadv_vec = .true. ! vector form (T) or flux form (F) - nn_dynkeg = 0 ! scheme for grad(KE): =0 C2 ; =1 Hollingsworth correction - ln_dynadv_cen2= .false. ! flux form - 2nd order centered scheme - ln_dynadv_ubs = .false. ! flux form - 3rd order UBS scheme - ln_dynzad_zts = .false. ! Use (T) sub timestepping for vertical momentum advection -/ -!----------------------------------------------------------------------- -&nam_vvl ! vertical coordinate options (default: zstar) -!----------------------------------------------------------------------- - ln_vvl_zstar = .true. ! zstar vertical coordinate - ln_vvl_ztilde = .false. ! ztilde vertical coordinate: only high frequency variations - ln_vvl_layer = .false. ! full layer vertical coordinate - ln_vvl_ztilde_as_zstar = .false. ! ztilde vertical coordinate emulating zstar - ln_vvl_zstar_at_eqtor = .false. ! ztilde near the equator - rn_ahe3 = 0.0e0 ! thickness diffusion coefficient - rn_rst_e3t = 30.e0 ! ztilde to zstar restoration timescale [days] - rn_lf_cutoff = 5.0e0 ! cutoff frequency for low-pass filter [days] - rn_zdef_max = 0.9e0 ! maximum fractional e3t deformation - ln_vvl_dbg = .true. ! debug prints (T/F) -/ -!----------------------------------------------------------------------- -&namdyn_vor ! Vorticity / Coriolis scheme (default: NO) -!----------------------------------------------------------------------- - ln_dynvor_ene = .false. ! enstrophy conserving scheme - ln_dynvor_ens = .false. ! energy conserving scheme - ln_dynvor_mix = .false. ! mixed scheme - ln_dynvor_een = .true. ! energy & enstrophy scheme - nn_een_e3f = 1 ! e3f = masked averaging of e3t divided by 4 (=0) or by the sum of mask (=1) - ln_dynvor_msk = .false. ! vorticity multiplied by fmask (=T) or not (=F) (all vorticity schemes) ! PLEASE DO NOT ACTIVATE -/ -!----------------------------------------------------------------------- -&namdyn_hpg ! Hydrostatic pressure gradient option (default: zps) -!----------------------------------------------------------------------- - ln_hpg_zco = .false. ! z-coordinate - full steps - ln_hpg_zps = .false. ! z-coordinate - partial steps (interpolation) - ln_hpg_sco = .false. ! s-coordinate (standard jacobian formulation) - ln_hpg_isf = .false. ! s-coordinate (sco ) adapted to isf - ln_hpg_djc = .false. ! s-coordinate (Density Jacobian with Cubic polynomial) - ln_hpg_prj = .true. ! s-coordinate (Pressure Jacobian scheme) -/ -!----------------------------------------------------------------------- -&namdyn_spg ! surface pressure gradient (default: NO) -!----------------------------------------------------------------------- - ln_dynspg_exp = .false. ! explicit free surface - ln_dynspg_ts = .true. ! split-explicit free surface - ln_bt_fw = .true. ! Forward integration of barotropic Eqs. - ln_bt_av = .true. ! Time filtering of barotropic variables - nn_bt_flt = 1 ! Time filter choice = 0 None - ! ! = 1 Boxcar over nn_baro sub-steps - ! ! = 2 Boxcar over 2*nn_baro " " - ln_bt_auto = .true. ! Number of sub-step defined from: - rn_bt_cmax = 0.5 ! =T : the Maximum Courant Number allowed - nn_baro = 30 ! =F : the number of sub-step in rn_rdt seconds - ln_ulimit = .true. - cn_ulimit = 0.9 ! maximum velocity inverse courant number - cnn_ulimit = 0.54 ! how much to reduce cn by in divergen flow -/ -!----------------------------------------------------------------------- -&namdyn_ldf ! lateral diffusion on momentum (default: NO) -!----------------------------------------------------------------------- - ! ! Type of the operator : - ! ! no diffusion: set ln_dynldf_lap=..._blp=F - ln_dynldf_lap = .false. ! laplacian operator - ln_dynldf_blp = .true. ! bilaplacian operator - ! ! Direction of action : - ln_dynldf_lev = .true. ! iso-level - ln_dynldf_hor = .false. ! horizontal (geopotential) - ln_dynldf_iso = .false. ! iso-neutral - ! ! Coefficient - nn_ahm_ijk_t = 0 ! space/time variation of eddy coef - ! ! =-30 read in eddy_viscosity_3D.nc file - ! ! =-20 read in eddy_viscosity_2D.nc file - ! ! = 0 constant - ! ! = 10 F(k)=c1d - ! ! = 20 F(i,j)=F(grid spacing)=c2d - ! ! = 30 F(i,j,k)=c2d*c1d - ! ! = 31 F(i,j,k)=F(grid spacing and local velocity) - ! ! = 32 F(i,j,k)=F(local gridscale and deformation rate) - ! Caution in 20 and 30 cases the coefficient have to be given for a 1 degree grid (~111km) - rn_ahm_0 = 60. ! horizontal laplacian eddy viscosity [m2/s] - rn_ahm_b = 0. ! background eddy viscosity for ldf_iso [m2/s] - rn_bhm_0 = -1.25e+10 ! horizontal bilaplacian eddy viscosity [m4/s] - ! ! Smagorinsky settings (nn_ahm_ijk_t = 32) : - rn_csmc = 3.5 ! Smagorinsky constant of proportionality - rn_minfac = 1.0 ! multiplier of theorectical lower limit - rn_maxfac = 1.0 ! multiplier of theorectical upper limit -/ - -!!====================================================================== -!! Tracers & Dynamics vertical physics namelists -!!====================================================================== -!! namzdf vertical physics -!! namzdf_ric richardson number dependent vertical mixing ("key_zdfric") -!! namzdf_tke TKE dependent vertical mixing ("key_zdftke") -!! namzdf_gls GLS vertical mixing ("key_zdfgls") -!! namzdf_ddm double diffusive mixing parameterization ("key_zdfddm") -!! namzdf_tmx tidal mixing parameterization ("key_zdftmx") -!!====================================================================== -! -!----------------------------------------------------------------------- -&namzdf ! vertical physics -!----------------------------------------------------------------------- - rn_avm0 = 1.2e-6 ! vertical eddy viscosity [m2/s] (background Kz if not "key_zdfcst") - rn_avt0 = 1.2e-6 ! vertical eddy diffusivity [m2/s] (background Kz if not "key_zdfcst") - nn_avb = 0 ! profile for background avt & avm (=1) or not (=0) - nn_havtb = 0 ! horizontal shape for avtb (=1) or not (=0) - ln_zdfevd = .false. ! enhanced vertical diffusion (evd) (T) or not (F) - nn_evdm = 1 ! evd apply on tracer (=0) or on tracer and momentum (=1) - rn_avevd = 100. ! evd mixing coefficient [m2/s] - ln_zdfnpc = .true. ! Non-Penetrative Convective algorithm (T) or not (F) - nn_npc = 1 ! frequency of application of npc - nn_npcp = 365 ! npc control print frequency - ln_zdfexp = .false. ! time-stepping: split-explicit (T) or implicit (F) time stepping - nn_zdfexp = 3 ! number of sub-timestep for ln_zdfexp=T - ln_zdfqiao = .false. ! Enhanced wave vertical mixing Qiao (2010) (T => ln_wave=.true. & ln_sdw=.true. & fill namsbc_wave) -/ -!----------------------------------------------------------------------- -&namzdf_ric ! richardson number dependent vertical diffusion ("key_zdfric" ) -!----------------------------------------------------------------------- - rn_avmri = 100.e-4 ! maximum value of the vertical viscosity - rn_alp = 5. ! coefficient of the parameterization - nn_ric = 2 ! coefficient of the parameterization - rn_ekmfc = 0.7 ! Factor in the Ekman depth Equation - rn_mldmin = 1.0 ! minimum allowable mixed-layer depth estimate (m) - rn_mldmax = 1000.0 ! maximum allowable mixed-layer depth estimate (m) - rn_wtmix = 10.0 ! vertical eddy viscosity coeff [m2/s] in the mixed-layer - rn_wvmix = 10.0 ! vertical eddy diffusion coeff [m2/s] in the mixed-layer - ln_mldw = .true. ! Flag to use or not the mixed layer depth param. -/ -!----------------------------------------------------------------------- -&namzdf_tke ! turbulent eddy kinetic dependent vertical diffusion ("key_zdftke") -!----------------------------------------------------------------------- - rn_ediff = 0.1 ! coef. for vertical eddy coef. (avt=rn_ediff*mxl*sqrt(e) ) - rn_ediss = 0.7 ! coef. of the Kolmogoroff dissipation - rn_ebb = 67.83 ! coef. of the surface input of tke (=67.83 suggested when ln_mxl0=T) - rn_emin = 1.e-6 ! minimum value of tke [m2/s2] - rn_emin0 = 1.e-4 ! surface minimum value of tke [m2/s2] - rn_bshear = 1.e-20 ! background shear (>0) currently a numerical threshold (do not change it) - nn_mxl = 3 ! mixing length: = 0 bounded by the distance to surface and bottom - ! = 1 bounded by the local vertical scale factor - ! = 2 first vertical derivative of mixing length bounded by 1 - ! = 3 as =2 with distinct disspipative an mixing length scale - nn_pdl = 1 ! Prandtl number function of richarson number (=1, avt=pdl(Ri)*avm) or not (=0, avt=avm) - ln_mxl0 = .true. ! surface mixing length scale = F(wind stress) (T) or not (F) - rn_mxl0 = 0.01 ! surface buoyancy lenght scale minimum value - ln_lc = .true. ! Langmuir cell parameterisation (Axell 2002) - rn_lc = 0.15 ! coef. associated to Langmuir cells - nn_etau = 1 ! penetration of tke below the mixed layer (ML) due to near intertial waves - ! = 0 no penetration - ! = 1 add a tke source below the ML - ! = 2 add a tke source just at the base of the ML - ! = 3 as = 1 applied on HF part of the stress (ln_cpl=T) - rn_efr = 0.05 ! fraction of surface tke value which penetrates below the ML (nn_etau=1 or 2) - nn_htau = 1 ! type of exponential decrease of tke penetration below the ML - ! = 0 constant 10 m length scale - ! = 1 0.5m at the equator to 30m poleward of 40 degrees -/ -!----------------------------------------------------------------------- -&namzdf_gls ! GLS vertical diffusion ("key_zdfgls") -!----------------------------------------------------------------------- - rn_emin = 1.e-6 ! minimum value of e [m2/s2] - rn_epsmin = 1.e-12 ! minimum value of eps [m2/s3] - ln_length_lim = .true. ! limit on the dissipation rate under stable stratification (Galperin et al., 1988) - rn_clim_galp = 0.267 ! galperin limit - ln_sigpsi = .true. ! Activate or not Burchard 2001 mods on psi schmidt number in the wb case - rn_crban = 100. ! Craig and Banner 1994 constant for wb tke flux - rn_charn = 70000. ! Charnock constant for wb induced roughness length - rn_hsro = 0.02 ! Minimum surface roughness - rn_frac_hs = 1.3 ! Fraction of wave height as roughness (if nn_z0_met=2) - nn_z0_met = 2 ! Method for surface roughness computation (0/1/2) - nn_bc_surf = 1 ! surface condition (0/1=Dir/Neum) - nn_bc_bot = 1 ! bottom condition (0/1=Dir/Neum) - nn_stab_func = 2 ! stability function (0=Galp, 1= KC94, 2=CanutoA, 3=CanutoB) - nn_clos = 1 ! predefined closure type (0=MY82, 1=k-eps, 2=k-w, 3=Gen) -/ -!----------------------------------------------------------------------- -&namzdf_ddm ! double diffusive mixing parameterization ("key_zdfddm") -!----------------------------------------------------------------------- - rn_avts = 1.e-4 ! maximum avs (vertical mixing on salinity) - rn_hsbfr = 1.6 ! heat/salt buoyancy flux ratio -/ -!----------------------------------------------------------------------- -&namzdf_tmx ! tidal mixing parameterization ("key_zdftmx") -!----------------------------------------------------------------------- - rn_htmx = 500. ! vertical decay scale for turbulence (meters) - rn_n2min = 1.e-8 ! threshold of the Brunt-Vaisala frequency (s-1) - rn_tfe = 0.333 ! tidal dissipation efficiency - rn_me = 0.2 ! mixing efficiency - ln_tmx_itf = .false. ! ITF specific parameterisation - rn_tfe_itf = 1. ! ITF tidal dissipation efficiency -/ -!----------------------------------------------------------------------- -&namzdf_tmx_new ! internal wave-driven mixing parameterization ("key_zdftmx_new" & "key_zdfddm") -!----------------------------------------------------------------------- - nn_zpyc = 1 ! pycnocline-intensified dissipation scales as N (=1) or N^2 (=2) - ln_mevar = .true. ! variable (T) or constant (F) mixing efficiency - ln_tsdiff = .true. ! account for differential T/S mixing (T) or not (F) -/ -!!====================================================================== -!! *** Miscellaneous namelists *** -!!====================================================================== -!! nammpp Massively Parallel Processing ("key_mpp_mpi) -!! namctl Control prints -!! namsto Stochastic parametrization of EOS -!!====================================================================== -! -!----------------------------------------------------------------------- -&nammpp ! Massively Parallel Processing ("key_mpp_mpi) -!----------------------------------------------------------------------- - cn_mpi_send = 'I' ! mpi send/recieve type ='S', 'B', or 'I' for standard send, - ! buffer blocking send or immediate non-blocking sends, resp. - nn_buffer = 0 ! size in bytes of exported buffer ('B' case), 0 no exportation - ln_nnogather= .false. ! activate code to avoid mpi_allgather use at the northfold - jpni = 30 ! standardqueue:30 ! shortqueue:11 ! jpni number of processors following i (set automatically if < 1) - jpnj = 16 ! standardqueue:16 ! shortqueue: 8 ! jpnj number of processors following j (set automatically if < 1) - jpnij = 480 ! standardqueue:480 ! shortqueue:88 ! jpnij number of local domains (set automatically if < 1) -/ -!----------------------------------------------------------------------- -&namctl ! Control prints -!----------------------------------------------------------------------- - ln_ctl = .false. ! trends control print (expensive!) - nn_print = 0 ! level of print (0 no extra print) - nn_ictls = 0 ! start i indice of control sum (use to compare mono versus - nn_ictle = 0 ! end i indice of control sum multi processor runs - nn_jctls = 0 ! start j indice of control over a subdomain) - nn_jctle = 0 ! end j indice of control - nn_isplt = 1 ! number of processors in i-direction - nn_jsplt = 1 ! number of processors in j-direction - nn_timing = 1 ! timing by routine activated (=1) creates timing.output file, or not (=0) - nn_diacfl = 0 ! Write out CFL diagnostics (=1) in cfl_diagnostics.ascii, or not (=0) -/ -!----------------------------------------------------------------------- -&namsto ! Stochastic parametrization of EOS (default: NO) -!----------------------------------------------------------------------- - ln_sto_eos = .false. ! stochastic equation of state - nn_sto_eos = 1 ! number of independent random walks - rn_eos_stdxy= 1.4 ! random walk horz. standard deviation (in grid points) - rn_eos_stdz = 0.7 ! random walk vert. standard deviation (in grid points) - rn_eos_tcor = 1440. ! random walk time correlation (in timesteps) - nn_eos_ord = 1 ! order of autoregressive processes - nn_eos_flt = 0 ! passes of Laplacian filter - rn_eos_lim = 2.0 ! limitation factor (default = 3.0) - ln_rststo = .false. ! start from mean parameter (F) or from restart file (T) - ln_rstseed = .true. ! read seed of RNG from restart file - cn_storst_in = "restart_sto" ! suffix of stochastic parameter restart file (input) - cn_storst_out = "restart_sto" ! suffix of stochastic parameter restart file (output) -/ - -!!====================================================================== -!! *** Diagnostics namelists *** -!!====================================================================== -!! namtrd dynamics and/or tracer trends (default F) -!! namptr Poleward Transport Diagnostics (default F) -!! namhsb Heat and salt budgets (default F) -!! namdiu Cool skin and warm layer models (default F) -!! namdiu Cool skin and warm layer models (default F) -!! namflo float parameters ("key_float") -!! nam_diaharm Harmonic analysis of tidal constituents ("key_diaharm") -!! namdct transports through some sections ("key_diadct") -!! nam_diatmb Top Middle Bottom Output (default F) -!! nam_dia25h 25h Mean Output (default F) -!! namnc4 netcdf4 chunking and compression settings ("key_netcdf4") -!!====================================================================== -! -!----------------------------------------------------------------------- -&namtrd ! trend diagnostics (default F) -!----------------------------------------------------------------------- - ln_glo_trd = .false. ! (T) global domain averaged diag for T, T^2, KE, and PE - ln_dyn_trd = .false. ! (T) 3D momentum trend output - ln_dyn_mxl = .false. ! (T) 2D momentum trends averaged over the mixed layer (not coded yet) - ln_vor_trd = .false. ! (T) 2D barotropic vorticity trends (not coded yet) - ln_KE_trd = .false. ! (T) 3D Kinetic Energy trends - ln_PE_trd = .false. ! (T) 3D Potential Energy trends - ln_tra_trd = .false. ! (T) 3D tracer trend output - ln_tra_mxl = .false. ! (T) 2D tracer trends averaged over the mixed layer (not coded yet) - nn_trd = 365 ! print frequency (ln_glo_trd=T) (unit=time step) -/ -!!gm nn_ctls = 0 ! control surface type in mixed-layer trends (0,1 or n /seconds ; =86400. -> /day) -!!gm cn_trdrst_in = "restart_mld" ! suffix of ocean restart name (input) -!!gm cn_trdrst_out = "restart_mld" ! suffix of ocean restart name (output) -!!gm ln_trdmld_restart = .false. ! restart for ML diagnostics -!!gm ln_trdmld_instant = .false. ! flag to diagnose trends of instantantaneous or mean ML T/S -!!gm -!----------------------------------------------------------------------- -&namptr ! Poleward Transport Diagnostic (default F) -!----------------------------------------------------------------------- - ln_diaptr = .false. ! Poleward heat and salt transport (T) or not (F) - ln_subbas = .false. ! Atlantic/Pacific/Indian basins computation (T) or not -/ -!----------------------------------------------------------------------- -&namhsb ! Heat and salt budgets (default F) -!----------------------------------------------------------------------- - ln_diahsb = .false. ! check the heat and salt budgets (T) or not (F) -/ -!----------------------------------------------------------------------- -&namdiu ! Cool skin and warm layer models (default F) -!----------------------------------------------------------------------- - ln_diurnal = .false. ! - ln_diurnal_only = .false. ! -/ -!----------------------------------------------------------------------- -&namflo ! float parameters ("key_float") -!----------------------------------------------------------------------- - jpnfl = 1 ! total number of floats during the run - jpnnewflo = 0 ! number of floats for the restart - ln_rstflo = .false. ! float restart (T) or not (F) - nn_writefl = 75 ! frequency of writing in float output file - nn_stockfl = 5475 ! frequency of creation of the float restart file - ln_argo = .false. ! Argo type floats (stay at the surface each 10 days) - ln_flork4 = .false. ! trajectories computed with a 4th order Runge-Kutta (T) - ! ! or computed with Blanke' scheme (F) - ln_ariane = .true. ! Input with Ariane tool convention(T) - ln_flo_ascii= .true. ! Output with Ariane tool netcdf convention(F) or ascii file (T) -/ -!----------------------------------------------------------------------- -&nam_diaharm ! Harmonic analysis of tidal constituents ("key_diaharm") -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&nam_diaharm_fast ! Harmonic analysis of tidal constituents ("key_diaharm_fast") -!----------------------------------------------------------------------- - ln_diaharm_store = .false. - ln_diaharm_compute = .true. - ln_diaharm_read_restart = .false. - ln_ana_ssh = .true. - ln_ana_uvbar = .false. - ln_ana_bfric = .false. - ln_ana_rho = .false. - ln_ana_uv3d = .false. - ln_ana_w3d = .false. - tname(1)='K1' - tname(2)='K2' - tname(3)='M2' - tname(4)='M4' - tname(5)='N2' - tname(6)='O1' - tname(7)='P1' - tname(8)='Q1' - tname(9)='S2' -!! FES2014 full list -! tname(1) ='2N2' -! tname(2)='EPS2' -! tname(3)='J1' -! tname(4)='K1' -! tname(5)='K2' -! tname(6)='L2' -! tname(7)='LA2' -! tname(8)='M2' -! tname(9)='M3' -! tname(10)='M4' -! tname(11)='M6' -! tname(12)='M8' -! tname(13)='MF' -! tname(14)='MKS2' -! tname(15)='MM' -! tname(16)='MN4' -! tname(17)='MS4' -! tname(18)='MSF' -! tname(19)='MSQM' -! tname(20)='MTM' -! tname(21)='MU2' -! tname(22)='N2' -! tname(23)='N4' -! tname(24)='NU2' -! tname(25)='O1' -! tname(26)='P1' -! tname(27)='Q1' -! tname(28)='R2' -! tname(29)='S1' -! tname(30)='S2' -! tname(31)='S4' -! tname(32)='SA' -! tname(33)='SSA' -! tname(34)='T2' -/ -!----------------------------------------------------------------------- -&namdct ! transports through some sections ("key_diadct") -!----------------------------------------------------------------------- - nn_dct = 15 ! time step frequency for transports computing - nn_dctwri = 15 ! time step frequency for transports writing - nn_secdebug= 112 ! 0 : no section to debug - ! ! -1 : debug all section - ! ! 0 < n : debug section number n -/ -!----------------------------------------------------------------------- -&nam_diatmb ! Top Middle Bottom Output (default F) -!----------------------------------------------------------------------- - ln_diatmb = .false. ! Choose Top Middle and Bottom output or not -/ -!----------------------------------------------------------------------- -&nam_dia25h ! 25h Mean Output (default F) -!----------------------------------------------------------------------- - ln_dia25h = .false. ! Choose 25h mean output or not -/ -!----------------------------------------------------------------------- -&namnc4 ! netcdf4 chunking and compression settings ("key_netcdf4") -!----------------------------------------------------------------------- - ln_diatmb = .false. ! Choose Top Middle and Bottom output or not -/ -!----------------------------------------------------------------------- -&nam_dia25h ! 25h Mean Output (default F) -!----------------------------------------------------------------------- - ln_dia25h = .false. ! Choose 25h mean output or not -/ -!----------------------------------------------------------------------- -&namnc4 ! netcdf4 chunking and compression settings ("key_netcdf4") -!----------------------------------------------------------------------- - nn_nchunks_i= 4 ! number of chunks in i-dimension - nn_nchunks_j= 4 ! number of chunks in j-dimension - nn_nchunks_k= 31 ! number of chunks in k-dimension - ! ! setting nn_nchunks_k = jpk will give a chunk size of 1 in the vertical which - ! ! is optimal for postprocessing which works exclusively with horizontal slabs - ln_nc4zip = .true. ! (T) use netcdf4 chunking and compression - ! ! (F) ignore chunking information and produce netcdf3-compatible files -/ - -!!====================================================================== -!! *** Observation & Assimilation *** -!!====================================================================== -!! namobs observation and model comparison -!! nam_asminc assimilation increments ('key_asminc') -!!====================================================================== -! -!----------------------------------------------------------------------- -&namobs ! observation usage switch -!----------------------------------------------------------------------- - ln_diaobs = .false. ! Logical switch for the observation operator - ln_t3d = .false. ! Logical switch for T profile observations - ln_s3d = .false. ! Logical switch for S profile observations - ln_sla = .false. ! Logical switch for SLA observations - ln_sst = .false. ! Logical switch for SST observations - ln_sic = .false. ! Logical switch for Sea Ice observations - ln_vel3d = .false. ! Logical switch for velocity observations - ln_altbias = .false. ! Logical switch for altimeter bias correction - ln_nea = .false. ! Logical switch for rejection of observations near land - ln_grid_global = .true. ! Logical switch for global distribution of observations - ln_grid_search_lookup = .false. ! Logical switch for obs grid search w/lookup table - ln_ignmis = .true. ! Logical switch for ignoring missing files - ln_s_at_t = .false. ! Logical switch for computing model S at T obs if not there - ln_sstnight = .false. ! Logical switch for calculating night-time average for SST obs -! All of the *files* variables below are arrays. Use namelist_cfg to add more files - cn_profbfiles = 'profiles_01.nc' ! Profile feedback input observation file names - cn_slafbfiles = 'sla_01.nc' ! SLA feedback input observation file names - cn_sstfbfiles = 'sst_01.nc' ! SST feedback input observation file names - cn_sicfbfiles = 'sic_01.nc' ! SIC feedback input observation file names - cn_velfbfiles = 'vel_01.nc' ! Velocity feedback input observation file names - cn_altbiasfile = 'altbias.nc' ! Altimeter bias input file name - cn_gridsearchfile='gridsearch.nc' ! Grid search file name - rn_gridsearchres = 0.5 ! Grid search resolution - rn_dobsini = 00010101.000000 ! Initial date in window YYYYMMDD.HHMMSS - rn_dobsend = 00010102.000000 ! Final date in window YYYYMMDD.HHMMSS - nn_1dint = 0 ! Type of vertical interpolation method - nn_2dint = 0 ! Type of horizontal interpolation method - nn_msshc = 0 ! MSSH correction scheme - rn_mdtcorr = 1.61 ! MDT correction - rn_mdtcutoff = 65.0 ! MDT cutoff for computed correction - nn_profdavtypes = -1 ! Profile daily average types - array - ln_sstbias = .false. ! - cn_sstbias_files = 'sstbias.nc' ! -/ -!----------------------------------------------------------------------- -&nam_asminc ! assimilation increments ('key_asminc') -!----------------------------------------------------------------------- - ln_bkgwri = .false. ! Logical switch for writing out background state - ln_trainc = .false. ! Logical switch for applying tracer increments - ln_dyninc = .false. ! Logical switch for applying velocity increments - ln_sshinc = .false. ! Logical switch for applying SSH increments - ln_asmdin = .false. ! Logical switch for Direct Initialization (DI) - ln_asmiau = .false. ! Logical switch for Incremental Analysis Updating (IAU) - nitbkg = 0 ! Timestep of background in [0,nitend-nit000-1] - nitdin = 0 ! Timestep of background for DI in [0,nitend-nit000-1] - nitiaustr = 1 ! Timestep of start of IAU interval in [0,nitend-nit000-1] - nitiaufin = 15 ! Timestep of end of IAU interval in [0,nitend-nit000-1] - niaufn = 0 ! Type of IAU weighting function - ln_salfix = .false. ! Logical switch for ensuring that the sa > salfixmin - salfixmin = -9999 ! Minimum salinity after applying the increments - nn_divdmp = 0 ! Number of iterations of divergence damping operator -/ diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_ice_cfg b/RUN_DIRECTORIES/EXP_eORCAR12/namelist_ice_cfg deleted file mode 100755 index 784d2d7..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_ice_cfg +++ /dev/null @@ -1,48 +0,0 @@ -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! LIM3 configuration namelist: Overwrites SHARED/namelist_ice_lim3_ref -!! 1 - Generic parameters (namicerun) -!! 2 - Diagnostics (namicediag) -!! 3 - Ice initialization (namiceini) -!! 4 - Ice discretization (namiceitd) -!! 5 - Ice dynamics and transport (namicedyn) -!! 6 - Ice diffusion (namicehdf) -!! 7 - Ice thermodynamics (namicethd) -!! 8 - Ice salinity (namicesal) -!! 9 - Ice mechanical redistribution (namiceitdme) -!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!------------------------------------------------------------------------------ -&namicerun ! Generic parameters -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicediag ! Diagnostics -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namiceini ! Ice initialization -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namiceitd ! Ice discretization -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicedyn ! Ice dynamics and transport -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicehdf ! Ice horizontal diffusion -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicethd ! Ice thermodynamics -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namicesal ! Ice salinity -!------------------------------------------------------------------------------ -/ -!------------------------------------------------------------------------------ -&namiceitdme ! Ice mechanical redistribution (ridging and rafting) -!------------------------------------------------------------------------------ -/ diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_ice_ref b/RUN_DIRECTORIES/EXP_eORCAR12/namelist_ice_ref deleted file mode 120000 index d298c6e..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_ice_ref +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/namelist_ice_lim3_ref \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_pisces_cfg b/RUN_DIRECTORIES/EXP_eORCAR12/namelist_pisces_cfg deleted file mode 100755 index 9c24e03..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_pisces_cfg +++ /dev/null @@ -1,63 +0,0 @@ -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! PISCES : Configuration namelist : used to overwrite defaults values defined in SHARED/namelist_pis_ref -!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisext ! air-sea exchange -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisatm ! Atmospheric prrssure -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisbio ! biological parameters -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampislim ! parameters for nutrient limitations -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisopt ! parameters for optics -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisprod ! parameters for phytoplankton growth -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampismort ! parameters for phytoplankton sinks -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampismes ! parameters for mesozooplankton -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampiszoo ! parameters for microzooplankton -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisfer ! parameters for iron chemistry -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisrem ! parameters for remineralization -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampiscal ! parameters for Calcite chemistry -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampissbc ! parameters for inputs deposition -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampisdmp ! Damping -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ -!''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -&nampismass ! Mass conservation -!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -/ diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_pisces_ref b/RUN_DIRECTORIES/EXP_eORCAR12/namelist_pisces_ref deleted file mode 120000 index e4b4056..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_pisces_ref +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/namelist_pisces_ref \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_ref b/RUN_DIRECTORIES/EXP_eORCAR12/namelist_ref deleted file mode 120000 index a1435a3..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_ref +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/namelist_ref \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_top_cfg b/RUN_DIRECTORIES/EXP_eORCAR12/namelist_top_cfg deleted file mode 100755 index 82732c6..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_top_cfg +++ /dev/null @@ -1,109 +0,0 @@ -!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!! NEMO/TOP1 : Configuration namelist : used to overwrite defaults values defined in SHARED/namelist_top_ref -!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -!----------------------------------------------------------------------- -&namtrc_run ! run information -!----------------------------------------------------------------------- - ln_top_euler = .true. -/ -!----------------------------------------------------------------------- -&namtrc ! tracers definition -!----------------------------------------------------------------------- - jp_bgc = 24 -! - ln_pisces = .true. - ln_my_trc = .false. - ln_age = .false. - ln_cfc11 = .false. - ln_cfc12 = .false. - ln_c14 = .false. -! - ln_trcdta = .true. ! Initialisation from data input file (T) or not (F) -! ! ! ! ! -! ! name ! title of the field ! units ! initial data from file or not ! -! ! ! ! ! - sn_tracer(1) = 'DIC ' , 'Dissolved inorganic Concentration ', 'mol-C/L' , .true. - sn_tracer(2) = 'Alkalini' , 'Total Alkalinity Concentration ', 'eq/L ' , .true. - sn_tracer(3) = 'O2 ' , 'Dissolved Oxygen Concentration ', 'mol-C/L' , .true. - sn_tracer(4) = 'CaCO3 ' , 'Calcite Concentration ', 'mol-C/L' , .false. - sn_tracer(5) = 'PO4 ' , 'Phosphate Concentration ', 'mol-C/L' , .true. - sn_tracer(6) = 'POC ' , 'Small organic carbon Concentration ', 'mol-C/L' , .false. - sn_tracer(7) = 'Si ' , 'Silicate Concentration ', 'mol-C/L' , .true. - sn_tracer(8) = 'PHY ' , 'Nanophytoplankton Concentration ', 'mol-C/L' , .false. - sn_tracer(9) = 'ZOO ' , 'Microzooplankton Concentration ', 'mol-C/L' , .false. - sn_tracer(10) = 'DOC ' , 'Dissolved organic Concentration ', 'mol-C/L' , .true. - sn_tracer(11) = 'PHY2 ' , 'Diatoms Concentration ', 'mol-C/L' , .false. - sn_tracer(12) = 'ZOO2 ' , 'Mesozooplankton Concentration ', 'mol-C/L' , .false. - sn_tracer(13) = 'DSi ' , 'Diatoms Silicate Concentration ', 'mol-C/L' , .false. - sn_tracer(14) = 'Fer ' , 'Dissolved Iron Concentration ', 'mol-C/L' , .true. - sn_tracer(15) = 'BFe ' , 'Big iron particles Concentration ', 'mol-C/L' , .false. - sn_tracer(16) = 'GOC ' , 'Big organic carbon Concentration ', 'mol-C/L' , .false. - sn_tracer(17) = 'SFe ' , 'Small iron particles Concentration ', 'mol-C/L' , .false. - sn_tracer(18) = 'DFe ' , 'Diatoms iron Concentration ', 'mol-C/L' , .false. - sn_tracer(19) = 'GSi ' , 'Sinking biogenic Silicate Concentration', 'mol-C/L' , .false. - sn_tracer(20) = 'NFe ' , 'Nano iron Concentration ', 'mol-C/L' , .false. - sn_tracer(21) = 'NCHL ' , 'Nano chlorophyl Concentration ', 'mol-C/L' , .false. - sn_tracer(22) = 'DCHL ' , 'Diatoms chlorophyl Concentration ', 'mol-C/L' , .false. - sn_tracer(23) = 'NO3 ' , 'Nitrates Concentration ', 'mol-C/L' , .true. - sn_tracer(24) = 'NH4 ' , 'Ammonium Concentration ', 'mol-C/L' , .false. -/ -!----------------------------------------------------------------------- -&namtrc_dta ! Initialisation from data input file -!----------------------------------------------------------------------- -! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! -! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! - sn_trcdta(1) = 'data_DIC_nomask' , -12 , 'DIC' , .false. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(2) = 'data_Alkalini_nomask' , -12 , 'Alkalini', .false. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(3) = 'data_O2_nomask' , -1 , 'O2' , .true. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(5) = 'data_PO4_nomask' , -1 , 'PO4' , .true. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(7) = 'data_Si_nomask' , -1 , 'Si' , .true. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(10) = 'data_DOC_nomask' , -12 , 'DOC' , .false. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(14) = 'data_Fer_nomask' , -12 , 'Fer' , .false. , .true. , 'yearly' , '' , '' , '' - sn_trcdta(23) = 'data_NO3_nomask' , -1 , 'NO3' , .true. , .true. , 'yearly' , '' , '' , '' - rn_trfac(1) = 1.0e-06 ! multiplicative factor - rn_trfac(2) = 1.0e-06 ! - - - - - rn_trfac(3) = 44.6e-06 ! - - - - - rn_trfac(5) = 122.0e-06 ! - - - - - rn_trfac(7) = 1.0e-06 ! - - - - - rn_trfac(10) = 1.0 ! - - - - - rn_trfac(14) = 1.0 ! - - - - - rn_trfac(23) = 7.6e-06 ! - - - - -/ -!----------------------------------------------------------------------- -&namtrc_adv ! advection scheme for passive tracer -!----------------------------------------------------------------------- - ln_trcadv_mus = .true. ! MUSCL scheme - ln_mus_ups = .false. ! use upstream scheme near river mouths -/ -!----------------------------------------------------------------------- -&namtrc_ldf ! lateral diffusion scheme for passive tracer -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namtrc_zdf ! vertical physics -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namtrc_rad ! treatment of negative concentrations -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namtrc_dmp ! passive tracer newtonian damping -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namtrc_ice ! Representation of sea ice growth & melt effects -!----------------------------------------------------------------------- -/ -!----------------------------------------------------------------------- -&namtrc_trd ! diagnostics on tracer trends ('key_trdtrc') -! or mixed-layer trends ('key_trdmld_trc') -!---------------------------------------------------------------------- -/ -!---------------------------------------------------------------------- -&namtrc_bc ! data for boundary conditions -!----------------------------------------------------------------------- -/ -!---------------------------------------------------------------------- -&namtrc_bdy ! Setup of tracer boundary conditions -!----------------------------------------------------------------------- diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_top_ref b/RUN_DIRECTORIES/EXP_eORCAR12/namelist_top_ref deleted file mode 120000 index 49690ad..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/namelist_top_ref +++ /dev/null @@ -1 +0,0 @@ -/work/n01/n01/jelt/SEAsia/trunk_NEMOGCM_r8395/CONFIG/SHARED/namelist_top_ref \ No newline at end of file diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/runscript b/RUN_DIRECTORIES/EXP_eORCAR12/runscript deleted file mode 100755 index aaeaddd..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/runscript +++ /dev/null @@ -1,30 +0,0 @@ -#!/bin/bash -#PBS -N SEAsia -#PBS -l select=21 -#PBS -l walltime=12:00:00 -#PBS -A n01-ACCORD -# mail alert at (b)eginning, (e)nd and (a)bortion of execution -#PBS -m bea -#PBS -M jelt@noc.ac.uk - -module swap PrgEnv-cray PrgEnv-intel -module load cray-netcdf-hdf5parallel -module load cray-hdf5-parallel - -export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR) -# echo $(readlink -f $PBS_O_WORKDIR) -# export OMP_NUM_THREADS=1 - -cd $PBS_O_WORKDIR -# - echo " "; - OCEANCORES=480 #92 - XIOSCORES=4 -ulimit -c unlimited -ulimit -s unlimited - -rm -f core - -aprun -b -n $XIOSCORES -N 4 ./xios_server.exe : -n $OCEANCORES -N 24 ./opa - -exit diff --git a/RUN_DIRECTORIES/EXP_eORCAR12/runscript_short b/RUN_DIRECTORIES/EXP_eORCAR12/runscript_short deleted file mode 100755 index d531813..0000000 --- a/RUN_DIRECTORIES/EXP_eORCAR12/runscript_short +++ /dev/null @@ -1,33 +0,0 @@ -#!/bin/bash -#PBS -N SEAsia -#PBS -l select=5 -#PBS -l walltime=00:20:00 -#PBS -A n01-ACCORD -# mail alert at (b)eginning, (e)nd and (a)bortion of execution -#PBS -m bea -#PBS -M jelt@noc.ac.uk -#PBS -q short - -module swap PrgEnv-cray PrgEnv-intel -module load cray-netcdf-hdf5parallel -module load cray-hdf5-parallel - -export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR) -# echo $(readlink -f $PBS_O_WORKDIR) -# export OMP_NUM_THREADS=1 - -cd $PBS_O_WORKDIR -# - echo " "; - OCEANCORES=88 - XIOSCORES=4 -ulimit -c unlimited -ulimit -s unlimited - -rm -f core - -#aprun -n $OCEANCORES -N 24 ./opa -aprun -b -n $XIOSCORES -N 4 ./xios_server.exe : -n $OCEANCORES -N 24 ./opa -#aprun -b -n $XIOCORES -N 1 ./xios_server.exe : -n $OCEANCORES -N 24 ./opa - -exit From 10380801333f091a66f6c4e0396e97d4490991a4 Mon Sep 17 00:00:00 2001 From: jpolton Date: Tue, 28 Sep 2021 09:27:24 +0100 Subject: [PATCH 09/12] update python2 --> python3: print syntax --- .../OFFICIAL_Generate_NEMO_Forcing_NEWERA.py | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/SCRIPTS/OFFICIAL_Generate_NEMO_Forcing_NEWERA.py b/SCRIPTS/OFFICIAL_Generate_NEMO_Forcing_NEWERA.py index f2272e7..8b6cfa8 100755 --- a/SCRIPTS/OFFICIAL_Generate_NEMO_Forcing_NEWERA.py +++ b/SCRIPTS/OFFICIAL_Generate_NEMO_Forcing_NEWERA.py @@ -90,7 +90,7 @@ def Read_NetCDF_Concatenate( fname, KeyVar ) : ## save if iF == 0 : out = Var; tout = Time else : out = np.concatenate( [out,Var], axis=0 ); tout = np.concatenate( [tout,Time], axis=0 ) - print tout[0], tout[-1], tout.shape, out.shape, LON.shape + print( tout[0], tout[-1], tout.shape, out.shape, LON.shape ) try : return tout, LON, LAT, out, dum.units, dum.long_name except : return tout, LON, LAT, out, dum.units, dum.standard_name @@ -106,7 +106,7 @@ def Read_NetCDF( fname, KeyVar ) : try : Tref = netcdftime.utime( Time_Var.units, calendar = Time_Var.calendar ) except : Tref = netcdftime.utime( Time_Var.units, calendar = "gregorian" ) Time = Tref.num2date( Time_H ) - print "====================++++" + print( "====================++++") ## Get Coordinates try : Lon = nc.variables[ 'longitude' ][:] @@ -125,7 +125,7 @@ def Read_NetCDF( fname, KeyVar ) : ind = (np.isnan(Var)) Var[ind] = -9999999 - print Time[0], Time[-1], Var.shape, Time.shape, np.sum(ind) + print( Time[0], Time[-1], Var.shape, Time.shape, np.sum(ind)) try : return Time, LON, LAT, Var, dum.units, dum.long_name except : return Time, LON, LAT, Var, dum.units, dum.standard_name @@ -135,7 +135,7 @@ def compute_scale_and_offset( Var, n ): 'http://james.hiebert.name/blog/work/2015/04/18/NetCDF-Scale-Factors/' Vmin = np.nanmin( Var ) Vmax = np.nanmax( Var ) - print "scaleoffset", Vmin, Vmax + print( "scaleoffset", Vmin, Vmax) # stretch/compress data to the available packed range scale_factor = (Vmax - Vmin) / (2 ** n - 1) # translate the range to be symmetric about zero @@ -199,7 +199,7 @@ def Extract( fin, fout, clean=True ) : if not os.path.exists( fout ) : command = "ncks -d latitude,{0},{1} -d longitude,{2},{3} {4} {5}".format( np.float(South), np.float(North),\ np.float(West), np.float(East), fin, fout ) - print command + print( command ) os.system( command ) def datetime_range(start, end, delta): @@ -219,7 +219,7 @@ def datetime_range(start, end, delta): ## Loop over each variable for dirVar, nameVar in var_path.iteritems() : - print "================== {0} - {1} ==================".format( dirVar, nameVar ) + print( "================== {0} - {1} ==================".format( dirVar, nameVar )) ##---------- EXTRACT ALL DATA FOR DOMAIN ---------------- for iY in range( Year_init, Year_end+1 ) : @@ -231,34 +231,34 @@ def datetime_range(start, end, delta): ##---------- LOAD FULLL TIME SERIES IN MEMORY ----------- Time, Lon, Lat, dum, Units, Name = Read_NetCDF_Concatenate( "./{1}/{0}_*.nc".format( nameVar, path_EXTRACT ), nameVar ) - print "Time" , Time + print("Time" , Time) dt = Time[1] - Time[0] ## assume to be constant in time dt2 = datetime.timedelta( seconds=dt.total_seconds() / 2. ) - print "dt", dt, dt2 + print( "dt", dt, dt2 ) ##---------- SOME PREPROCESSING ------------------------- ## Add time step for last hour - copy the last input dumA = np.concatenate( [ dum, dum[-1][np.newaxis,...] ], axis = 0 ) TimeA = np.array( Time.tolist() + [Time[-1],] ) - print "Time" , Time - print "TimeA", TimeA + print( "Time" , Time ) + print( "TimeA", TimeA ) ## instantaneous field every hour. we center it in mid-time step (00:30) as it ## is what NEMO assumes according to documentation dumC = ( dumA[0:-1] + dumA[1::] ) / 2.0 TimeC = TimeA[0:-1] + dt2 ## shift half time step positively due to averaging suffix = '' - print "TimeC", TimeC + print( "TimeC", TimeC ) ##---------- OUTPUT A FILE PER YEAR --------------------- for iY in range( Year_init, Year_end+1 ) : - print datetime.datetime( iY ,1,1 ), datetime.datetime( iY+1,1,1 ) + print( datetime.datetime( iY ,1,1 ), datetime.datetime( iY+1,1,1 ) ) indT = ( np.array(TimeC) >= datetime.datetime( iY ,1,1,0,0,0 ) ) \ * ( np.array(TimeC) < datetime.datetime( iY+1,1,1,0,0,0 ) ) - print "indT",np.sum(indT) + print( "indT",np.sum(indT)) if nameVar in [ "d2m", "sp" ] : Fout = "./{2}/forSPH_ERA5_{0}_y{1}.nc".format( nameVar.upper(), iY, path_FORCING ) From 3b0434f2d95d02af15815520d78d7edc1ea17e14 Mon Sep 17 00:00:00 2001 From: mpayopayo Date: Thu, 14 Oct 2021 16:41:06 +0200 Subject: [PATCH 10/12] added slurm script slurm script to create weights for atmospheric forcing --- create_weight_ERA5.sh | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 create_weight_ERA5.sh diff --git a/create_weight_ERA5.sh b/create_weight_ERA5.sh new file mode 100644 index 0000000..791a640 --- /dev/null +++ b/create_weight_ERA5.sh @@ -0,0 +1,22 @@ +#ERA5 files have been downloaded in livlojobs and transferred to $SBC in ARCHER2 + +cd $SBC + +#update namelists to reflect paths and names (only if doing something new) +# namelist_reshape_bicubic_atmos +# namelist_reshape_bilin_atmos + +#link coordinate file +ln -s $DOMAIN/coordinates.nc $SBC/. + +#load modules +module -s restore /work/n01/shared/acc/n01_modules/ucx_env + +#generate weights +$TDIR/WEIGHTS/scripgrid.exe namelist_reshape_bilin_atmos +$TDIR/WEIGHTS/scrip.exe namelist_reshape_bilin_atmos +$TDIR/WEIGHTS/scripshape.exe namelist_reshape_bilin_atmos +$TDIR/WEIGHTS/scrip.exe namelist_reshape_bicubic_atmos +$TDIR/WEIGHTS/scripshape.exe namelist_reshape_bicubic_atmos + +cd $WDIR From c99953431d7b9783e8697b6a8eec239a80632e2b Mon Sep 17 00:00:00 2001 From: not populated Date: Mon, 18 Oct 2021 10:49:02 +0100 Subject: [PATCH 11/12] slurm script for ERA5 weights generation --- SCRIPTS/create_weight_ERA5.sh | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 SCRIPTS/create_weight_ERA5.sh diff --git a/SCRIPTS/create_weight_ERA5.sh b/SCRIPTS/create_weight_ERA5.sh new file mode 100644 index 0000000..791a640 --- /dev/null +++ b/SCRIPTS/create_weight_ERA5.sh @@ -0,0 +1,22 @@ +#ERA5 files have been downloaded in livlojobs and transferred to $SBC in ARCHER2 + +cd $SBC + +#update namelists to reflect paths and names (only if doing something new) +# namelist_reshape_bicubic_atmos +# namelist_reshape_bilin_atmos + +#link coordinate file +ln -s $DOMAIN/coordinates.nc $SBC/. + +#load modules +module -s restore /work/n01/shared/acc/n01_modules/ucx_env + +#generate weights +$TDIR/WEIGHTS/scripgrid.exe namelist_reshape_bilin_atmos +$TDIR/WEIGHTS/scrip.exe namelist_reshape_bilin_atmos +$TDIR/WEIGHTS/scripshape.exe namelist_reshape_bilin_atmos +$TDIR/WEIGHTS/scrip.exe namelist_reshape_bicubic_atmos +$TDIR/WEIGHTS/scripshape.exe namelist_reshape_bicubic_atmos + +cd $WDIR From 04f584d8d1c95a240cb76c82e0f91bc4c2d0d0f3 Mon Sep 17 00:00:00 2001 From: mpayopayo Date: Mon, 18 Oct 2021 14:01:56 +0200 Subject: [PATCH 12/12] Delete create_weight_ERA5..sh because wrong location --- create_weight_ERA5.sh | 22 ---------------------- 1 file changed, 22 deletions(-) delete mode 100644 create_weight_ERA5.sh diff --git a/create_weight_ERA5.sh b/create_weight_ERA5.sh deleted file mode 100644 index 791a640..0000000 --- a/create_weight_ERA5.sh +++ /dev/null @@ -1,22 +0,0 @@ -#ERA5 files have been downloaded in livlojobs and transferred to $SBC in ARCHER2 - -cd $SBC - -#update namelists to reflect paths and names (only if doing something new) -# namelist_reshape_bicubic_atmos -# namelist_reshape_bilin_atmos - -#link coordinate file -ln -s $DOMAIN/coordinates.nc $SBC/. - -#load modules -module -s restore /work/n01/shared/acc/n01_modules/ucx_env - -#generate weights -$TDIR/WEIGHTS/scripgrid.exe namelist_reshape_bilin_atmos -$TDIR/WEIGHTS/scrip.exe namelist_reshape_bilin_atmos -$TDIR/WEIGHTS/scripshape.exe namelist_reshape_bilin_atmos -$TDIR/WEIGHTS/scrip.exe namelist_reshape_bicubic_atmos -$TDIR/WEIGHTS/scripshape.exe namelist_reshape_bicubic_atmos - -cd $WDIR