| 1 | ### =========================================================================== |
|---|
| 2 | ### |
|---|
| 3 | ### Build coordnates mask |
|---|
| 4 | ### |
|---|
| 5 | ### =========================================================================== |
|---|
| 6 | # creates file coordinates_mask.nc used by mosaix from NEMO netcdf files |
|---|
| 7 | # coordinates.nc and bathymetry.nc (on the same grid as coordinates.nc) |
|---|
| 8 | |
|---|
| 9 | import numpy as np |
|---|
| 10 | import xarray as xr |
|---|
| 11 | import nemo |
|---|
| 12 | import datetime, os, platform, argparse |
|---|
| 13 | |
|---|
| 14 | ## SVN information |
|---|
| 15 | __Author__ = "$Author$" |
|---|
| 16 | __Date__ = "$Date$" |
|---|
| 17 | __Revision__ = "$Revision$" |
|---|
| 18 | __Id__ = "$Id$" |
|---|
| 19 | __HeadURL__ = "$HeadURL: $" |
|---|
| 20 | ### |
|---|
| 21 | |
|---|
| 22 | ### ===== Handling command line parameters ================================================== |
|---|
| 23 | # Creating a parser |
|---|
| 24 | parser = argparse.ArgumentParser ( |
|---|
| 25 | description = """Read coordinates and bathymetry to build masks, grid bounds and areas for MOSAIX""", |
|---|
| 26 | epilog='-------- End of the help message --------', |
|---|
| 27 | formatter_class=argparse.ArgumentDefaultsHelpFormatter) |
|---|
| 28 | |
|---|
| 29 | # Adding arguments |
|---|
| 30 | parser.add_argument ('--model' , help='oce model name', type=str, default='eORCA1.2', choices=('paleORCA', 'ORCA2.3', 'ORCA2.4', 'eORCA1.2', 'eORCA025', 'eORCA025.1') ) |
|---|
| 31 | parser.add_argument ('--bathy' , help='bathymetry file name', type=str, default='bathy_meter.nc' ) |
|---|
| 32 | parser.add_argument ('--coord' , help='coordinates file name', type=str, default='coordinates.nc' ) |
|---|
| 33 | parser.add_argument ('--fout' , help='output file name (given as an input to MOSAIX)', type=str, default='coordinates_mask.nc' ) |
|---|
| 34 | parser.add_argument ('--ocePerio', help='periodicity of ocean grid, if not given is imposed according to --model', type=int, default=0, choices=range(1, 7) ) |
|---|
| 35 | parser.add_argument ('--nemo4Ubug',help='reproduce NEMO lbc_lnk bug for U grid and periodicity 4', type=bool, default=False, choices=(True, False) ) |
|---|
| 36 | parser.add_argument ('--straits' , help='modify grid metrics for selected strait points (depends on model name)', type=bool, default=False, choices=(True, False) ) |
|---|
| 37 | parser.add_argument ('--coordPerio', help='impose periodicity of coordinates and areas through lbc', type=bool, default=False, choices=(True, False) ) |
|---|
| 38 | parser.add_argument ('--maskbathy', help='use the same formula as in NEMO to compute mask_T from the bathymetry file. Does not always give the same result as NEMO ???', type=bool, default=False, choices=(True, False) ) |
|---|
| 39 | |
|---|
| 40 | # Parse command line |
|---|
| 41 | myargs = parser.parse_args() |
|---|
| 42 | |
|---|
| 43 | # ocean model name |
|---|
| 44 | model = myargs.model |
|---|
| 45 | |
|---|
| 46 | # bathymetry input file |
|---|
| 47 | n_bathy = myargs.bathy |
|---|
| 48 | # coordinates input file |
|---|
| 49 | n_coord = myargs.coord |
|---|
| 50 | # coordinates and mask output file |
|---|
| 51 | n_out = myargs.fout |
|---|
| 52 | |
|---|
| 53 | # reproduce periodicity lbclnk bug for U and nperio = 4 |
|---|
| 54 | nemoUbug = myargs.nemo4Ubug |
|---|
| 55 | # change metrics (and bathymetry) for straits |
|---|
| 56 | straits = myargs.straits |
|---|
| 57 | # periodicity imposed on coordinates, metrics and areas |
|---|
| 58 | coordperio = myargs.coordPerio |
|---|
| 59 | # function used to compute mask_T from bathymetry |
|---|
| 60 | maskbathynemo = myargs.maskbathy |
|---|
| 61 | |
|---|
| 62 | # type of grid periodicity |
|---|
| 63 | nperio = myargs.ocePerio |
|---|
| 64 | |
|---|
| 65 | # check of periodicity with type of grid |
|---|
| 66 | if model in ('eORCA1.2', 'paleORCA', 'ORCA025', 'eORCA025', 'eORCA025.1') : |
|---|
| 67 | if nperio != 0 : |
|---|
| 68 | if nperio != 6 : |
|---|
| 69 | print(f'Warning ! model = {model} and ocePerio = {nperio} instead of 6 !') |
|---|
| 70 | else : |
|---|
| 71 | nperio = 6 |
|---|
| 72 | |
|---|
| 73 | if model in ('ORCA2.3', 'ORCA2.4') : |
|---|
| 74 | if nperio != 0 : |
|---|
| 75 | if nperio != 4 : |
|---|
| 76 | print(f'Attention ! model = {model} and ocePerio = {nperio} instead of 4 !') |
|---|
| 77 | else : |
|---|
| 78 | nperio = 4 |
|---|
| 79 | |
|---|
| 80 | print(f' model = {model}\n ocePerio = {nperio}\n bathy = {n_bathy}\n coord = {n_coord}\n fout = {n_out}') |
|---|
| 81 | print(f' Switchs : nemo4Ubug = {nemoUbug}, straits = {straits}, coordPerio = {coordperio}, maskbathy = {maskbathynemo}') |
|---|
| 82 | |
|---|
| 83 | ## |
|---|
| 84 | #!!! bathymetry and coordinates files |
|---|
| 85 | ## |
|---|
| 86 | |
|---|
| 87 | # open input files while removing the time dimension |
|---|
| 88 | f_coord = xr.open_dataset (n_coord, decode_times=False).squeeze() |
|---|
| 89 | f_bathy = xr.open_dataset (n_bathy, decode_times=False).squeeze() |
|---|
| 90 | |
|---|
| 91 | # Suppress time if necessary |
|---|
| 92 | try : |
|---|
| 93 | del f_coord['time'] |
|---|
| 94 | print ('time successfully removed') |
|---|
| 95 | except : |
|---|
| 96 | pass |
|---|
| 97 | print ('failed to suppress time') |
|---|
| 98 | |
|---|
| 99 | # rename latitude, longitude and grid variables in bathymetry |
|---|
| 100 | Bathymetry = f_bathy['Bathymetry'].copy() |
|---|
| 101 | |
|---|
| 102 | nav_lon_grid_T = f_bathy['nav_lon'].data |
|---|
| 103 | nav_lat_grid_T = f_bathy['nav_lat'].data |
|---|
| 104 | Bathymetry = xr.DataArray (Bathymetry, coords = { "nav_lat_grid_T": (["y", "x"], nav_lat_grid_T), |
|---|
| 105 | "nav_lon_grid_T": (["y", "x"], nav_lon_grid_T) } ) |
|---|
| 106 | |
|---|
| 107 | Bathymetry = Bathymetry.rename ({'y':'y_grid_T', 'x':'x_grid_T'}) |
|---|
| 108 | |
|---|
| 109 | # modify Bathymetry in straits for select grids (might change computed mask_T) |
|---|
| 110 | if straits : |
|---|
| 111 | # Open straits for usual grids |
|---|
| 112 | if model == 'ORCA2.3' : |
|---|
| 113 | # orca_r2: Gibraltar strait open |
|---|
| 114 | Bathymetry[101,139] = 284. |
|---|
| 115 | # orca_r2: Bab el Mandeb strait open |
|---|
| 116 | Bathymetry[87,159] = 137. |
|---|
| 117 | |
|---|
| 118 | # impose periodicity of bathymetry |
|---|
| 119 | Bathymetry = nemo.lbc (Bathymetry, nperio=nperio, cd_type='T') |
|---|
| 120 | # suppress ocean points at southernmost position only if nperio in {3, 4, 5, 6} |
|---|
| 121 | if nperio in (3, 4, 5, 6) : |
|---|
| 122 | Bathymetry[0,:] = 0.0 |
|---|
| 123 | |
|---|
| 124 | ## |
|---|
| 125 | #!!! Create masks from bathymetry |
|---|
| 126 | ## |
|---|
| 127 | |
|---|
| 128 | # Creation of mask_T following choosed option maskbathy |
|---|
| 129 | if maskbathynemo : |
|---|
| 130 | # Use same formula as domzgr. |
|---|
| 131 | mask_T = xr.where (Bathymetry - 1. + 0.1 >= 0.0, 1, 0).astype (dtype='f4') |
|---|
| 132 | else : |
|---|
| 133 | mask_T = xr.where (Bathymetry > 0.0, 1, 0).astype (dtype='f4') |
|---|
| 134 | |
|---|
| 135 | # Creation of U, V, W, F masks from mask_T |
|---|
| 136 | mask_U = mask_T * mask_T.shift (x_grid_T=-1) |
|---|
| 137 | mask_V = mask_T * mask_T.shift (y_grid_T=-1) |
|---|
| 138 | mask_F = mask_T * mask_T.shift (y_grid_T=-1) * mask_T.shift (x_grid_T=-1) * mask_T.shift (y_grid_T=-1, x_grid_T=-1) |
|---|
| 139 | mask_W = mask_T |
|---|
| 140 | |
|---|
| 141 | # loop on TUVFW to modify coordinates and attributes of mask_[TUVFW] and maskutil_[TUVFW] |
|---|
| 142 | for cd_type in ['T', 'U', 'V', 'F', 'W'] : |
|---|
| 143 | MaskName = 'mask_' + cd_type |
|---|
| 144 | UtilName = 'maskutil_' + cd_type |
|---|
| 145 | # impose periodicity of chosen grid model on masks |
|---|
| 146 | locals()[MaskName] = nemo.lbc (locals()[MaskName], nperio=nperio, cd_type=cd_type, nemo_4U_bug=nemoUbug).astype (dtype='f4') |
|---|
| 147 | # rename masks coordinates |
|---|
| 148 | if cd_type != 'T' : |
|---|
| 149 | locals()[MaskName] = locals()[MaskName].rename \ |
|---|
| 150 | ( {'y_grid_T' : 'y_grid_'+cd_type, 'x_grid_T' : 'x_grid_'+cd_type, |
|---|
| 151 | 'nav_lat_grid_T': 'nav_lat_grid_'+cd_type, 'nav_lon_grid_T': 'nav_lon_grid_'+cd_type} ) |
|---|
| 152 | |
|---|
| 153 | # create masks without duplicate points : maskutil_[TUVWF] |
|---|
| 154 | locals()[UtilName] = nemo.lbc_mask (locals()[MaskName].copy(), nperio=nperio, cd_type=cd_type) |
|---|
| 155 | |
|---|
| 156 | #set name attribute of mask dataset |
|---|
| 157 | locals()[MaskName].name = MaskName |
|---|
| 158 | locals()[UtilName].name = UtilName |
|---|
| 159 | |
|---|
| 160 | # remove _FillVallue from mskutil |
|---|
| 161 | locals()[MaskName].encoding['_FillValue'] = None |
|---|
| 162 | locals()[UtilName].encoding['_FillValue'] = None |
|---|
| 163 | |
|---|
| 164 | # add masks attributes |
|---|
| 165 | locals()[MaskName].attrs['cell_measures'] = 'area: area_grid_'+cd_type |
|---|
| 166 | locals()[UtilName].attrs['cell_measures'] = 'area: area_grid_'+cd_type |
|---|
| 167 | |
|---|
| 168 | ## |
|---|
| 169 | #!!! create grid coordinates from NEMO coordinates.nc file |
|---|
| 170 | ## |
|---|
| 171 | |
|---|
| 172 | angle = { 'lon' : 'glam', 'lat' : 'gphi' } |
|---|
| 173 | gridv = { 'T' : 't', 'U' : 'u', 'V' : 'v', 'F' : 'f', 'W' : 't' } |
|---|
| 174 | for cd_type in ['T', 'U', 'V', 'F', 'W'] : |
|---|
| 175 | for dir_type in ['lon', 'lat'] : |
|---|
| 176 | coord_name = 'nav_' + dir_type + '_grid_' + cd_type |
|---|
| 177 | dir_name = angle[dir_type]+gridv[cd_type] |
|---|
| 178 | # impose or not periodicity on coordinates read from file |
|---|
| 179 | if coordperio : |
|---|
| 180 | locals()[coord_name] = nemo.lbc (f_coord[dir_name].copy(), nperio=nperio, cd_type=cd_type, nemo_4U_bug=nemoUbug) |
|---|
| 181 | else : |
|---|
| 182 | locals()[coord_name] = f_coord[dir_name].copy() |
|---|
| 183 | |
|---|
| 184 | locals()[coord_name] = locals()[coord_name].rename( {'y':'y_grid_'+cd_type, 'x':'x_grid_'+cd_type} ) |
|---|
| 185 | |
|---|
| 186 | # remove _FillValue and missing_value |
|---|
| 187 | locals()[coord_name].encoding['_FillValue'] = None |
|---|
| 188 | locals()[coord_name].encoding['missing_value'] = None |
|---|
| 189 | |
|---|
| 190 | # define name attribute |
|---|
| 191 | locals()[coord_name].name = coord_name |
|---|
| 192 | |
|---|
| 193 | # add coordinates attributes |
|---|
| 194 | locals()[coord_name].attrs['bounds'] ='bounds_' + dir_type + '_grid_' + cd_type |
|---|
| 195 | |
|---|
| 196 | locals()['nav_lon_grid_'+cd_type].attrs['standard_name'] = 'longitude' |
|---|
| 197 | locals()['nav_lon_grid_'+cd_type].attrs['long_name'] = 'Longitude' |
|---|
| 198 | locals()['nav_lon_grid_'+cd_type].attrs['units'] = 'degrees_east' |
|---|
| 199 | locals()['nav_lat_grid_'+cd_type].attrs['standard_name'] = 'latitude' |
|---|
| 200 | locals()['nav_lat_grid_'+cd_type].attrs['long_name'] = 'Latitude' |
|---|
| 201 | locals()['nav_lat_grid_'+cd_type].attrs['units'] = 'degrees_north' |
|---|
| 202 | |
|---|
| 203 | ## |
|---|
| 204 | #!!! compute areas of cells at coordinate points |
|---|
| 205 | ## |
|---|
| 206 | |
|---|
| 207 | # create areas variables for grid cells from NEMO coordinates.nc file |
|---|
| 208 | # create new variables e1 e2 to keep f_coord the same |
|---|
| 209 | for cd_type in ['t', 'u', 'v', 'f'] : |
|---|
| 210 | for axis in ['1', '2'] : |
|---|
| 211 | coordName = 'e' + axis + cd_type |
|---|
| 212 | locals()[coordName]=f_coord[coordName].copy() |
|---|
| 213 | # remove zero values from areas |
|---|
| 214 | # need to be define for the extended grid south of -80S |
|---|
| 215 | # some point are undefined but you need to have e1 and e2 .NE. 0 |
|---|
| 216 | locals()[coordName]=xr.where(locals()[coordName] == 0.0, 1.0e2, locals()[coordName]) |
|---|
| 217 | |
|---|
| 218 | # Correct areas for straits |
|---|
| 219 | if straits : |
|---|
| 220 | # ORCA R2 configuration |
|---|
| 221 | if model == 'ORCA2.3' : |
|---|
| 222 | # Gibraltar : e2u reduced to 20 km |
|---|
| 223 | e2u[101,138:140] = 20.e3 |
|---|
| 224 | # Bab el Mandeb : e2u reduced to 30 km |
|---|
| 225 | # e1v reduced to 18 km |
|---|
| 226 | e1v[87,159] = 18.e3 |
|---|
| 227 | e2u[87,159] = 30.e3 |
|---|
| 228 | # Danish Straits: e2u reduced to 10 km |
|---|
| 229 | e2u[115,144:146] = 10.e3 |
|---|
| 230 | # ORCA R1 configuration |
|---|
| 231 | if model == 'eORCA1.2' : |
|---|
| 232 | # Gibraltar : e2u reduced to 20 km |
|---|
| 233 | e2u[240,281:283] = 20.e3 |
|---|
| 234 | # Bhosporus : e2u reduced to 10 km |
|---|
| 235 | e2u[247,313:315] = 10.e3 |
|---|
| 236 | # Lombok : e1v reduced to 13 km |
|---|
| 237 | e1v[163:165,43] = 13.e3 |
|---|
| 238 | # Sumba : e1v reduced to 8 km |
|---|
| 239 | e1v[163:165,47] = 8.e3 |
|---|
| 240 | # Ombai : e1v reduced to 13 km |
|---|
| 241 | e1v[163:165,52] = 13.e3 |
|---|
| 242 | # Timor Passage : e1v reduced to 20 km |
|---|
| 243 | #e1v[163:165,55] = 20.e3 |
|---|
| 244 | # W Halmahera : e1v reduced to 30 km |
|---|
| 245 | e1v[180:182,54] = 30.e3 |
|---|
| 246 | # E Halmahera : e1v reduced to 50 km |
|---|
| 247 | e1v[180:182,57] = 50.e3 |
|---|
| 248 | # ORCA R05 configuration |
|---|
| 249 | if model == 'ORCA.05' : |
|---|
| 250 | # Reduced e2u at the Gibraltar Strait |
|---|
| 251 | e2u[326,562:564] = 20.e3 |
|---|
| 252 | # Reduced e2u at the Bosphore Strait |
|---|
| 253 | e2u[342,626:628] = 10.e3 |
|---|
| 254 | # Reduced e2u at the Sumba Strait |
|---|
| 255 | e2u[231,92:94] = 40.e3 |
|---|
| 256 | # Reduced e2u at the Ombai Strait |
|---|
| 257 | e2u[231,102] = 15.e3 |
|---|
| 258 | # Reduced e2u at the Palk Strait |
|---|
| 259 | e2u[269,14] = 10.e3 |
|---|
| 260 | # Reduced e1v at the Lombok Strait |
|---|
| 261 | e1v[231:233,86] = 10.e3 |
|---|
| 262 | # Reduced e1v at the Bab el Mandeb |
|---|
| 263 | e1v[275,661] = 25.e3 |
|---|
| 264 | |
|---|
| 265 | # compute cells areas |
|---|
| 266 | |
|---|
| 267 | for cd_type in ['T', 'U', 'V', 'F', 'W'] : |
|---|
| 268 | areaName = 'area_grid_' + cd_type |
|---|
| 269 | if coordperio : |
|---|
| 270 | locals()[areaName] = nemo.lbc (locals()['e1'+gridv[cd_type]]*locals()['e2'+gridv[cd_type]], |
|---|
| 271 | nperio=nperio, cd_type=cd_type, nemo_4U_bug=nemoUbug) |
|---|
| 272 | else : |
|---|
| 273 | locals()[areaName] = locals()['e1'+gridv[cd_type]]*locals()['e2'+gridv[cd_type]] |
|---|
| 274 | |
|---|
| 275 | # rename indices |
|---|
| 276 | locals()[areaName] = locals()[areaName].rename ({'y':'y_grid_'+cd_type, 'x':'x_grid_'+cd_type}) |
|---|
| 277 | |
|---|
| 278 | # add attributes |
|---|
| 279 | locals()[areaName].name = areaName |
|---|
| 280 | locals()[areaName].attrs['standard_name'] = 'cell_area' |
|---|
| 281 | locals()[areaName].attrs['units'] = 'm2' |
|---|
| 282 | |
|---|
| 283 | # remove fill values |
|---|
| 284 | locals()[areaName].encoding['_FillValue'] = None |
|---|
| 285 | |
|---|
| 286 | ## |
|---|
| 287 | #!!! compute grid bounds !!! |
|---|
| 288 | ## |
|---|
| 289 | |
|---|
| 290 | #--------------------------------------------------------------- |
|---|
| 291 | # function to generate grid bounds from NEMO coordinates.nc file |
|---|
| 292 | def set_bounds (cdgrd) : |
|---|
| 293 | ''' |
|---|
| 294 | Constructs lon/lat bounds |
|---|
| 295 | Bounds are numerated counter clockwise, from bottom left |
|---|
| 296 | See NEMO file OPA_SRC/IOM/iom.F90, ROUTINE set_grid_bounds, for more details |
|---|
| 297 | ''' |
|---|
| 298 | # Define offset of coordinate representing bottom-left corner |
|---|
| 299 | if cdgrd in ['T', 'W'] : |
|---|
| 300 | icnr = -1 ; jcnr = -1 |
|---|
| 301 | corner_lon = f_coord['glamf'].copy() ; corner_lat = f_coord['gphif'].copy() |
|---|
| 302 | center_lon = f_coord['glamt'].copy() ; center_lat = f_coord['gphit'].copy() |
|---|
| 303 | if cdgrd == 'U' : |
|---|
| 304 | icnr = 0 ; jcnr = -1 |
|---|
| 305 | corner_lon = f_coord['glamv'].copy() ; corner_lat = f_coord['gphiv'].copy() |
|---|
| 306 | center_lon = f_coord['glamu'].copy() ; center_lat = f_coord['gphiu'].copy() |
|---|
| 307 | if cdgrd == 'V' : |
|---|
| 308 | icnr = -1 ; jcnr = 0 |
|---|
| 309 | corner_lon = f_coord['glamu'].copy() ; corner_lat = f_coord['gphiu'].copy() |
|---|
| 310 | center_lon = f_coord['glamv'].copy() ; center_lat = f_coord['gphiv'].copy() |
|---|
| 311 | if cdgrd == 'F' : |
|---|
| 312 | icnr = -1 ; jcnr = -1 |
|---|
| 313 | corner_lon = f_coord['glamt'].copy() ; corner_lat = f_coord['gphit'].copy() |
|---|
| 314 | center_lon = f_coord['glamf'].copy() ; center_lat = f_coord['gphif'].copy() |
|---|
| 315 | |
|---|
| 316 | jpj, jpi = corner_lon.shape ; |
|---|
| 317 | nvertex = 4 |
|---|
| 318 | dims = ['y_grid_' + cdgrd, 'x_grid_' + cdgrd, 'nvertex_grid_' + cdgrd] |
|---|
| 319 | |
|---|
| 320 | bounds_lon = xr.DataArray (np.zeros ((jpj, jpi, nvertex)), dims=dims) |
|---|
| 321 | bounds_lat = xr.DataArray (np.zeros ((jpj, jpi, nvertex)), dims=dims) |
|---|
| 322 | |
|---|
| 323 | idx = [(jcnr,icnr), (jcnr,icnr+1), (jcnr+1,icnr+1), (jcnr+1,icnr)] |
|---|
| 324 | |
|---|
| 325 | # Compute cell vertices that can be defined, |
|---|
| 326 | # and complete with periodicity |
|---|
| 327 | for nn in range (nvertex) : |
|---|
| 328 | tmp = np.roll (corner_lon, shift=tuple(-1*np.array(idx[nn])), axis=(-2,-1)) |
|---|
| 329 | bounds_lon[1:jpj,1:jpi,nn] = tmp[1:jpj,1:jpi] |
|---|
| 330 | tmp = np.roll (corner_lat, shift=tuple(-1*np.array(idx[nn])), axis=(-2,-1)) |
|---|
| 331 | bounds_lat[1:jpj,1:jpi,nn] = tmp[1:jpj,1:jpi] |
|---|
| 332 | bounds_lon[:,:,nn] = nemo.lbc (bounds_lon[:,:,nn], nperio=nperio, cd_type=cdgrd, nemo_4U_bug=nemoUbug) |
|---|
| 333 | bounds_lat[:,:,nn] = nemo.lbc (bounds_lat[:,:,nn], nperio=nperio, cd_type=cdgrd, nemo_4U_bug=nemoUbug) |
|---|
| 334 | |
|---|
| 335 | # Zero-size cells at closed boundaries if cell points provided, |
|---|
| 336 | # otherwise they are closed cells with unrealistic bounds |
|---|
| 337 | if not (nperio == 1 or nperio == 4 or nperio == 6) : |
|---|
| 338 | for nn in range (nvertex) : |
|---|
| 339 | bounds_lon[:,0,nn] = center_lon[:,0] # (West or jpni = 1), closed E-W |
|---|
| 340 | bounds_lat[:,0,nn] = center_lat[:,0] |
|---|
| 341 | bounds_lon[:,jpi,nn] = center_lon[:,jpi] # (East or jpni = 1), closed E-W |
|---|
| 342 | bounds_lat[:,jpi,nn] = center_lat[:,jpi] |
|---|
| 343 | if nperio != 2 : |
|---|
| 344 | for nn in range (nvertex) : |
|---|
| 345 | bounds_lon[0,:,nn] = center_lon[0,:] # (South or jpnj = 1), not symmetric |
|---|
| 346 | bounds_lat[0,:,nn] = center_lat[0,:] |
|---|
| 347 | if nperio < 3 : |
|---|
| 348 | for nn in range (nvertex) : |
|---|
| 349 | bounds_lon[jpj,:,nn] = center_lon[jpj,:] # (North or jpnj = 1), no north fold |
|---|
| 350 | bounds_lat[jpj,:,nn] = center_lat[jpj,:] |
|---|
| 351 | |
|---|
| 352 | # Rotate cells at the north fold |
|---|
| 353 | if nperio >= 3 : |
|---|
| 354 | # Working array for location of northfold |
|---|
| 355 | z_fld = nemo.lbc (np.ones ((jpj, jpi)), nperio=nperio, cd_type=cdgrd, psgn=-1., nemo_4U_bug=nemoUbug) |
|---|
| 356 | z_fld = np.repeat((z_fld == -1.0)[...,np.newaxis],4,axis=2) |
|---|
| 357 | # circular shift of 2 indices in bounds third index |
|---|
| 358 | bounds_lon_tmp = np.roll (bounds_lon, shift=-2, axis=2) |
|---|
| 359 | bounds_lat_tmp = np.roll (bounds_lat, shift=-2, axis=2) |
|---|
| 360 | bounds_lon[:,:,:] = np.where (z_fld, bounds_lon_tmp[:,:,:] , bounds_lon[:,:,:] ) |
|---|
| 361 | bounds_lat[:,:,:] = np.where (z_fld, bounds_lat_tmp[:,:,:] , bounds_lat[:,:,:] ) |
|---|
| 362 | |
|---|
| 363 | # Invert cells at the symmetric equator |
|---|
| 364 | if nperio == 2 : |
|---|
| 365 | bounds_lon_tmp = np.roll (bounds_lon, shift=-2, axis=2) |
|---|
| 366 | bounds_lat_tmp = np.roll (bounds_lat, shift=-2, axis=2) |
|---|
| 367 | bounds_lon[0,:,:] = bounds_lon[0,:,:] |
|---|
| 368 | bounds_lat[0,:,:] = bounds_lat[0,:,:] |
|---|
| 369 | |
|---|
| 370 | #bounds_lon.attrs['coordinates'] = 'nav_lat_grid_' + cdgrd + ' nav_lon_grid_' + cdgrd |
|---|
| 371 | #bounds_lat.attrs['coordinates'] = 'nav_lat_grid_' + cdgrd + ' nav_lon_grid_' + cdgrd |
|---|
| 372 | bounds_lon.attrs['units'] = 'degrees_east' |
|---|
| 373 | bounds_lat.attrs['units'] = 'degrees_north' |
|---|
| 374 | bounds_lon.name = 'bounds_lon_grid_' + cdgrd |
|---|
| 375 | bounds_lat.name = 'bounds_lat_grid_' + cdgrd |
|---|
| 376 | # remove _FillValue |
|---|
| 377 | bounds_lon.encoding['_FillValue'] = None |
|---|
| 378 | bounds_lat.encoding['_FillValue'] = None |
|---|
| 379 | |
|---|
| 380 | return bounds_lon, bounds_lat |
|---|
| 381 | #------------------------------------------------------------ |
|---|
| 382 | |
|---|
| 383 | bounds_lon_grid_T, bounds_lat_grid_T = set_bounds ('T') |
|---|
| 384 | bounds_lon_grid_U, bounds_lat_grid_U = set_bounds ('U') |
|---|
| 385 | bounds_lon_grid_V, bounds_lat_grid_V = set_bounds ('V') |
|---|
| 386 | bounds_lon_grid_W, bounds_lat_grid_W = set_bounds ('W') |
|---|
| 387 | bounds_lon_grid_F, bounds_lat_grid_F = set_bounds ('F') |
|---|
| 388 | |
|---|
| 389 | # build xarray dataset to be saved |
|---|
| 390 | ds = xr.Dataset ({ |
|---|
| 391 | 'mask_T' : mask_T , |
|---|
| 392 | 'mask_U' : mask_U , |
|---|
| 393 | 'mask_V' : mask_V , |
|---|
| 394 | 'mask_W' : mask_W , |
|---|
| 395 | 'mask_F' : mask_F , |
|---|
| 396 | 'area_grid_T' : area_grid_T, |
|---|
| 397 | 'area_grid_U' : area_grid_U, |
|---|
| 398 | 'area_grid_V' : area_grid_V, |
|---|
| 399 | 'area_grid_W' : area_grid_W, |
|---|
| 400 | 'area_grid_F' : area_grid_F, |
|---|
| 401 | 'maskutil_T' : maskutil_T , |
|---|
| 402 | 'maskutil_U' : maskutil_U , |
|---|
| 403 | 'maskutil_V' : maskutil_V , |
|---|
| 404 | 'maskutil_W' : maskutil_W , |
|---|
| 405 | 'maskutil_F' : maskutil_F , |
|---|
| 406 | 'bounds_lon_grid_T': bounds_lon_grid_T, |
|---|
| 407 | 'bounds_lat_grid_T': bounds_lat_grid_T, |
|---|
| 408 | 'bounds_lon_grid_U': bounds_lon_grid_U, |
|---|
| 409 | 'bounds_lat_grid_U': bounds_lat_grid_U, |
|---|
| 410 | 'bounds_lon_grid_V': bounds_lon_grid_V, |
|---|
| 411 | 'bounds_lat_grid_V': bounds_lat_grid_V, |
|---|
| 412 | 'bounds_lon_grid_W': bounds_lon_grid_W, |
|---|
| 413 | 'bounds_lat_grid_W': bounds_lat_grid_W, |
|---|
| 414 | 'bounds_lon_grid_F': bounds_lon_grid_F, |
|---|
| 415 | 'bounds_lat_grid_F': bounds_lat_grid_F, |
|---|
| 416 | }) |
|---|
| 417 | |
|---|
| 418 | #replace nav_lon nav_lat with variables obtained from NEMO coordinates.nc file |
|---|
| 419 | #by construction nav_lon nav_lat come from the bathymetry |
|---|
| 420 | for cd_type in ['T', 'U', 'V', 'F', 'W'] : |
|---|
| 421 | for dir_type in ['lon', 'lat'] : |
|---|
| 422 | coord_name = 'nav_' + dir_type + '_grid_' + cd_type |
|---|
| 423 | ds.coords[coord_name]=locals()[coord_name] |
|---|
| 424 | |
|---|
| 425 | ds.attrs['name'] = 'coordinates_mask' |
|---|
| 426 | ds.attrs['description'] = 'coordinates and mask for MOSAIX' |
|---|
| 427 | ds.attrs['title'] = 'coordinates_mask' |
|---|
| 428 | ds.attrs['source'] = 'IPSL Earth system model' |
|---|
| 429 | ds.attrs['group'] = 'ICMC IPSL Climate Modelling Center' |
|---|
| 430 | ds.attrs['Institution'] = 'IPSL https.//www.ipsl.fr' |
|---|
| 431 | ds.attrs['Model'] = model |
|---|
| 432 | ds.attrs['timeStamp'] = '{:%Y-%b-%d %H:%M:%S}'.format (datetime.datetime.now ()) |
|---|
| 433 | ds.attrs['history'] = 'Build from ' + n_coord + ' and ' + n_bathy |
|---|
| 434 | ds.attrs['directory'] = os.getcwd () |
|---|
| 435 | try: |
|---|
| 436 | ds.attrs['user'] = os.getlogin () |
|---|
| 437 | except: |
|---|
| 438 | ds.attrs['user'] = 'NoUser' |
|---|
| 439 | ds.attrs['HOSTNAME'] = platform.node () |
|---|
| 440 | ds.attrs['Python'] = 'Python version: ' + platform.python_version () |
|---|
| 441 | ds.attrs['xarray'] = 'xarray version: ' + xr.__version__ |
|---|
| 442 | ds.attrs['OS'] = platform.system () |
|---|
| 443 | ds.attrs['release'] = platform.release () |
|---|
| 444 | ds.attrs['hardware'] = platform.machine () |
|---|
| 445 | |
|---|
| 446 | ds.attrs['SVN_Author'] = "$Author$" |
|---|
| 447 | ds.attrs['SVN_Date'] = "$Date$" |
|---|
| 448 | ds.attrs['SVN_Revision'] = "$Revision$" |
|---|
| 449 | ds.attrs['SVN_Id'] = "$Id$" |
|---|
| 450 | ds.attrs['SVN_HeadURL'] = "$HeadURL: http://forge.ipsl.jussieu.fr/igcmg/svn/TOOLS/MOSAIX/Build_coordinates_mask.py $" |
|---|
| 451 | |
|---|
| 452 | # save to output file |
|---|
| 453 | ds.to_netcdf (n_out) |
|---|
