Merge pull request #16 from NOC-MSM/master

NEMO-RELOC --> SWOT
JMMP-Group · May 27, 2021 · a786036 · a786036
2 parents 92a8d01 + aceb4c8
commit a786036
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diff --git a/SCRIPTS/make_bathymetry_from_gebco.sh b/SCRIPTS/make_bathymetry_from_gebco.sh
@@ -53,41 +53,36 @@
   # If necessary, edit namelist to point to correct input file and variable names
   cd $DOMAIN
 
+  # Link in the new coordinates file
+  ln -s $TDIR/NESTING/1_coordinates_AMM15.nc coordinates.nc
+
   # Execute first SCRIP process::
   $TDIR/WEIGHTS/scripgrid.exe namelist_reshape_bilin_gebco
 
-#:'
-#
 #  Output files::
 #
 #    remap_nemo_grid_gebco.nc
 #    remap_data_grid_gebco.nc
-#'
-#::
 
   #Execute second SCRIP process:
   $TDIR/WEIGHTS/scrip.exe namelist_reshape_bilin_gebco
 
-#:'
-#
 #  Output files::
 #
 #    data_nemo_bilin_gebco.nc
-#'
-#::
+
 
   # Execute third SCRIP process:
   $TDIR/WEIGHTS/scripinterp.exe namelist_reshape_bilin_gebco
 
-#:'
-#
 #  Output files::
 #
 #    bathy_meter.nc
 #
 #  Finally, load ``nco`` tools to tidy some grid scale issues
-#'
-#::
+
+#
+# Finally make minor modifications to the bathymetry file
 #
 #  # load nco modules (this was done locally)
 #  module load nco
@@ -106,4 +101,5 @@
 #  # E.g. ncap2 -s 'Bathymetry(0,0)=0' bathy_meter_10m.nc bathy_meter_10m.nc -O
 
 
+
   cd $WORK
diff --git a/SCRIPTS/make_coordinates_from_parent_SEAsia.sh b/SCRIPTS/make_coordinates_from_parent_SEAsia.sh
@@ -10,101 +10,22 @@ Make a netCDF coordinates file holds that holds the horizontal grid coordinate
 position and spacings information. This is used to construct the 3D version:
 the domain_cfg.nc file.
 
-This script generates a coordinates.nc file using the gebco bathymetry data.
+This script generates a coordinates.nc file using a parent NEMO coordinates file.
 
 '
-
-
-
-
-
-Hmm try and jump straight to DOMAINcfg with only lat and lon points
-
-
-Extract from the parent bathymetry the size, start lat and lon, and resolution::
-
-
-  y = 1363
-        x = 2410
-
-::
-
-  vi namelist_cfg
-
-  jpidta      =    2410   !  1st lateral dimension ( >= jpi )
-  jpjdta      =    1363   !  2nd    "         "    ( >= jpj )
-  ...
-  jpiglo      =    2410   !  1st dimension of global domain --> i =jpidta
-  jpjglo      =    1363   !  2nd    -                  -    --> j  =jpjdta
-
-
-  !-----------------------------------------------------------------------
-  &namdom        !   space and time domain (bathymetry, mesh, timestep)
-  !-----------------------------------------------------------------------
-    jphgr_msh   =       1               !  type of horizontal mesh
-    ppglam0     =  -1.6638888888888899             !  longitude of first raw and column T-point (jphgr_msh = 1)
-    ppgphi0     =  50.53833333333690803             ! latitude  of first raw and column T-point (jphgr_msh = 1)
-    ppe1_deg    =  0.0002777777778             !  zonal      grid-spacing (degrees)
-    ppe2_deg    =  0.0002777777778             !  meridional grid-spacing (degrees)
-    ppdzmin     =  999999.              !  Minimum vertical spacing
-    pphmax      =  999999.              !  Maximum depth
-    ldbletanh   =  .FALSE.              !  Use/do not use double tanf function for vertical coordinates
-    ppa2        =  999999.              !  Double tanh function parameters
-    ppkth2      =  999999.              !
-    ppacr2      =  999999.              !
-  /
-
-
-
-This seems to work, in populating e1 and e2 fields.
-
-NExt steps:
-Do rigourously.
-
-
-Then build into a coordinate.nc file::
-
-  $archer
-  module load nco
-
-  # copy the desired variables
-  ncks -O -C -a -v nav_lon,nav_lat,glamt,glamu,glamv,glamf,gphit,gphiu,gphiv,gphif,e1t,e1u,e1v,e1f,e2t,e2u,e2v,e2f,ff_f,ff_t domain_cfg.nc coordinates_Solent_R3600.nc
-
-
-This creates a new coordinates file with contents, which is now copied to
-  INPUTS::
-
-    cp coordinates_Solent_R3600.nc $INPUTS/coordinates.nc
-
-
-
-Now we need to generate a bathymetry on this new grid.
-
-
-
-
-
 #::
 
-
-
   cd $TDIR/NESTING
 
   #load modules
-  module unload nco cray-netcdf cray-hdf5
-  module swap PrgEnv-cray PrgEnv-intel
-  module load cray-netcdf-hdf5parallel
-  module load cray-hdf5-parallel
+  module -s restore /work/n01/shared/acc/n01_modules/ucx_env
 
   # subdomain of ORCA global
   # you can download the ORCA R12 coordinates
   wget http://gws-access.jasmin.ac.uk/public/nemo/runs/ORCA0083-N06/domain/coordinates.nc -O $TDIR/NESTING/coordinates_ORCA_R12.nc
 
-  #  or in ARCHER you can take it from my directory
-  # cp /work/n01/n01/jelt/EXTRA_TOOLS/GRIDS/coordinates_ORCA_R12.nc $TDIR/NESTING/.
-
   # Get the namelist file from the cloned NEMO-RELOC repository
-  cp $GITCLONE/DOMAIN/namelist.input $TDIR/NESTING/
+  cp $DOMAIN/namelist.input $TDIR/NESTING/
 
 :'
 
@@ -115,8 +36,6 @@ coordinates. rho=rhot=7 with increase the resolution by a factor of 7.
 
 #::
 
-  cd $TDIR/NESTING/
-
   # Generate the new coordinates file with the namelist.input settings
   ./agrif_create_coordinates.exe