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   Nicolas Jourdain, IGE-CNRS, Feb. 2017
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Pre-processing tools to build a regional NEMO configuration laterally forced by a global ocean simulation.
Tested with NEMO-3.6 but should work with previous NEMO-3.x versions.

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Before you start, make sure your system has the following:
- a fortran compiler
- netcdf and fortran-netcdf libraries.

To download NEMO, you need to register on http://www.nemo-ocean.eu/user/register

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Last updates:

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## 0-- First of all, choose a configuration name, e.g. WED12, AMU12, PERIANT025, etc, and save it.

	export CONFIG='WED12'   ## NB: to redo if you start a new session along the following steps !!


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## 1-- Get and install NEMO and XIOS (required for the preprocessing to build the mesh_mask file)

        ## NB: on froggy (Grenoble), you will need to run this command to enable svn functions:
        export ftp_proxy=http://www-cache.ujf-grenoble.fr:3128

        cd $WORKDIR
	mkdir models
	cd models

        ## Choose if you install XIOS-1 or XIOS-2 :
        svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0 XIOS  ## XIOS-1
        svn co -r 1011 http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk XIOS     ## XIOS-2

        ## Install XIOS :
        cd XIOS
        chmod +x make_xios
        ./make_xios --avail      ## find your architecture if it exists (e.g. X64_ADA) 
                                 ## or create a new one in the arch directory.
        time ./make_xios --prod --full --arch X64_ADA --jobs 8 &> compil.log &
        tail -f compil.log       ## to follow the compilation
        ls bin/xios_server.exe   ## to check that it went ok
        cd ..

        ## Choose one of these NEMO releases (or any other branch and version) :
        svn co http://forge.ipsl.jussieu.fr/nemo/svn/trunk MY_NEMO         ## for the last trunk version
	svn co -r 6402 http://forge.ipsl.jussieu.fr/nemo/svn/trunk MY_NEMO ## for version 6402 of the trunk
        svn co http://forge.ipsl.jussieu.fr/nemo/svn/branches/2015/nemo_v3_6_STABLE MY_NEMO ## NEMO3.6 STABLE

        ## Compile for a new configuration, e.g. the WED12 configuration (you can have several ones)
        cd MY_NEMO/NEMOGCM/CONFIG
        echo "$CONFIG OPA_SRC LIM_SRC_3" >> cfg.txt  ## here for OPA+LIM3 (see cfg.txt for other options)
        ./makenemo -h                ## find your architecture if it exists (e.g. X64_ADA)
                                     ## or create a new one in the MY_NEMO/NEMOGCM/ARCH directory.
        vi ../ARCH/arch-X64_ADA.fcm  ## adapt XIOS pathway accordingly with the previous installation.
        mkdir $CONFIG
        ## Choose fppkeys prior to compilation (see NEMO documentations or examples in existing configurations,
        ## e.g. MY_NEMO/NEMOGCM/CONFIG/AMM12/cpp_AMM12.fcm), e.g. : 
        echo " bld::tool::fppkeys key_bdy key_dynspg_ts key_lim3 key_ldfslp key_iomput key_mpp_mpi" > AMU12/cpp_${CONFIG}.fcm
        time ./makenemo -n $CONFIG -m X64_ADA -j 8 &> compile.log &
        tail -f compile.log            ## to follow the compilation
        ls -al ${CONFIG}/BLD/bin/nemo.exe  ## to check that everything went fine
        ## if you recompile, it is recommended to remove these directories: rm -rf ${CONFIG}/WORK ${CONFIG}/BLD
        cd ..

       ## Compile REBUILD_NEMO (used to recombine outputs at the end of the jobs):
       cd TOOLS
       ./maketools -h  ## use same architecture as for NEMO's compilation (e.g. X64_ADA)
       ./maketools -m X64_ADA -n REBUILD_NEMO
       ls -al REBUILD_NEMO/BLD/bin/  ## to check that everything went fine
       cd ..

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## 2-- Prepare the pre-processing tools:

        ##### GSW TOOLBOX #####
        # First you may need the TEOS10 toolbox to convert from EOS80 to TEOS10.
        # To avoid issues with updates on the GSW-Fortran tools, I've cloned the 2016 GSW-Fortran
        # in this repository. In case you want to check for updates (not recommended), you can still do:
        # git clone https://github.com/TEOS-10/GSW-Fortran.git
        cd GSW-Fortran/test
        # edit makefile (in particular fill the FC and NETCDF_INCDIR variables)
        make
        ./gsw_check  ## to check (some have to work, maybe not all of them)
        cd ../..
        # The gsw_data_v3_0.nc file provided in this repository should be fine, but in case you start again 
        # from the original file (i.e. from github.com/TEOS-10/GSW-Fortran.git), you will need to modify it
        # to avoid NaN in some places (otherwise, skip the next 4 lines):
        ./compile.sh remove_NaN_from_gsw_data_v3_0.f90 
        ./remove_NaN_from_gsw_data_v3_0
        ncks -x -v ocean_ref,ndepth_ref,deltaSA_ref,SA_ref,SAAR_ref GSW-Fortran/test/gsw_data_v3_0.nc gsw_data_v3_0.nc
        ncks -A gsw_data_v3_0_to_be_ncks-A.nc gsw_data_v3_0.nc 

        # Edit your own namelist, e.g. namelist_WED12, and link namelist_pre to it:
        vi namelist_${CONFIG}
        ln -s -v namelist_${CONFIG} namelist_pre
        # Edit compile_ALL.sh, adapt fortran compiler (and maybe netcdf path), then execute it:
        ./compile_ALL.sh
        # Create a directory where you will store all the netcdf files created along the following steps, e.g.:
        mkdir $WORKDIR/input/nemo_${CONFIG}  # WARNING: this must correspond to the namelist entry "config_dir"

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## 3-- Build the bathymetry (and ice shelf draft if needed) and coordinates files for the regional domain.

        ./submit.sh extract_bathy_coord 01  ## -> should create the bathy and coordinate files,
                                            ##    e.g. bathy_meter_WED12.nc and coordinates_WED12.nc
                                            ##    (stored in directory defined as config_dir in the namelist)

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## 4- Create mesh_mask file.

        cd xxxxx ## TO BE IMPROVED
        ## NB: set jpni=jpnj=jpnij=0 in the &nammpp section of NEMO's namelist.
        ##     and use the same &namdom parameters as in the simulation used as BDYs.
        qsub run_nemo.sh    ## this will create mesh_mask_${CONFIG}.nc before crashing
        ./rebuild_mesh_mask.sh 0
        mv mesh_mask.nc $WORKDIR/input/nemo_${CONFIG}/mesh_mask_${CONFIG}.nc ## directory defined as config_dir

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## 5- Create the initial state (temperature and salinity)

        ./submit.sh extract_istate 01  ## -> should create the initial state for temperature and salinity 
                                       ##    e.g. dta_temp_WED12.nc and dta_sal_WED12.nc
                                       ##    (stored in directory defined as config_dir in the namelist)

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## 5- Create the lateral boundary conditions (u, v, T, S, SSH, sea-ice thic, sea-ice frac)

	./submit.sh build_coordinates_bdy 01  ## -> creates the coordinate file for lateral boundaries
                                              ##    e.g. coordinates_bdy_WED12.nc

        ./submit.sh extract_bdy_gridT 01 15   ## -> creates T,S bdy files and store them in a BDY folder
                                              ##    itself located in directory defined as config_dir

        ./submit.sh extract_bdy_gridU 01 15   ## -> creates U   bdy files and store them in a BDY folder
        ./submit.sh extract_bdy_gridV 01 15   ## -> creates V   bdy files and store them in a BDY folder
        ./submit.sh extract_bdy_icemod 01     ## -> creates ice bdy files and store them in a BDY folder
        ./submit.sh extract_bdy_ssh 01        ## -> creates SSH bdy files and store them in a BDY folder

        ./concatenate_yearly_BDY.sh           ## Edit this file first.
                                              ## -> concatenate the bdy files into yearly files

        ./submit.sh extract_bdy_tides 01      ## if you want to put tidal signals along the BDYs

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## 6- Other files (SSS for restoring, runoff, chlorophyll)

	./submit.sh extract_SSS_restoring 01 15  ## -> creates SSS files and store them in a SSS folder
        ./concatenate_yearly_SSS.sh              ## Edit this file first.
                                                 ## -> concatenate the bdy files into yearly files

	./submit.sh extract_runoff_icebergs 01   ## -> creates iceberg runoff file
                                                 ##    (stored in config_dir defined in the namelist)

        ./submit.sh extract_chloro 01            ## -> creates chlorophyll file
                                                 ##    (stored in config_dir defined in the namelist)
    
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## 7- Weights for the interpolation of atmospheric forcing

	# here it is assumed that you have NEMO downloaded and installed as explained in step #1

	cd $WORKDIR/models/MY_NEMO/NEMOGCM/TOOLS
	maketools -m X64_ADA -n WEIGHTS           ## Adapt for any machine different from ADA (try makenemo -h)
        cd WEIGHTS                                ## See nice README file in this directoy.
	cp -p nocsutil/namelist_example_bilin namelist_WEIGHTS_${CONFIG}_bilin ## Edit this namelist
	#NB: you may have to increase char_len in src/kinds_mod.f90 if you include long path for file names.

       ## Below is an example for namelist_WEIGHTS_${CONFIG}_bilin :
       ##      
       ##      &grid_inputs
       ##          input_file = 'drowned_precip_DFS5.2_y1993.nc'
       ##          nemo_file = 'coordinates_WED12.nc'
       ##          datagrid_file = 'remap_data_grid.nc'
       ##          nemogrid_file = 'remap_nemo_grid.nc'
       ##          method = 'regular'
       ##          input_lon = 'lon'
       ##          input_lat = 'lat'
       ##          nemo_lon = 'glamt'
       ##          nemo_lat = 'gphit'
       ##          nemo_mask = 'none'
       ##          nemo_mask_value = 10
       ##          input_mask = 'none'
       ##          input_mask_value = 10
       ##      /
       ##      
       ##      &remap_inputs
       ##          num_maps = 1
       ##          grid1_file = 'remap_data_grid.nc'
       ##          grid2_file = 'remap_nemo_grid.nc'
       ##          interp_file1 = 'data_nemo_bilin.nc'
       ##          interp_file2 = 'nemo_data_bilin.nc'
       ##          map1_name = 'data to nemo bilin Mapping'
       ##          map2_name = 'nemo to data bilin Mapping'
       ##          map_method = 'bilinear'
       ##          normalize_opt = 'frac'
       ##          output_opt = 'scrip'
       ##          restrict_type = 'latitude'
       ##          num_srch_bins = 90
       ##          luse_grid1_area = .false.
       ##          luse_grid2_area = .false.
       ##      /
       ##      
       ##      &interp_inputs
       ##          input_file = "drowned_precip_DFS5.2_y1993.nc"
       ##          interp_file = "data_nemo_bilin.nc"
       ##          input_name = "snow"
       ##          input_start = 1,1,1,1
       ##          input_stride = 1,1,1,1
       ##          input_stop = 0,0,0,1
       ##          input_vars = 'initial_time0_hours'
       ##      /
       ##      
       ##      &interp_outputs
       ##          output_file = "snow_orca.nc"
       ##          output_mode = "create"
       ##          output_dims = 'x', 'y', 'time_counter'
       ##          output_scaling = "snow|1.0", "time_counter|86400.0"
       ##          output_name = 'snow'
       ##          output_lon = 'x'
       ##          output_lat = 'y'
       ##          output_vars = 'time_counter'
       ##          output_attributes = 'time_counter|units|seconds since 1995-00-00 00:00:00',
       ##                              'time_counter|calendar|noleap',
       ##                              'snow|units|mm/s'
       ##      /
       ##      

       ## Then, execute these things:
	./scripgrid.exe   ## namelist_${CONFIG}_bilin
	./scrip.exe       ## namelist_${CONFIG}_bilin
	./scripshape.exe  ## namelist_${CONFIG}_bilin

       ## Then create another namelist:  namelist_${CONFIG}_bicub and just change these parameters:
       ##      interp_file1 = 'data_nemo_bicubic.nc'
       ##      interp_file2 = 'nemo_data_bicubic.nc'
       ##      map1_name = 'data to nemo bicubic Mapping'
       ##      map2_name = 'nemo to data bicubic Mapping'
       ##      map_method = 'bicubic'
       ##      interp_file = "data_nemo_bicubic.nc"
       ##      interp_file = 'data_nemo_bicubic.nc'
       ##      output_file = 'weights_bicubic.nc'
       ## Then execute :
	./scrip.exe       ## namelist_${CONFIG}_bicub
	./scripshape.exe  ## namelist_${CONFIG}_bicub