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CF standard: add a dummy variable crs and add all grid mapping related meta-data as attributes.
The ADAGUC WMS/WCS software requires some additional attributes that contain the same information as the CF grid_mapping attributes: proj4_params and epsg_code. In the Dutch National Model and Data Centre NMDC.eu ADAGUC is used as a central component, so for NMDC these additional attributes are highly recommended.
netcdf test_map { variables: double var(n); var:proj4_params = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs" ; var:EPSG_code = "EPSG:4326"; }

Proposal for multiple coordinate systems: https://cf-pcmdi.llnl.gov/trac/wiki/MultipleProjections
proposed extension: add a WKT (well-known text) string of all grid mapping related meta-data (the WKT quite laborious for parsing though). Note that the plethora of brackets and slashes can ruin opendap access to a netCDF file, see the following slash*.nc examples.
proposed extension: make sure that the dummy variable crs it an integer and that its value is the EPSG code of the coordinate system, e.g:
- 28992 for Dutch Rijksdriehoek (projection_x_coordinate,projection_y_coordinate)
- 4326 for WGS84 global ellipsoid (latitude, longitude)
- 32631 for WGS 84 / UTM zone 31N (projection_x_coordinate,projection_y_coordinate)

Examples

D-Flow FM map file on local xy-grid (e.g., Amersfoort / RD New).

Currently lacks lon/lat for x/y-grids.
The RD projection (oblique stereographic) is not recognized in CF-1.4 (and many others), in PROJ.4 'sterea' is used: http://www.spatialreference.org/ref/epsg/28992/

More details are here: unstructured grid format.

netcdf test_map {
// Only relevant parts for crs are shown!
dimensions:
        nNetCell = 665 ;
        time = UNLIMITED ; // (1 currently)
variables:
        double time(time) ;
                time:units = "seconds since 2010-01-01 00:00:00" ;
        double NetCell_xc(nNetCell) ;
                NetCell_xc:units = "m" ;
                NetCell_xc:standard_name = "projection_x_coordinate" ;
                NetCell_xc:long_name = "Net cell circumcenter x" ;
                NetCell_xc:bounds = "NetCellContour_x" ;
        double NetCell_yc(nNetCell) ;
                NetCell_yc:units = "m" ;
                NetCell_yc:standard_name = "projection_y_coordinate" ;
                NetCell_yc:long_name = "Net cell circumcenter y" ;
                NetCell_yc:bounds = "NetCellContour_y" ;
        double s1(time, nNetCell) ;
                s1:cell_methods = "area: mean" ;
                s1:coordinates = "NetCell_xc Netcell_yc" ;
                s1:grid_mapping = "crs" ;
        int crs ;
                crs:grid_mapping_name = "oblique_stereographic" ;
                crs:projection_name = "Amersfoort / RD New" ;
                crs:semi_major_axis = 6377397.f ;
                crs:inverse_flattening = 299.1528f ;
                crs:latitude_of_projection_origin = 52.15616f ;
                crs:longitude_of_central_meridian = 5.387639f ;
                crs:scale_factor_at_projection_origin = 0.9999079f ;
                crs:false_easting = 155000 ;
                crs:false_northing = 463000 ;
                crs:proj4_params = "+proj=sterea +lat_0=52.15616055555555 +lon_0=5.38763888888889 +k=0.999908 +x_0=155000 +y_0=463000 +ellps=bessel +units=m +towgs84=565.4174,50.3319,465.5542,-0.398957388243134,0.343987817378283,-1.87740163998045,4.0725 +no_defs" // ADAGUC extension
                crs:EPSG_code = "EPSG:28992" // ADAGUC extension

// note that the default proj4 (epsg) string for the Dutch RD system (EPSG:28992 & EPSG:7415) is wrong, it contains an erroneous ellipse reference, hence the full ellipse values need to be supplied.

//...
crs = 28992 ;

D-Flow FM map file on lon/lat-grid (e.g., WGS 1984)

More details are here: unstructured grid format.

netcdf test_map {
// Only relevant parts for crs are shown!
dimensions:
        nNetCell = 184324 ;
        time = UNLIMITED ; // (1 currently)
variables:
        double time(time) ;
                time:units = "seconds since 2010-01-01 00:00:00" ;
        double NetCell_xc(nNetCell) ;
                NetCell_xc:units = "degrees_east" ;
                NetCell_xc:standard_name = "longitude" ;
                NetCell_xc:long_name = "Net cell circumcenter x" ;
                NetCell_xc:bounds = "NetCellContour_x" ;
        double NetCell_yc(nNetCell) ;
                NetCell_yc:units = "degrees_north" ;
                NetCell_yc:standard_name = "latitude" ;
                NetCell_yc:long_name = "Net cell circumcenter y" ;
                NetCell_yc:bounds = "NetCellContour_y" ;
        double s1(time, nNetCell) ;
                s1:cell_methods = "area: mean" ;
                s1:coordinates = "NetCell_xc Netcell_yc" ;
                s1:grid_mapping = "crs" ;
        int crs ;
                crs:grid_mapping_name = "latitude_longitude" ;
                crs:longitude_of_prime_meridian = 0.f ;
                crs:semi_major_axis = 6378137.f ;
                crs:inverse_flattening = 298.2572f ;
                NetCell_xc:proj4_params = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"  // ADAGUC extension
                NetCell_xc:EPSG_code = "EPSG:4326";  // ADAGUC extension
//...
crs = 4326 ;