convert_grid_to_nc.md

Convert grid to netCDF that CDO understands

We are going to use spheRlab for conversion. You have to have R already installed.

Clone spheRlab

git clone https://github.com/FESOM/spheRlab.git spheRlab

Build package:

cd spheRlab/
R CMD build spheRlab

Make sure you have cdo installed (cdo -V) and launch R (type R). Install the package:

R>install.packages("spheRlab_1.1.0.tar.gz",repos=NULL)

If you don;t have netCDF library installed, you also have to do:

R>install.packages("ncdf4")

Load libraries:

R>library(spheRlab)
R>library(ncdf4)

You can get help (for any function) by typing, e.g.:

R>?sl.grid.writeCDO

Define path to the mesh

R>meshpath="/work/ollie/dsidoren/input/fesom2.0/meshes/mesh_CORE2_final/"

Read the grid in to R structure (the arguments rot etc. might be different for different meshes, but this is the standard): For rotated meshes:

R>grid = sl.grid.readFESOM(griddir=meshpath,rot=TRUE,rot.invert=TRUE,rot.abg=c(50,15,-90))

For unrotated meshes:

R>grid = sl.grid.readFESOM(griddir=meshpath,rot=FALSE,rot.invert=FALSE,rot.abg=c(0,0,0), threeD=FALSE)

Define path to the output file:

R>ofile = paste0(meshpath, "sl.grid.CDO", sep = "")

Directrly write netCDF file with mesh description:

R>sl.grid.writeCDO(grid, ofile=ofile, netcdf=TRUE, depth=FALSE)

Conservative remapping with cdo (interpolate topography to mesh)

$bash> export MESHPATH=/work/ollie/dsidoren/input/fesom2.0/meshes/mesh_CORE2_final/
$bash> export DATAPATH=/work/ollie/dsidoren/ETOPO5/etopo5_lonlat.nc
$bash> cdo remapycon,$MESHPATH/sl.grid.CDO.nc -selname,topo $DATAPATH $MESHPATH/topo.nc