Other NEMO packages¶
Some useful tools that come with NEMO are available in the analog of the
TOOLS folder. These are built using the ARCH files as you would for
building an experiment with e.g.
./maketools -n REBUILD_NEMO -m HKUST_HPC2
Notes on the ones I have used may be found here.
REBUILD_NEMO¶
XIOS can combine the output-per-CPU cells into one global file, but by default
the restart files and mesh_mask.nc files are output per CPU, so it is useful
to recombine them. This can be done through the REBUILD_NEMO package.
Build as usual, and the resulting output should be a rebuild_nemo.exe in the
folder, to be driven by the script rebuild_nemo. The way to use it is to
call the script as, for example,
$BASE_DIR/tools/REBUILD_NEMO/rebuild_nemo ${MODEL}_${RES_TIMESTAMP}_restart $NUM_CPU
where $BASE_DIR is wherever the folder lives, the things to be combined look
like ${MODEL}_${RES_TMESTAMP}_restart_0000.nc (e.g. mesh_mask_00??.nc,
UNAGI_00051840_restart[_ice].nc, etc.), and $NUM_CPU are the number of
files to combine (e.g. if we use 96 cores then we get mesh_mask_0000.nc to
mesh_mask_0095.nc, and we should do export NUM_CPU=96).
Note
In NEMO 4.0 versions an error may come up with undefined reference to iarg_ and getarg_. This seems to arise from src/rebuild_nemo.f90 where both iarg and getarg are defined as extrinsic. With gfortran this seems to be fixed by simply changing the attribute to intrinsic.
SECTIONS_DIADCT¶
WEIGHTS¶
DOMAINcfg¶
This package generates the domain_cfg.nc file that encodes the grid
locations and spacings, and is recommended for creating new configurations,
mostly because the vertical grid spacings with partial steps correction are a
bit weird to try and do manually. From the readme file in there, you seem
to need to use xios1 to compile this; see the :ref:`README <sec:nemo36:>`_ for
how various things to watch out for.
When compiled the executable is called make_domain_cfg.exe, and it expects
to read a bathy_meter.nc (links are ok) and a namelist_cfg file. The
namelist_cfg file should contain the various settings for horizontal and
vertical grid spacing, which should be consistent with the content in
bathy_meter.nc. An example namelist_cfg is the following:
!-----------------------------------------------------------------------
&namcfg ! parameters of the configuration
!-----------------------------------------------------------------------
!
ln_e3_dep = .true. ! =T : e3=dk[depth] in discret sens.
! ! ===>>> will become the only possibility in v4.0
! ! =F : e3 analytical derivative of depth function
! ! only there for backward compatibility test with v3.6
! !
cp_cfg = "UNAGI" ! name of the configuration
jp_cfg = 100 ! resolution of the configuration
jpidta = 90 ! 1st lateral dimension ( >= jpi )
jpjdta = 26 ! 2nd " " ( >= jpj )
jpkdta = 31 ! number of levels ( >= jpk )
jpiglo = 90 ! 1st dimension of global domain --> i =jpidta
jpjglo = 26 ! 2nd - - --> j =jpjdta
jpizoom = 1 ! left bottom (i,j) indices of the zoom
jpjzoom = 1 ! in data domain indices
jperio = 1 ! lateral cond. type (between 0 and 6) [1 is EW periodicity]
/
!-----------------------------------------------------------------------
&namzgr ! vertical coordinate
!-----------------------------------------------------------------------
ln_zps = .true. ! z-coordinate - partial steps
ln_linssh = .true. ! linear free surface
/
!-----------------------------------------------------------------------
&namdom !
!-----------------------------------------------------------------------
jphgr_msh = 3 ! type of horizontal mesh
ppglam0 = 0.0 ! longitude of first raw and column T-point (jphgr_msh = 1)
ppgphi0 = -50.0 ! latitude of first raw and column T-point (jphgr_msh = 1)
ppe1_deg = 999999.0 ! zonal grid-spacing (degrees)
ppe2_deg = 999999.0 ! meridional grid-spacing (degrees)
ppe1_m = 100000.0 ! zonal grid-spacing (metres)
ppe2_m = 100000.0 ! meridional grid-spacing (metres)
ppsur = 999999.0 ! ORCA r4, r2 and r05 coefficients
ppa0 = 999999.0 ! (default coefficients)
ppa1 = 999999.0 !
ppkth = 18.0 !
ppacr = 10.0 !
ppdzmin = 10.0 ! Minimum vertical spacing
pphmax = 3000.0 ! Maximum depth
ldbletanh = .FALSE. ! Use/do not use double tanf function for vertical coordinates
ppa2 = 999999.0 ! Double tanh function parameters
ppkth2 = 999999.0 !
ppacr2 = 999999.0 !
/
Here, the configuration is called UNAGI. The jp[ijk]data is the number
of grid cells in \((x,y,z)\), and I chose jp[ij]glo to be consistent
with the choice of horizontal sizes. The jperio denotes the periodicities
(see src/domcfg.f90 for the choices). The present model uses a Cartesian
grid on a \(\beta\)-plane corresponding to jphgr_msh = 3 (see
src/domhgr.f90 for choices), and is centred at longitude 0 and latitude 50 S
(see ppglam0 and ppgphi0). The grid spacing here is 100 km,
correpsonding to ppe[12]_m; the values of 999999.0 are options that are
not used.
For the vertical grid, ln_zps switches on the partial step correction and
takes into account bathy_meter.nc. The vertical spacing is governed through
the parameters ppkth, ppacr, ppdzmin and pphmax
([MI96]; unless you use the double tanh option).
Note
Note NEMO 4.2 seems to be using different namings and convention (see here). As of writing
DOMAINcfg still reads the jperio option but separately defines the
l_[IJ]perio and ldNFold logical flags for NEMO to read.