Moving an AMM12 Configuration to JPP Configuration : Part One
par_oce
Note
Bottom Line: you need par_JPP.h90 and the new par_oce.F90 from the SALISH_amm/MY_SRC in your MY_SRC
The grid shape for a run is in a par_***.h90. So we need to create a par_JPP.h90 with the correct grid. These are just the changes
cp_cfg = "WCSD" !: name of the configuration jp_cfg = 120 , & !: resolution of the configuration (degrees) -- 1/120 jpidta = 398, & !: first horizontal dimension > or = to jpi jpjdta = 345, & !: second > or = to jpj jpkdta = 40, & !: number of levels > or = to jpk jpisl = 150, & !: number of islands jpnisl = 3000 !: maximum number of points per island ppkth = 25.00_wp , & !: (non dimensional): gives the approximate ppacr = 3.00000000000_wp !: (non dimensional): stretching factor !: layer number above which stretching will !: be maximum. Usually of order jpk/2. ppdzmin = 1._wp , & !: (meters) vertical thickness of the top layer pphmax = 500._wp !: (meters) Maximum depth of the ocean gdepw(jpk)
Notes:
jp_cfg has no effect as we are reading the coordinate files
Islands copied from JPP
pp’s define vertical grid
And this needs to be referenced in par_oce.F90. So add:
#elif defined key_jpp !!--------------------------------------------------------------------- !! 'key_jpp': Strait of Georgia Subdomain: JPP !!--------------------------------------------------------------------- # include "par_JPP.h90"
Recompile
In your CONFIG directory (assuming you are using SALISH_amm as your config name)
./makenemo -n SALISH_amm add_key "key_jpp" del_key "key_amm_12km"
Initialization Files
Clone the nemo-forcing repository from here https://github.com/SalishSeaCast/NEMO-Forcing
Note
Bottom Line: you need files: SubDom_bathy_meter_NOBCchancomp.nc linked to bathy_meter.nc and SubDom_coordinates_seagrid_WestCoast.nc linked to coordinates.nc
Namelist File
Changes from AMM12 namelist file
experience name cn_exp
last time step nn_itend
start date nn_date0
frequency of restart file nn_stock
frequency of write in output file nn_write probably superceded
DIMG file format ln_dimgnnn probably superceded
vertical coordinate ln_zps ln_sco
minimum depth of ocean rn_hmin
partial step thickness rn_e3sps_min rn_e3zps_rat
time step for the dynamics rn_rdt
zero surface forcing ln_ana ln_flx rn_utau0 to be changed later!!
zero run off ln_rnf to be changed later!!
light penetration ln_traqsr
amount of slip on lateral boundaries rn_shlat
climatological obs files ln_obc_clim
total volume conservation ln_vol_cst
use initial state for open boundary conditions nn_obcdta to be changed later!!
time scales for open boundary relaxation rn_dpeXob
turn tidal potential off ln_tide_pot
number of tidal harmonics (for potential) & names nb_harmo clname()
number of open boundary sets nb_bdy to be changed next!
name of tide files, component names and speed filtid tide_cpt() tide_speed()
bottom drag coefficient rn_bfri2
bottom turbulent kinetic energy background rn_bfeb2
geothermal heat flux nn_geoflx
lateral mixing coefficient in the bbl rn_ahtbbl
horizontal eddy diffusivity for tracers rn_aht_0
treatment of hydrostatic pressure ln_phg_sco ln_phg_prj
bilaplacian operator ln_dynldf_bilap
horizontal laplacian eddy viscosity rn_ahm_0_lap
vertical eddy viscosity and diffusivity rn_avm0 rn_avt0
enhanced vertical diffusion and coefficient ln_zdfevd rn_avevd
surface tke input coefficient rn_ebb
surface mixing length scale, Langmuir parameterization ln_mx10, ln_lc
penetration of tke below mixed layer and its exponential decrease nn_etau nn_htau
maximum iterations for the SOR solver and its coefficient nn_nmax rn_sor
number of processors in various directions jpni jpnj jpnij
control sums nn_ictlX nn_jctlX
time step frequency for dynamics and tracer trends nn_trd
time steps used for harmonic analysis nit000_han nitend_han nstep_han
names for harmonic analysis tname()
Note
Bottom Line: you need to clone the namelist from https://github.com/SalishSeaCast/SS-run-sets see JPP. This run is based on git revision: 3647b5e84ad0.
Run
From inside your EXP00 directory, where you have linked to your forcing files you can run
mpiexec -n 16 ./opa