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://bitbucket.org/salishsea/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  • frequency of write in output file nn_write probably superceded

  • DIMG file format ln_dimgnnn probably superceded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://bitbucket.org/salishsea/ss-run-sets see JPP. This run is based on hg changeset: b501af941889

Run

From inside your EXP00 directory, where you have linked to your forcing files you can run

mpiexec -n 16 ./opa