okadate / roms_b4dvar

ROMS with Biological 4DVAR -- adding 4D-Var codes for Fennel et al. (2006) biology model.

ROMS with Biological 4D-Var

This is Regional Ocean Modelling System with 4D-Var data assimilation codes for Fennel et al. (2006) biology model, and under development. Original ROMS codes can be obtained at https://www.myroms.org/.

Additional CPP flags

Fennel et al.(2006) biology model OPTIONS:

PHOSPHORUS          use to add phosphorus variables (PO4, LdetritusP and SdetritusP)
TDEPENDANCE         use to multiply reaction rate by coefficient depending on temperature
BIO_SED_CONSTANT    use to add constant bottom fluxes of DO, NH4 and PO4
NPFLUX_BY_DO        use if bottom fluxes of NH4 and PO4 depending on DO
BIO_SED_DIAGENESIS  (not maintenance) use to activate diagenesis model for bottom fluxes
H2S                 (not maintenance) use to add hydrogen sulfide (H2S)
GROWTH1             (not maintenance) use if growth rate of optimal temperature

Biogeochemical 4D-Var OPTIONS:

ADJUST_PARAM        use if including biogeochemical parameters in 4D-Var state
RESTART_PARAM       use to read biochemical parameters
POSITIVE_T          use to make tracers positive
POSITIVE_PARAM      use to make parameters positive
UV_FIXED_TL         use if physical model is fixed in B4D-Var
OBS_DEPTH_SSH       use if obs_depth=0 is SSH
EXP_PARAM           (not maintenance) use if exponential parameters

Checker for 4D-Var OPTIONS:

CHECKER             use to print user's diagnostic informations
POSITIVE_CG_DELTA   use to make cg_delta positive
POSITIVE_CG_RITZ    use to make cg_ritz positive

Other OPTIONS:

DSTARTSEC           use to change units of dstart from days to seconds
USER_ENSEMBLE       use if ensemble runs by user parameters in ocean.in