Anomalous namelist usage early in the code to set parameters

[charliestock]

There are a small number of parameters being defined in a name list at the beginning of the code:

ocean_BGC/generic_tracers/generic_COBALT.F90

Lines 197 to 227 in bfa0211

	! Namelist Options
	character(len=10) :: co2_calc = 'ocmip2' ! other option is 'mocsy'
	logical :: do_14c = .false.
	logical :: debug = .false.
	logical :: do_nh3_atm_ocean_exchange = .false.
	! namelist capabilities for half-sats not used in this run
	logical :: do_vertfill_pre = .false.
	real :: k_nh4_small = 1.e-8
	real :: k_nh4_diazo = 1.e-7
	real :: k_nh4_large = 5.e-8
	real :: k_no3_small = 5.e-7
	real :: k_no3_diazo = 5.0e-6
	real :: k_no3_large = 2.5e-6
	real :: o2_min_nit= 0.01e-6
	real :: k_o2_nit = 3.9e-6
	real :: irr_inhibit = 10.
	real :: gamma_nitrif= 3.5e6 !month(-1)
	real :: k_nh3_nitrif= 3.1e-9 !mol/kg
	real :: imbalance_tolerance=1.0e-10 !the tolerance for non-conservation in C,N,P,Sc,Fe
	integer :: scheme_no3_nh4_lim = 2 !1-Frost and Franzen (1992)
	!2-O'Neill
	integer :: scheme_nitrif = 3 !1-default COBALT
	!2-update with no temperature dependence
	!3-update with temperature dependence
	namelist /generic_COBALT_nml/ do_14c, co2_calc, debug, do_nh3_atm_ocean_exchange, scheme_nitrif, &
	k_nh4_small,k_nh4_large,k_nh4_diazo,scheme_no3_nh4_lim,k_no3_small,k_no3_large,k_no3_diazo, &
	o2_min_nit,k_o2_nit,irr_inhibit,k_nh3_nitrif,gamma_nitrif,do_vertfill_pre,imbalance_tolerance

Many of these are a legacy from Fabien Paulot's development of dynamic ammonia exchanges across the air-sea interface and can likely be either removed and/or set as the other parameters are set. I can put together a pull request to remove these once we agree on the best approach for handling the setting of parameter values.

[yichengt900]

@charliestock , thanks for bringing this up. I also noticed that during my code cleanup & inline doc process (#17). At this moment I simply commented out those lines in branch feature/inline_documentation:

ocean_BGC/generic_tracers/generic_COBALT.F90

Lines 204 to 212 in 9fceed8

	! namelist capabilities for half-sats not used in this run
	! YC TODO: I commented out the following unused namelists now, but should we consider to remove them?
	!real :: k_nh4_small = 1.e-8
	!real :: k_nh4_diazo = 1.e-7
	!real :: k_nh4_large = 5.e-8
	!real :: k_no3_small = 5.e-7
	!real :: k_no3_diazo = 5.0e-6
	!real :: k_no3_large = 2.5e-6
	!logical :: debug = .false.

But we definitely should remove them if they are not used anymore.

Regarding how to handle the setting of parameter values, I like the g_tracer_add_param way because we can always overwrite default values through field_table, but I am open to any ideas.

[yichengt900]

Some of the unused parameters defined in a namelist have been removed in PR #23. The remaining parameters have now been moved to cobalt_types.F90:

  character(len=10), public ::  co2_calc = 'mocsy'           !< carbonate formalation options. Default is 'mocsy'
  logical, public :: do_14c             = .false.            !< If true, then simulate radiocarbon 
  logical, public :: do_nh3_atm_ocean_exchange = .false.     ! If true, then do NH3 air-sea exchange 
  !
  logical, public :: do_vertfill_pre = .false.             !< Returns tracer arrays with sensible values
  logical, public :: debug           = .false.             !< not use   
  real, public    :: o2_min_nit= 0.01e-6                   !< Oxygen threshold for nitrification (mol O2 kg-1)
  real, public    :: k_o2_nit  = 3.9e-6                    !< Oxygen half saturation constant for nitrification
  real, public    :: irr_inhibit = 10.                     !< Irradiance inhibition term for nitrification (W m-2)
  real, public    :: gamma_nitrif= 3.5e6                   !< Rate constant for nitrification (month-1)
  real, public    :: k_nh3_nitrif= 3.1e-9                  !< NH3 half-saturation for nitrification (mol NH3 kg-1)  
  real, public    :: imbalance_tolerance=1.0e-10           !< the tolerance for non-conservation in C,N,P,Sc,Fe

  integer, public :: scheme_no3_nh4_lim = 2 !< Nitrate and ammonia limitation scheme options
                                            !! 1-Frost and Franzen (1992)
                                            !! 2-O'Neill

  integer, public :: scheme_nitrif = 3      !< nitrification scheme options:
                                            !! 1-default COBALT
                                            !! 2-update with no temperature dependence
                                            !! 3-update with temperature dependence

@charliestock we may consider move some of them to g_tracer_add_param.