update documentation and 3 bgc namelist defaults

CICE-Consortium · Sep 12, 2024 · 066ffc7 · 066ffc7
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diff --git a/cicecore/drivers/unittest/opticep/ice_init_column.F90 b/cicecore/drivers/unittest/opticep/ice_init_column.F90
@@ -1053,15 +1053,15 @@ subroutine input_zbgc
       tr_bgc_N        = .true.   !
 
       ! brine height parameter
-      phi_snow        = -0.3_dbl_kind      ! snow porosity
+      phi_snow        = -1.0_dbl_kind      ! snow porosity
 
       ! skl biology parameters
       bgc_flux_type   = 'Jin2006'! type of ocean-ice poston velocity ('constant')
 
       ! z biology parameters
       grid_o             = 0.006           ! for bottom flux
       grid_o_t           = 0.006           ! for top flux
-      l_sk               = 20.0_dbl_kind   ! characteristic diffusive scale (m)
+      l_sk               = 2.0_dbl_kind    ! characteristic diffusive scale (m)
       initbio_frac       = c1              ! fraction of ocean trcr concentration in bio trcrs
       frazil_scav        = 0.8_dbl_kind    ! increase in initial bio tracer from ocean scavenging
       ratio_Si2N_diatoms = 1.8_dbl_kind    ! algal Si to N (mol/mol)
@@ -1081,7 +1081,7 @@ subroutine input_zbgc
       ratio_Fe2DOC_l     = 0.033_dbl_kind  ! Fe to C of DOC (nmol/umol) lipids
       fr_resp            = 0.05_dbl_kind   ! frac of algal growth lost due to respiration
       tau_min            = 3600.0_dbl_kind ! rapid mobile to stationary exchanges (s)
-      tau_max            = 7776000_dbl_kind! long time mobile to stationary exchanges (s)
+      tau_max            = 604800._dbl_kind! long time mobile to stationary exchanges (s)
       algal_vel          = 1.0e-7_dbl_kind ! 0.5 cm/d(m/s) Lavoie 2005  1.5 cm/day
       R_dFe2dust         = 0.035_dbl_kind  !  g/g (3.5% content) Tagliabue 2009
       dustFe_sol         = 0.005_dbl_kind  ! solubility fraction

diff --git a/cicecore/shared/ice_init_column.F90 b/cicecore/shared/ice_init_column.F90
@@ -1053,15 +1053,15 @@ subroutine input_zbgc
       tr_bgc_N        = .true.   !
 
       ! brine height parameter
-      phi_snow        = -0.3_dbl_kind      ! snow porosity
+      phi_snow        = -1.0_dbl_kind      ! snow porosity
 
       ! skl biology parameters
       bgc_flux_type   = 'Jin2006'! type of ocean-ice poston velocity ('constant')
 
       ! z biology parameters
       grid_o             = 0.006           ! for bottom flux
       grid_o_t           = 0.006           ! for top flux
-      l_sk               = 20.0_dbl_kind   ! characteristic diffusive scale (m)
+      l_sk               = 2.0_dbl_kind    ! characteristic diffusive scale (m)
       initbio_frac       = c1              ! fraction of ocean trcr concentration in bio trcrs
       frazil_scav        = 0.8_dbl_kind    ! increase in initial bio tracer from ocean scavenging
       ratio_Si2N_diatoms = 1.8_dbl_kind    ! algal Si to N (mol/mol)
@@ -1081,7 +1081,7 @@ subroutine input_zbgc
       ratio_Fe2DOC_l     = 0.033_dbl_kind  ! Fe to C of DOC (nmol/umol) lipids
       fr_resp            = 0.05_dbl_kind   ! frac of algal growth lost due to respiration
       tau_min            = 3600.0_dbl_kind ! rapid mobile to stationary exchanges (s)
-      tau_max            = 7776000_dbl_kind! long time mobile to stationary exchanges (s)
+      tau_max            = 604800._dbl_kind! long time mobile to stationary exchanges (s)
       algal_vel          = 1.0e-7_dbl_kind ! 0.5 cm/d(m/s) Lavoie 2005  1.5 cm/day
       R_dFe2dust         = 0.035_dbl_kind  !  g/g (3.5% content) Tagliabue 2009
       dustFe_sol         = 0.005_dbl_kind  ! solubility fraction

diff --git a/doc/source/user_guide/ug_case_settings.rst b/doc/source/user_guide/ug_case_settings.rst
@@ -828,7 +828,7 @@ zbgc_nml
    "``K_Sil_phaeo``", "real", "silicate half saturation phaeocystis mmol/m^3", "0.0"
    "``K_Sil_sp``", "real", "silicate half saturation small plankton mmol/m^3", "0.0"
    "``kn_bac_protein``", "real", "bacterial degradation of DON per day", "0.2"
-   "``l_sk``", "real", "characteristic diffusive scale in m", "20.0"
+   "``l_sk``", "real", "characteristic diffusive scale in m", "2.0"
    "``l_skS``", "real", "zsalinity DEPRECATED", ""
    "``max_dfe_doc1``", "real", "max ratio of dFe to saccharides in the ice in nm Fe / muM C", "0.2"
    "``max_loss``", "real", "restrict uptake to percent of remaining value", "0.9"
@@ -844,7 +844,7 @@ zbgc_nml
    "``mu_max_sp``", "real", "maximum growth rate small plankton per day", "0.41"
    "``nitratetype``", "real", "mobility type between stationary and mobile nitrate", "-1.0"
    "``op_dep_min``", "real", "light attenuates for optical depths exceeding min", "0.1"
-   "``phi_snow``", "real", "snow porosity for brine height tracer", "-0.3"
+   "``phi_snow``", "real", "snow porosity for brine height tracer", "-1.0"
    "``ratio_chl2N_diatoms``", "real", "algal chl to N in mg/mmol diatoms", "2.1"
    "``ratio_chl2N_phaeo``", "real", "algal chl to N in mg/mmol phaeocystis", "0.84"
    "``ratio_chl2N_sp``", "real", "algal chl to N in mg/mmol small plankton", "1.1"
@@ -877,7 +877,7 @@ zbgc_nml
    "``skl_bgc``", "logical", "skeletal biogeochemistry DEPRECATED", "``.false.``"
    "``solve_zbgc``", "logical", "", "``.false.``"
    "``solve_zsal``", "logical", "zsalinity DEPRECATED, update salinity tracer profile", "``.false.``"
-   "``tau_max``", "real", "long time mobile to stationary exchanges", "7776000."
+   "``tau_max``", "real", "long time mobile to stationary exchanges", "604800."
    "``tau_min``", "real", "rapid module to stationary exchanges", "3600."
    "``tr_bgc_Am``", "logical", "ammonium tracer", "``.false.``"
    "``tr_bgc_C``", "logical", "algal carbon tracer", "``.false.``"