3.4. Case Settings¶

There are two important files that define the case, icepack.settings and icepack_in. icepack.settings is a list of env variables that define many values used to setup, build and run the case. icepack_in is the input namelist file for the icepack driver. Variables in both files are described below.

3.4.1. Table of Icepack Settings¶

The icepack.settings file is reasonably well self documented. Several of the variables defined in the file are not used in Icepack. They exist to support the CICE model.

*Icepack settings*¶
variable	options/format	description	recommended value
ICE_CASENAME		case name	set by icepack.setup
ICE_SANDBOX		sandbox directory	set by icepack.setup
ICE_MACHINE		machine name	set by icepack.setup
ICE_COMPILER		environment name	set by icepack.setup
ICE_MACHCOMP		machine_environment name	set by icepack.setup
ICE_SCRIPTS		scripts directory	set by icepack.setup
ICE_CASEDIR		case directory	set by icepack.setup
ICE_RUNDIR		run directory	set by icepack.setup
ICE_OBJDIR		compile directory	${ICE_RUNDIR}/compile
ICE_RSTDIR		unused	${ICE_RUNDIR}/restart
ICE_HSTDIR		unused	${ICE_RUNDIR}/history
ICE_LOGDIR		log directory	${ICE_CASEDIR}/logs
ICE_RSTPFILE		unused	undefined
ICE_DRVOPT		unused	icepack
ICE_IOTYPE		unused	none
ICE_CLEANBUILD	true,false	automatically clean before building	true
ICE_GRID	col	grid	col
ICE_NXGLOB	4	number of gridcells	4
ICE_NTASKS	1	number of tasks, must be set to 1	1
ICE_NTHRDS	1	number of threads per task, must be set to 1	1
ICE_TEST		test setting if using a test	set by icepack.setup
ICE_TESTNAME		test name if using a test	set by icepack.setup
ICE_BASELINE		baseline directory name, associated with icepack.setup -bd	set by icepack.setup
ICE_BASEGEN		baseline directory name for regression generation, associated with icepack.setup -bg	set by icepack.setup
ICE_BASECOM		baseline directory name for regression comparison, associated with icepack.setup -bc	set by icepack.setup
ICE_BFBCOMP		location of case for comparison, associated with icepack.setup -td	set by icepack.setup
ICE_SPVAL		unused	UnDeFiNeD
ICE_RUNLENGTH		batch run length default	00:10:00
ICE_ACCOUNT		batch account number	set by icepack.setup or by default
ICE_THREADED	true,false	force threading in compile, will always compile threaded if NTHRDS is gt 1	false
NICELYR		number of vertical layers in the ice	7
NSNWLYR		number of vertical layers in the snow	1
NICECAT		number of ice thickness categories	5
TRAGE	0,1	ice age tracer	1
TRFY	0,1	first-year ice area tracer	1
TRLVL	0,1	deformed ice tracer	1
TRPND	0,1	melt pond tracer	1
NTRAERO		number of aerosol tracers	1
TRBRI	0,1	brine height tracer	0
TRZS	0,1	zsalinity tracer, needs TRBRI=1	0
TRBGCS	0,1	skeletal layer tracer, needs TRBGCZ=0	0
TRBGCZ	0,1	zbgc tracers, needs TRBGCS=0 and TRBRI=1	0
NBGCLYR		number of zbgc layers	7
TRZAERO	0-6	number of z aerosol tracers	0
TRALG	0,1,2,3	number of algal tracers	0
TRDOC	0,1,2,3	number of dissolved organic carbon	0
TRDIC	0,1	number of dissolved inorganic carbon	0
TRDON	0,1	number of dissolved organic nitrogen	0
TRFEP	0,1,2	number of particulate iron tracers	0
TRFED	0,1,2	number of dissolved iron tracers	0
CAM_ICE		unused	no
DITTO		unused	no
BARRIERS		unused	no
ICE_BLDDEBUG	true,false	turn on compile debug flags	false
NUMIN		unused	11
NUMAX		unused	99

3.4.2. Table of Namelist Inputs¶

Namelist is part of the icepack driver code and is used to setup testing of the column physics.

*Namelist Inputs*¶
variable	options/format	description	recommended value
setup_nml
		Time, Diagnostics
`days_per_year`	`360` or `365`	number of days in a model year	365
`use_leap_years`	true/false	if true, include leap days
`year_init`	yyyy	the initial year, if not using restart
`istep0`	integer	initial time step number	0
`dt`	seconds	thermodynamics time step length
`npt`	integer	total number of time steps to take
`ndtd`	integer	number of dynamics/advection/ridging/steps per thermo timestep	1
		Initialization/Restarting
`ice_ic`	`default`	latitude and sst dependent	default
	`none`	no ice
	path/file	restart file name
`restart_dir`	path/	path to restart directory
`dumpfreq`	`y`	write restart every `dumpfreq_n` years	y
	`m`	write restart every `dumpfreq_n` months
	`d`	write restart every `dumpfreq_n` days
`dump_last`	true/false	write restart at end of run	false
		Model Output
`diagfreq`	integer	frequency of diagnostic output in `dt`	24
	e.g., 10	once every 10 time steps
`diag_file`	filename	diagnostic output file (script may reset)

grid_nml
		Grid
`kcatbound`	`0`	original category boundary formula	0
	`1`	new formula with round numbers
	`2`	WMO standard categories
	`-1`	one category

tracer_nml
		Tracers
`tr_iage`	true/false	ice age
`tr_FY`	true/false	first-year ice area
`tr_lvl`	true/false	level ice area and volume
`tr_pond_cesm`	true/false	CESM melt ponds
`tr_pond_topo`	true/false	topo melt ponds
`tr_pond_lvl`	true/false	level-ice melt ponds
`tr_aero`	true/false	aerosols

thermo_nml
		Thermodynamics
`kitd`	`0`	delta function ITD approximation	1
	`1`	linear remapping ITD approximation
`ktherm`	`0`	zero-layer thermodynamic model
	`1`	Bitz and Lipscomb thermodynamic model
	`2`	mushy-layer thermodynamic model
`conduct`	`Maykut71`	conductivity [39]
	`bubbly`	conductivity [42]
`a_rapid_mode`	real	brine channel diameter	0.5x10 \(^{-3}\) m
`Rac_rapid_mode`	real	critical Rayleigh number	10
`aspect_rapid_mode`	real	brine convection aspect ratio	1
`dSdt_slow_mode`	real	drainage strength parameter	-1.5x10 \(^{-7}\) m/s/K
`phi_c_slow_mode`	\(0<\phi_c < 1\)	critical liquid fraction	0.05
`phi_i_mushy`	\(0<\phi_i < 1\)	solid fraction at lower boundary	0.85

dynamics_nml
		Dynamics
`kstrength`	`0`	ice strength formulation [20]	1
	`1`	ice strength formulation [44]
`krdg_partic`	`0`	old ridging participation function	1
	`1`	new ridging participation function
`krdg_redist`	`0`	old ridging redistribution function	1
	`1`	new ridging redistribution function
`mu_rdg`	real	e-folding scale of ridged ice
`Cf`	real	ratio of ridging work to PE change in ridging

shortwave_nml
		Shortwave
`shortwave`	`ccsm3`	NCAR CCSM3 distribution method	‘dEdd’
	`dEdd`	Delta-Eddington method
`albedo_type`	`ccsm3`	NCAR CCSM3 albedos	‘ccsm3’
	`constant`	four constant albedos
`albicev`	\(0<\alpha <1\)	visible ice albedo for thicker ice
`albicei`	\(0<\alpha <1\)	near infrared ice albedo for thicker ice
`albsnowv`	\(0<\alpha <1\)	visible, cold snow albedo
`albsnowi`	\(0<\alpha <1\)	near infrared, cold snow albedo
`ahmax`	real	albedo is constant above this thickness	0.3 m
`R_ice`	real	tuning parameter for sea ice albedo from Delta-Eddington shortwave
`R_pnd`	real	… for ponded sea ice albedo …
`R_snw`	real	… for snow (broadband albedo) …
`dT_mlt`	real	\(\Delta\) temperature per \(\Delta\) snow grain radius
`rsnw_mlt`	real	maximum melting snow grain radius
`kalg`	real	absorption coefficient for algae

ponds_nml
		Melt Ponds
`hp1`	real	critical ice lid thickness for topo ponds	0.01 m
`hs0`	real	snow depth of transition to bare sea ice	0.03 m
`hs1`	real	snow depth of transition to pond ice	0.03 m
`dpscale`	real	time scale for flushing in permeable ice	\(1\times 10^{-3}\)
`frzpnd`	`hlid`	Stefan refreezing with pond ice thickness	‘hlid’
	`cesm`	CESM refreezing empirical formula
`rfracmin`	\(0 \le r_{min} \le 1\)	minimum melt water added to ponds	0.15
`rfracmax`	\(0 \le r_{max} \le 1\)	maximum melt water added to ponds	1.0
`pndaspect`	real	aspect ratio of pond changes (depth:area)	0.8

forcing_nml
		Forcing
`formdrag`	true/false	calculate form drag
`atmbndy`	`default`	stability-based boundary layer	‘default’
	`constant`	bulk transfer coefficients
`fyear_init`	yyyy	first year of atmospheric forcing data
`ycycle`	integer	number of years in forcing data cycle
`atm_data_type`	`default`	constant values defined in the code
	`clim`	monthly climatology (see Forcing data)
	`CFS`	CFS model output (see Forcing data)
	`ISPOL`	ISPOL experiment data (see Forcing data)
	`NICE`	N-ICE experiment data (see Forcing data)
`data_dir`	path/	path to forcing data directory
`atm_data_file`	filename	file containing atmospheric data
`ocn_data_file`	filename	file containing ocean data
`ice_data_file`	filename	file containing ice opening, closing data
`bgc_data_file`	filename	file containing biogeochemistry data
`calc_strair`	true	calculate wind stress and speed
	false	read wind stress and speed from files
`highfreq`	true/false	high-frequency atmo coupling
`natmiter`	integer	number of atmo boundary layer iterations
`calc_Tsfc`	true/false	calculate surface temperature	`.true.`
`precip_units`	`mks`	liquid precipitation data units
	`mm_per_month`
	`mm_per_sec`	(same as MKS units)
`tfrz_option`	`minus1p8`	constant ocean freezing temperature (\(-1.8^\circ C\))
	`linear_salt`	linear function of salinity (ktherm=1)
	`mushy`	matches mushy-layer thermo (ktherm=2)
`default_season`	`winter`	Sets initial values of forcing and is overwritten when forcing read in. Default is winter
	`summer`	typical summer values
	`spring`	typical spring values
`ustar_min`	real	minimum value of ocean friction velocity	0.0005 m/s
`emissivity`	real	emissivity of snow and ice	0.95
`fbot_xfer_type`	`constant`	constant ocean heat transfer coefficient
	`Cdn_ocn`	variable ocean heat transfer coefficient
`update_ocn_f`	true	include frazil water/salt fluxes in ocn fluxes
	false	do not include (when coupling with POP)
`l_mpond_fresh`	true	retain (topo) pond water until ponds drain
	false	release (topo) pond water immediately to ocean
`oceanmixed_ice`	true/false	active ocean mixed layer calculation	`.true.` (if uncoupled)
`ocn_data_type`	`default`	constant values defined in the code
	`ISPOL`	ISPOL experiment data (see Forcing data)
	`NICE`	N-ICE experiment data (see Forcing data)
	`SHEBA`	Opening/closing dataset from SHEBA
`oceanmixed_file`	filename	data file containing ocean forcing data
`restore_ocn`	true/false	restore sst to data
`trestore`	integer	sst restoring time scale (days)

zbgc_nml
		Biogeochemistry
`tr_brine`	true/false	brine height tracer (needs TRBRI 1 in comp_ice)	`.true.`
`restart_hbrine`	true/false	restart the brine height tracer (automatically turned on if restart = .true.)	`.false.`
`tr_zaero`	true/false	turns on black carbon and dust aerosols	`.false.`
`modal_aero`	true/false	turns on a modal aerosol option	`.false.`
`skl_bgc`	true/false	turns on a single bottom layer biogeochemistry. z_tracers and solve_zbgc must be false	`.false.`
`z_tracers`	true/false	turns on a vertically resolved transport	`.true.`
`dEdd_algae`	true/false	Include radiative impact of algae and aerosols in the delta-Eddington shortwave scheme. Requires shortwave = ‘dEdd’.	`.false.`
`solve_zbgc`	true/false	turns on the biochemistry using z_tracers (specify algal numbers in comp_ice TRALG)	`.true.`
`bgc_flux_type`	`Jin2006` or `default`	ice–ocean flux type for bottom layer tracers only [27]	`Jin2006`
`restore_bgc`	true/false	restores upper ocean concentration fields to data values for nitrate and silicate	`.false.`
`restart_bgc`	true/false	restarts biogeochemical tracers (automatically turned on if restart = .true.)	`.false.`
`scale_bgc`	true/false	Initialize biogeochemical profiles to scale with prognosed salinity profile	`.false.`
`solve_zsal`	true/false	prognostic salinity tracer used with ktherm = 1	`.false.`
`restart_zsal`	true/false	restarts zsalinity	`.false.`
`bgc_data_type`	`default`	fixed, spatially homogeneous constant values defined in the code
	`clim`	monthly climatology data file (see icedrv_forcing_bgc.F90) [18]
	`NICE`	N-ICE experiment data
	`ISPOL`	ISPOL experiment data
`tr_bgc_Nit`	true/false	nitrate tracer	`.true.`
`tr_bgc_C`	true/false	dissolved organic carbon tracers and dissolved inorganic carbon tracers (not yet implemented)	`.true.`
`tr_bgc_chl`	true/false	dummy variable for now. Chl is simply fixed ratio of algal Nitrogen	`.false.`
`tr_bgc_Am`	true/false	Ammonium	`.true.`
`tr_bgc_Sil`	true/false	Silicate	`.true.`
`tr_bgc_DMS`	true/false	Three tracers: DMS dimethyl sulfide, DMSPp (particulate, assumed to be a fixed ratio of sulfur to algal nitrogen) and DMSPd (dissolved)	`.true.`
`tr_bgc_PON`	true/false	passive purely mobile ice tracer with ocean concentration equivalent to nitrate	`.false.`
`tr_bgc_hum`	true/false	refractory DOC or DON (units depend on the ocean source)	`.true.`
`tr_bgc_DON`	true/false	dissolved organic nitrogen	`.true.`
`tr_bgc_Fe`	true/false	dissolved iron and particulate iron	`.true.`
`grid_o`	real	ice-ocean surface layer thickness (bgc transport scheme)	0.006
`l_sk`	real	length scale in gravity drainage parameterization (bgc transport scheme)	0.024
`grid_oS`	real	ice-ocean surface layer thickness (zsalinity transport scheme)	0.0
`l_skS`	real	ice-atmosphere surface layer thickness (zsalinity transport scheme)	0.028
`phi_snow`	real	snow porosity at the ice-snow interface. if \(<0\) then phi_snow is computed from snow density	-0.3
`initbio_frac`	real	for each bgc tracer, specifies the fraction of the ocean concentration that is retained in the ice during initial new ice formation	0.8
`frazil_scav`	real	for each bgc tracer, specifies the fraction or multiple of the ocean concentration that is retained in the ice from frazil ice formation	0.8
`ratio_si2N_diatoms`	real	algal Si to N (\(mol/mol\)) for diatoms	1.8
`ratio_si2N_sp`	real	algal Si to N (\(mol/mol\)) for small phytoplankton	0.0
`ratio_si2N_phaeo`	real	algal Si to N (\(mol/mol\)) for phaeocystis	0.0
`ratio_S2N_diatoms`	real	algal S to N (\(mol/mol\)) for diatoms	0.03
`ratio_S2N_sp`	real	algal S to N (\(mol/mol\)) for small phytoplankton	0.03
`ratio_S2N_phaeo`	real	algal S to N (\(mol/mol\)) for phaeocystis	0.03
`ratio_Fe2C_diatoms`	real	algal Fe to C (\(\mu mol/mol\)) for diatoms	0.0033
`ratio_Fe2C_sp`	real	algal Fe to C (\(\mu mol/mol\)) for small phytoplankton	0.0033
`ratio_Fe2C_phaeo`	real	algal Fe to C (\(\mu mol/mol\)) for phaeocystis	0.1
`ratio_Fe2N_diatoms`	real	algal Fe to N (\(\mu mol/mol\)) for diatoms	0.023
`ratio_Fe2N_sp`	real	algal Fe to N (\(\mu mol/mol\)) for small phytoplankton	0.023
`ratio_Fe2N_phaeo`	real	algal Fe to N (\(\mu mol/mol\)) for phaeocystis	0.7
`ratio_Fe2DON`	real	Fe to N of DON (\(nmol/mol\))	0.023
`ratio_Fe2DOC_s`	real	Fe to C of DOC for saccharids (\(nmol/mol\))	0.1
`ratio_Fe2DOC_l`	real	Fe to C of DOC for lipids (\(nmol/mol\))	0.033
`fr_resp`	real	fraction of algal growth lost due to respiration	0.05
`tau_min`	real	rapid mobile to stationary exchanges (\(s\))	5200.0
`tau_max`	real	long time mobile to stationary exchanges (\(s\))	1.73e5
`algal_vel`	real	0.5 \(cm/day (m/s)\)	1.11e-8
`R_dFe2dust`	real	g/g (3.5% content)	0.035
`dustFe_sol`	real	solubility fraction	0.005
`chlabs_diatoms`	real	diatoms chl absorption (\(1/m/(mg/m^3)\))	0.03
`chlabs_sp`	real	small phytoplankton chl absorption (\(1/m/(mg/m^3)\))	0.01
`chlabs_phaeo`	real	phaeocystis chl absorption (\(1/m/(mg/m^3)\))	0.05
`alpha2max_low_diatoms`	real	diatoms light limitation (\((W/m^2)^{-1}\))	0.8
`alpha2max_low_sp`	real	small phytoplankton light limitation (\((W/m^2)^{-1}\))	0.67
`alpha2max_low_phaeo`	real	phaeocystis light limitation (\((W/m^2)^{-1}\))	0.67
`beta2max_diatoms`	real	diatoms light inhibition (\((W/m^2)^{-1}\))	0.018
`beta2max_sp`	real	small phytoplankton light inhibition (\((W/m^2)^{-1}\))	0.0025
`beta2max_phaeo`	real	phaeocystis light inhibition (\((W/m^2)^{-1}\))	0.01
`mu_max_diatoms`	real	diatoms maximum growth rate (\(day^{-1}\))	1.2
`mu_max_sp`	real	small phytoplankton maximum growth rate (\(day^{-1}\))	0.851
`mu_max_phaeo`	real	phaeocystis maximum growth rate (\(day^{-1}\))	0.851
`grow_Tdep_diatoms`	real	diatoms Temperature dependence of growth (\(^o\)C\(^{-1})\)	0.06
`grow_Tdep_sp`	real	small phytoplankton Temperature dependence of growth \(^o\)C\(^{-1}\)	0.06
`grow_Tdep_phaeo`	real	phaeocystis Temperature dependence of growth \(^o\)C\(^{-1}\)	0.06
`fr_graze_diatoms`	real	diatoms fraction grazed	0.01
`fr_graze_sp`	real	small phytoplankton fraction grazed	0.1
`fr_graze_phaeo`	real	phaeocystis fraction grazed	0.1
`mort_pre_diatoms`	real	diatoms mortality (\(day^{-1}\))	0.007
`mort_pre_sp`	real	small phytoplankton mortality (\(day^{-1}\))	0.007
`mort_pre_phaeo`	real	phaeocystis mortality (\(day^{-1}\))	0.007
`mort_Tdep_diatoms`	real	diatoms temperature dependence of mortality \(^o\)C\(^{-1}\)	0.03
`mort_Tdep_sp`	real	small phytoplankton temperature dependence of mortality (\(^o\)C\(^{-1}\))	0.03
`mort_Tdep_phaeo`	real	phaeocystis temperature dependence of mortality (\(^o\)C\(^{-1}\))	0.03
`k_exude_diatoms`	real	diatoms algal exudation (\(day^{-1}\))	0.0
`k_exude_sp`	real	small phytoplankton algal exudation (\(day^{-1}\))	0.0
`k_exude_phaeo`	real	phaeocystis algal exudation (\(day^{-1}\))	0.0
`K_Nit_diatoms`	real	datoms nitrate half saturation (\(mmol/m^3\))	1.0
`K_Nit_sp`	real	small phytoplankton nitrate half saturation (\(mmol/m^3\))	1.0
`K_Nit_phaeo`	real	phaeocystis nitrate half saturation (\(mmol/m^3\))	1.0
`K_Am_diatoms`	real	diatoms ammonium half saturation (\(mmol/m^3\))	0.3
`K_Am_sp`	real	small phytoplankton ammonium half saturation (\(mmol/m^3\))	0.3
`K_Am_phaeo`	real	phaeocystis ammonium half saturation (\(mmol/m^3\))	0.3
`K_Sil_diatoms`	real	diatoms silicate half saturation (\(mmol/m^3\))	4.0
`K_Sil_sp`	real	small phytoplankton silicate half saturation (\(mmol/m^3\))	0.0
`K_Sil_phaeo`	real	phaeocystis silicate half saturation (\(mmol/m^3\))	0.0
`K_Fe_diatoms`	real	diatoms iron half saturation (\(nM\))	1.0
`K_Fe_sp`	real	small phytoplankton iron half saturation (\(nM\))	0.2
`K_Fe_phaeo`	real	phaeocystis iron half saturation (\(nM\))	0.1
`f_don_protein`	real	fraction of spilled grazing to proteins	0.6
`kn_bac_protein`	real	Bacterial degredation of DON (\(day^{-1}\))	0.03
`f_don_Am_protein`	real	fraction of remineralized DON to ammonium	0.25
`f_doc_s`	real	fraction of mortality to DOC saccharids	0.4
`f_doc_l`	real	fraction of mortality to DOC lipids	0.4
`f_exude_s`	real	fraction of exudation to DOC saccharids	1.0
`f_exude_l`	real	fraction of exudation to DOC lipids	1.0
`k_bac_s`	real	bacterial degredation of DOC (\(day^{-1}\)) saccharids	0.03
`k_bac_l`	real	bacterial degredation of DOC (\(day^{-1}\)) lipids	0.03
`T_max`	real	maximum temperature (\(^o\)C)	0.0
`fsal`	real	Salinity limitation (ppt)	1.0
`op_dep_min`	real	Light attenuates for optical depths exceeding min	0.1
`fr_graze_s`	real	fraction of grazing spilled or slopped	0.5
`fr_graze_e`	real	fraction of assimilation excreted	0.5
`fr_mort2min`	real	fractionation of mortality to Am	0.5
`fr_dFe`	real	fraction of remineralized nitrogen (algal iron)	0.3
`k_nitrif`	real	nitrification rate (\(day^{-1}\))	0.0
`t_iron_conv`	real	desorption loss pFe to dFe (day)	3065.0
`max_loss`	real	restrict uptake to % of remaining value	0.9
`max_dfe_doc1`	real	max ratio of dFe to saccharides in the ice (\(nM Fe/\mu M C\))	0.2
`fr_resp_s`	real	DMSPd fraction of respiration loss as DMSPd	0.75
`y_sk_DMS`	real	fraction conversion given high yield	0.5
`t_sk_conv`	real	Stefels conversion time (\(day\))	3.0
`t_sk_ox`	real	DMS oxidation time (\(day\))	10.0
`algaltype_diatoms`	real	mobility type between stationary <–> mobile for diatoms	0.0
`algaltype_sp`	real	mobility type between stationary <–> mobile for small phytoplankton	0.5
`algaltype_phaeo`	real	mobility type between stationary <–> mobile for phaeocystis	0.5
`nitratetype`	real	mobility type between stationary <–> mobile for nitrate	-1.0
`ammoniumtype`	real	mobility type between stationary <–> mobile for ammonium	1.0
`silicatetype`	real	mobility type between stationary <–> mobile for silicate	-1.0
`dmspptype`	real	mobility type between stationary <–> mobile for DMSP particulate	0.5
`dmspdtype`	real	mobility type between stationary <–> mobile for DMSP dissolved	-1.0
`humtype`	real	mobility type between stationary <–> mobile for humic matter	1.0
`doctype_s`	real	mobility type between stationary <–> mobile for DOC saccharids	0.5
`doctype_l`	real	mobility type between stationary <–> mobile for DOC lipids	0.5
`dontype_protein`	real	mobility type between stationary <–> mobile for proteins	0.5
`fedtype_1`	real	mobility type between stationary <–> mobile for FeD	0.5
`feptype_1`	real	mobility type between stationary <–> mobile for FeP	0.5
`zaerotype_bc1`	real	mobility type between stationary <–> mobile for zaerotype_bc1	1.0
`zaerotype_bc2`	real	mobility type between stationary <–> mobile for zaerotype_bc2	1.0
`zaerotype_dust1`	real	mobility type between stationary <–> mobile for dust1	1.0
`zaerotype_dust2`	real	mobility type between stationary <–> mobile for dust2	1.0
`zaerotype_dust3`	real	mobility type between stationary <–> mobile for dust3	1.0
`zaerotype_dust4`	real	mobility type between stationary <–> mobile for dust4	1.0
`ratio_C2N_diatoms`	real	diatom algal C to N ratio (\(mol/mol\))	7.0
`ratio_C2N_sp`	real	small phytoplankton algal C to N ratio (\(mol/mol\))	7.0
`ratio_C2N_phaeo`	real	phaeocystis algal C to N ratio (\(mol/mol\))	7.0
`ratio_chl2N_diatoms`	real	diatom algal chlorophyll to N ratio (\(mg/mmol\))	2.1
`ratio_chl2N_sp`	real	small phytoplankton algal chlorophyll to N ratio (\(mg/mmol\))	1.1
`ratio_chl2N_phaeo`	real	phaeocystis algal chlorophyll to N ratio (\(mg/mmol\))	0.84
`F_abs_chl_diatoms`	real	diatom scales absorbed radiation for dEdd	2.0
`F_abs_chl_sp`	real	small phytoplankton scales absorbed radiation for dEdd	4.0
`F_abs_chl_phaeo`	real	phaeocystis scales absorbed radiation for dEdd	5.0
`ratio_C2N_proteins`	real	ratio of C to N in proteins (\(mol/mol\))	7.0

3.4.3. BGC Tuning Parameters¶

Biogeochemical tuning parameters are specified as namelist options in icepack_in. Table Biogeochemical Reaction Parameters provides a list of parameters used in the reaction equations, their representation in the code, a short description of each and the default values. Please keep in mind that there has only been minimal tuning of the model.

*Biogeochemical Reaction Parameters*¶
Text Variable	Variable in code	Description	Value	units
\(f_{graze}\)	fr_graze(1:3)	fraction of growth grazed	0, 0.1, 0.1	1
\(f_{res}\)	fr_resp	fraction of growth respired	0.05	1
\(l_{max}\)	max_loss	maximum tracer loss fraction	0.9	1
\(m_{pre}\)	mort_pre(1:3)	maximum mortality rate	0.007, 0.007, 0.007	day\(^{-1}\)
\(m_{T}\)	mort_Tdep(1:3)	mortality temperature decay	0.03, 0.03, 0.03	\(^o\)C\(^{-1}\)
\(T_{max}\)	T_max	maximum brine temperature	0	\(^o\)C
\(k_{nitr}\)	k_nitrif	nitrification rate	0	day\(^{-1}\)
\(f_{ng}\)	fr_graze_e	fraction of grazing excreted	0.5	1
\(f_{gs}\)	fr_graze_s	fraction of grazing spilled	0.5	1
\(f_{nm}\)	fr_mort2min	fraction of mortality to \({\mbox{NH$_4$}}\)	0.5	1
\(f_{dg}\)	f_don	frac. spilled grazing to \({\mbox{DON}}\)	0.6	1
\(k_{nb}\)	kn_bac \(^a\)	bacterial degradation of \({\mbox{DON}}\)	0.03	day\(^{-1}\)
\(f_{cg}\)	f_doc(1:3)	fraction of mortality to \({\mbox{DOC}}\)	0.4, 0.4, 0.2	1
\(R_{c:n}^c\)	R_C2N(1:3)	algal carbon to nitrogen ratio	7.0, 7.0, 7.0	mol/mol
\(k_{cb}\)	k_bac1:3\(^a\)	bacterial degradation of DOC	0.03, 0.03, 0.03	day\(^{-1}\)
\(\tau_{fe}\)	t_iron_conv	conversion time pFe \(\leftrightarrow\) dFe	3065.0	day
\(r^{max}_{fed:doc}\)	max_dfe_doc1	max ratio of dFe to saccharids	0.1852	nM Fe\(/\mu\)M C
\(f_{fa}\)	fr_dFe	fraction of remin. N to dFe	0.3	1
\(R_{fe:n}\)	R_Fe2N(1:3)	algal Fe to N ratio	0.023, 0.023, 0.7	mmol/mol
\(R_{s:n}\)	R_S2N(1:3)	algal S to N ratio	0.03, 0.03, 0.03	mol/mol
\(f_{sr}\)	fr_resp_s	resp. loss as DMSPd	0.75	1
\(\tau_{dmsp}\)	t_sk_conv	Stefels rate	3.0	day
\(\tau_{dms}\)	t_sk_ox	DMS oxidation rate	10.0	day
\(y_{dms}\)	y_sk_DMS	yield for DMS conversion	0.5	1
\(K_{{\mbox{NO$_3$}}}\)	K_Nit(1:3)	\({\mbox{NO$_3$}}\) half saturation constant	1,1,1	mmol/m\(^{3}\)
\(K_{{\mbox{NH$_4$}}}\)	K_Am(1:3)	\({\mbox{NH$_4$}}\) half saturation constant	0.3, 0.3, 0.3	mmol/m\(^{-3}\)
\(K_{{\mbox{SiO$_3$}}}\)	K_Sil(1:3)	silicate half saturation constant	4.0, 0, 0	mmol/m\(^{-3}\)
\(K_{{\mbox{fed}}}\)	K_Fe(1:3)	iron half saturation constant	1.0, 0.2, 0.1	\(\mu\)mol/m\(^{-3}\)
\(op_{min}\)	op_dep_min	boundary for light attenuation	0.1	1
\(chlabs\)	chlabs(1:3)	light absorption length per chla conc.	0.03, 0.01, 0.05	1\(/\)m\(/\)(mg\(/\)m\(^{3}\))
\(\alpha\)	alpha2max_low(1:3)	light limitation factor	0.25, 0.25, 0.25	m\(^2\)/W
\(\beta\)	beta2max(1:3)	light inhibition factor	0.018, 0.0025, 0.01	m\(^2\)/W
\(\mu_{max}\)	mu_max(1:3)	maximum algal growth rate	1.44, 0.851, 0.851	day\(^{-1}\)
\(\mu_T\)	grow_Tdep(1:3)	temperature growth factor	0.06, 0.06, 0.06	day\(^{-1}\)
\(f_{sal}\)	fsal	salinity growth factor	1	1
\(R_{si:n}\)	R_Si2N(1:3)	algal silicate to nitrogen	1.8, 0, 0	mol/mol

\(^a\) only (1:2) of DOC and DOC parameters have physical meaning