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
NFSDCAT		number of floe size categories	12
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
ICE_BLDDEBUG	true,false	turn on compile debug flags	false

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
tr_fsd	true/false	floe size distribution
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 [40]
	bubbly	conductivity [44]
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 [50]
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)
wave_spec_type	none	no ocean wave spectrum data - no wave-ice interactions
	constant	ocean wave spectrum data present*, sea surface height field generated using constant phase, for testing FSD
	random	ocean wave spectrum data present*, sea surface height field generated using random phase
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 [28]	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

• = If Icepack is run stand-alone and wave_spec_type is not set to none, then a fixed wave spectrum is defined in the code to use for testing. As with other input data, this spectrum should not be used for production runs or publications.

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