3.4. Case Settings, Model Namelist, and CPPs

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. In addition, the first table documents available C Preprocessor Macros.

3.4.1. Table of C Preprocessor (CPP) Macros

The Icepack model supports a few C Preprocessor (CPP) Macros. These can be turned on during compilation to activate different pieces of source code. The main purpose is to introduce build-time code modifications to include or exclude certain libraries or Fortran language features, in part to support CICE or other applications. More information can be found in C Preprocessor (CPP) Macros. The following CPPs are available.

CPP Macros

CPP name	description
General Macros
NO_I8	Converts integer*8 to integer*4.
NO_R16	Converts real*16 to real*8.
NO_SNICARHC	Does not compile hardcoded (HC) 5 band snicar tables tables needed by shortwave=dEdd_snicar_ad. May reduce compile time.
USE_NETCDF	Turns on netcdf capabilities in Icepack. By default and generally, Icepack does not need netcdf.
Application Macros
CESMCOUPLED	Turns on code changes for the CESM coupled application
CICE_IN_NEMO	Turns on code changes for coupling in the NEMO ocean model

3.4.2. Table of Icepack Settings

The icepack.settings file contains a number of environment variables that define configuration, file system, run, and build settings. Several variables are set by the icepack.setup script. This file is created on a case by case basis and can be modified as needed.

Icepack settings

variable	options/format	description	default value
ICE_CASENAME	string	case name	set by icepack.setup
ICE_SANDBOX	string	sandbox directory	set by icepack.setup
ICE_MACHINE	string	machine name	set by icepack.setup
ICE_ENVNAME	string	compilation environment	set by icepack.setup
ICE_MACHCOMP	string	machine_environment name	set by icepack.setup
ICE_SCRIPTS	string	scripts directory	set by icepack.setup
ICE_CASEDIR	string	case directory	set by icepack.setup
ICE_RUNDIR	string	run directory	set by icepack.setup
ICE_OBJDIR	string	compile directory	${ICE_RUNDIR}/compile
ICE_RSTDIR	string	unused	${ICE_RUNDIR}/restart
ICE_HSTDIR	string	unused	${ICE_RUNDIR}/history
ICE_LOGDIR	string	log directory	${ICE_CASEDIR}/logs
ICE_RSTPFILE	string	unused	undefined
ICE_DRVOPT	string	unused	icepack
ICE_IOTYPE	none,netcdf	IO options	none
ICE_CLEANBUILD	true,false	automatically clean before building	true
ICE_CPPDEFS	string	user defined preprocessor macros for build	null
ICE_QUIETMODE	true, false	reduce build output to the screen	false
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	string	test setting if using a test	set by icepack.setup
ICE_TESTNAME	string	test name if using a test	set by icepack.setup
ICE_BASELINE	string	baseline directory name, associated with icepack.setup -bd	set by icepack.setup
ICE_BASEGEN	string	baseline directory name for regression generation, associated with icepack.setup -bg	set by icepack.setup
ICE_BASECOM	string	baseline directory name for regression comparison, associated with icepack.setup -bc	set by icepack.setup
ICE_BFBCOMP	string	location of case for comparison, associated with icepack.setup -td	set by icepack.setup
ICE_SPVAL	string	unused	UnDeFiNeD
ICE_RUNLENGTH	string	batch run length default	00:10:00
ICE_ACCOUNT	string	batch account number	set by icepack.setup or by default
ICE_QUEUE	string	batch queue name	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	integer	number of vertical layers in the ice	7
NSNWLYR	integer	number of vertical layers in the snow	1
NICECAT	integer	number of ice thickness categories	5
NFSDCAT	integer	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	integer	number of aerosol tracers	1
NTRISO	integer	number of water isotope tracers	1
TRBRI	0,1	brine height tracer	0
TRZS		DEPRECATED
TRBGCS	0,1	skeletal layer tracer, needs TRBGCZ=0	0
TRBGCZ	0,1	zbgc tracers, needs TRBGCS=0 and TRBRI=1	0
NBGCLYR	integer	number of zbgc layers	1
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_SNICARHC	true,false	include hardcoded (HC) snicar tables	false
ICE_BLDDEBUG	true,false	turn on compile debug flags	false
ICE_COVERAGE	true,false	turn on code coverage flags	false

3.4.3. Tables of Namelist Options

The Icepack driver reads a namelist input file, icepack_in, consisting of several namelist groups. The tables below summarize the different groups and the variables in each group. The variables are organized alphabetically and the default values listed are the values defined in the source code. Those values will be used unless overridden by the Icepack namelist file, icepack_in. The source code default values as listed in the table are not necessarily the recommended production values.

3.4.3.1. setup_nml

setup_nml namelist options

variable	options/format	description	default value
conserv_check	logical	check conservation	.false.
cpl_bgc	logical	couple bgc thru driver	.false.
days_per_year	integer	number of days in a model year	365
diagfreq	integer	frequency of diagnostic output in timesteps	24
diag_file	string	diagnostic output filename	‘ice_diag’
dumpfreq	d	write restart every dumpfreq_n days	y
	m	write restart every dumpfreq_n months
	y	write restart every dumpfreq_n years
dump_last	true/false	write restart at end of run	false
dt	seconds	thermodynamics time step length
history_format	cdf	history file output in netcdf format	none
	none	no history output
ice_ic	default	latitude and sst dependent initial condition	default
	none	no ice
	‘path/file’	restart file name
istep0	integer	initial time step number	0
ndtd	integer	number of dynamics/advection/ridging/steps per thermo timestep	1
npt	integer	total number of time steps to take	99999
restart	logical	initialize using restart file	.false.
restart_dir	string	path to restart directory	‘./’
restart_file	string	output file prefix for restart dump	‘iced’
restart_format	bin	restart file output in binary format	bin
	cdf	restart file output in netcdf format
use_leap_years	logical	include leap days	.false.
year_init	integer	the initial year if not using restart	0

3.4.3.2. grid_nml

grid_nml namelist options

variable	options/format	description	default value
kcatbound	-1	single category formulation	1
	0	old formulation
	1	new formulation with round numbers
	2	WMO standard categories
	3	asymptotic scheme

3.4.3.3. tracer_nml

tracer_nml namelist options

variable	options/format	description	default value
tr_aero	logical	aerosols	.false.
tr_fsd	logical	floe size distribution	.false.
tr_FY	logical	first-year ice area	.false.
tr_iage	logical	ice age	.false.
tr_iso	logical	isotopes	.false.
tr_lvl	logical	level ice area and volume	.false.
tr_pond_lvl	logical	level-ice melt ponds	.false.
tr_pond_topo	logical	topo melt ponds	.false.
tr_snow	logical	advanced snow physics	.false.

3.4.3.4. thermo_nml

thermo_nml namelist options

variable	options/format	description	default value
a_rapid_mode	real	brine channel diameter in m	0.5e-3
aspect_rapid_mode	real	brine convection aspect ratio	1.0
conduct	bubbly	conductivity scheme [50]	bubbly
	MU71	conductivity [45]
dSdt_slow_mode	real	slow drainage strength parameter m/s/K	-1.5e-7
floediam	real	effective floe diameter for lateral melt in m	300.0
hfrazilmin	real	min thickness of new frazil ice in m	0.05
hi_min	real	minimum ice thickness allowed for thermo in m	0.01
kitd	0	delta function ITD approximation	1
	1	linear remapping ITD approximation
ksno	real	snow thermal conductivity	0.3
ktherm	-1	thermodynamic model disabled	1
	1	Bitz and Lipscomb thermodynamic model
	2	mushy-layer thermodynamic model
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
Rac_rapid_mode	real	critical Rayleigh number	10.0
Tliquidus_max	real	maximum liquidus temperature of mush (C)	0.0
tscale_pnd_drain	real	mushy pond macroscopic drainage timescale in days

3.4.3.5. dynamics_nml

dynamics_nml namelist options

variable	options/format	description	default value
Cf	real	ratio of ridging work to PE change in ridging	17.0
kstrength	0	ice strength formulation [21]	1
	1	ice strength formulation [57]
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 for krdg_partic = 1 in m^0.5	3.0

3.4.3.6. shortwave_nml

shortwave_nml namelist options

variable	options/format	description	default value
ahmax	real	albedo is constant above this thickness in meters	0.3
albedo_type	ccsm3	NCAR CCSM3 albedo implementation	ccsm3
	constant	four constant albedos
albicei	\(0<\alpha <1\)	near infrared ice albedo for thicker ice	0.36
albicev	\(0<\alpha <1\)	visible ice albedo for thicker ice	0.78
albsnowi	\(0<\alpha <1\)	near infrared, cold snow albedo	0.70
albsnowv	\(0<\alpha <1\)	visible, cold snow albedo	0.98
dT_mlt	real	\(\Delta\) temperature per \(\Delta\) snow grain radius	1.5
kalg	real	absorption coefficient for algae	0.6
rsnw_mlt	real	maximum melting snow grain radius
R_ice	real	tuning parameter for sea ice albedo from Delta-Eddington shortwave	0.0
R_pnd	real	tuning parameter for ponded sea ice albedo from Delta-Eddington shortwave	0.0
R_snw	real	tuning parameter for snow (broadband albedo) from Delta-Eddington shortwave	1.5
shortwave	ccsm3	NCAR CCSM3 shortwave distribution method	dEdd
	dEdd	Delta-Eddington method (3-band)
	dEdd_snicar_ad	Delta-Eddington method with 5-band snow
snw_ssp_table	snicar	lookup table for dEdd_snicar_ad
	test	reduced lookup table for dEdd_snicar_ad testing
sw_dtemp	real	temperature from melt for sw_redist	0.02
sw_frac	real	fraction of shortwave redistribution	0.9
sw_redist	logical	shortwave redistribution	.false.

3.4.3.7. ponds_nml

ponds_nml namelist options

variable	options/format	description	default value
dpscale	real	scaling factor for flushing in permeable ice (ktherm=1)	1.e-3
frzpnd	cesm	CESM pond refreezing forumulation	cesm
	hlid	Stefan refreezing with pond ice thickness
hp1	real	critical ice lid thickness for topo ponds in m	0.01
hs0	real	snow depth of transition to bare sea ice in m
hs1	real	snow depth of transition to pond ice in m	0.03
pndaspect	real	aspect ratio of pond changes (depth:area)	0.8
rfracmax	\(0 \le r_{max} \le 1\)	maximum melt water added to ponds	0.85
rfracmin	\(0 \le r_{min} \le 1\)	minimum melt water added to ponds	0.15

3.4.3.8. snow_nml

snow_nml namelist options

variable	options/format	description	default value
drhosdwind	real	wind compaction factor for snow	27.3
rhosmin	real	minimum snow density	100.0
rhosmax	real	maximum snow density	450.0
rhosnew	real	new snow density	100.0
rsnw_fall	real	radius of new snow (um)	54.526
rsnw_tmax	real	maximum snow radius (um)	1500.0
snw_aging_table	test	snow aging lookup table	test
	snicar	(not available in Icepack)
snwgrain	logical	snow grain metamorphosis	.true.
snwlvlfac	real	fraction increase in bulk snow redistribution	0.3
snwredist	snwITDrdg	snow redistribution using ITD/ridges	snwITDrdg
	bulk	bulk snow redistribution
	none	no snow redistribution
use_smliq_pnd	logical	use liquid in snow for ponds	.true.
windmin	real	minimum wind speed to compact snow	10.0

3.4.3.9. forcing_nml

forcing_nml namelist options

variable	options/format	description	default value
atmbndy	string	bulk transfer coefficients	similarity
	similarity	stability-based boundary layer
	constant	constant-based boundary layer
	mixed	stability-based, but constant for sensible+latent heatfluxes
atmiter_conv	real	convergence criteria for ustar	0.0
atm_data_file	string	file containing atmospheric data	‘ ‘
atm_data_format	bin	read direct access binary forcing files	bin
atm_data_type	clim	monthly climatology (see Forcing data)	default
	CFS	CFS model output (see Forcing data)
	default	constant values defined in the code
	ISPOL	ISPOL experiment data (see Forcing data)
	NICE	N-ICE experiment data (see Forcing data)
bgc_data_file	string	file containing biogeochemistry data	‘ ‘
bgc_data_format	bin	read direct access binary forcing files	bin
bgc_data_type	clim	bgc climatological data	default
	default	constant values defined in the code
	ncar	POP ocean forcing data
calc_strair	.false.	read wind stress and speed from files	.true.
	.true.	calculate wind stress and speed
calc_Tsfc	logical	calculate surface temperature	.true.
cpl_frazil	external	frazil water/salt fluxes are handled outside of Icepack	fresh_ice_correction
	fresh_ice_correction	correct fresh-ice frazil water/salt fluxes for mushy physics
	internal	send full frazil water/salt fluxes for mushy physics
data_dir	string	path to forcing data directory	‘ ‘
default_season	summer	forcing initial summer values	winter
	winter	forcing initial winter values
emissivity	real	emissivity of snow and ice	0.985
fbot_xfer_type	Cdn_ocn	variabler ocean heat transfer coefficient scheme	constant
	constant	constant ocean heat transfer coefficient
formdrag	logical	calculate form drag	.false.
fyear_init	integer	first year of atmospheric forcing data	1998
highfreq	logical	high-frequency atmo coupling	.false.
lateral_flux_type	uniform_ice	flux ice with identical properties into the cell when closing (Icepack only)
	none	advect open water into the cell when closing (Icepack only)
ice_data_file	string	file containing ice opening, closing data	‘ ‘
l_mpond_fresh	.false.	release pond water immediately to ocean	.false.
	true	retain (topo) pond water until ponds drain
natmiter	integer	number of atmo boundary layer iterations	5
oceanmixed_ice	logical	active ocean mixed layer calculation	.false.
ocn_data_file	string	file containing ocean data	‘ ‘
ocn_data_format	bin	read direct access binary forcing files	bin
ocn_data_type	default	constant values defined in the code	default
	ISPOL	ISPOL experiment data (see Forcing data)
	NICE	N-ICE experiment data (see Forcing data)
	SHEBA	Opening/closing dataset from SHEBA
precip_units	mks	liquid precipitation data units	mks
	mm_per_month
	mm_per_sec	(same as MKS units)
	m_per_sec
restore_ocn	logical	restore sst to data	.false.
saltflux_option	constant	salt flux is referenced to a constant salinity	constant
	prognostic	use actual sea ice bulk salinity in flux
tfrz_option	constant	constant ocean freezing temperature (Tocnfrz)	mushy
	linear_salt	linear function of salinity (ktherm=1)
	minus1p8	constant ocean freezing temperature (\(-1.8^{\circ} C\))
	mushy	matches mushy-layer thermo (ktherm=2)
trestore	integer	sst restoring time scale (days)	90
update_ocn_f	.false.	do not include frazil water/salt fluxes in ocn fluxes	.false.
	true	include frazil water/salt fluxes in ocn fluxes
ustar_min	real	minimum value of ocean friction velocity in m/s	0.005
wave_spec_type	constant	wave data file is provided, sea surface height generated using constant phase (1 iteration of wave fracture)	none
	none	no wave data provided, no wave-ice interactions (not recommended when using the FSD)
	profile	no wave data file is provided, use fixed dummy wave spectrum, for testing, sea surface height generated using constant phase (1 iteration of wave fracture)
	random	wave data file is provided, sea surface height generated using random number (multiple iterations of wave fracture)
ycycle	integer	number of years in forcing data cycle	1

3.4.3.10. zbgc_nml

zbgc_nml namelist options

variable	options/format	description	default value
algaltype_diatoms	real	mobility type between stationary and mobile algal diatoms	0.0
algaltype_phaeo	real	mobility type between stationary and mobile algal phaeocystis	0.5
algaltype_sp	real	mobility type between stationary and mobile small plankton	0.5
algal_vel	real	[33]	1.11e-8
alpha2max_low_diatoms	real	light limitation diatoms 1/(W/m^2)	0.8
alpha2max_low_phaeo	real	light limitation phaeocystis 1/(W/m^2)	0.67
alpha2max_low_sp	real	light limitation small plankton 1/(W/m^2)	0.67
ammoniumtype	real	mobility type between stationary and mobile ammonium	1.0
beta2max_diatoms	real	light inhibition diatoms 1/(W/m^2)	0.18
beta2max_phaeo	real	light inhibition phaeocystis 1/(W/m^2)	0.01
beta2max_sp	real	light inhibition small plankton 1/(W/m^2)	0.0025
bgc_data_type	clim	bgc climatological data	default
	default	constant values defined in the code
	ncar	POP ocean forcing data
bgc_flux_type	constant	constant ice–ocean flux velocity	Jin2006
	Jin2006	ice–ocean flux velocity of [30]
chlabs_diatoms	real	chl absorbtion diatoms 1/m/(mg/m^3)	0.03
chlabs_phaeo	real	chl absorbtion phaeocystis 1/m/(mg/m^3)	0.05
chlabs_sp	real	chl absorbtion small plankton 1/m/(mg/m^3)	0.01
dEdd_algae	logical		.false.
dmspdtype	real	mobility type between stationary and mobile dmspd	-1.0
dmspptype	real	mobility type between stationary and mobile dmspp	0.5
doctype_l	real	mobility type between stationary and mobile doc lipids	0.5
doctype_s	real	mobility type between stationary and mobile doc saccharids	0.5
dontype_protein	real	mobility type between stationary and mobile don proteins	0.5
dustFe_sol	real	solubility fraction	0.005
fedtype_1	real	mobility type between stationary and mobile fed lipids	0.5
feptype_1	real	mobility type between stationary and mobile fep lipids	0.5
frazil_scav	real	increase in initial bio bracer from ocean scavenging	1.0
fr_dFe	real	fraction of remineralized nitrogen in units of algal iron	0.3
fr_graze_diatoms	real	fraction grazed diatoms	0.01
fr_graze_e	real	fraction of assimilation excreted	0.5
fr_graze_phaeo	real	fraction grazed phaeocystis	0.1
fr_graze_s	real	fraction of grazing spilled or slopped	0.5
fr_graze_sp	real	fraction grazed small plankton	0.1
fr_mort2min	real	fractionation of mortality to Am	0.5
fr_resp	real	frac of algal growth lost due to respiration	0.05
fr_resp_s	real	DMSPd fraction of respiration loss as DMSPd	0.75
fsal	real	salinity limitation ppt	1.0
F_abs_chl_diatoms	real	scales absorbed radiation for dEdd chl diatoms	2.0
F_abs_chl_phaeo	real	scales absorbed radiation for dEdd chl phaeocystis	5.0
F_abs_chl_sp	real	scales absorbed radiation for dEdd small plankton	4.0
f_doc_l	real	fraction of mortality to DOC lipids	0.4
f_doc_s	real	fraction of mortality to DOC saccharides	0.4
f_don_Am_protein	real	fraction of remineralized DON to ammonium	0.25
f_don_protein	real	fraction of spilled grazing to proteins	0.6
f_exude_l	real	fraction of exudation to DOC lipids	1.0
f_exude_s	real	fraction of exudation to DOC saccharids	1.0
grid_o	real	z biology for bottom flux	5.0
grid_oS	real	DEPRECATED
grow_Tdep_diatoms	real	temperature dependence growth diatoms per degC	0.06
grow_Tdep_phaeo	real	temperature dependence growth phaeocystis per degC	0.06
grow_Tdep_sp	real	temperature dependence growth small plankton per degC	0.06
humtype	real	mobility type between stationary and mobile hum	1.0
initbio_frac	real	fraction of ocean trcr concentration in bio tracers	1.0
K_Am_diatoms	real	ammonium half saturation diatoms mmol/m^3	0.3
K_Am_phaeo	real	ammonium half saturation phaeocystis mmol/m^3	0.3
K_Am_sp	real	ammonium half saturation small plankton mmol/m^3	0.3
k_bac_l	real	Bacterial degredation of DOC lipids per day	0.03
k_bac_s	real	Bacterial degredation of DOC saccharids per day	0.03
k_exude_diatoms	real	algal exudation diatoms per day	0.0
k_exude_phaeo	real	algal exudation phaeocystis per day	0.0
k_exude_sp	real	algal exudation small plankton per day	0.0
K_Fe_diatoms	real	iron half saturation diatoms nM	1.0
K_Fe_phaeo	real	iron half saturation phaeocystis nM	0.1
K_Fe_sp	real	iron half saturation small plankton nM	0.2
k_nitrif	real	nitrification rate per day	0.0
K_Nit_diatoms	real	nitrate half saturation diatoms mmol/m^3	1.0
K_Nit_phaeo	real	nitrate half saturation phaeocystis mmol/m^3	1.0
K_Nit_sp	real	nitrate half saturation small plankton mmol/m^3	1.0
K_Sil_diatoms	real	silicate half saturation diatoms mmol/m^3	4.0
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	0.03
l_sk	real	characteristic diffusive scale in m	7.0
l_skS	real	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
modal_aero	logical	modal aersols	.false.
mort_pre_diatoms	real	mortality diatoms	0.007
mort_pre_phaeo	real	mortality phaeocystis	0.007
mort_pre_sp	real	mortality small plankton	0.007
mort_Tdep_diatoms	real	temperature dependence of mortality diatoms per degC	0.03
mort_Tdep_phaeo	real	temperature dependence of mortality phaeocystis per degC	0.03
mort_Tdep_sp	real	temperature dependence of mortality small plankton per degC	0.03
mu_max_diatoms	real	maximum growth rate diatoms per day	1.2
mu_max_phaeo	real	maximum growth rate phaeocystis per day	0.851
mu_max_sp	real	maximum growth rate small plankton per day	0.851
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	0.5
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
ratio_C2N_diatoms	real	algal C to N in mol/mol diatoms	7.0
ratio_C2N_phaeo	real	algal C to N in mol/mol phaeocystis	7.0
ratio_C2N_proteins	real	algal C to N in mol/mol proteins	7.0
ratio_C2N_sp	real	algal C to N in mol/mol small plankton	7.0
ratio_Fe2C_diatoms	real	algal Fe to C in umol/mol diatoms	0.0033
ratio_Fe2C_phaeo	real	algal Fe to C in umol/mol phaeocystis	1.0
ratio_Fe2C_sp	real	algal Fe to C in umol/mol small plankton	0.0033
ratio_Fe2N_diatoms	real	algal Fe to N in umol/mol diatoms	0.23
ratio_Fe2N_phaeo	real	algal Fe to N in umol/mol phaeocystis	0.7
ratio_Fe2N_sp	real	algal Fe to N in umol/mol small plankton	0.23
ratio_Fe2DOC_s	real	Fe to C of DON saccharids nmol/umol	1.0
ratio_Fe2DOC_l	real	Fe to C of DOC lipids nmol/umol	0.033
ratio_Fe2DON	real	Fe to C of DON nmol/umol	0.023
ratio_Si2N_diatoms	real	algal Si to N in mol/mol diatoms	1.8
ratio_Si2N_phaeo	real	algal Si to N in mol/mol phaeocystis	0.0
ratio_Si2N_sp	real	algal Si to N in mol/mol small plankton	0.0
ratio_S2N_diatoms	real	algal S to N in mol/mol diatoms	0.03
ratio_S2N_phaeo	real	algal S to N in mol/mol phaeocystis	0.03
ratio_S2N_sp	real	algal S to N in mol/mol small plankton	0.03
restore_bgc	logical	restore bgc to data	.false.
R_dFe2dust	real	g/g [66]	0.035
scale_bgc	logical		.false.
silicatetype	real	mobility type between stationary and mobile silicate	-1.0
skl_bgc	logical	biogeochemistry	.false.
solve_zbgc	logical		.false.
solve_zsal	logical	DEPRECATED	.false.
tau_max	real	long time mobile to stationary exchanges	1.73e-5
tau_min	real	rapid module to stationary exchanges
tr_bgc_Am	logical	ammonium tracer	.false.
tr_bgc_C	logical	algal carbon tracer	.false.
tr_bgc_chl	logical	algal chlorophyll tracer	.false.
tr_bgc_DMS	logical	DMS tracer	.false.
tr_bgc_DON	logical	DON tracer	.false.
tr_bgc_Fe	logical	iron tracer	.false.
tr_bgc_hum	logical		.false.
tr_bgc_Nit	logical		.false.
tr_bgc_PON	logical	PON tracer	.false.
tr_bgc_Sil	logical	silicate tracer	.false.
tr_brine	logical	brine height tracer	.false.
tr_zaero	logical	vertical aerosol tracers	.false.
t_iron_conv	real	desorption loss pFe to dFe in days
t_sk_conv	real	Stefels conversion time in days	3.0
t_sk_ox	real	DMS oxidation time in days	10.0
T_max	real	maximum temperature degC	0.0
y_sk_DMS	real	fraction conversion given high yield	0.5
zaerotype_bc1	real	mobility type between stationary and mobile zaero bc1	1.0
zaerotype_bc2	real	mobility type between stationary and mobile zaero bc2	1.0
zaerotype_dust1	real	mobility type between stationary and mobile zaero dust1	1.0
zaerotype_dust2	real	mobility type between stationary and mobile zaero dust2	1.0
zaerotype_dust3	real	mobility type between stationary and mobile zaero dust3	1.0
zaerotype_dust4	real	mobility type between stationary and mobile zaero dust4	1.0
z_tracers	logical		.false.

• = 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.

3.4.4. 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