3.4. Case Settings

There are two important files that define the case, cice.settings and ice_in. cice.settings is a list of env variables that define many values used to setup, build and run the case. ice_in is the input namelist file for CICE. Variables in both files are described below. In addition, the first table lists available preprocessor macros to activate or deactivate various features when compiling.

3.4.1. Table of C Preprocessor (CPP) Macros

The CICE model supports a number of 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. More information can be found in C Preprocessor (CPP) Macros. The following CPPs are available.

CPP Macros

CPP name	description
General Macros
CESM1_PIO	Provide backwards compatible support for PIO interfaces/version released with CESM1 in about 2010
ESMF_INTERFACE	Turns on ESMF support in a subset of driver code. Also USE_ESMF_LIB and USE_ESMF_METADATA
FORTRANUNDERSCORE	Used in ice_shr_reprosum86.c to support Fortran-C interfaces. This should generally be turned on at all times. There are other CPPs (FORTRANDOUBULEUNDERSCORE, FORTRANCAPS, etc) in ice_shr_reprosum.c that are generally not used in CICE but could be useful if problems arise in the Fortran-C interfaces
GPTL	Turns on GPTL initialization if needed for PIO
NO_F2003	Turns off some Fortran 2003 features
NO_I8	Converts integer*8 to integer*4. This could have adverse affects for certain algorithms including the ddpdd implementation associated with the bfbflag
NO_R16	Converts real*16 to real*8. This could have adverse affects for certain algorithms including the lsum16 implementation associated with the bfbflag
USE_NETCDF	Turns on netcdf code. This is normally on and is needed for released configurations. An older value, ncdf, is still supported
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
CICE_DMI	Turns on code changes for the DMI coupled model application
ICE_DA	Turns on code changes in the hadgem driver
RASM_MODS	Turns on code changes for the RASM coupled application
Library Macros
_OPENMP	Automatically defined when compiling with OpenMP
_OPENACC	Automatically defined when compiling with OpenACC

3.4.2. Table of CICE Settings

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

CICE settings

variable	options/format	description	default value
ICE_CASENAME	string	case name	set by cice.setup
ICE_SANDBOX	string	sandbox directory	set by cice.setup
ICE_MACHINE	string	machine name	set by cice.setup
ICE_ENVNAME	string	environment name	set by cice.setup
ICE_MACHCOMP	string	machine_environment name	set by cice.setup
ICE_SCRIPTS	string	scripts directory	set by cice.setup
ICE_CASEDIR	string	case directory	set by cice.setup
ICE_RUNDIR	string	run directory	set by cice.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_DRVOPT	string	unused	standalone/cice
ICE_TARGET	string	build target	set by cice.setup
ICE_IOTYPE	string	I/O format	set by cice.setup
	netcdf	serial netCDF
	pio	parallel netCDF
	none	netCDF library is not available
ICE_CLEANBUILD	true, false	automatically clean before building	true
ICE_CPPDEFS	user defined preprocessor macros for build	null
ICE_QUIETMODE	true, false	reduce build output to the screen	false
ICE_GRID	string (see below)	grid	set by cice.setup
	gx3	3-deg displace-pole (Greenland) global grid
	gx1	1-deg displace-pole (Greenland) global grid
	tx1	1-deg tripole global grid
	gbox80	80x80 box
	gbox128	128x128 box
ICE_NTASKS	integer	number of tasks, must be set to 1	set by cice.setup
ICE_NTHRDS	integer	number of threads per task, must be set to 1	set by cice.setup
ICE_TEST	string	test setting if using a test	set by cice.setup
ICE_TESTNAME	string	test name if using a test	set by cice.setup
ICE_BASELINE	string	baseline directory name, associated with cice.setup -bdir	set by cice.setup
ICE_BASEGEN	string	baseline directory name for regression generation, associated with cice.setup -bgen	set by cice.setup
ICE_BASECOM	string	baseline directory name for regression comparison, associated with cice.setup -bcmp	set by cice.setup
ICE_BFBCOMP	string	location of case for comparison, associated with cice.setup -td	set by cice.setup
ICE_SPVAL	string	special value for cice.settings strings	set by cice.setup
ICE_RUNLENGTH	integer (see below)	batch run length default	set by cice.setup
	-1	15 minutes (default)
	0	30 minutes
	1	59 minutes
	2	2 hours
	other \(2 < N < 8\)	N hours
	8 or larger	8 hours
ICE_ACCOUNT	string	batch account number	set by cice.setup, .cice_proj or by default
ICE_QUEUE	string	batch queue name	set by cice.setup or by default
ICE_THREADED	true, false	force threading in compile, will always compile threaded if ICE_NTHRDS \(> 1\)	false
ICE_BLDDEBUG	true, false	turn on compile debug flags	false
ICE_COVERAGE	true, false	turn on code coverage flags	false

3.4.3. Table of namelist options

CICE reads a namelist input file, ice_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 CICE namelist file, ice_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
bfbflag	off	local reduction then global scalar sum	off
	lsum4	local reduction with real*4 then global scalar sum
	lsum8	local reduction with real*8 then global scalar sum
	lsum16	local reduction with real*16 then global scalar sum
	ddpdd	parallel double double algorithm
	reprosum	fixed point double integer sum
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
day_init	integer	the initial day of the month if not using restart	1
dbug	logical	write extra diagnostics	.false.
diagfreq	integer	frequency of diagnostic output in timesteps	24
diag_type	stdout	write diagnostic output to stdout	stdout
	file	write diagnostic output to file
diag_file	string	diagnostic output file	‘ice_diag.d’
dt	real	thermodynamics time step length in seconds
dumpfreq	d	write restart every dumpfreq_n days	y
	h	write restart every dumpfreq_n hours
	m	write restart every dumpfreq_n months
	y	write restart every dumpfreq_n years
	1	write restart every dumpfreq_n time step
dumpfreq_n	integer	write restart frequency with dumpfreq	1
dump_last	logical	write restart on last time step of simulation	.false.
hist_avg	logical	write time-averaged data	.true.
histfreq	d	write history every histfreq_n days	‘1’,’h’,’d’,’m’,’y’
	h	write history every histfreq_n hours
	m	write history every histfreq_n months
	x	unused frequency stream (not written)
	y	write history every histfreq_n years
	1	write history every histfreq_n time step
histfreq_n	integer array	frequency history output is written with histfreq	1,1,1,1,1
history_dir	string	path to history output directory	‘./’
history_file	string	output file for history	‘iceh’
history_format	default	read/write history files in default format	default
	pio_pnetcdf	read/write restart files with pnetcdf in pio
history_precision	integer	history file precision: 4 or 8 byte	4
ice_ic	default	latitude and sst dependent initial condition	default
	none	no ice
	‘path/file’	restart file name
incond_dir	string	path to initial condition directory	‘./’
incond_file	string	output file prefix for initial condition	‘iceh_ic’
istep0	integer	initial time step number	0
latpnt	real	latitude of (2) diagnostic points	90.0,-65.0
lcdf64	logical	use 64-bit netcdf format	.false.
lonpnt	real	longitude of (2) diagnostic points	0.0,-45.0
month_init	integer	the initial month if not using restart	1
ndtd	integer	number of dynamics/advection/ridging/steps per thermo timestep	1
npt	integer	total number of npt_units to run the model	99999
npt_unit	d	run npt days	1
	h	run npt hours
	m	run npt months
	s	run npt seconds
	y	run npt years
	1	run npt timesteps
numin	integer	minimum internal IO unit number	11
numax	integer	maximum internal IO unit number	99
pointer_file	string	restart pointer filename	‘ice.restart_file’
print_global	logical	print global sums diagnostic data	.true.
print_points	logical	print diagnostic data for two grid points	.false.
restart	logical	initialize using restart file	.false.
restart_dir	string	path to restart directory	‘./’
restart_ext	logical	read/write halo cells in restart files	.false.
restart_file	string	output file prefix for restart dump	‘iced’
restart_format	default	read/write restart file with default format	default
	pio_pnetcdf	read/write restart files with pnetcdf in pio
runid	string	label for run (currently CESM only)	‘unknown’
runtype	continue	restart using pointer_file	initial
	initial	start from ice_ic
sec_init	integer	the initial second if not using restart	0
use_leap_years	logical	include leap days	.false.
use_restart_time	logical	set initial date using restart file	.true.
version_name	string	model version	‘unknown_version_name’
write_ic	logical	write initial condition	.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
bathymetry_file	string	name of bathymetry file to be read	‘unknown_bathymetry_file’
bathymetry_format	default	NetCDF depth field	‘default’
	pop	pop thickness file in cm in ascii format
dxrect	real	x-direction grid spacing for rectangular grid in cm	0.0
dyrect	real	y-direction grid spacing for rectangular grid in cm	0.0
gridcpl_file	string	input file for coupling grid info	‘unknown_gridcpl_file’
grid_file	string	name of grid file to be read	‘unknown_grid_file’
grid_format	bin	read direct access grid and kmt files	bin
	nc	read grid and kmt files
grid_type	displaced_pole	read from file in popgrid	rectangular
	rectangular	defined in rectgrid
	regional	read from file in popgrid
	tripole	read from file in popgrid
kcatbound	-1	single category formulation	1
	0	old formulation
	1	new formulation with round numbers
	2	WMO standard categories
	3	asymptotic scheme
kmt_file	string	name of land mask file to be read	‘unknown_kmt_file’
nblyr	integer	number of zbgc layers	0
ncat	integer	number of ice thickness categories	0
nfsd	integer	number of floe size categories	1
nilyr	integer	number of vertical layers in ice	0
nslyr	integer	number of vertical layers in snow	0
orca_halogrid	logical	use orca haloed grid for data/grid read	.false.
use_bathymetry	logical	use read in bathymetry file for seabedstress option	.false.

3.4.3.3. domain_nml

domain_nml namelist options

variable	options/format	description	default value
add_mpi_barriers	logical	throttle communication	.false.
block_size_x	integer	block size in x direction	-1
block_size_y	integer	block size in y direction	-1
debug_blocks	logical	add additional print statements to debug the block decomposition	.false.
distribution_type	cartesian	2D cartesian block distribution method	cartesian
	rake	redistribute blocks among neighbors
	roundrobin	1 block per proc until blocks are used
	sectcart	blocks distributed to domain quadrants
	sectrobin	several blocks per proc until used
	spacecurve	distribute blocks via space-filling curves
	spiralcenter	distribute blocks via roundrobin from center of grid outward in a spiral
	wghtfile	distribute blocks based on weights specified in distribution_wght_file
distribution_wght	block	full block size distribution weight method	latitude
	latitude	latitude/ocean sets work_per_block
distribution_wght_file	string	distribution weight file when distribution_type is wghtfile	‘unknown’
ew_boundary_type	cyclic	periodic boundary conditions in x-direction	cyclic
	open	Dirichlet boundary conditions in x
maskhalo_dyn	logical	mask unused halo cells for dynamics	.false.
maskhalo_remap	logical	mask unused halo cells for transport	.false.
maskhalo_bound	logical	mask unused halo cells for boundary updates	.false.
max_blocks	integer	maximum number of blocks per MPI task for memory allocation	-1
nprocs	integer	number of processors to use	-1
ns_boundary_type	cyclic	periodic boundary conditions in y-direction	open
	open	Dirichlet boundary conditions in y
	tripole	U-fold tripole boundary conditions in y
	tripoleT	T-fold tripole boundary conditions in y
nx_global	integer	global grid size in x direction	-1
ny_global	integer	global grid size in y direction	-1
processor_shape	slenderX1	1 processor in the y direction used with distribution_type=cartesian	slenderX2
	slenderX1	1 processor in the y direction (tall, thin)
	slenderX2	2 processors in the y direction (thin)
	square-ice	more processors in x than y, \(\sim\) square
	square-pop	more processors in y than x, \(\sim\) square

3.4.3.4. tracer_nml

tracer_nml namelist options

variable	options/format	description	default value
n_aero	integer	number of aerosol tracers	0
n_algae	0,1,2,3	number of algal tracers	0
n_dic	0,1	number of dissolved inorganic carbon	0
n_doc	0,1,2,3	number of dissolved organic carbon	0
n_don	0,1	number of dissolved organize nitrogen	0
n_fed	0,1,2	number of dissolved iron tracers	0
n_fep	0,1,2	number of particulate iron tracers	0
n_iso	integer	number of isotope tracers	0
n_zaero	0,1,2,3,4,5,6	number of z aerosol tracers in use	0
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_cesm	logical	CESM melt ponds	.false.
tr_pond_lvl	logical	level-ice melt ponds	.false.
tr_pond_topo	logical	topo melt ponds	.false.
restart_aero	logical	restart tracer values from file	.false.
restart_age	logical	restart tracer values from file	.false.
restart_fsd	logical	restart floe size distribution values from file	.false.
restart_FY	logical	restart tracer values from file	.false.
restart_iso	logical	restart tracer values from file	.false.
restart_lvl	logical	restart tracer values from file	.false.
restart_pond_cesm	logical	restart tracer values from file	.false.
restart_pond_lvl	logical	restart tracer values from file	.false.
restart_pond_topo	logical	restart tracer values from file	.false.

3.4.3.5. 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 [40]	bubbly
	MU71	conductivity [35]
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
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
	0	zero-layer thermodynamic model
	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

3.4.3.6. dynamics_nml

dynamics_nml namelist options

variable	options/format	description	default value
advection	remap	linear remapping advection scheme	remap
	upwind	donor cell advection
algo_nonlin	anderson	use nonlinear anderson algorithm for implicit solver	picard
	picard	use picard algorithm
alphab	real	\(\alpha_{b}\) factor in [29]	20.0
arlx	real	revised_evp value	300.0
brlx	real	revised_evp value	300.0
Cf	real	ratio of ridging work to PE change in ridging	17.0
coriolis	constant	constant coriolis value = 1.46e-4 s\(^{-1}\)	latitude
	latitude	coriolis variable by latitude
	zero	zero coriolis
Cstar	real	constant in Hibler strength formula	20
e_ratio	real	EVP ellipse aspect ratio	2.0
dim_fgmres	integer	maximum number of Arnoldi iterations for FGMRES solver	50
dim_pgmres	integer	maximum number of Arnoldi iterations for PGMRES preconditioner	5
kdyn	-1	dynamics algorithm OFF	1
	0	dynamics OFF
	1	EVP dynamics
	2	EAP dynamics
	3	VP dynamics
kevp_kernel	0	standard 2D EVP memory parallel solver	0
	2	1D shared memory solver (not fully validated)
kstrength	0	ice strength formulation [11]	1
	1	ice strength formulation [46]
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
kridge	-1	ridging disabled	1
	1	ridging enabled
ktransport	-1	transport disabled	1
	1	transport enabled
Ktens	real	Tensile strength factor (see [2])	0.0
k1	real	1st free parameter for landfast parameterization	8.0
k2	real	2nd free parameter (N/m\(^3\)) for landfast parameterization	15.0
maxits_nonlin	integer	maximum number of nonlinear iterations for VP solver	1000
maxits_fgmres	integer	maximum number of restarts for FGMRES solver	1
maxits_pgmres	integer	maximum number of restarts for PGMRES preconditioner	1
monitor_nonlin	logical	write velocity norm at each nonlinear iteration	.false.
monitor_fgmres	logical	write velocity norm at each FGMRES iteration	.false.
monitor_pgmres	logical	write velocity norm at each PGMRES iteration	.false.
mu_rdg	real	e-folding scale of ridged ice for krdg_partic = 1 in m^0.5	3.0
ndte	integer	number of EVP subcycles	120
ortho_type	cgs	Use classical Gram-Shchmidt in FGMRES solver	mgs
	mgs	Use modified Gram-Shchmidt in FGMRES solver
precond	diag	Use Jacobi preconditioner for the FGMRES solver	pgmres
	ident	Don’t use a preconditioner for the FGMRES solver
	pgmres	Use GMRES as preconditioner for FGMRES solver
Pstar	real	constant in Hibler strength formula (N/m\(^2\))	2.75e4
reltol_nonlin	real	relative tolerance for nonlinear solver	1e-8
reltol_fgmres	real	relative tolerance for FGMRES solver	1e-2
reltol_pgmres	real	relative tolerance for PGMRES preconditioner	1e-6
revised_evp	logical	use revised EVP formulation	.false.
seabed_stress	logical	use seabed stress parameterization for landfast ice	.false.
seabed_stress_method	LKD	linear keel draft method [29]	LKD
	probabilistic	probability of contact method (Dupont et al., in prep)
ssh_stress	coupled	computed from coupled sea surface height gradient	geostrophic
	geostropic	computed from ocean velocity
threshold_hw	real	Max water depth for grounding (see [1])
yield_curve	ellipse	elliptical yield curve	ellipse
use_mean_vrel	logical	Use mean of two previous iterations for vrel in VP	.true.

3.4.3.7. 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	ccsm3
	dEdd	Delta-Eddington method
sw_dtemp	real	temperature difference from melt to start redistributing	0.02
sw_frac	real	fraction redistributed	0.9
sw_redist	logical	redistribute internal shortwave to surface	.false.

3.4.3.8. ponds_nml

ponds_nml namelist options

variable	options/format	description	default value
dpscale	real	time scale for flushing in permeable ice	1.0
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	0.03
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

3.4.3.9. forcing_nml

forcing_nml namelist options

variable	options/format	description	default value
atmbndy	constant	bulk transfer coefficients	default
	default	stability-based boundary layer
atmiter_conv	real	convergence criteria for ustar	0.0
atm_data_dir	string	path to atmospheric forcing data directory
atm_data_format	bin	read direct access binary atmo forcing file format	bin
	nc	read netcdf atmo forcing files
atm_data_type	box2001	forcing data for [17] box problem	default
	default	constant values defined in the code
	hycom	HYCOM atm forcing data in netcdf format
	JRA55_gx1	JRA55 forcing data for gx1 grid [55]
	JRA55_gx3	JRA55 forcing data for gx3 grid [55]
	JRA55_tx1	JRA55 forcing data for tx1 grid [55]
	LYq	COREII Large-Yeager (AOMIP) forcing data [26]
	monthly	monthly forcing data
	ncar	NCAR bulk forcing data
	oned	column forcing data
bgc_data_dir	string	path to oceanic forcing data directory	‘unknown_bgc_data_dir’
bgc_data_type	clim	bgc climatological data	default
	default	constant values defined in the code
	hycom	HYCOM ocean forcing data in netcdf format
	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.
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	variable ocean heat transfer coefficient scheme	constant
	constant	constant ocean heat transfer coefficient
fe_data_type	clim	ocean climatology forcing value for iron	default
	default	default forcing value for iron
formdrag	logical	calculate form drag	.false.
fyear_init	integer	first year of atmospheric forcing data	1900
highfreq	logical	high-frequency atmo coupling	.false.
ice_data_type	boxslotcyl	initialize ice concentration and velocity for boxslotcyl test ([61])	default
	box2001	initialize ice concentration for box2001 test ([17])
	default	no special initialization
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
nfreq	integer	number of frequencies in ocean surface wave spectral forcing	25
oceanmixed_file	string	data file containing ocean forcing data	‘unknown_oceanmixed_file’
oceanmixed_ice	logical	active ocean mixed layer calculation	.false.
ocn_data_dir	string	path to oceanic forcing data directory	‘unknown_ocn_data_dir’
ocn_data_format	bin	read direct access binary ocean forcing files	bin
	nc	read netcdf ocean forcing files
ocn_data_type	clim	ocean climatological data formulation	default
	default	constant values defined in the code
	hycom	HYCOM ocean forcing data in netcdf format
	ncar	POP ocean forcing data
precip_units	mks	liquid precipitation data units	mks
	mm_per_month
	mm_per_sec	(same as MKS units)
	m_per_sec
restart_coszen	logical	read/write coszen in restart files	.false.
restore_ocn	logical	restore sst to data	.false.
restore_ice	logical	restore ice state along lateral boundaries	.false.
rotate_wind	logical	rotate wind from east/north to computation grid	.true.
tfrz_option	linear_salt	linear functino of salinity (ktherm=1)	mushy
	minus1p8	constant ocean freezing temperature (\(-1.8^{\circ} C\))
	mushy	matches mushy-layer thermo (ktherm=2)
trestore	integer	sst restoring time scale (days)	90
ustar_min	real	minimum value of ocean friction velocity	0.0005 m/s
update_ocn_f	.false.	do not include frazil water/salt fluxes in ocn fluxes	.false.
	true	include frazil water/salt fluxes in ocn fluxes
wave_spec_file	string	data file containing wave spectrum forcing data
wave_spec_type	constant	wave data file is provided, constant wave spectrum, for testing	none
	none	no wave data provided, no wave-ice interactions
	profile	no wave data file is provided, use fixed dummy wave spectrum, for testing
	random	wave data file is provided, wave spectrum generated using random number
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	[27]	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_flux_type	constant	constant ice–ocean flux velocity	Jin2006
	Jin2006	ice–ocean flux velocity of [23]
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_o_t	real	z biology for top flux	5.0
grid_oS	real	z salinity for bottom flux	5.0
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	z salinity characteristic diffusive scale in m	7.0
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
restart_bgc	logical	restart tracer values from file	.false.
restart_hbrine	logical		.false.
restart_zsal	logical		.false.
restore_bgc	logical	restore bgc to data	.false.
R_dFe2dust	real	g/g [51]	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	update salinity tracer profile	.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.

3.4.3.11. icefields_nml

icefields_nml namelist options

variable	options/format	description	default value
f_<var>	d	write field var every histfreq_n days
	h	write field var every histfreq_n hours
	m	write field var every histfreq_n months
	x	do not write var to history
	y	write field var every histfreq_n years
	1	write field var every time step
	md	e.g., write both monthly and daily files
f_<var>_ai	d	write field cell average var every histfreq_n days
	h	write field cell average var every histfreq_n hours
	m	write field cell average var every histfreq_n months
	x	do not write cell average var to history
	y	write field cell average var every histfreq_n years
	1	write field cell average var every time step
	md	e.g., write both monthly and daily files