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.

3.4.1. Table of CICE Settings

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

CICE settings

variable	options/format	description	recommended 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_COMPILER	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	cice
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_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
	0	15 minutes (default)
	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

3.4.2. Table of namelist options

Namelist options

also in Icepack	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
	runtype	initial	start from ice_ic
		continue	restart using pointer_file
*	ice_ic	default	latitude and sst dependent	default
		none	no ice
		path/file	restart file name
	restart	true/false	initialize using restart file	.true.
	use_restart_time	true/false	set initial date using restart file	.true.
	restart_format	nc	read/write  restart files (use with PIO)
		bin	read/write binary restart files
	lcdf64	true/false	if true, use 64-bit  format
	numin	integer	minimum internal IO unit number	11
	numax	integer	maximum internal IO unit number	99
*	restart_dir	path/	path to restart directory
	restart_ext	true/false	read/write halo cells in restart files
	restart_file	filename prefix	output file for restart dump	‘iced’
	pointer_file	pointer filename	contains restart filename
*	dumpfreq	y	write restart every dumpfreq_n years	y
		m	write restart every dumpfreq_n months
		d	write restart every dumpfreq_n days
		h	write restart every dumpfreq_n hours
		1	write restart every dumpfreq_n time step
	dumpfreq_n	integer	frequency restart data is written	1
*	dump_last	true/false	if true, write restart on last time step of simulation
			Model Output
	bfbflag	off/lsum4/lsum8/lsum16/ddpdd/reprosum	global sum methods	off
*	diagfreq	integer	frequency of diagnostic output in dt	24
		e.g., 10	once every 10 time steps
*	diag_type	stdout	write diagnostic output to stdout
		file	write diagnostic output to file
	diag_file	filename	diagnostic output file (script may reset)
	print_global	true/false	print diagnostic data, global sums	.false.
	print_points	true/false	print diagnostic data for two grid points	.false.
	latpnt	real	latitude of (2) diagnostic points
	lonpnt	real	longitude of (2) diagnostic points
	dbug	true/false	if true, write extra diagnostics	.false.
	histfreq	string array	defines output frequencies
		y	write history every histfreq_n years
		m	write history every histfreq_n months
		d	write history every histfreq_n days
		h	write history every histfreq_n hours
		1	write history every histfreq_n time step
		x	unused frequency stream (not written)
	histfreq_n	integer array	frequency history output is written
		0	do not write to history
	hist_avg	true	write time-averaged data	.true.
		false	write snapshots of data
	history_dir	path/	path to history output directory
	history_file	filename prefix	output file for history	‘iceh’
	write_ic	true/false	write initial condition
	incond_dir	path/	path to initial condition directory
	incond_file	filename prefix	output file for initial condition	‘iceh’
	runid	string	label for run (currently CESM only)
	grid_nml
			Grid
	grid_format	nc	read  grid and kmt files	‘bin’
		bin	read direct access, binary file
	grid_type	rectangular	defined in rectgrid
		displaced_pole	read from file in popgrid
		tripole	read from file in popgrid
		regional	read from file in popgrid
	grid_file	filename	name of grid file to be read	‘grid’
	bathymetry_file	filename	name of bathymetry file to be read	‘grid’
	use_bathymetry	true/false	use read in bathymetry file for basalstress option
	kmt_file	filename	name of land mask file to be read	‘kmt’
	gridcpl_file	filename	input file for coupling grid info
*	kcatbound	0	original category boundary formula	0
		1	new formula with round numbers
		2	WMO standard categories
		-1	one category
	dxrect	real	x-direction grid spacing (cm) for rectangular grid
	dyrect	real	y-direction grid spacing (cm) for rectangular grid
	ncat	integer	number of ice thickness categories	5
	nilyr	integer	number of vertical layers in ice	7
	nslyr	integer	number of vertical layers in snow	1
	nblyr	integer	number of zbgc layers	7
	domain_nml
			Domain
	nprocs	integer	number of processors to use
	nx_global	integer	global grid size in x direction
	ny_global	integer	global grid size in y direction
	block_size_x	integer	block size in x direction
	block_size_y	integer	block size in y direction
	max_blocks	integer	maximum number of blocks per MPI task for memory allocation
	processor_shape	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
	distribution_type	cartesian	distribute blocks in 2D Cartesian array
		roundrobin	1 block per proc until blocks are used
		sectcart	blocks distributed to domain quadrants
		sectrobin	several blocks per proc until used
		rake	redistribute blocks among neighbors
		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 sets work_per_block
		latitude	latitude/ocean sets work_per_block
	distribution_wght_file	filename	distribution weight file when distribution_type is wghtfile
	ew_boundary_type	cyclic	periodic boundary conditions in x-direction
		open	Dirichlet boundary conditions in x
	ns_boundary_type	cyclic	periodic boundary conditions in y-direction
		open	Dirichlet boundary conditions in y
		tripole	U-fold tripole boundary conditions in y
		tripoleT	T-fold tripole boundary conditions in y
	maskhalo_dyn	true/false	mask unused halo cells for dynamics
	maskhalo_remap	true/false	mask unused halo cells for transport
	maskhalo_bound	true/false	mask unused halo cells for boundary updates
	tracer_nml
			Tracers
	n_aero	integer	number of aerosol tracers	1
	n_zaero	0,1,2,3,4,5,6	number of z aerosol tracers in use	0
	n_algae	0,1,2,3	number of algal tracers	0
	n_doc	0,1,2,3	number of dissolved organic carbon	0
	n_dic	0,1	number of dissolved inorganic 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
*	tr_iage	true/false	ice age
	restart_age	true/false	restart tracer values from file
*	tr_FY	true/false	first-year ice area
	restart_FY	true/false	restart tracer values from file
*	tr_lvl	true/false	level ice area and volume
	restart_lvl	true/false	restart tracer values from file
*	tr_pond_cesm	true/false	CESM melt ponds
	restart_pond_cesm	true/false	restart tracer values from file
*	tr_pond_topo	true/false	topo melt ponds
	restart_pond_topo	true/false	restart tracer values from file
*	tr_pond_lvl	true/false	level-ice melt ponds
	restart_pond_lvl	true/false	restart tracer values from file
*	tr_aero	true/false	aerosols
	restart_aero	true/false	restart tracer values from file
	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
		-1	thermodynamics disabled
*	conduct	Maykut71	conductivity [30]
		bubbly	conductivity [35]
*	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
	kdyn	-1	dynamics OFF	1
		0	dynamics OFF
		1	EVP dynamics
		2	EAP dynamics
		1	dynamics ON
	revised_evp	true/false	use revised EVP formulation
	ndte	integer	number of EVP subcycles	240
	advection	remap	linear remapping advection	‘remap’
		upwind	donor cell advection
*	kstrength	0	ice strength formulation [11]	1
		1	ice strength formulation [39]
*	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
	coriolis	latitude	Coriolis variable by latitude	‘latitude’
		constant	Constant coriolis value = 1.46e-4
		zero	Zero coriolis
	kridge	1	Ridging Enabled	1
		-1	Ridging Disabled
	ktransport	1	Transport Enabled	1
		-1	Transport Disabled
	basalstress	true/false	use basal stress parameterization for landfast ice
	k1	real	1st free parameter for landfast parameterization
	e_ratio	real	EVP ellipse aspect ratio	2.0
	Ktens	real	Tensile strength factor (see [2])	0.0
	shortwave_nml
			Shortwave
*	shortwave	ccsm3	NCAR CCSM3 distribution method
		dEdd	Delta-Eddington method
*	albedo_type	ccsm3	NCAR CCSM3 albedos	‘default’
		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
*	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.
*	default_season	winter	Sets initial values of forcing and is overwritten if forcing is read in.
*	precip_units	mks	liquid precipitation data units
		mm_per_month
		mm_per_sec	(same as MKS units)
		m_per_sec
*	tfrz_option	minus1p8	constant ocean freezing temperature (\(-1.8^{\circ} C\))
		linear_salt	linear function of salinity (ktherm=1)
		mushy_layer	matches mushy-layer thermo (ktherm=2)
*	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)
*	restore_ocn	true/false	restore sst to data
*	trestore	integer	sst restoring time scale (days)
	restore_ice	true/false	restore ice state along lateral boundaries
*	atm_data_type	default	constant values defined in the code
		LYq	AOMIP/Large-Yeager forcing data
		monthly	monthly forcing data
		ncar	NCAR bulk forcing data
		box2001	forcing data for [15] box problem
		oned	column forcing data
		hycom	HYCOM atm forcing data in netcdf format
*	ocn_data_type	default	constant values defined in the code
		clim	climatological data
		ncar	POP ocean forcing data
		hycom	HYCOM ocean forcing data in netcdf format	Constant initial forcing
	bgc_data_type	default	constant values defined in the code
		clim	climatological data
		ncar	POP ocean forcing data
		hycom	HYCOM ocean forcing data in netcdf format	Constant initial forcing
	fe_data_type	default	default forcing value for iron
		clim	iron forcing from ocean climatology
	ice_data_type	string	ice initialization for special tests	default
		default	no special initialization
		box2001	initialize ice concentration for box2001 test ([15])
		boxslotcyl	initialize ice concentration and velocity for boxslotcyl test ([51])
	atm_data_format	nc	read  atmo forcing files
		bin	read direct access, binary files
	ocn_data_format	nc	read  ocean forcing files
		bin	read direct access, binary files
*	oceanmixed_file	filename	data file containing ocean forcing data
	atm_data_dir	path/	path to atmospheric forcing data directory
	ocn_data_dir	path/	path to oceanic forcing data directory
	bgc_data_dir	path/	path to oceanic forcing data directory
	zbgc_nml
			Biogeochemistry	More information about the BGC tuning can be found in the Icepack Documentation.
*	tr_brine	true/false	brine height tracer
*	tr_zaero	true/false	vertical aerosol tracers
*	modal_aero	true/false	modal aersols
	restore_bgc	true/false	restore bgc to data
	solve_zsal	true/false	update salinity tracer profile
*	skl_bgc	true/false	biogeochemistry
	bgc_flux_type	Jin2006	ice–ocean flux velocity of [21]
		constant	constant ice–ocean flux velocity
	restart_bgc	true/false	restart tracer values from file
	tr_bgc_C_sk	true/false	algal carbon tracer
	tr_bgc_chl_sk	true/false	algal chlorophyll tracer
	tr_bgc_Am_sk	true/false	ammonium tracer
	tr_bgc_Sil_sk	true/false	silicate tracer
	tr_bgc_DMSPp_sk	true/false	particulate DMSP tracer
	tr_bgc_DMSPd_sk	true/false	dissolved DMSP tracer
	tr_bgc_DMS_sk	true/false	DMS tracer
	phi_snow	real	snow porosity for brine height tracer
	icefields_nml
			History Fields
	f_<var>	string	frequency units for writing <var> to history
		y	write history every histfreq_n years
		m	write history every histfreq_n months
		d	write history every histfreq_n days
		h	write history every histfreq_n hours
		1	write history every time step
		x	do not write <var> to history
		md	e.g., write both monthly and daily files
	f_<var>_ai		grid cell average of <var> (\(\times a_i\))