3.1. Implementation¶
Icepack is written in FORTRAN90 and runs on platforms using UNIX, LINUX, and other operating systems. The code is not parallelized. (CHANGE IF OPENMP IS IMPLEMENTED)
Icepack consists of the sea ice column physics code, contained in the columnphysics/ directory, and a configuration/ directory that includes a driver for testing the column physics and a set of scripts for configuring the tests. Icepack is designed such that the column physics code may be used by a host sea ice model without direct reference to the driver or scripts, although these may be consulted for guidance when coupling the column physics code to the host sea ice model (CICE may also be useful for this.) Information about the interface between the column physics and the driver or host sea ice model is located in the Initialization and Forcing section.
3.1.1. Directory structure¶
The present code distribution includes source code for the column physics, source code for the driver, and the scripts. Forcing data is available from the ftp site. The directory structure of Icepack is as follows. All columnphysics filename have a prefix of icepack_ and all driver files are prefixed with icedrv_*.
- LICENSE.pdf
license for using and sharing the code
- DistributionPolicy.pdf
policy for using and sharing the code
- README.md
basic information and pointers
- columnphysics/
columnphysics source code, see Icepack Column Physics
- configuration/scripts/
support scripts, see Scripts Implementation
- configuration/driver/
icepack driver code, see Driver Implementation
- doc/
documentation
- icepack.setup
main icepack script for creating cases
A case (compile) directory is created upon initial execution of the script
icepack.setup at the user-specified location provided after the -c flag.
Executing the command ./icepack.setup -h provides helpful information for
this tool.
3.1.2. Grid and boundary conditions¶
The driver configures a collection of grid cells on which the column physics code
will be run. This “horizontal” grid is a vector of length nx, with a minimum length
of 4.
The grid vector is initialized with different sea ice conditions, such as open
water, a uniform slab of ice, a multi-year ice thickness distribution with snow,
and land. For simplicity, the same forcing values are applied to all grid cells.
Icepack includes two vertical grids. The basic vertical grid contains
nilyr equally spaced grid cells.
History variables available for column output are ice and snow
temperature, Tinz and Tsnz. These variables also include thickness
category as a fourth dimension.
In addition, there is a bio-grid that
can be more finely resolved and includes additional nodes for boundary conditions.
It is used for solving the brine height variable \(h_b\) and for
discretizing the vertical transport equations of biogeochemical tracers.
The bio-grid is a non-dimensional vertical grid which takes the value
zero at \(h_b\) and one at the ice–ocean interface. The number of
grid levels is specified during compilation by setting
the variable NBGCLYR equal to an integer (\(n_b\)) .
Ice tracers and microstructural properties defined on the bio-grid are
referenced in two ways: as bgrid \(=n_b+2\) points and as
igrid\(=n_b+1\) points. For both bgrid and igrid, the first and
last points reference \(h_b\) and the ice–ocean interface,
respectively, and so take the values \(0\) and \(1\),
respectively. For bgrid, the interior points \([2, n_b+1]\) are
spaced at \(1/n_b\) intervals beginning with bgrid(2) =
\(1/(2n_b)\). The igrid interior points \([2, n_b]\) are also
equidistant with the same spacing, but physically coincide with points
midway between those of bgrid.
3.1.3. Initialization and Forcing¶
Icepack’s parameters and variables are initialized in several steps. Many constants and physical parameters are set in icepack_parameters.F90. In the current driver implementation, a namelist file is read to setup the model. Namelist values are given default values in the code, which may then be changed when the input file icepack_in is read. Other physical constants, numerical parameters, and variables are first set in initialization routines for each ice model component or module. Then, if the ice model is being restarted from a previous run, core variables are read and reinitialized in restartfile, while tracer variables needed for specific configurations are read in separate restart routines associated with each tracer or specialized parameterization. Finally, albedo and other quantities dependent on the initial ice state are set. Some of these parameters will be described in more detail in the Tables of Namelist Options.
Two namelist variables control model initialization, ice_ic
and restart. Setting ice_ic = ‘default’ causes the model to run using
initial values set in the code. To start
from a file filename, set
restart = .true. and ice_ic = filename. When restarting using the Icepack
driver, for simplicity the tracers are assumed to be set the same way (on/off) as in the
run that created the restart file; i.e. that the restart file contains exactly the
information needed for the new run. CICE is more flexible in this regard.
For stand-alone runs, routines in icedrv_forcing.F90 read and interpolate data from files, and are intended merely for testing, although they can also provide guidance for the user to write his or her own routines.
3.1.4. Choosing an appropriate time step¶
Transport in thickness space imposes a restraint on the time step, given by the ice growth/melt rate and the smallest range of thickness among the categories, \(\Delta t<\min(\Delta H)/2\max(f)\), where \(\Delta H\) is the distance between category boundaries and \(f\) is the thermodynamic growth rate. For the 5-category ice thickness distribution used as the default in this distribution, this is not a stringent limitation: \(\Delta t < 19.4\) hr, assuming \(\max(f) = 40\) cm/day.
3.1.5. Model output¶
The Icepack model provides diagnostic output files, binary or netCDF restart files, and a primitive netCDF history file capability. The sea ice model CICE provides more extensive options for model output, including many derived output variables.
3.1.5.1. Diagnostic files¶
Icepack writes diagnostic information for each grid cell as a separate file, ice_diag.*, identified by the initial ice state of the grid cell (no ice, slab, land, etc).
3.1.5.2. Restart files¶
Icepack provides restart data in binary unformatted format or netCDF. The restart files
created by the Icepack driver contain all of the variables needed
for a full, exact restart. The filename begins with the character string
‘iced.’ and is placed in the directory specified by the namelist variable
restart_dir. The restart dump frequency is given by the namelist
variable dumpfreq. The namelist variable ice_ic contains the
pointer to the filename from which the restart data is to be read and
the namelist option restart must be set to .true. to use the file.
dump_last namelist can also be set to true to trigger restarts automatically
at the end of runs. The default restart file format is binary, set in
namelist with restart_format = ‘bin’. For netCDF, set restart_format = ‘nc’
or use icepack.setup -s restcdf.
The default configuration of Icepack does not support netCDF. If netCDF restart files are
desired, the USE_NETCDF C preprocessor directive must be set during compilation. This
is done by setting ICE_IOTYPE to netcdf in icepack.settings or using the
icepack.setup -s option ionetcdf. If netCDF is used on a particular machine,
the machine env and Macros file must support compilation with netCDF.
3.1.5.3. History files¶
Icepack has a primitive netCDF history capability that is turned on with the
history_format namelist. When history_format is set to ‘nc’, history files
are created for each run with a naming convention of icepack.h.yyyymmdd.nc
in the run directory history directory. The yyyymmdd is the start date for each run.
Use icepack.setup -s histcdf to turn on netCDF history files automatically.
When Icepack history files are turned on, data for a set of fixed fields is written to the history file for each column at every timestep without ability to control fields, frequencies, or temporal averaging. All output fields are hardwired into the implementation in configuration/driver/icedrv_history.F90 file. The netCDF file does NOT meet netCDF CF conventions and is provided as an amenity in the standalone Icepack model. Users are free to modify the output fields or extend the implementation and are encouraged to share any updates with the Consortium.
The default configuration of Icepack does not support netCDF. If netCDF history files are
desired, the USE_NETCDF C preprocessor directive must be set during compilation. This
is done by setting ICE_IOTYPE to netcdf in icepack.settings or using the
icepack.setup -s option ionetcdf. If netCDF is used on a particular machine,
the machine env and Macros file must support compilation with netCDF.
3.1.5.4. Biogeochemistry History Fields¶
History output is not provided with Icepack. This documentation indicates what is available for output and is implemented in CICE.
Table Biogeochemical History variables lists the biogeochemical tracer history flags along with a short description and the variable or variables saved. Not listed are flags appended with _ai, i.e. f_fbio_ai. These fields are identical to their counterpart. i.e. f_fbio, except they are averaged by ice area.
History Flag |
Definition |
Variable(s) |
Units |
|---|---|---|---|
f_fiso_atm |
atmospheric water isotope deposition flux |
fiso_atm |
kg m\(^{-2}\) s\(^{-1}\) |
f_fiso_ocn |
water isotope flux from ice to ocean |
fiso_ocn |
kg m\(^{-2}\) s\(^{-1}\) |
f_iso |
isotope mass (snow and ice) |
isosno, isoice |
kg/kg |
f_faero_atm |
atmospheric aerosol deposition flux |
faero_atm |
kg m\(^{-2}\) s\(^{-1}\) |
f_faero_ocn |
aerosol flux from ice to ocean |
faero_ocn |
kg m\(^{-2}\) s\(^{-1}\) |
f_aero |
aerosol mass (snow and ice ssl and int) |
aerosnossl, aerosnoint,aeroicessl, aeroiceint |
kg/kg |
f_fbio |
biological ice to ocean flux |
fN, fDOC, fNit, fAm,fDON,fFep\(^a\), fFed\(^a\), fSil,fhum, fPON, fDMSPd,fDMS, fDMSPp, fzaero |
mmol m\(^{-2}\) s\(^{-1}\) |
f_zaero |
bulk z-aerosol mass fraction |
zaero |
kg/kg |
f_bgc_S |
DEPRECATED |
bgc_S |
ppt |
f_bgc_N |
bulk algal N concentration |
bgc_N |
mmol m\(^{-3}\) |
f_bgc_C |
bulk algal C concentration |
bgc_C |
mmol m\(^{-3}\) |
f_bgc_DOC |
bulk DOC concentration |
bgc_DOC |
mmol m\(^{-3}\) |
f_bgc_DON |
bulk DON concentration |
bgc_DON |
mmol m\(^{-3}\) |
f_bgc_DIC |
bulk DIC concentration |
bgc_DIC |
mmol m\(^{-3}\) |
f_bgc_chl |
bulk algal chlorophyll concentration |
bgc_chl |
mg chl m\(^{-3}\) |
f_bgc_Nit |
bulk nitrate concentration |
bgc_Nit |
mmol m\(^{-3}\) |
f_bgc_Am |
bulk ammonium concentration |
bgc_Am |
mmol m\(^{-3}\) |
f_bgc_Sil |
bulk silicate concentration |
bgc_Sil |
mmol m\(^{-3}\) |
f_bgc_DMSPp |
bulk particulate DMSP concentration |
bgc_DMSPp |
mmol m\(^{-3}\) |
f_bgc_DMSPd |
bulk dissolved DMSP concentration |
bgc_DMSPd |
mmol m\(^{-3}\) |
f_bgc_DMS |
bulk DMS concentration |
bgc_DMS |
mmol m\(^{-3}\) |
f_bgc_Fe |
bulk dissolved and particulate iron conc. |
bgc_Fed, bgc_Fep |
\(\mu\,\)mol m\(^{-3}\) |
f_bgc_hum |
bulk humic matter concentration |
bgc_hum |
mmol m\(^{-3}\) |
f_bgc_PON |
bulk passive mobile tracer conc. |
bgc_PON |
mmol m\(^{-3}\) |
f_upNO |
Total algal \({\mbox{NO$_3$}}\) uptake rate |
upNO |
mmol m\(^{-2}\) d\(^{-1}\) |
f_upNH |
Total algal \({\mbox{NH$_4$}}\) uptake rate |
upNH |
mmol m\(^{-2}\) d\(^{-1}\) |
f_bgc_ml |
upper ocean tracer concentrations |
ml_N, ml_DOC, ml_Nit,ml_Am, ml_DON, ml_Fep\(^b\),ml_Fed\(^b\), ml_Sil, ml_hum, ml_PON,ml_DMS, ml_DMSPd, ml_DMSPp |
mmol m\(^{-3}\) |
f_bTin |
ice temperature on the bio grid |
bTizn |
\(^o\)C |
f_bphi |
ice porosity on the bio grid |
bphizn |
% |
f_iDin |
brine eddy diffusivity on the interface bio grid |
iDin |
m\(^{2}\) d\(^{-1}\) |
f_iki |
ice permeability on the interface bio grid |
ikin |
mm\(^{2}\) |
f_fbri |
ratio of brine tracer height to ice thickness |
fbrine |
1 |
f_hbri |
brine tracer height |
hbrine |
m |
f_zfswin |
internal ice PAR on the interface bio grid |
zfswin |
W m\(^{-2}\) |
f_bionet |
brine height integrated tracer concentration |
algalN_net, algalC_net, chl_net, pFe\(^c\)_net, dFe\(^c\)_net, Sil_net, Nit_net, Am_net, hum_net, PON_net, DMS_net, DMSPd_net, DMSPp_net, DOC_net, zaero_net, DON_net |
mmol m\(^{-2}\) |
f_biosnow |
snow integrated tracer concentration” |
algalN_snow, algalC_snow,chl_snow, pFe\(^c\)_snow, dFe\(^c\)_snow,Sil_snow, Nit_snow, Am_snow, hum_snow, PON_snow, DMS_snow, DMSPd_snow, DMSPp_snow, DOC_snow, zaero_snow, DON_snow |
mmol m\(^{-2}\) |
f_grownet |
Net specific algal growth rate |
grow_net |
m d\(^{-1}\) |
f_PPnet |
Net primary production |
PP_net |
mgC m\(^{-2}\) d\(^{-1}\) |
f_algalpeak |
interface bio grid level of peak chla |
peak_loc |
1 |
f_zbgc_frac |
mobile fraction of tracer |
algalN_frac, chl_frac, pFe_frac,dFe_frac, Sil_frac, Nit_frac,Am_frac, hum_frac, PON_frac,DMS_frac, DMSPd_frac, DMSPp_frac,DOC_frac, zaero_frac, DON_frac |
1 |
\(^a\) units are \(\mu\)mol m\(^{-2}\) s\(^{-1}\)
\(^b\) units are \(\mu\)mol m\(^{-3}\)
\(^c\) units are \(\mu\)mol m\(^{-2}\)