sitrack

A Lagrangian Sea-Ice Particule Tracker for SI3 (or any sea-ice GCM running on the Arakawa C-grid).

Dependencies

mojito

• clone mojito into the <somewhere> directory on your computer

cd <somewhere>/
git clone git@github.com:brodeau/mojito.git

• make python able to locate the mojito modules, so add the following line to your .bashrc, .profile, or equivalent:

export PYTHONPATH=<absolute_path_to_somewhere>/mojito:${PYTHONPATH}

python-basemap

Required if you want to use the plotting functionality (usually triggered with iplot=1 in the various scripts).

Getting started with sitrack

• download and extract the tarball sitrack_demo.tar of the directory containing the netCDF files for the demo test: sitrack_demo
• the absolute path to the content of this directory is hereafter referred to as <PATH_TO_DEMO_DIR>

Generation of the seeding file (netCDF)

This is done by means of script tools/generate_idealized_seeding.py of sitrack

• generate the seeding file that si3_part_tracker.py will use

generate_idealized_seeding.py -d '1996-12-15_00:00:00' \
                              -m <PATH_TO_DEMO_DIR>/NANUK4/mesh_mask_NANUK4_L31_4.2_1stLev.nc \
                              -i <PATH_TO_DEMO_DIR>/NANUK4/NANUK4-BBM23U06_1h_19961215_19970420_icemod.nc \
                              -k 0 -S 5 \
                              -f  <PATH_TO_DEMO_DIR>/NANUK4/mask_SeedInit_TrackIce_NANUK4.nc \
                              -N NANUK4

Basically, we are telling generate_idealized_seeding.py:

• that the seeding occurs at 1996-12-15_00:00:00
• to find SI3 coordinates, mask, metrics, etc, into mesh_mask_NANUK4_L31_4.2_1stLev.nc
• to use a sea-ice/open-ocean mask based on the sea-ice fraction read in file NANUK4-BBM23U06_1h_19961215_19970420_icemod.nc at record k=0
• to use a sub-sampling of 5 in terms of model grid points
• to restrict the seeding to the horizontal subdomain defined as a mask in file NANUK4/mask_SeedInit_TrackIce_NANUK4.nc
• that the NEMO config is NANUK4

If everything goes according to plan, you should have obtained:

• an image showing you the to-be-seeded virtual buoys on a map of the Arctic: ./figs/SEEDING/sitrack_seeding_nemoTsi3_19961215_00_HSS5.png
• the netCDF files do be used by sitrack that contains the location of virtual buoys to seed: nc/sitrack_seeding_nemoTsi3_19961215_00_HSS5.nc

Alternatively, you can create your own netCDF seeding file, provided you respect the following organization and naming convention:

dimensions:
        time = UNLIMITED ; // (1 currently)
        buoy = 986 ;
variables:
        int time(time) ;
                time:units = "seconds since 1970-01-01 00:00:00" ;
        int buoy(buoy) ;
        int id_buoy(buoy) ;
                id_buoy:units = "ID of buoy" ;
        float latitude(time, buoy) ;
                latitude:_FillValue = -9999.f ;
                latitude:units = "degrees north" ;
        float longitude(time, buoy) ;
                longitude:_FillValue = -9999.f ;
                longitude:units = "degrees south" ;
        float y_pos(time, buoy) ;
                y_pos:_FillValue = -9999.f ;
                y_pos:units = "km" ;
        float x_pos(time, buoy) ;
                x_pos:_FillValue = -9999.f ;
                x_pos:units = "km" ;

Tracking of the seeded virtual buoys

Now that the seeding file is generated you can fire si3_part_tracker.py to track the buoys. Example:

si3_part_tracker.py -i <PATH_TO_DEMO_DIR>/NANUK4/NANUK4-BBM23U06_1h_19961215_19970420_icemod.nc \
                    -m <PATH_TO_DEMO_DIR>/NANUK4/mesh_mask_NANUK4_L31_4.2_1stLev.nc \
                    -s ./nc/sitrack_seeding_nemoTsi3_19961215_00_HSS5.nc
                    -e 1997-04-20 -N NANUK4 -p 24

• -s: specifies the seeding file to use
• -e: specifies the end date
• -p 24: create an image of the positions of the buoys every 24 model records (i.e. daily in this case)

Trajectories of virtual buoys are saved into file:
nc/NEMO-SI3_NANUK4_BBM23U06_tracking_nemoTsi3_idlSeed_19961215h00_19970420h00.nc

Maps showing the positions of the buoys are generated into the figs/tracking/ directory.

Using non-SI3 input data: A-grid data

First, create the coordinates_mesh_mask.nc file based on the A-grid on which the data is provided:

./tools/xy_arctic_to_meshmask.py -i <path_data>/20240110_hr-nersc-MODEL-nextsimf-ARC-b20240111-fv00.0.nc -o <path_data>/coordinates_mesh_mask.nc

Keep this file.

Now, you should generate a seeding file, containing the initial position, in space (geographical aka GPS coordinates) and time, of the buoys you wish to track. Here, in the example we are just using the debug functionality that seeds buoys with their initial positions hard-coded into function debugSeeding() of sitrack/tracking.py:

./tools/generate_idealized_seeding.py -d 2024-01-10_00:00:00

The seeding file ./nc/sitrack_seeding_debug_20240110_00.nc has been generated and the image ./figs/SEEDING/sitrack_seeding_debug_20240110_00.png shows you the initial position of the buoys on the map...

Now you can run the tracking of these buoys:

./si3_part_tracker.py -i <path_data>/20240110_hr-nersc-MODEL-nextsimf-ARC-b20240111-fv00.0.nc \
                      -m <path_data>/coordinates_mesh_mask.nc \
                      -s ./nc/sitrack_seeding_debug_20240110_00.nc \
                      -g A -R 3 -u vxsi -v vysi -p 12

• -g A: input data is on the A-grid, not a C-grid as for SI3 data
• -R 3: nominal spatial resolution of the input data is 3 km
• -u vxsi -v vysi: name of u,v into into input netCDF file
• -p 12: create an image of the positions of the buoys every 12 model records (i.e. 12 hours in this case)