Adding Passive Tracers to SalishSea

This page provides instructions on how a configuration including tracers was built for the Salish Sea model and how to use it and modify it. More information on adding passive tracers can also be found here.

Compile SalishSea_TRC

The configuration including the tracers is SalishSea_TRC. The NEMO ARCH files use the XIOS_HOME environment variable to find the XIOS-2 library you built above. XIOS_HOME must be an absolute path to your XIOS-2 clone directory. You can set XIOS_HOME on the command-line before the makenemo and maketools commands as shown below, or you can set and export the value of XIOS_HOME in your $HOME/.bashrc file.

XIOS_HOME=/data/$USER/MEOPAR/XIOS-2/ ./makenemo -n SalishSea_TRC -m GCC_SALISH -j8

New MY_SRC Files

There are three extra modified fortran files to be found in MY_SRC (most of the other files are symlinked to the SalishSea and SMELT configuration).

The file par_my_trc.F90 specifies that six passive tracers are to be used and will have the last index of jpmyt1, jpmyt2, jpmty3, jpmty4, jpmty5, jpmty6 respectively.

The file trcini_my_trc.F90 has been barely changed from the original (in NEMO-3.6-code/NEMOGCM/NEMO/TOP_SRC/MY_TRC). It now writes out the number of tracers and sets the tracer concentration to 1 below depth level 10, 15, 19, 22, 24, and 25 corresponding to depths 10, 15, 20, 30, 45, and 60 m respectively. If you wished to initialize the tracers differently, that would go here.

The file trcsms_my_trc.F90 defines the chemistry/biology to be done to the tracers. It now dictates that the tracers decay when they are above depths 10, 15, 20, 30, 45, and 60 m respectively. For example, if a tracer was at concentration 1 in the ‘decay’ zone, after one model day, their concentration would be ~0.3679 (1/e). The decay time for each tracer could be modified by changing the factor used to multiply the trb array on lines 73, 78, 83, 88, 93, and 98 in the file.

An old version of this file is available at nemo-code in NEMOGCM/CONFIG/SalishSea_TRC/MY_SRC. Here we just specify the value of each tracer to be 1 in the grid cell we think contains the sewage outfall for each of Clover, Macaulay, Iona, Nanaimo and Campbell River outfalls. Note that cells are defined by lats and lons. Specifying grid locations plays havoc when running mpi.

New Namelist Files

Two new namelist files are included: namlist_top_ref and namelist_top_cfg. The main namelist_ref and namelist_cfg should be copied or symlinked from an appropriate SalishSea namelist.

namelist_top_ref defines the output names of the tracer. You could also add tracer damping using this namelist. Also change this file to use a restart file for the tracers.

New IODEF.xml

Writing out of the tracers goes into its own netcdf4 file with key prtc. The example given writes out 1h data.

Grid/Input Files

Use appropriate files from the SalishSea configuration.