FESOM

The Finite Element Sea-ice Ocean Model (FESOM) is an unstructured mesh global ocean model using finite element methods to solve the hydro-static primitive equations with the Boussinesq approximation (Danilov et al., 2004 [1]; Wang et al., 2008 [2]). FESOM v1.4 is interfaced with DART by Aydoğdu et al. (2018a) [3] using a regional implementation in Turkish Straits System (Gürses et al. 2016 [4], Aydoğdu et al. 2018b [5]).

There is a recent version of the model called the Finite-volumE Sea ice–Ocean Model (FESOM2, Danilov et al. 2017 [6]). A version for coastal applications FESOM-C v.2 (Androsov et al., 2019 [7]) has also been published.

The FESOM V1.4 source code can be downloaded from https://fesom.de/models/fesom14

The FESOM/DART interfaces, diagnostics and support scripting were contributed by Ali Aydoğdu. Thanks Ali!

Overview

model_mod.f90

A module called fesom_modules is provided to pass the information from FESOM to DART. fesom_modules.f90 includes fortran routines adopted from FESOM v1.4 to read the mesh, set the variables and dimensions of the arrays. fesom_modules should have access to nod2d.out, nod3d.out, elem2d.out, elem3d.out, aux3d.out, depth.out and m3d.ini mesh files.

Forward operators use an interpolation using the closest model node in the horizontal, given that the application in Aydoğdu et al. (2018a) uses a very high-resolution mesh. In the vertical, a linear interpolation is performed between two enclosing model layers. Interpolation in model_interpolate routine can be improved, if needed.

Note that because the FESOM-native code explicitly types reals, the DART mechanism of being able to run in reduced precision by defining real(r8) to be the same as real(r4) via ‘types_mod.f90’ is not supported.

Workflow

1. environment.load Must be modified to contain the specifics of an experiment. This file is sourced by every other script below.

2. experiment.launch Takes the information from environment.load and creates runnable scripts from the template script files. This also initiates the first cycle of the experiment.

   2.1. ensemble.sh

   2.1.1. initialize.template (first cycle only)

   2.1.2. advance_model.template (job array to advance the ensemble)

   2.1.3. check_ensemble.sh (if all goes well, assimilate)

   2.1.3.1. filter.template (assimilate)

   2.1.3.2. finalize.sh if all goes well and experiment is not finished …

   continue to 2.1

Shell Scripts

Shell scripts are written in bash for LSF queuing system. They should be modified to work with others such as SLURM. FESOM executables are called externally detached from DART therefore no need for an advance model.

Script	Queue	Definition
environment.load	serial	Includes environment variables, relevant directories, experiment specifications. This file is sourced by every other script below.
experiment.launch	serial	Main script which modifies ensemble.sh and calls ensemble.${EXPINFO}.sh. An experiment-specific summary which should be modified before launching the scripts.
ensemble.sh	serial	Calls and submits initialize.template, advance_model.template check_ensemble.sh one after the other.
initialize.template	serial	Called only once at the beginning of the experiment. Sets the experiment directory, copies initial ensemble, namelists.
advance_model.template	parallel	Submits a job array for all ensemble members.
check_ensemble.sh	serial	Checks if the forwarding for all members is finished. If so, first calls filter.template and then calls finalize.sh to conclude current assimilation cycle.
filter.template	parallel	Runs the filter to perform the assimilation.
finalize.sh	serial	Checks if the whole experiment is finished. If so, stops. Otherwise, resubmits ensemble.${EXPINFO}.sh for the next assimilation cycle.

Diagnostics

A toolbox for diagnostics is provided. Some are written for a specific regional application using Ferrybox observations of temperature and salinity. However, it shouldn’t be difficult to add new tools following the present ones. A fortran toolbox post-processes the FESOM outputs and visualization is done using Generic Mapping Tools (GMT). DART post-processed netCDF outputs are visualized using FERRET. Please see the expanded description inside each source file.

Directory	code file	description
src/
	fesom_post_main.F90	main fortran routine calling each tool selected in the namelist
	fesom_ocean_mod.F90	ocean diagnostic routines
	fesom_dart_mod.F90	DART diagnostic output routines
	fesom_forcing_mod.F90	forcing diagnostic routines
	fesom_observation_mod.F90	observation diagnostic routines
	gen_input.F90	routines for I/O (adapted from FESOM)
	gen_modules_clock.F90	routines for timing (adapted from FESOM)
	gen_modules_config.F90	routines for configuration (adapted from FESOM)
	mesh_read.F90	routines for reading the mesh (adapted from FESOM)
	Makefile	Makefile (adapted from FESOM) but reads DART environment
	oce_dens_press.F90	routines to compute density and pressure (adapted from FESOM)
	oce_mesh_setup.F90	routines for mesh setup (adapted from FESOM)
	oce_modules.F90	routines for ocean modules (adapted from FESOM)
	random_perturbation.F90	random perturbation to observation sampling
	utilities.F90	various utilities
script/
	compute_ensemble_mean	computes ensemble mean and extracts a transect or level
	compute_increment	computes increment using DART diagnostic output
	compute_NR_diff	computes the difference between a nature run and the ensemble prior mean
	dart_obs_seq_diag	DART observation-space statistics from obs_epoch.nc and obs_diag.nc
	dart.postproc.env	DART environment variables
	fesom.postproc.env	FESOM environment variables
	observe_nature_run	creates synthetic observations from a nature run
	transect_daily_mean	extracts and plots a transect of an individual ensemble member
	zlevel_daily_mean	extracts and plots a level of an individual ensemble member
gmt/
	plot_ensemble_mean.gmt	plots ensemble mean created by compute_ensemble_mean
	plot_increment.gmt	plots increment created by compute_increment
	plot_NR_diff.gmt	plots difference created by compute_NR_diff
	transect_daily_mean.gmt	plots transects created by transect_daily_mean
	zlevel_yearly_mean.gmt	plots levels created by zlevel_daily_mean
ferret/
	frt.obs_diag_TeMPLaTe.jnl	plot DART diags created by dart_obs_seq_diag
	frt.obs_epoch_TeMPLaTe.jnl	plot DART diags created by dart_obs_seq_diag

References

[1]

Danilov, S., Kivman, G., and Schröter, J.: A finite-element ocean model: principles and evaluation, Ocean Modell., 6, 125–150, 2004.

[2]

Wang, Q., Danilov, S., and Schröter, J.: Finite element ocean circulation model based on triangular prismatic elements, with application in studying the effect of topography representation, J. Geophys. Res.-Oceans (1978–2012), 113, C05015, doi:10.1029/2007JC004482, 2008.

[3]

Aydoğdu, A., Hoar, T. J., Vukicevic, T., Anderson, J. L., Pinardi, N., Karspeck, A., Hendricks, J., Collins, N., Macchia, F., and Özsoy, E.: OSSE for a sustainable marine observing network in the Sea of Marmara, Nonlin. Processes Geophys., 25, 537-551, doi:10.5194/npg-25-537-2018, 2018a.

[4]

Gürses, Ö., Aydoğdu, A., Pinardi, N., and Özsoy, E.: A finite element modeling study of the Turkish Straits System, in: The Sea of Marmara – Marine Biodiversity, Fisheries, Conservations and Governance, edited by: Özsoy E., Çaǧatay, M. N., Balkis, N., and Öztürk, B., TUDAV Publication, 169–184, 2016.

[5]

Aydoğdu, A., Pinardi, N., Özsoy, E., Danabasoglu, G., Gürses, Ö., and Karspeck, A.: Circulation of the Turkish Straits System under interannual atmospheric forcing, Ocean Sci., 14, 999-1019, doi:10.5194/os-14-999-2018, 2018b.

[6]

Danilov, S., Sidorenko, D., Wang, Q., and Jung, T.: The Finite-volumE Sea ice–Ocean Model (FESOM2), Geosci. Model Dev., 10, 765-789, doi:10.5194/gmd-10-765-2017, 2017.

[7]

Androsov, A., Fofonova, V., Kuznetsov, I., Danilov, S., Rakowsky, N., Harig, S., Brix, H., and Wiltshire, K. H.: FESOM-C v.2: coastal dynamics on hybrid unstructured meshes, Geosci. Model Dev., 12, 1009-1028, doi:10.5194/gmd-12-1009-2019, 2019.