Ocean Modelling

The patch for implementing iceshelf cavities into FVCOM4.0 consits of 1. A text file, git_diff_FVCOM4.0_iceshelf.txt, containing all the code modifications related to the inclusion of ice shelf cavities into FVCOM4.0 source code, generated by git diff. The FVCOM4.0 source code that has been used for this implementataion is published on https://gitlab.ecosystem-modelling.pml.ac.uk/fvcom/uk-fvcom/tags/FVCOM-v4.0. Alternatively, the source can also be obatined from the official FVCOM website http://fvcom.smast.umassd.edu/ and is available to all members of the FVCOM community. 2. A folder, R1CON, contains the input files, namelists and apps options to run the testcase R1CON. Do not hesitate to contact the authors for further instructions / help for applying FVCOM-ice-shelf applications!

Data used in manuscript "Relevance of wind stress and wave-dependent ocean surface roughness on the generation of winter meteotsunamis in the Northern Gulf of Mexico" by Luming Shi, Maitane Olabarrieta, Arnoldo Valle-Levinson and John.C Warner.

The netcfd files in this repository are the result of the correction procedure described in the article. The wave height related variables present both the original and the corrected values. The text files have the calculated directional coefficients for sea and swell. Fake sea and fake swell corrections are the values obtained by the linear regression model despite the statistical significance analysis.

Details of the UH8to2 model set up may be found in the associated manuscript. Fields were averaged using NCO and MATLAB.

The Matlab code included in this repository is used to perform the deterministic formulation of the Ensemble Kalman Filter (DEnKF) in the Regional Ocean Modelling System (ROMS). This code was developed by the MEMG group at Dalhousie University, Canada. It is a supplement to the paper "Ocean biogeochemical modelling" by K. Fennel, J.P. Mattern, S.C. Doney, L. Bopp, A.M. Moore, B. Wang, and L. Yu. in Nature Reviews Methods Primers (Sept 2022). The code in this repository is configured for a 3-dimensional ocean biogeochemical model (using ROMS) in an idealized channel that experiences wind-driven upwelling as in Yu et al. (2018, doi.org/10.1016/j.ocemod.2018.04.005). This code will initiate the ensemble runs with perturbed wind forcing and biological parameters, then assimilate observations to update the model state variables, and restart the ensemble runs from the updated initial state. In this application, we have two assimilation steps. In the first step, we assimilate the physical observations (i.e., sea surface height, sea surface temperature, and in-situ profiles of temperature) to update both physical and biological model state variables (i.e., temperature and NO₃). In the second step, we assimilate the biological observations (i.e., surface chlorophyll and in-situ profiles of NO₃) to update only biological model state variables (i.e., chlorophyll, phytoplankton, zooplankton, and NO₃).

Here we provide two ArcGIS map packages with georeferenced files on the spatial distribution of sponges and echinoderms in the wider Weddell Sea (Antarctica), which were created in the context of the development of a marine protected area (MPA) in the Weddell Sea. Sponges: The map of interpolated occurrence of sponges is based on quantitative abundance data (Gerdes 2014 a - o) and on semi-quantitative data obtained by W. Arntz (retired; formerly AWI) (see Teschke & Brey 2019a for presence / absence records of the latter dataset). The abundance data were classified to be merged with the semi-quantitative data and an inverse distance weighted method was performed on the united dataset. Areas with very common occurrence of sponges occurred on the shelf near Brunt Ice Shelf along Riiser - Larsen Ice Shelf to Ekstrøm Ice Shelf. Echinoderms: A cluster analysis with species x station datasets of asteroids (Teschke & Brey 2019b), ophiuroids (Teschke & Brey 2019c) and holothurians (Gutt et al. 2014) from the Antarctic Weddell Sea indicated a particular cold-water echinoderm fauna on the Filchner shelf. We approximated this potential habitat by bottom temperature ≤ -1°, based on seawater temperature data from the Finite Element Sea Ice - Ocean Model provided by R. Timmermann (AWI). More information on the spatial analysis is given in working paper WG-EMM-16/03 submitted to the CCAMLR Working Group on Ecosystem Monitoring and Management (available at https://www.ccamlr.org/en/wg-emm-16).

Here we provide an ArcGIS map package on the pelagic regionalisation in the wider Weddell Sea (Antarctica), which were created in the context of the development of a marine protected area (MPA) in the Weddell Sea. For the pelagic regionalisation following parameters were incorporated: (i) ice coverage from AMSR-E sea ice maps, (ii) bathymetric data from the International Bathymetric Chart of the Southern Ocean (IBCSO), and (iii) seawater temperature and salinity data from the Finite Element Sea Ice - Ocean Model (FESOM) provided by R. Timmermann (AWI). To classify different pelagic areas we have applied K-means clustering algorithm and 'clusGap' function from R package 'cluster'. Coastal polynyas mainly occurred east and west of the Prime Meridian (between 20°W to 30°E) as well as around the tip of Antarctic Peninsula, whereas the inner Weddell Sea was characterised by perennial ice-coverage. The largest area proportion of the wider Weddell Sea were classified by above average large water depths and relative high probabilities of ice-free days. More information on the spatial analysis is given in working paper WG-EMM-16/03 submitted to the CCAMLR Working Group on Ecosystem Monitoring and Management (available at https://www.ccamlr.org/en/wg-emm-16).

Observational data set from the Columbia River estuary North Channel. The data were collected during two campaigns during May and October-November 2012. Included are Automated Underwater (AUV) mission, and ship-mounted whiched profiler (WP) data sets. Outputs from numerical circulation model are also included. See the README.txt in each zip file for further information.