Dataset Submitted

Atlantis model ecosystem restoration simulation results

Authors: Ainsworth, C.
Identified On: Jun 12 2025 19:57 UTC
DOI: https://doi.org/10.7266/20px9qk8
UDI: F4.x180.000:0002
Project Information

Funded By:
Florida RESTORE Act Centers of Excellence Program

Funding Cycle:
FLRACEP 4

Research Group:
Estimating combined effects of FL TIG restoration projects in Florida using an end-to-end ecosystem model

Point of Contact

Cameron Ainsworth
University of South Florida / College of Marine Science
ainsworth@usf.edu

Data Collection Period
2024-01-01
to
2025-06-02
Theme keywords

Ecosystem model, Ecosystem resstoration, Seagrass, Mangrove, Fisheries, Juvenile fish

Abstract:

These Atlantis ecosystem model input and output files accompany the article, “You can’t reach the Lost Valley by boat: navigating bottom-up restoration pathways” accepted for publication in Fish and Fisheries in April 2025 by Ainsworth, C.H., Repeta, H.C. and Scott, R.L. 2025. Fish and Fisheries, 26(4): 546-560. The directory contains all the files necessary to run the historical, present day and restored future scenarios. The model is presently configured to run the present day scenario but changes can be made in the forcing file (at_force_SG_Dynamic_nuts.prm) under variables use_external_scaling and externalBiologyForcingFile to point to historical or restored future versions of files. Contents include both input and output files for Atlantis. Other baseline conditions are described in Ainsworth et al. (2015) (e.g., realistic spatial fishing is turned on, e.g., box1MPA.ts). A complete description of Atlantis and input file syntax is available in Audzijonyte et al. 2017. Input files • Run file: at_run.prm • Initial conditions file: GOM_CDF_sg_historical.nc; GOM_CDF_sg_present.nc; GOM_CDF_sg_restored.nc • Biology parameter file: gom_prm_2021_sg.prm • Nitrogen forcing files: Present day and restored scenarios use n_p5_p.ts, n_p33_p.ts, n_p34_p.ts, n_p55_p.ts. Historical scenario uses n_p5_h.ts, n_p33_h.ts, n_p34_h.ts, n_p55_h.ts. • harvest file: at_harvest_Dec2021.prm • physics file: at_physics.nutsB.prm • box geometry file: GOM_BGM.bgm Output files • Biological, chemical, and physical outputs: GOM_OUT.nc. This file contains age-structure species data by polygon and depth layers for volumetric functional groups (numbers, reserve Nitrogen and structural Nitrogen (mgN/m^3)) and epibenthic functional groups (mgN/m^2). • Fishery outputs: GOM_OUTCATCH.nc. This file contains age-structured fishery catch data by functional group, polygon and depth layer in either (mgN/m^3) or (mgN/m^2). • Simplified biological outputs (GOM_OUT_BiomIndx.txt) and catch outputs (GOM_OUTCatch.txt) are available.

Suggested Citation:

Ainsworth, C.. Atlantis model ecosystem restoration simulation results. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/20px9qk8

Purpose:

The Atlantis simulations were conducted as part of a project funded by the Florida RESTORE Act Centers of Excellence Program Project entitled, "Estimating combined effects of FL TIG restoration projects in Florida using an end-to-end ecosystem model." These simulations represent the ecosystem in the 1990s, pre-restoration, the present, and a restored future.

Data Parameters and Units:

Data structure for vertebrates: Structural nitrogen: (mg N * m^-3) Reserve nitrogen: (mg N * m^-3) Numbers Data structure for invertebrates: Epibenthic: Biomass (mg N * m^-2) Volumetric: Biomass (mg N * m^-3) Other variables are in meters (e.g., Depth of oxygen horizon, max depth of detritus) Unitless (e.g., percent reef cover) Salinity (Practical Salinity Unity, PSU) Temperature (degrees celsius) Dissolved Oxygen (mg O2 * m^-3) Dissolved Silica (mg Si * m^-3)

Methods:

NetCDF files (Network Common Data Form) are self-describing binary format files used to encode multidimensional data. NetCDF files can be viewed in NC viewers such as OLIVE. Units are found in the NC file header section. The Atlantis model is described in NOAA technical memoranda by Ainsworth et al. (2015) and Perryman et al. (2023).