Atlantis model ecosystem restoration simulation results

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.