Abstract:
These data include input and output files from the Gulf of Mexico Atlantis model. The simulations are published in Dornberger et al., 2019. The dataset includes every file needed to recreate the simulations: 1) the 18 spatial forcing files needed to recreate the sensitivity analysis; these vary the oil sensitivity threshold K, the fish oil threshold and the invertebrate oil threshold. The file naming scheme indicates parameter values used. 2) the three .prm files needed to recreate the different levels of fishing mortality (F=0.5, 1, 2.0, 10), The F rate indicates an increase in fishing mortality across all fishing sectors relative to baseline F=1 conditions, 3) seven detritus point-source input forcing .ts files corresponding to the Mississippi River input polygons discussed in the paper, 4) a complete Atlantis run folder set up to run the F=1 baseline scenario (1X base fishing mortality for all fleets) used in the paper (K1000, fish threshold 362, invert threshold 1000). Note, this folder contains a complete set of outputs files for the base case. The other runs (varying oil and fishing and detritus inputs) can be recreated by substituting the appropriate spatial forcing .nc, .prm and .ts files into this base case and re-running the simulation. This dataset supports the publication: Dornberger, L. N., Ainsworth, C. H., Coleman, F., & Wetzel, D. L. (2019). A Synthesis of Top-Down and Bottom-Up Impacts of the Deepwater Horizon Oil Spill Using Ecosystem Modeling. In S. A. Murawski, C. H. Ainsworth, S. A. Gilbert, D. J. Hollander, C. B. Paris, M. Schlüter., Wetzel D. (Eds.), Deep Oil Spills - Facts, Fate and Effects (pp. 536-550). Springer International. doi:10.1007/978-3-030-11605-7_31
Suggested Citation:
Ainsworth, Cameron and Lindsey Dornberger. 2020. Input, output and complete run files for the Atlantis ecosystem model Deepwater Horizon oil spill simulations including fish and invertebrate effects. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-dx3q-4y78
Purpose:
This dataset shows the ecological impacts of the Deepwater Horizon oil spill on living functional groups described by Atlantis under various fishing levels. The innovation of this data set over previous simulation results is that this includes effects on invertebrates as well as vertebrates and variations in fishing intensity.
Data Parameters and Units:
The primary output files of interest will be the GOM_OUT.NC files, which can be read with a standard NC reader such as OLIVE. For vertebrate groups (fish and some heavily exploited invertebrates) the data include numbers at age (numbers), reserve Nitrogen per individual at age (mgN) and structural Nitrogen per individual at age (mgN). These data are provided per Atlantis polygon and Depth layer. Data are provided in the following format: LRF10_ResN represents the reserve Nitrogen for group LRF (large reef fish) age class 10 of 10; the corresponding matrix is 66 by 7 elements large (for 66 horizontal polygons and 7 depth layers). See the documentation on the model for the definition and codes for all functional groups. Other variables are described by the: long_name attribute. Units for other data found in the NC file are provided in the header section of the NC file itself. Other non-exploited invertebrates are described as epibenthic, meaning that they are 2 dimensional, and biomass density (grams wet weight per square meter) is expressed.
Description of Atlantis file types:
Ts – time-series input files for Atlantis containing forcing functions for state variables
txt – contains simplified output from Atlantis
nc – NetCDF files includes both input and output data
prm – contains input data matrices for Atlantis
xml – these files are generated internally by Atlantis and are not to be accessed by users
cdf – NetCDF files for user reference
bat – batch file to run Atlantis executable with proper command-line arguments
dll – dynamic link library file required by Atlantis
csv – comma-separated values files containing input data required by Atlantis
exe – Atlantis executable files
bgm – box geometry file containing polygon data
Note: empty files are outputted by Atlantis to indicate task completion during run time and are not to be accessed by users.
Error Analysis:
Atlantis is a deterministic model, however, the sensitivity runs which vary K, invertebrate threshold and vertebrate threshold are designed to explore the potential output parameter space.
Provenance and Historical References:
Output products from Atlantis include biological, nutrient, and fishery data by polygon, depth layer, and time step. These are contained in out.nc and fisheries_out.nc. These NC files may be viewed by NC viewers such as OLIVE. Additional output files in text format (e.g., log.txt, biom_out.txt) summarize smaller subsets of the output data and are viewable in a text editor (Examples could include wind speeds, salinity, temperature, etc.).