# Numerical experiments examining water quality impacts during Hurricane Irene (2011) in a large coastal-plain estuary (Chesapeake Bay)

## Introduction

  The archive features 3-D numerical experiments examining water quality impacts during Hurricane Irene (2011) in a large coastal-plain estuary (Chesapeake Bay). The 3-D results cover the period shortly before/during/after the hurricane (25 August 2011 to 2 September 2011) and originate from an implementation of the Regional Ocean Modeling System (ROMS, Shchepetkin & McWilliams 2005) for the Chesapeake Bay (St-Laurent & Friedrichs 2024) including the Estuarine-Carbon-Biogeochemistry module (ECB, Feng et al. 2015). This ROMS-ECB configuration is forced by an ensemble of 50 atmospheric simulations conducted with E3SM (version 2, Golaz et al. 2022) initialized from a reanalysis on 26 August 00:00 (ERA5, Hersbach et al. 2020) and evolving freely afterward (Ensemble 1 in Deb et al. 2024). The ensemble is leveraged to assess the sensitivity of the hurricane's water quality impacts in the Chesapeake Bay as a function of the hurricane's characteristics (maximum sustained winds, minimum sea level pressure, distance to the Bay, etc). The 3-D outputs of ROMS-ECB are provided in the NetCDF format, which is an open file format that can be exploited from a vast suite of programs and languages (Python, R, Matlab, Julia, GNU Octave...) with metadata (information about field dimensions, units...) directly embedded inside the NetCDF files.

## tracks50e3sm_atcf.tempestextremes.2011082600 (331 KiB)

  The file tracks50e3sm_atcf.tempestextremes.2011082600 contains statistics on the 50 atmospheric simulations of Irene. The statistics are generated by the software TempestExtremes (Ullrich et al. 2021) based on the original E3SM outputs and include information over time about the track of the hurricane, its maximum sustained wind speed, etc. See the documentation of TempestExtremes for additional information.

## code_ecb_roms.zip (7.2 MiB)

  The computer code used for the 3-D simulations of water quality in Chesapeake Bay is included in this file. The first subdirectory (ecb_chesapeake) contains the Chesapeake implementation and the ECB code. The second subdirectory (rutgers_roms20220512rev1125) contains the ROMS code from myroms.org that was used to generate the 3-D simulations of water quality. The code can be combined with the files from "inputs_roms.zip" in order to re-create the simulations of the Chesapeake Bay and their outputs.

## inputs_roms.zip (11 GiB)

The file contains the input information (also known as "forcings") required by the ROMS-ECB code in order to re-create the experiments and the outputs:

1. atm_n_depos_chesbay_2011_v20231010.nc

  Information about atmospheric nitrogen deposition over the Chesapeake Bay region (see Da et al. 2018). See the metadata information embedded inside the NetCDF file for further information.

2. bry_chesbay336x564x20_2011_v20210413.nc

  Information about water levels and oceanic conditions on the continental shelf of the Mid-Atlantic Bight (also known as lateral boundary conditions). See the metadata information embedded inside the NetCDF file for further information.

3. roms_ini.nc

  Initial condition for ROMS-ECB valid on 16 August 2011 00:00. This is the starting point of the 50 ROMS-ECB simulations. See the metadata information embedded inside the NetCDF file for further information.

4. tides_chesbay336x564_v20210914.nc

  Tidal harmonics prescribed at the open boundary of the ROMS-ECB domain (continental shelf). See the metadata information embedded inside the NetCDF file for further information.

5. waves_ches_swan_era5_2011_v20231101.nc

  Wind waves conditions over the Chesapeake Bay. See the metadata information embedded inside the NetCDF file for further information.

6. grd_chesbay336x564_v20230418.nc

  Information about the grid of the ROMS-ECB implementation (topography, longitude/latitude of the grid cells, etc). See the metadata information embedded inside the NetCDF file for further information.

7. frc_ches_era5_2011_v20231010.nc **or** frc_ches_era5_2011_benedict_present_day_t44_ensXXX_v20231212.nc

  The first file contains atmospheric forcings from ERA5, while the second set of files (001 <= XXX <= 050) holds the E3SM atmospheric fields for ensemble member XXX over the period 26 August to 4 September (and ERA5 the rest of the year). The ensemble of E3SM atmospheric outputs is thus available inside these ROMS atmospheric forcing files. See the metadata information embedded inside the NetCDF file for further information.

8. riv_chesbay336x564x20_v20231215.nc **or** riv_chesbay336x564x20_present_day_t44_membXX_v20240109.nc

  The first file contains terrestrial inputs from Phase6 (Bhatt et al. 2023), while the second set of files (01 <= XX <= 50) has been modified to reflect the amount of precipitation simulated by each of the 50 E3SM ensemble member in the different hydrological sub-regions of the Chesapeake Bay Watershed. See the metadata information embedded inside the NetCDF file for further information.

## outputs_roms.zip (63 GiB)

  The file contains a set of 50 subdirectories (roms_runXX, with 01 <= XX <= 50), each containing the ROMS-ECB results corresponding to ensemble member XX over the period 25 August to 2 September 2011. The results are saved in 3 types of files:

1. roms_avg_yyyy.nc (with 0010 <= yyyy <= 0018)

  Daily-averaged estuarine fields computed by ROMS-ECB in day `yyyy' of the simulation. See the metadata information embedded inside the NetCDF file for further information.

2. roms_dia_yyyy.nc (with 0010 <= yyyy <= 0018)

  Daily-averaged diagnostics computed by ROMS-ECB in day `yyyy' of the simulation. The diagnostics notably include the air/sea flux for CO2 and O2. See the metadata information embedded inside the NetCDF file for further information.

3. roms_sta.nc

  3-hourly instantaneous estuarine fields at specific longitudes/latitudes ("stations") of the Chesapeake Bay region. The file notably includes the water levels, water temperature, salinity... at the location of coastal tidal gauges and moored buoys. The list of "stations" is available inside inputs_roms.zip (file code_ecb_roms/ecb_chesapeake/stations600m_v20230927.in). Only one file of this type is included and it originates from a ROMS-ECB hindast simulation forced by the atmospheric reanalysis ERA5. See the metadata information embedded inside the NetCDF file for further information.

## airseafluxes1985_2023hindcast_era5.nc (431 KiB)

  The file contains daily air/sea fluxes of CO2 and O2 horizontally-integrated over the Chesapeake Bay region. The fluxes are derived from a 1985-2023 hindcast simulation with ROMS-ECB forced by ERA5. The air/sea flux timeseries distinguish between ingassing and outgassing. See the metadata information embedded inside the NetCDF file for further information.

## References

Bhatt, G., L. Linker, G. Shenk, I. Bertani, R. Tian, J. Rigelman, K. Hinson, P. Claggett (2023) Water quality impacts of climate change, land use, and population growth in the Chesapeake Bay watershed, J. Am. Water. Resour. Assoc., 00:1-29, doi:10.1111/1752-1688.13144

Da, F., Friedrichs, M. A. M., St-Laurent, P. (2018). Impacts of atmospheric nitrogen deposition and coastal nitrogen fluxes on oxygen concentrations in Chesapeake Bay. Journal of Geophysical Research: Oceans, 123, 5004–5025. https://doi.org/ 10.1029/2018JC014009

Deb, M., J. J. Benedict, N. Sun, Z. Yang, R. D. Hetland, D. Judi, and T. Wang (2024), Estuarine hurricane wind can intensify surge-dominated extreme water level in shallow and converging coastal systems, Nat. Hazards Earth Syst. Sci., 24, 2461–2479, doi:10.5194/nhess-24-2461-2024

Feng, Y., M. A. M. Friedrichs, J. Wilkin, H. Tian, Q. Yang, E. E. Hofmann, J. D. Wiggert, and R. R. Hood (2015) Chesapeake Bay nitrogen fluxes derived from a land-estuarine ocean biogeochemical modeling system: Model description, evaluation, and nitrogen budgets, J. Geophys. Res. Biogeosci., 120, doi:10.1002/2015JG002931

Golaz, J.-C., L. P. Van Roeke, X. Zheng, A. F. Roberts, J. D. Wolfe, W. Lin, A. M. Bradley, Q. Tang, M. E. Maltrud, R. M. Forsyth, C. Zhang, T. Zhou, K. Zhang, C. S. Zender, M. Wu, H. Wang, A. K. Turner, B. Singh, J. H. Richter, Y. Qin, M. R. Petersen, A. Mametjanov, P.-L. Ma, V. E. Larson, J. Krishna, N. D. Keen, N. Jeffery, E. C. Hunke, W. M. Hannah, O. Guba, B. M. Griffin, Y. Feng, D. Engwirda, A. V. Di Vittorio, C. Dang, L. M. Conlon, C. Chen, M. A. Brunke, G. Bisht, J. J. Benedict, X. S. Asay-Davis, Y. Zhang, M. Zhang, X. Zeng, S. Xie1, P. J. Wolfram, T. Vo, M. Veneziani, T. K. Tesfa, S. Sreepathi, A. G. Salinger, J. Eyre, M. J. Prather, S. Mahajan, Q. Li, P. W. Jones, R. L. Jacob, G. W. Huebler, X. Huang, B. R. Hillman, B. E. Harrop, J. G. Foucar, Y. Fang, D. S. Comeau, P. M. Caldwell, T. Bartoletti, K. Balaguru, M. A. Taylor, R. B. McCoy, L. R. Leung, and D. C. Bader (2022), The DOE E3SM model version 2: Overview of the physical model and initial model evaluation, Journal of Advances in Modeling Earth Systems, 14 (e2022MS003156), doi:10.1029/2022MS003156

Hersbach, H., B. Bell, P. Berrisford, S. Hirahara, A. Horńyi, J. Munoz-Sabater, J. Nicolas, C. Peubey, R. Radu, D. Schepers, A. Simmons, C. Soci, S. Abdalla, X. Abellan, G. Balsamo, P. Bechtold, G. Biavati, J. Bidlot, M. Bonavita, C. G. De P. Dahlgren, D. Dee, M. Diamantakis, R. Dragani, J. Flemming, R. Forbes, M. Fuentes, A. Geer, L. Haimberger, S. Healy, R. J. Hogan, E. Hólm, M. Janisková, S. Keeley, P. Laloyaux, P. Lopez, C. Lupu, G. Radnoti, R. P. de I. Rozum, F. Vamborg, S. Villaume, and J.-N. Thépaut (2020), The ERA5 global reanalysis, Q J R Meteorol Soc., 146, 1999-2049, doi:10.1002/qj.3803

Shchepetkin, A.F., J.C. McWilliams (2005) The regional oceanic modeling system (ROMS): a split-explicit, free-surface, topography-following-coordinate oceanic model, Ocean Modelling, 9, 347-404, doi:10.1016/j.ocemod.2004.08.002

St-Laurent, P., and Friedrichs, M.A.M. (2024). On the sensitivity of coastal hypoxia to its external physical forcings. J. Adv. Model. Earth Syst. 16(1). doi:10.1029/2023ms003845

Ullrich, P. A., C. M. Zarzycki, E. E. McClenny, M. C. Pinheiro, A. M. Stansfield, and K. A. Reed (2021), TempestExtremes v2.1: A community framework for feature detection, tracking, and analysis in large datasets, Geosci. Model Dev., 14, 5023–5048, doi:10.5194/gmd-14-5023-2021