Numerical Modeling of the Flow Circulation and ...

Numerical Modeling of the Flow Circulation and Hydrological Cycle in Florida Bay

Candidate ABU BAKAR SIDDKE

Thesis proposal submitted in partial fulfillment of a Master degree in Ocean Engineering

Advisory Committee Laurent Chérubin, Ph.D Manhar R. Dhanak, Ph.D Pierre Philippe Beaujean, Ph.D Caiyun Zhang, Ph.D

August 3, 2017

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1. Introduction Florida Bay is located between the southern end of mainland Florida and enclaved by the Everglades National Park on-north, Florida Keys on east and south and Gulf of Mexico on west. Florida bay is a unique estuary with abundance of fish, wild life and different endangered species. The bay supports a $59-million-dollar shrimp industry and $22-million-dollar stone crab fishery. The key element of this unique bio-diversity is having the correct water properties. For a shallow tropical lagoon like Florida bay’s its salinity which matters. Salinity has been recognized as the key driving factor in this bay (Salinity and Hydrology of Florida Bay: Status and Trends 1990-2009, Technical Report) Florida bay has one of the most complex hydrological mechanism in this world. It shows the nature of both estuary and tropical lagoon at the same place. This complex place receives a huge freshwater input through Everglades National park via rivers, canals and channels. It also receives salt water from Gulf of Mexico at its west boundary and from Atlantic Ocean through the Florida Keys at its southern boundary. The bathymetry of this place is also complex. A shallow lagoon typically ranging from less than 1.5 meters to couple of feet at some places resulting in grassy mud banks and small basins. Florida bays bathymetry, hydrology and mixing of sea water with fresh water makes it a uniquely complex ecosystem. To understand the mechanism of salinity we need to understand the other relevant atmospheric forcing which contributes to salinity. Like rainfall, river discharge, tide, heat fluxes etc. A numerical model can be described as a computer model that is designed to simulate and reproduce the mechanism of a system. Numerical model of an earth-based system can be represented as a computer-based model that uses bathymetry and meteorological parameters to determine the dynamics of an ecosystem. Numerical modeling of shallow depth estuarine could 2

provide both quantitative and mechanistic understanding of critical hydrodynamics process and a powerful tool to predict the water movement and other key properties like temperature and salinity. Due to practical reason, it is not possible to measure the water properties of a vast region by field data collection method, here numerical modeling provides a great opportunity to access the dataset of a vast or relatively inaccessible region at a relatively reasonable cost. Developing a numerical model for a complex place like Florida bay is challenging. The numerical model must adapt to all atmospheric driving forces like solar radiation, evaporation, precipitation, wind stress, air temperature, humidity, etc. Adapting to the bottom friction at very shallow depth makes the modeling process more complex. Apart from the regular atmospheric forcing parameter like heat flux or hydrological parameter like evaporation or precipitation, Florida bay goes through wet and dry season every year when the small basins go through hyper saline activity and few basins on western portion of Florida Bay are protected by mud banks in such a way that it allows only limited exchange of water between Florida Bay and Gulf of Mexico (Smith 1994, Wang et al.1994). Also, these small basins are connected by natural and man-made water channels (Sogard et al.1987). The physical separation by the banks reduce the effects of tidal variance on water level and mixing within Florida Bay and creates a pathway of exchanging salinity and water flow with their nearby basins (Hudson et al.1970). All these parameters make the modeling of this place quite complex. 2. Research Objectives The objective will be to reproduce the salinity of Florida bay for past years (2004-2006). Since the model is relatively high resolution (500m) throughout the grid. So, we will get high resolution salinity data all over the grid and if not then we will identify model shortcomings

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towards improvement of the model physics to be able to resolve the hydrological cycle in Florida Bay. 3. Literature Review 3.a. Background

Numerous study has been done on salinity mapping on everglades and Florida bay portion. Most of them are focused on everglades and northern portion of Florida bay (Marshall and Nuttle,2008). Starting from boat based survey from United States Geological Survey ranging to statistical and mechanistic model (Marshall and Nuttle,2008) and most recent is Landsat TM mapping (Zhang et al. ,2006). Since we are doing a numerical model that consist on atmospheric and hydrological forcing parameter our focus will be on mechanistic model. Mechanistic model can be grouped in to two categories: a) Mass Balance model (Marshall and Nuttle,2008) and b) hydrological model (Hamrick and Moustafa, 2003). Both model relay on accurate accounting for physical process which drives the changes in salinity (Zhang et al., 2006). Accuracy of these model is limited by the data availability to describe pattern of salinity and their driving process (Marshall and Nuttle, 2008). Typically, a numerical model describes the physical relationship between driving process and salinity (Marshall et al., 2008). Mass balance models account for the inputs and outputs of water from basins delineated by geomorphologic features and accounts for minimum flows and levels modeling where Hydrodynamic models are based on the solution of simultaneous differential equations of continuity and hydrodynamics (momentum) in one, two, or three dimensions and can be used for both surface and groundwater applications. Currently Four-Box Florida Bay Mass Model and FATHOM ,41-basin dynamic model are mass balance models that are widely used due to their simplicity and less computational cost. But their configuration should change based on the circulation of the flow in that area. So recent development of hydrological model like environmental fluid dynamic code model(EFDC) and 4

Tides and inflow in the mangrove ecotone (TIME) model is in progress (Marshall et al.,2008). Considering the recent progression of hydrological model, we tried to develop a shallow water hydrological model that will include all the complexity of Florida Bay (wetting and drying, River Discharge, exchange through canal and wide-open boundary on the west Florida shelf) and try to reproduce the observed salinity regardless of the circulation of the flow of different locations on the Bay. 3.b. Flow pattern and Hydrology

Everglades National Park is part of a massive freshwater system called the KissimmeeLake Okeechobee-Everglades Watershed, which encompasses nearly 11,000 square miles in south-central Florida (NPS 1997,2013a). Historically, freshwater sheet flow moved south through the Everglades system and emptied into Florida Bay or the Ten Thousand Islands (SFWMD 2000).

Fig1: Historic and current flow pattern Currently, Taylor Slough provides the major freshwater flow in the eastern portion of Everglades National Park and empties into the northeastern portion of Florida Bay (NPS 2013b).

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Shark River Slough is the largest slough in Everglades National Park and flows in a southwestern direction through Everglades National Park toward Whitewater Bay and the Gulf coast of Florida (Livingston 1990). Shark River Slough drains into the small stream and mangrove estuaries that feed the northwestern portions of Florida Bay (NPS 2013b). The highly subdivided nature of Florida Bay and its shallow water depths reduce the effects of tidal flows and water mixing within the bay and leave the area highly subject to evaporation and freshwater influxes directly from Taylor Slough and indirectly from Shark River Slough via Whitewater Bay (Hall et al. 2007). Historically, Florida Bay was dominated by freshwater runoff during the wet season and became a hypersaline marine lagoon during the dry season (Draft Seagrass Habitat Restoration and Management Plan,2013). However, during the 20th century, two major anthropogenic changes altered the input and output flow patterns of Florida Bay (Swart et al. 1999, Rudnick et al. 2005). First, alteration of freshwater flow from the mainland began in the late 1800s and accelerated after 1920 with the construction of drainage canals, the Tamiami Trail, the Central and South Florida Flood Control Project, and the South Dade Conveyance System (Rudnick et al. 2005). Diversion of water from the Everglades via drainage canals, agricultural use, and other development has cut the freshwater influx to Florida Bay by as much as 60% over the past 100 years (Madden et al.2009). A second major anthropogenic alteration was the construction of the Flagler Railway through the Florida Keys, which filled in several passes connecting Florida Bay to the Atlantic Ocean (Swart et al.,1996). This resulted in an immediate change of salinity regimes within Florida Bay, likely due to increased water residence times (Swart et al. 1999, Rudnick et al. 2005). Salinity levels in Florida Bay can reach 60 parts per thousand (ppt) during the peak dry season in late spring, particularly in the central portion of the bay where water circulation is most limited. Salinities

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over 70 ppt are not uncommon in central Florida Bay during extended drought periods (Hall et al. 2007) since central zone contains the most isolated basins in the bay. Large freshwater discharges that have occurred are likely to be “pulsed” due to flood control measures, i.e. water releases, resulting in large, rapid variations in salinity that can potentially stress flora and fauna. (Draft Seagrass Habitat Restoration and Management Plan,2013). Based on the analysis shown above, to control the salinity of the Bay it is a crucial task to develop a freshwater budget that will prevent the hypersaline event and will not allow the salinity of the Bay to be reduced less than 30 PSU at any instance (salinity and Hydrology of Florida Bay: status and trends 1990-2009). From our study, we hope to see the impact of freshwater discharge through four major freshwater discharge point (see figure) and how they co-relate to the overall salinity of the Florida Bay which will hopefully led to a more effective water management of river and canals which discharge on Florida Bay.

Fig2: Location of major freshwater discharge points

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4. Study area Florida Bay is a shallow inner shelf lagoon located at the southern end of the south Florida watershed. It is an area where fresh water from the Everglades mixes with the salty water from Gulf of Mexico to form an estuary that is surrounded by mangroves forests and encompasses over 200 mangrove islands. Its nearly 1000 square mile of interconnected basins, grassy mud banks and mangrove island are nesting, nursing and feeding ground for a host of marine animals. (Christine Rapozo, 2001) Located at the southernmost tip of Florida peninsula, Florida bay lies between the mainland and the chain of islands known as Florida Keys. The Keys and Florida reef tract extend 220 miles south and west of Florida peninsula. The bay is characterized by many interconnected shallow basins (Madden et al.2009) with an average depth of less than 1.5 meter (Schomer and Drew,1982).

Fig3: Florida Bay

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5. Numerical modeling approach A hydrodynamic model has been developed for Florida Bay covering the southern portion of Florida mainland, Florida Keys, Gulf of Mexico and Atlantic Ocean. The model is based on an open source software called ROMS (Regional Ocean Modeling System). ROMS is a hydrostatic, primitive equation ocean model that solves the Reynolds averaged form of the Navier Stokes equations on a horizontal orthogonal curvilinear Arakawa ‘‘C’’ grid and uses stretched terrain following coordinates in the vertical. The model can be configured with choices from several advection schemes, pressure-gradient algorithms, turbulence closures, and types of boundary conditions (Warner et al., 2004). ROMS is an earth system modeling framework convenient for model coupling, initialization, run and finalization. Our model stretches from 84° 54' 0" East to 78° 30' 0" East and 22° North to 28° 24' 0" North and uses a terrain following curvilinear coordinate with 25 sigma layers. The model was designed to represent complex coastline and rapidly changing bathymetry in Florida bay and Everglades region. The model is driven by freshwater inputs (river discharge and precipitation), tides and metrological forcing. The river discharge were derived from data collected by USGS river gauge (https://sofia.usgs.gov/exchange/sfl_hydro_data/) . The metrological forcing was derived from 3hourly output of the NCEP North American Regional Reanalysis (NARR) website (https://rda.ucar.edu/NARR) which has a 32-Km spatial resolution. The NARR dataset is an extension of the NCEP Global Reanalysis which is run over the North American Region. The NARR model uses the very high resolution NCEP Eta Model (32km/45 layer) together with the Regional Data Assimilation System (RDAS) which, significantly, assimilates precipitation along with other variables. Two key parameters temperature and salinity was calculated from model

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using the other parameters like SST and air temp as input. Another key component tide was derived from Oregon State university’s global model of ocean tide TPX07.

Fig4: Bathymetry of our model

Fig5: Grid developed for our model

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6. Available data 6.a. Net Longwave radiation Net longwave radiation is a measure of the difference between outgoing longwave radiation from the earth surface and incident atmospheric longwave counter-radiation. Thus, net longwave radiation can be expressed by: net longwave radiation (W/m2) = incident longwave counter-radiation (W/m2) - outgoing longwave radiation (W/m2) Values of NLWR was obtained for entire North America region and then interpolated on our grid.

Fig6: Net Longwave radition (Hour 00 and 12 ,Day17,2003) 6.b. Net Shortwave radiation Net shortwave radiation is a measure of the difference between incoming solar shortwave radiation and outgoing shortwave radiation from the earth surface. Net shortwave radiation can be expressed by the amount of incident solar shortwave radiation absorbed on the earth surface per unit of area:

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net shortwave radiation (W/m^2) = {direct shortwave radiation (W/m^2) + diffused shortwave radiation (W/m^2)} (1 – surface albedo) Values of NSWR was obtained for entire North America region and then interpolated on our grid.

Fig7: Net Shortwave radiation (Hour 00 and 12 ,Day17,2003) 6.c. Sensible heat flux Sensible heat flux is the process where heat energy is transferred from the Earth’s surface to the atmosphere by conduction and convection. The heat energy then can move horizontally by atmospheric circulation. Sensible heat flux can be expressed by the amount of heat transmitted per unit of area per unit of time.

6.d. Latent heat flux latent heat flux is the flux of heat from the Earth's surface to the atmosphere that is associated with evaporation or transpiration of water at the surface and subsequent condensation of water vapor in the troposphere.

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6.e. Net heat flux Net heat flux is the summation of all the major heat component that goes inside the model and coming out of the model. e.g. solar shortwave radiation brings heat inside the model and solar longwave radiation brings heat outside of the model. Net heat flux sums up all those major heat component and gives the model the net heat to work with. Qnet= Net shortwave radiation +Net Longwave radiation +Latent heat +sensible heat Downward flux is positive: heating Upward flux is negative: cooling

Fig8: Net Heat (Hour 00 and 12 ,Day17,2003) 6.f. Sea surface temperature A Group for High Resolution Sea Surface Temperature (GHRSST) Level 4 sea surface temperature analysis produced as a retrospective dataset (four day latency) and near-real-time dataset (one day latency) at the JPL Physical Oceanography DAAC using wavelets as basis functions in an optimal interpolation approach on a global 0.01 degree grid. The version 4 Multiscale Ultrahigh Resolution (MUR) L4 analysis is based upon nighttime GHRSST L2P skin

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and sub skin SST observations from several instruments including the NASA Advanced Microwave Scanning Radiometer-EOS (AMSRE), the Moderate Resolution Imaging Spectro radiometer (MODIS) on the NASA Aqua and Terra platforms, the US Navy microwave WinSAT radiometer, Advanced Very High Resolution Radiometer (AVHRR) on several NOAA satellites, and in situ SST observations from the NOAA aqua project.

Fig9: SST (Day 17 and 18,2003)

6.g. Relative humidity and specific humidity Water vapor is a greenhouse gas, it plays an important role in radiative balance of atmosphere (Raval and Ramanathan,1989). The distribution of water vapor in the atmosphere affect climate change through radiative balance and surface evaporation (Liu et al.,1990). Specially the vertical distribution of water vapor in atmosphere it affects surface evaporation and latent heat flux (Liu,1998) and it is more important over the ocean since oceans are the largest reservoir of water on earth and considered to be the global heat engine (Liu et al.,1990). Both relative and specific humidity has a close tie to evaporation. Humidity content on air relates

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directly to evaporation and evaporation directly relates to heat balance. We obtained both relative and specific humidity from NARR and then interpolated it to our grid.

Fig10: Relative Humidity (Hour 00 and 12 ,Day17,2003) 6.h. Wind Wind plays a vital role on ocean model. Both Zonal and meridional wind stress in their respective direction which can cause the model to blowup. So only wind speed is included in the model and using bulk formulation wind stress is calculated internally from the model. Again, we used NARR data and interpolated in our grid.

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Fig11: Zonal wind (Hour 00 and 12 ,Day17,2003)

Fig12: Zonal wind (Hour 00 and 12 ,Day17,2003) 6.h. Evaporation, Precipitation and Fresh water flux Typically, fresh water flux is defined as FWflux= Evaporation – Precipitation Evaporation is the heat that is required for water to evaporated. Evaporation cools the ocean and has a huge impact on ocean model. On the other hand, precipitation adds water to the model. 16

Balance between these two are the net amount of fresh water that’s been added to the model. It is defined as fresh water flux. In our model since evaporation cools the model so it is taken as negative and precipitation is taken as positive so that it can be consistent with model’s other parameters direction.

Fig13: Precipitation Rate (Hour 00 and 12 ,Day17,2003)

Fig14: Freshwater flux (Hour 00 and 12 ,Day17,2003)

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7. ROMS model and methodology Like any other ocean model, the basic principle of ROMS is that if it knows the ocean state at a certain time and proper boundary conditions are given than it uses the primitive equations to compute the ocean states. It solves Naiver stokes equations but with approximations. The common hypothesis is: 1. Hydrostatic: a. H/L