Three-dimensional hydrodynamic modeling of San Pablo Bay on an unstructured grid

Proceedings of the Seventh International Conference on Hydroscience and Engineering, Philadelphia, PA, September 2006. http://hdl.handle.net/1860/732A three-dimensional hydrodynamic model of San Francisco Bay was developed using the three-dimensional hydrodynamic model UnTRIM. The model was calibrated using continuous water level measurements and ADCP data in San Francisco Bay, and validated during an additional simulation period using current velocity measurements. The model was developed to support the Hamilton Wetlands Restoration Project, a joint undertaking by the U.S. Army Corps of Engineers and the California Coastal Conservancy to restore 2.6 km2 of tidal marsh bordering San Pablo Bay. The restoration effort is expected to make use of more than 8.1 million m3 of dredged materials to raise the elevation of subsided wetlands. The placement of an Aquatic Transfer Facility (ATF) in San Pablo Bay is being considered by the U. S. Army Corps of Engineers to serve as a temporary holding site for dredge sediments before they are transferred to the Hamilton Wetlands restoration site. The San Francisco Bay model presented in this paper was developed as part of a larger study to evaluate potential impacts of the proposed ATF on circulation and sediment transport dynamics in San Pablo Bay. This paper presents the model calibration and validation, while the full analysis of proposed ATF conditions is presented in a separate technical report

The Extent of Seasonally Suitable Habitats May Limit Forage Fish Production in a Temperate Estuary

The sustained production of sufficient forage is critical to advancing ecosystem-based management, yet factors that affect local abundances and habitat conditions necessary to support aggregate forage production remain largely unexplored. We quantified suitable habitat in the Chesapeake Bay and its tidal tributaries for four key forage fishes: juvenile spotted hake Urophycis regia, juvenile spot Leiostomus xanthurus, juvenile weakfish Cynoscion regalis, and bay anchovy Anchoa mitchilli. We used information from monthly fisheries surveys from 2000 to 2016 coupled with hindcasts from a spatially interpolated model of dissolved oxygen and a 3-D hydrodynamic model of the Chesapeake Bay to identify influential covariates and construct habitat suitability models for each species. Suitable habitat conditions resulted from a complex interplay between water quality and geophysical properties of the environment and varied among species. Habitat suitability indices ranging between 0 (poor) and 1 (superior) were used to estimate seasonal and annual extents of suitable habitats. Seasonal variations in suitable habitat extents in Chesapeake Bay, which were more pronounced than annual variations during 2000–2016, reflected the phenology of estuarine use by these species. Areas near shorelines served as suitable habitats in spring for juvenile spot and in summer for juvenile weakfish, indicating the importance of these shallow areas for production. Tributaries were more suitable for bay anchovy in spring than during other seasons. The relative baywide abundances of juvenile spot and bay anchovy were significantly related to the extent of suitable habitats in summer and winter, respectively, indicating that Chesapeake Bay habitats may be limiting for these species. In contrast, the relative baywide abundances of juvenile weakfish and juvenile spotted hake varied independently of the spatial extent of suitable habitats. In an ecosystem-based approach, areas that persistently provide suitable conditions for forage species such as shoreline and tributary habitats may be targeted for protection or restoration, thereby promoting sufficient production of forage for predators. Further, quantitative habitat targets or spatial thresholds may be developed for habitat-limited species using estimates of the minimum habitat area required to produce a desired abundance or biomass; such targets or thresholds may serve as spatial reference points for management

Seasonal and Annual Variation in the Extent of Suitable Habitats for Forage Fishes in Chesapeake Bay, 2000-2016

The sustained production of sufficient forage is critical to advancing ecosystem-based management in Chesapeake Bay. Yet factors that affect local abundances and habitat conditions necessary to support forage production remain largely unexplored. Here, we quantified suitable habitat in the Chesapeake Bay region for four key forage fishes: bay anchovy Anchoa mitchilli, juvenile spot Leiostomus xanthurus, juvenile weakfish Cynoscion regalis, and juvenile spotted hake Urophycis regia. We coupled information from 17 years of monthly fisheries surveys with hindcasts from a numerical model of dissolved oxygen (DO) conditions and a 3-D hydrodynamic model of the Bay that provided estimates of habitat conditions across 18 covariates of salinity, temperature, DO, depth, and current speed for the period 2000 to 2016. Sediment composition and distance to shore metrics were also considered. The hindcast covariates were subsampled at the times and locations of the fisheries surveys to provide dynamic habitat metrics that are not generally observed at the time of fish sampling (e.g., current velocity, salinity stratification). Hindcast covariates were also used to describe habitat conditions in areas of Chesapeake Bay that are not sampled routinely by fisheries-independent surveys such as the Potomac River and Mobjack Bay. Boosted regression trees were used to identify influential habitat covariates for each species, and these influential covariates were then used to construct habitat suitability models. Habitat suitability indices, which ranged between 0 (poor habitat) and 1 (superior habitat), were assigned to each location in the 3-D model grid for each season in 2000-2016. Based on the estimated habitat suitability index and using a GIS approach, we quantified suitable habitat (defined as habitats with a habitat suitability index \u3e 0.5) throughout the Chesapeake Bay and its tidal tributaries. Furthermore, we validated the modeling approach using out-of-sample observations from Mobjack Bay in 2010-2012. Suitable seasonal habitat extents for forage species exhibited strong seasonal and annual signals reflecting temporal heterogeneity in habitat conditions in Chesapeake Bay. Current speed, water depth, and either temperature or dissolved oxygen were identified as important covariates for the four forage species we examined, and distance to shore was important for three of the four species; thus, suitable habitat conditions resulted from a complex interplay between water quality and the physical properties of the habitat. In our study, two species exhibited a relationship between relative abundance and extent of suitable habitats – juvenile spot in summer and bay anchovy in winter; as such, estimates of the minimum habitat area required to produce a desired abundance (or biomass) of forage fish can be used to establish quantitative habitat targets or spatial thresholds that may serve as spatial reference points for management. In an ecosystem-based approach, important habitats may be targeted for protection (e.g., by limiting fishing activities that may incidentally capture or injure forage fishes) or restoration (e.g., by improving water quality conditions), thereby ensuring production of sufficient forage for predators. In addition, the consequences of aquatic habitat alterations, whether due to climate change or physical disturbances can be investigated using projections of environmental conditions and habitat suitability in the region, though these projections will introduce additional uncertainty

Flow convergence routing hypothesis for pool-riffle maintenance in alluvial rivers

The velocity reversal hypothesis is commonly cited as a mechanism for the maintenance of pool-riffle morphology. Although this hypothesis is based on the magnitude of mean flow parameters, recent studies have suggested that mean parameters are not sufficient to explain the dominant processes in many pool-riffle sequences. In this study, two- and three-dimensional models are applied to simulate flow in the pool-riffle sequence on Dry Creek, California, where the velocity reversal hypothesis was first proposed. These simulations provide an opportunity to evaluate the hydrodynamics underlying the observed reversals in near-bed and section-averaged velocity and are used to investigate the influence of secondary currents, the advection of momentum, and cross-stream flow variability. The simulation results support the occurrence of a reversal in mean velocity and mean shear stress with increasing discharge. However, the results indicate that the effects of flow convergence due to an upstream constriction and the routing of flow through the system are more significant in influencing pool-riffle morphology than the occurrence of a mean velocity reversal. The hypothesis of flow convergence routing is introduced as a more meaningful explanation of the mechanisms acting to maintain pool-riffle morphology

Implementation of higher-order absorbing boundary conditions for the Einstein equations

We present an implementation of absorbing boundary conditions for the Einstein equations based on the recent work of Buchman and Sarbach. In this paper, we assume that spacetime may be linearized about Minkowski space close to the outer boundary, which is taken to be a coordinate sphere. We reformulate the boundary conditions as conditions on the gauge-invariant Regge-Wheeler-Zerilli scalars. Higher-order radial derivatives are eliminated by rewriting the boundary conditions as a system of ODEs for a set of auxiliary variables intrinsic to the boundary. From these we construct boundary data for a set of well-posed constraint-preserving boundary conditions for the Einstein equations in a first-order generalized harmonic formulation. This construction has direct applications to outer boundary conditions in simulations of isolated systems (e.g., binary black holes) as well as to the problem of Cauchy-perturbative matching. As a test problem for our numerical implementation, we consider linearized multipolar gravitational waves in TT gauge, with angular momentum numbers l=2 (Teukolsky waves), 3 and 4. We demonstrate that the perfectly absorbing boundary condition B_L of order L=l yields no spurious reflections to linear order in perturbation theory. This is in contrast to the lower-order absorbing boundary conditions B_L with L<l, which include the widely used freezing-Psi_0 boundary condition that imposes the vanishing of the Newman-Penrose scalar Psi_0.Comment: 25 pages, 9 figures. Minor clarifications. Final version to appear in Class. Quantum Grav

Hydrodynamic Simulation of Circulation and Residence Time in Clifton Court Forebay

Circulation in Clifton Court Forebay (CCF) was simulated using the three-dimensional (3–D) hydrodynamic model UnTRIM. These numerical simulations were performed to provide a better understanding of circulation patterns, flow pathways, and residence time in Clifton Court Forebay in support of ongoing studies of pre-screen loss and fish facility efficiency for delta smelt (Hypomesus transpacificus) at the California State Water Project (SWP) export facilities. The 3–D hydrodynamic model of CCF was validated through comparisons to observed water surface elevations inside CCF, and comparisons to observed drifter paths and velocity measurements collected by the U.S. Geological Survey as part of this study. Flow measurements collected near the radial gates for 2 days during relatively low inflows suggest that the Hills (1988) gate equations may over-estimate inflow by as much as 39% when the CCF radial gates are only partially opened. Several alternative approaches to improve the implementation of the radial gate flows in the UnTRIM model were evaluated. The resulting model accurately predicts water surface elevations and currents inside CCF over a range of wind and operating conditions. The validated model was used to predict residence time and other transport time scales for two 21-day simulation periods, one of very low daily SWP export pumping averaging 19.3 m3 s-1 and one for moderate daily SWP export pumping averaging 66.6 m3 s-1. The average transit time, indicating the time from entering CCF to reaching the fish facility, was estimated as 9.1 days for low export conditions and 4.3 days for moderate export conditions.  These transport time scale estimates may be used to inform estimates of pre-screen losses inside CCF due to predation or other causes

Hydrodynamic Simulation of Circulation and Residence Time in Clifton Court Forebay

Circulation in Clifton Court Forebay (CCF) was simulated using the three-dimensional (3–D) hydrodynamic model UnTRIM. These numerical simulations were performed to provide a better understanding of circulation patterns, flow pathways, and residence time in Clifton Court Forebay in support of ongoing studies of pre-screen loss and fish facility efficiency for delta smelt (Hypomesus transpacificus) at the California State Water Project (SWP) export facilities. The 3–D hydrodynamic model of CCF was validated through comparisons to observed water surface elevations inside CCF, and comparisons to observed drifter paths and velocity measurements collected by the U.S. Geological Survey as part of this study. Flow measurements collected near the radial gates for 2 days during relatively low inflows suggest that the Hills (1988) gate equations may over-estimate inflow by as much as 39% when the CCF radial gates are only partially opened. Several alternative approaches to improve the implementation of the radial gate flows in the UnTRIM model were evaluated. The resulting model accurately predicts water surface elevations and currents inside CCF over a range of wind and operating conditions. The validated model was used to predict residence time and other transport time scales for two 21-day simulation periods, one of very low daily SWP export pumping averaging 19.3 m3 s-1 and one for moderate daily SWP export pumping averaging 66.6 m3 s-1. The average transit time, indicating the time from entering CCF to reaching the fish facility, was estimated as 9.1 days for low export conditions and 4.3 days for moderate export conditions.  These transport time scale estimates may be used to inform estimates of pre-screen losses inside CCF due to predation or other causes

Variation of Fish Habitat and Extent of the Low-Salinity Zone with Freshwater Flow in the San Francisco Estuary

We used the UnTRIM San Francisco Bay–Delta hydrodynamic model to examine the spatial distribution of salinity as a function of freshwater flow in the San Francisco Estuary. Our particular focus was the covariation of flow with the spatial extent of the low-salinity zone (LSZ: salinity = 0.5 to 6), and with the extent of habitat for common species of -nekton as defined by their salinity ranges. The UnTRIM model has an unstructured grid which allowed us to refine earlier estimates of the availability of suitable salinity ranges, particularly for species resident in low salinity. The response of the salinity field to flow was influenced by the bathymetry of the estuary. Area and volume of the LSZ were bimodal with X2, the distance up the axis of the estuary to a near-bottom salinity of 2, roughly the middle of the LSZ. The smallest area and volume occurred when the LSZ was in the Delta or Carquinez Strait, moderate values when it was in Suisun Bay, and the highest values when it was in broad, shallow San Pablo Bay. Resource selection functions for the distributions of common nekton species in salinity space were up-dated from previous values and used to calculate salinity-based habitat indices using the UnTRIM results. These indices generally increased with decreasing X2 (increasing flow), but the slopes of these relationships were mostly inconsistent with corresponding relationships of abundance to flow. Thus, although the salinity range used by most nekton expands as flow increases, other mechanisms relating population size to flow are likely more important than the physical extent of suitable salinity.