Multi-layer model simulation and data assimilation in the Serangoon Harbor of Singapore

In June of 2009, a sea trial was carried out around Singapore to study and monitor physical, biological and chemical oceanographic parameters. Temperature, salinity and velocities were collected from multiple vehicles. The extensive data set collected in the Serangoon Harbour provides an opportunity to study barotropic and baroclinic circulation in the harbour and to apply data assimilation methods in the estuarine area. In this study, a three-dimensional, primitive equation coastal ocean model (FVCOM) with a number of vertical layers is used to simulate barotropic and baroclinic flows and reconstruct the vertical velocity structures. The model results are validated with in situ ADCP observations to assess the realism of the model simulations. EnKF data assimilation method is successively implemented to assimilate all the available ADCP data, and thus correct for the model forecast deficiencies.Singapore. National Research FoundationSingapore-MIT AllianceSingapore-MIT Alliance. Center for Environmental Sensing and Monitorin

Multi-vehicle oceanographic feature exploration

URL to conference page. Scroll down to 2009 conference (June 21-26), click "Paper and session list," and search under Patrikalakis' name.Oceanographic features such as jets and vortices are often found downstream of obstacles and landforms such as islands or peninsulas. Such features have high spatial and temporal variability and are, hence, interesting but difficult to measure and quantify. This paper discusses an experiment to identify and resolve such oceanographic features in Selat Pauh, in the Straits of Singapore. The deployment formation for multiple robotic vehicles (Autonomous Surface Craft - ASC), the measurement instruments, and the algorithms developed in extracting oceanographic field variables are described. These were based on two ocean field predictions from well-known geophysical flow dynamic models. Field experiments were carried out and comparison of the forecasts with measurements was attempted. To investigate an unexpected behaviour of one ASC, hindcasts with wind effects and simulation with vortex feature extraction on a larger domain with more involved bathymetry were also partially carried out.Singapore-MIT Alliance for Research and TechnologySingapore. National Research Foundation (SMART/CENSAM initiative

Modelling sea level surges in the Firth of Clyde, a fjordic embayment in south-west Scotland

Storm surges are an abnormal enhancement of the water level in response to weather perturbations. They have the capacity to cause damaging flooding of coastal regions, expecially when they coincide with astronomical high spring tides. Some areas of the UK have suffered particularly damaging surge events, and the Firth of Clyde is a region with high risk due to its location and morphology. Here we use a three-dimensional high spatial resolution hydrodynamic model to simulate the local bathymetric and morphological enhancement of surge in the Clyde, and disaggregate the effects of far-field atmospheric pressure distribution and local scale wind forcing of surges. A climatological analysis, based on 30 years of data from Millport tide gauges is also discussed. The results suggest that floods are not only caused by extreme surge events, but also by the coupling of spring high tides with moderate surges. Water level is also enhanced by a funnelling effect due to the bathymetry and the morphology of fjordic sealochs and the River Clyde estuary. In a world of rising sea level, studying the propagation and the climatology of surges and high water events is fundamental. In addition, high-resolution hydrodynamic models are essential to forecast extreme events and prevents the loss of lives, or to plan coastal defences solutions

Impact of high-frequency nonlinear internal waves on plankton dynamics in Massachusetts Bay

Author Posting. © Sears Foundation for Marine Research, 2010. This article is posted here by permission of Sears Foundation for Marine Research for personal use, not for redistribution. The definitive version was published in Journal of Marine Research 68 (2010): 259-281, doi:10.1357/002224010793721415.A simple Nutrient-Phytoplankton-Zooplankton (NPZ) model was coupled with the non-hydrostatic Finite-Volume Coastal Ocean Model (FVCOM-NH) to study the impact of high-frequency nonlinear internal waves on plankton dynamics in Massachusetts Bay (MB) during the stratified summer season. The temporal and spatial variability of phytoplankton concentration follows the vertical isopycnal displacement to the lowest order as the waves are generated by the semidiurnal tidal flow over Stellwagen Bank (SB) and propagate westward across MB. The tidally-averaged distribution of phytoplankton is characterized by three distinct zones of low subsurface concentration: (I) the western flank of Stellwagen Bank; (II) the center of Stellwagen Basin; and (III) the upper western flank of Stellwagen Basin. The result of a model dye experiment suggests that these zones are created by the following physical processes which are dominant in each zone: (I) hydraulic jump; (II) strong internal wave-tidal current nonlinear interaction; and (III) energetic internal wave dissipation and subsequent mixing processes. The nonlinear interaction of the internal waves and offshore tidal currents significantly enhances the vertical velocity, and increases wave dissipation, thus causing an onshore transport of phytoplankton in zone II. Although the phytoplankton patchy structure can be produced using the hydrostatic FVCOM, the resulting phytoplankton concentration is overestimated due to the unrealistic intensification of vertical velocity and thus vertical nutrient flux from the deep water. It suggests that non-hydrostatic dynamics should be considered for certain small-scale biological processes that are driven primarily by the physics.This project is supported by NOAA grants DOC/NOAA/NA04NMF4720332 and DOC/NOAA/NA05NMF4721131, US GLOBEC Northwest Atlantic/Georges Bank Program NSF grants (OCE-0234545; OCE-0227679; OCE-0606928; OCE-0712903; OCE-0732084; OCE- 0726851), and MIT Sea Grant funds (2006-RC-103, 2010-R/RC-116) and NOAA NERACOOS grant NA100558 for the UMassD team, and a NOAA grant (NA-17RJ1223) for R. C. Beardsley. C. Chen’s contribution is also supported by Shanghai Ocean University International Cooperation Program (No. A-2302–10-0003), the Program of Science and Technology Commission of Shanghai Municipality (No. 09320503700), the Leading Academic Discipline Project of Shanghai Municipal Education Commission (Project number: J50702), and Zhi jiang Scholar and 111 project funds of the State Key Laboratory for Estuarine and Coastal Research, East China Normal University (ECNU)

Comparison of observed and model-computed low frequency circulation and hydrography on the New England Shelf

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C09015, doi:10.1029/2007JC004394.The finite volume coastal ocean model (FVCOM) is configured to study the interannual variability of circulation in the Gulf of Maine (GoM) and Georges Bank. The FVCOM-GoM system incorporates realistic time-dependent surface forcing derived from a high-resolution mesoscale meteorological model (MM5) and assimilation of observed quantities including sea surface temperature and salinity and temperature fields on the open boundary. An evaluation of FVCOM-GoM model skill on the New England shelf is made by comparison of computed fields and data collected during the Coastal Mixing and Optics (CMO) Program (August 1996–June 1997). Model mean currents for the full CMO period compare well in both magnitude and direction in fall and winter but overpredict the westward flow in spring. The direction and ellipticity of the subtidal variability correspond but computed magnitudes are around 20% below observed, partially due to underprediction of the variability by MM5. Response of subtidal currents to wind-forcing shows the model captures the directional dependence, as well as seasonal variability of the lag. Hydrographic results show that FVCOM-GoM resolves the spatial and temporal evolution of the temperature and salinity fields. The model-computed surface salinity field compares well, except in May when there is no indication of the fresh surface layer from the Connecticut River discharge noted in the observations. Analysis of model-computed results indicates that the plume was unable to extend to the mooring location due to the presence of a westward mean model-computed flow during that time that was stronger than observed. Overall FVCOM-GoM captures well the dynamics of the mean and subtidal flow on the New England shelf.G. Cowles was supported by the Massachusetts Marine Fisheries Institute (MFI) through NOAA grants DOC/NOAA/ NA04NMF4720332 and DOC/NOAA/NA05NMF4721131, S. Lentz by the NSF Ocean Sciences Division through grants OCE-841292 and OCE- 848961, C. Chen and Q. Xu through the NSF/NOAA GLOBEC/Northwest Atlantic/Georges Bank Program under NSF grants OCE-0234545 and OCE-0227679 and NOAA grants NA-16OP2323, and R. Beardsley through NOAA grant NA-17RJ1223

Application and comparison of Kalman filters for coastal ocean problems : an experiment with FVCOM

Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 114 (2009): C05011, doi:10.1029/2007JC004548.Twin experiments were made to compare the reduced rank Kalman filter (RRKF), ensemble Kalman filter (EnKF), and ensemble square-root Kalman filter (EnSKF) for coastal ocean problems in three idealized regimes: a flat bottom circular shelf driven by tidal forcing at the open boundary; an linear slope continental shelf with river discharge; and a rectangular estuary with tidal flushing intertidal zones and freshwater discharge. The hydrodynamics model used in this study is the unstructured grid Finite-Volume Coastal Ocean Model (FVCOM). Comparison results show that the success of the data assimilation method depends on sampling location, assimilation methods (univariate or multivariate covariance approaches), and the nature of the dynamical system. In general, for these applications, EnKF and EnSKF work better than RRKF, especially for time-dependent cases with large perturbations. In EnKF and EnSKF, multivariate covariance approaches should be used in assimilation to avoid the appearance of unrealistic numerical oscillations. Because the coastal ocean features multiscale dynamics in time and space, a case-by-case approach should be used to determine the most effective and most reliable data assimilation method for different dynamical systems.P. Malanotte-Rizzoli and J. Wei were supported by the Office of Naval Research (ONR grant N00014-06-1- 0290); C. Chen and Q. Xu were supported by the U.S. GLOBEC/Georges Bank program (through NSF grants OCE-0234545, OCE-0227679, OCE- 0606928, OCE-0712903, OCE-0726851, and OCE-0814505 and NOAA grant NA-16OP2323), the NSF Arctic research grants ARC0712903, ARC0732084, and ARC0804029, and URI Sea Grant R/P-061; P. Xue was supported through the MIT Sea Grant 2006-RC-103; Z. Lai, J. Qi, and G. Cowles were supported through the Massachusetts Marine Fisheries Institute (NOAA grants NA04NMF4720332 and NA05NMF4721131); and R. Beardsley was supported through U.S. GLOBEC/Georges Bank NSF grant OCE-02227679, MIT Sea Grant NA06OAR1700019, and the WHOI Smith Chair in Coastal Oceanography

Connectivity of the bay scallop (Argopecten irradians) in Buzzards Bay, Massachusetts, U.S.A.

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Fisheries Oceanography 24 (2015): 364-382, doi:10.1111/fog.12114.The harvest of bay scallops (Argopecten irradians) from Buzzards Bay, Massachusetts, USA undergoes large interannual fluctuations, varying by more than an order of magnitude in successive years. To investigate the extent to which these fluctuations may be due to yearly variations in the transport of scallop larvae from spawning areas to suitable juvenile habitat (settlement zones), a high-resolution hydrodynamic model was used to drive an individual-based model of scallop larval transport. Model results revealed that scallop spawning in Buzzards Bay occurs during a time when nearshore bay currents were principally directed up-bay in response to a persistent southwesterly sea breeze. This nearshore flow results in substantial transport of larvae from lower-bay spawning areas to settlement zones further up-bay. Averaged over the entire bay, the spawning-to-settlement zone connectivity exhibits little interannual variation. However, connectivities between individual spawning and settlement zones vary by up to an order of magnitude. The model results identified spawning areas that have the greatest probability of transporting larvae to juvenile habitat. Because managers may aim to increase scallop populations either locally or broadly, the high-connectivity spawning areas were divided into: 1) high larval retention and relatively little larval transport to adjoining settlement areas, 2) both significant larval retention and transport to more distant settlement areas, and 3) little larval retention but significant transport to distant settlement areas.This project was supported by the Woods Hole Sea Grant through award NA10OAR4170083. All modeling computations were made on the University of Massachusetts at Dartmouth’s (UMD’s) GPGPU cluster, which was acquired with support from NSF award CNS-0959382 and AFOSR DURIP award FA9550-10-1-0354.2016-07-1

FVCOM validation experiments : comparisons with ROMS for three idealized barotropic test problems

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C07042, doi:10.1029/2007JC004557.The unstructured-grid Finite-Volume Coastal Ocean Model (FVCOM) is evaluated using three idealized benchmark test problems: the Rossby equatorial soliton, the hydraulic jump, and the three-dimensional barotropic wind-driven basin. These test cases examine the properties of numerical dispersion and damping, the performance of the nonlinear advection scheme for supercritical flow conditions, and the accuracy of the implicit vertical viscosity scheme in barotropic settings, respectively. It is demonstrated that FVCOM provides overall a second-order spatial accuracy for the vertically averaged equations (i.e., external mode), and with increasing grid resolution the model-computed solutions show a fast convergence toward the analytic solutions regardless of the particular triangulation method. Examples are provided to illustrate the ability of FVCOM to facilitate local grid refinement and speed up computation. Comparisons are also made between FVCOM and the structured-grid Regional Ocean Modeling System (ROMS) for these test cases. For the linear problem in a simple rectangular domain, i.e., the wind-driven basin case, the performance of the two models is quite similar. For the nonlinear case, such as the Rossby equatorial soliton, the second-order advection scheme used in FVCOM is almost as accurate as the fourth-order advection scheme implemented in ROMS if the horizontal resolution is relatively high. FVCOM has taken advantage of the new development in computational fluid dynamics in resolving flow problems containing discontinuities. One salient feature illustrated by the three-dimensional barotropic wind-driven basin case is that FVCOM and ROMS simulations show different responses to the refinement of grid size in the horizontal and in the vertical.For this work, H. Huang and G. Cowles were supported by the Massachusetts Marine Fisheries Institute (MFI) through NOAA grants DOC/NOAA/NA04NMF4720332 and DOC/ NOAA/NA05NMF472113; C. Chen was supported by NSF grants (OCE0234545, OCE0606928, OCE0712903, OCE0732084, and OCE0726851), NOAA grants (NA160P2323, NA06RG0029, and NA960P0113), MIT Sea grant (2006-RC-103), and Georgia Sea grant (NA26RG0373 and NA66RG0282); C. Winant was supported through NSF grant OCE-0726673; R. Beardsley was supported through NSF OCE—0227679 and the WHOI Smith Chair; K. Hedstrom was supported through NASA grant NAG13– 03021 and the Arctic Region Supercomputing Center; and D. Haidvogel was supported through grants ONR N00014- 03-1-0683 and NSF OCE 043557

A dike–groyne algorithm in a terrain-following coordinate ocean model (FVCOM) : development, validation and application

Author Posting. © The Author(s), 2012. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Ocean Modelling 47 (2012): 26-40, doi:10.1016/j.ocemod.2012.01.006.A dike-groyne module is developed and implemented into the unstructured-grid, three dimensional primitive equation Finite-Volume Coastal Ocean Model (FVCOM) for the study of the hydrodynamics around human-made construction in the coastal area. The unstructured-grid finite-volume flux discrete algorithm makes this module capable of realistically including narrow-width dikes and groynes with free exchange in the upper column and solid blocking in the lower column in a terrain-following coordinate system. This algorithm used in the module is validated for idealized cases with emerged and/or submerged dikes and a coastal seawall where either analytical solutions or laboratory experiments are available for comparison. As an example, this module is applied to the Changjiang Estuary where a dike-groyne structure was constructed in the Deep Waterway channel in the inner shelf of the East China Sea (ECS). Driven by the same forcing under given initial and boundary conditions, a comparison was made for model-predicted flow and salinity via observations between dike-groyne and bed-conforming slope algorithms. The results show that with realistic resolution of water transport above and below the dike-groyne structures, the new method provides more accurate results. FVCOM with this MPI-architecture parallelized dike-groyne module provides a new tool for ocean engineering and inundation applications in coastal regions with dike, seawall and/or dam structures.J. Ge and P. Ding have been supported by the Fund for Creative Research Groups of NSFC (No. 41021064), the PhD Program Scholarship Fund (2009010) of East China Normal University (ECNU), and the State Scholarship Fund from China Scholarship Council. C. Chen, J. Qi and R. C. Beardsley have been funded by the Northeast Regional Association of Coastal Ocean Observing Systems (NERACOOS), the IOOS/SURA Super-Regional Coastal Modeling Testbed, MIT Sea Grant NA06OAR4170019 and 571000271, and NSF grants OCE0606928, OCE0712903, OCE0732084, OCE0726851, OCE0814505, and OCE0804029

A nonhydrostatic version of FVCOM : 2. Mechanistic study of tidally generated nonlinear internal waves in Massachusetts Bay

Author Posting. © American Geophysical Union, 2010. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 115 (2010): C12049, doi:10.1029/2010JC006331.The generation, propagation, and dissipation processes of large-amplitude nonlinear internal waves in Massachusetts Bay during the stratified season were examined using the nonhydrostatic Finite-Volume Coastal Ocean Model (FVCOM-NH). The model reproduced well the characteristics of the high-frequency internal waves observed in Massachusetts Bay in August 1998. The model experiments suggested that internal waves over Stellwagen Bank are generated by the interaction of tidal currents with steep bottom topography through a process of forming a large-density front on the western slope of the bank by the release of an initial density perturbation near ebb-flood transition, nonlinear steepening of the density front into a deep density depression, and disintegrating of the density depression into a wave train. Earth's rotation tends to transfer the cross-bank tidal kinetic energy into the along-bank direction and thus reduces the intensity of the density perturbation at ebb-flood transition and density depression in the flood period. The internal wave packet propagates as a leading edge feature of the internal tidal wave, and the faster propagation speed of the high-frequency internal waves in Massachusetts Bay is caused by Earth's rotation. The model experiments suggested that bottom friction can significantly influence the cross-bank scale of the density perturbation and thus the density depression during wave generation and the dissipation during the wave's shoaling. Inclusion of vertical mixing using the Mellor-Yamada level 2.5 turbulence closure model had only a marginal effect on wave evolution. The model results support the internal wave theory proposed by Lee and Beardsley (1974) but are in disagreement with the lee-wave mechanism proposed by Maxworthy (1979).This research was supported by NOAA g r a n t s DOC/NOAA/NA04NMF4720332 and DOC/NOAA/ NA05NMF4721131, U.S. GLOBEC Northwest Atlantic/Georges Bank Program NSF grants (OCE‐0606928, OCE‐0712903, OCE‐0732084, OCE‐0726851, OCE0814505), and MIT Sea Grant funds (2006‐RC‐103 and 2010‐R/RC‐116), NOAA NERACOOS Program for the UMASSD team and the Smith Chair in Coastal Oceanography, and NOAA grant (NA‐17RJ1223) for R.C. Beardsley. C. Chen’s contribution is also supported by Shanghai Ocean University under grants A‐2302‐10‐0003 and 09320503700 and the State Key Laboratory for Estuarine and Coastal Research, East China Normal University