Ramiro Neves

3D modelling in the Sado estuary using a new generic vertical discretization approach

Abstract Sado estuary (Portugal) is a mesotidal well-mixed estuary. The flow however, displays strong three-dimensional features associated with bathymetry variations. The flow is simulated using a three-dimensional primitive equation model based on the finite-volume method and incorporating a new concept for the vertical discretization. The innovative features of the model are analysed and the advantages of the finite-volume method to implement the generic vertical discretization are put into evidence. The model was validated using water level, velocity and salinity measurements in several stations along the estuary. Results show the influence of main channels strong curvature on the generation of secondary flows inside the estuary. The steep bathymetry of the outer platform gives rise to a recirculation flow in the vertical plane that lasts for most of the tidal cycle. This structure is considered important for the sediment transport in that region. The above mentioned non-linear effects leave their print in both the transient and residual velocity fields. The results obtained help to understand the role of three-dimensional structures on the water exchange and sediment transport in the estuary. The results also confirm the suitability of the approach used in this model to simulate estuarine and coastal flows with strong three-dimensional effects.

A model for ocean circulation on the Iberian coast

We used a three-dimensional model with generic vertical coordinate to investigate the structure of flow and transports on the Iberian shelf-slope region. Two different types of experiments were conducted. The first was a process-oriented study to investigate the role of thermohaline forcing in the generation and meridional variability of the poleward slope current. The second experiment was a more realistic simulation for the year of 1994, a period for which there are several long-term current meter data sets available. Comparisons between model, data and other published works have shown a reasonable agreement both qualitatively and quantitatively. The results obtained included the seasonal cycle with upwelling during the summer and a winter surface poleward current over the shelf, with a permanent undercurrent transporting Mediterranean Water along the Portuguese and Spanish slopes. The along-slope transports were predominant especially in the OMEX II–II study area. The meridional transport is poleward all year round, decreasing from winter to summer and from the south to the north. D 2002 Elsevier Science B.V. All rights reserved.

Hydrodynamic and sediment suspension modelling in estuarine systems: Part I: Description of the numerical models

Abstract A fully-3D finite difference baroclinic model system for hydrodynamics and fine suspended sediment transport is described. The hydrodynamic model is based on the hydrostatic and Boussinesq approximations, and uses a vertical double sigma co-ordinate with a staggered grid and a semi-implicit two-time level scheme. In addition to the momentum and continuity equations, the model solves two transport equations for salt and temperature and an equation of state to include the baroclinic effects. The simulation of cohesive sediment transport processes is performed solving the 3D-conservative advection–diffusion equation, in the same grid used by the hydrodynamic model. Flocculation, erosion and deposition of sediments on the bottom are represented by means of empirical formulations parameterized by field data. The models were tested and calibrated by simulating tidal flows and suspended sediment transport in several estuaries (two applications are described in Part II). The results show good agreement between the numerical predictions and the corresponding field measurements.

A two-dimensional particle tracking model for pollution dispersion in A Coruna and Vigo Rias (NW Spain)

A two-dimensional hydrodynamic model coupled to a particle tracking model is applied to study the dispersion processes and residence time in two Galician rias (A Coruna and Vigo, NW Spain) under summer conditions. In A Coruna a long residence time was found in the harbour area due to the existence of a dock, and a short one in the river area. On the contrary, in Vigo, the residence time is smaller in the harbour area, due to the Rande Strait, beyond which the river effect is negligible.

Hydrodynamic and sediment suspension modelling in estuarine systems: Part II: Application to the Western Scheldt and Gironde estuaries

Applications of the 3D-baroclinic numerical model described in Part I of this paper were performed in the Western Scheldt (The Netherlands) and Gironde (France) estuaries. Simulations provide an insight into cohesive sediment transport and its dependency on 3D flow features. In the Scheldt estuary, non-linear processes associated with the geometry of the estuary and the vertical profile of horizontal velocity generate effective upward and downward movements promoting vertical mixing. These movements are responsible for the small vertical gradient of density. The sediment distribution is characterised by two zones of high concentration associated with the different characteristics of bottom sediments. The maximum turbidity is not directly associated with the density currents but mainly with the variation in estuarine width and its effects on flow field. In the Gironde estuary, the vertical gradient of the residual velocity is small. Until pk70, the flow is seaward over the whole cross-section. Between pk70 and the estuarine mouth there is a large eddy with seaward flow in the northern channel. The inward velocity is stronger near the surface, suggesting that the residual flow is associated with the tidal movement and, to a less extent, with the density. The simulation of cohesive sediment transport accounting for the effects of the density current shows that the location of the turbidity maximum is strongly controlled by the fluvial discharges.

Modelling the main features of the Algarve coastal circulation during July 2004: A downscaling approach

This article presents a methodology for simulating the Algarve coastal circulation using realistic forcing (e.g. low-frequency circulation, tide, high-resolution atmospheric forcing). Low-frequency open boundary conditions are defined via a downscaling of the HYCOM-US operational solution for the Gulf of Cadiz. Atmospheric forcing is imposed using the MM5 high-resolution mesoscale model (9 km resolution near the coast). A 3-level nesting system based on the MOHID numerical system is implemented. The higher nesting level has a horizontal resolution of 0.02° along the Algarve coast. The methodology is first validated qualitatively. A comparison between the numerical results and the conceptual model of the circulation described in the literature is presented. A quantitative validation is also performed, based mainly on remote sensing data (sea surface temperature and altimetry) available for July 2004. The numerical system is able to reproduce many of the circulation features described in the literature (e.g...

Modelling the influence of nutrient loads on Portuguese estuaries

The effects of implementing Directive 91/271/EEC of 21 May 1991 (Waste Water Treatment Plan Directive) and Directive 91/676/EEC of 12 December (Nitrates Directive) are analysed in 7 Portuguese estuaries (Minho, Lima, Douro, Mondego, Tagus, Sado and Guadiana) and two coastal lagoons (Ria de Aveiro and Ria Formosa), with a modelling approach. MOHID Water Modelling System was used to perform simulations with three nitrogen load scenarios for each system: a reference scenario, a 50% nitrate removal by agriculture scenario and another with a 100% nutrients removal by waste water treatment plants (WWTP). It is shown that the interaction between hydrodynamic and ecological processes is an important feature to study trophic problems in estuaries. Ecological processes such as primary production only occur inside the system if the residence time of water is high enough to enable organismal activity and if the adequate conditions are found (e.g. light, nutrients, temperature). From the model results it is possible to conclude: (i) in systems with short residence time a reduction in nutrient load will only produce a decrease in nutrient transit and will not affect the system’s global ecological status (e.g. Douro Estuary); (ii) in systems with long residence time the effects will range from significant, when primary production is mostly limited by nutrients (e.g. Ria de Aveiro), to non-significant, when primary production in the system is light-limited (e.g. Tagus Estuary).

An advanced modelling tool for simulating complex river systems

The present paper describes MOHID River Network (MRN), a 1D hydrodynamic model for river networks as part of MOHID Water Modelling System, which is a modular system for the simulation of water bodies (hydrodynamics and water constituents). MRN is capable of simulating water quality in the aquatic and benthic phase and its development was especially focused on the reproduction of processes occurring in temporary river networks (flush events, pools formation, and transmission losses). Further, unlike many other models, it allows the quantification of settled materials at the channel bed also over periods when the river falls dry. These features are very important to secure mass conservation in highly varying flows of temporary rivers. The water quality models existing in MOHID are base on well-known ecological models, such as WASP and ERSEM, the latter allowing explicit parameterization of C, N, P, Si, and O cycles. MRN can be coupled to the basin model, MOHID Land, with computes runoff and porous media transport, allowing for the dynamic exchange of water and materials between the river and surroundings, or it can be used as a standalone model, receiving discharges at any specified nodes (ASCII files of time series with arbitrary time step). These features account for spatial gradients in precipitation which can be significant in Mediterranean-like basins. An interface has been already developed for SWAT basin model.

MOHID 2000 - A coastal integrated object oriented model

Mathematical modeling, although a recent science, can be considered old when the time scale used to measure its age is the information technology evolution. FORTRAN 77 has been the most popular programming language among hydrodynamic modelers over the last two decades. This language was adequate to the (low) complexity of the models, limited by the exiting computers. The fast increase of the computing capacity allowed the development of more complex and multidisciplinary models. The necessity of new programming techniques became clear. It was started the era of the Object Oriented programming. Object Oriented programming isolates different parts of the code and allows communication among them using simple and robust interfaces. MOHID 2000 is an integrated modeling tool programmed in FORTRAN 95, using an Object Oriented strategy. It is the evolution of a set of models originally programmed in FORTRAN 77. Taking advantage of the new language possibilities, with a single code it is possible to perform different simulations (1D, 2D or 3D) and use a variety of vertical discretizations. This technique has also turned easy to integrate hydrodynamic, water quality, sediment transport and pollutants dispersion simulations using eulerian or lagrangian formulations. Having in mind the development of a tool accessible to the final user, the modeler must think about on the algorithms and code, but also on pre and post processing of the model data. MOHID 2000 input data files can be constructed by a graphical user interface. Output files use the standard HDF format making results exploring simple and allows the use of different graphic packages.

Mercury levels assessment in hair of riverside inhabitants of the Tapajós River, Pará State, Amazon, Brazil: Fish consumption as a possible route of exposure

The study present evaluated the levels of mercury (Hg) and methylmercury (MeHg) in hair samples of people from Barreiras community, riverside inhabitants of the Tapajós River (Pará, Brazil), an area impacted by clandestine gold mining, as well as we analyzed the levels of Hg and Se (selenium) in nine fish species (carnivores and non-carnivorous) from the Tapajós River, which stand out as the main species consumed by riverside inhabitants, to evaluate a relationship between frequency of fish consumption and Hg concentration, and also to evaluate possible mechanisms of fish protection (or non-protection) to Hg exposure by Se. Furthermore we analyze the water quality to evaluate the environmental trophic state, fact responsible by creating conditions that can potentiate the effects of toxic mercury. Concentrations of Hg and MeHg were analyzed in hair samples of 141 volunteers in different age band. Of those, 84.40% of samples present values above the threshold for biological tolerance, which is 6.00μgg(-1) of total Hg in hair. Total Hg, in men there was a variation of 2.07-24.93μgg(-1), while for women the variation was 4.84-27.02μgg(-1). Consequently, the level of MeHg in men presented a variation of 1.49-19.57μgg(-1), with an average of 11.68μgg(-1), while with women the variation was from 3.73 to 22.35μgg(-1), with an average of 10.38μgg(-1). In fish species, Hg concentrations in carnivorous species had an average of 0.66μgg(-1), higher than that permitted by current legislation, ranging from 0.30 to 0.98μgg(-1), while the non-carnivorous species have values below the recommended by the legislation averaging 0.09μgg(-1), ranging between 0.02 and 0.44μgg(-1). For Se in fish, show that among carnivores, the contents of Se ranged between 0.18 and 0.54μgg(-1) with a mean of 0.34μgg(-1), while for non-carnivores these values were of the order of 0.16-0.56μgg(-1), with an average of 0.32μgg(-1). In surface water quality variables at the sampling points all showed values in accordance with the range established by current legislation. In this regard, the results provided by this study, while not conclusive, are strong indicators that despite not having been shown the relationship between the concentration of mercury in hair and feeding habits along the Tapajós River basin communities showed that a plausible correlation exists between levels of mercury and selenium in fish. This fact may serve as a subsidy to research human health, because in the Amazon, there is still a lot to examine with regards to the full understanding of the Se cycle.