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In this paper, hydrogeological and geophysical data are used to validate a numerical model developed to predict seawater intrusion into coastal aquifers. The cell-centered finite volume method is adopted here to solve the set of coupled partial differential equations describing the motion of saltwater and freshwater separated by a sharp interface. These equations are based on the Dupuit approximation and are obtained from integration of 3D flow equations for fresh and salt water zones over the vertical dimension. In order to have flexibility upon complex configurations domain, non structured grid meshing is utilized. To approximate the diffusion fluxes, Green-Gauss type reconstruction, based on diamond-cell and least squares interpolation, is performed. The model is first validated using academic test case studies with known closed form solutions. The mathematical model has been calibrated using hydrogeochemical and geophysical data. The geophysical method applied in this study has been a frequency domain electromagnetic method. In this method the apparent electrical conductivity is measured by induction using two separate hand-held transmitter and receiver coils. During the operation the transmitter coil is energized by a low frequency alternating current that radiates an electromagnetic field and the receiver coil detects the resulting field. Taking into account the relationship between the bulk conductivity of the subsoil and the conductivity of groundwater, EM soundings have been interpreted to provide complementary information to hydrogeochemical data to outline the fresh–saltwater interface. This methodology has been applied to the case of saltwater intrusion into the Llobregat delta aquifer, near Barcelona, Spain.