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Exchange of material across the nearshore region, extending from the shoreline to a few kilometers offshore, determines the concentrations of pathogens and nutrients near the coast and the transport of larvae, whose cross-shore positions influence dispersal and recruitment. Here, we describe a framework for estimating the relative importance of cross-shore exchange mechanisms, including winds, Stokes drift, rip currents, internal waves, and diurnal heating and cooling. For each mechanism, we define an exchange velocity as a function of environmental conditions. The exchange velocity applies for organisms that keep a particular depth due to swimming or buoyancy. A related exchange diffusivity quantifies horizontal spreading of particles without enough vertical swimming speed or buoyancy to counteract turbulent velocities. This framework provides a way to determinewhich processes are important for cross-shore exchange for a particular study site, time period, and particle behavior. 

{"Abstract":["This is an archive of model output from the Regional Ocean Modeling System (ROMS) with two grids and two-way nesting. The parent grid resolution (referred to as Doppio) is 7 km and spans the Atlantic Ocean off the northeast United States from Cape Hatteras to Nova Scotia. The refinement grid (referred to as Snaildel) focuses on Delaware Bay and the adjacent coastal ocean at 1 km resolution. This ROMS configuration uses turbulence kinetic energy flux and significant wave height from Simulating Waves Nearshore (SWAN) as surface boundary conditions for turbulence closure.Ocean state variables computed are sea level, velocity, temperature, and salinity. Also inclued are surface and bottom stresses, as well as vertical diffusivity of tracer and momentum. \nThe files uploaded here are examples of one time record from each of this dataset. Outputs for the full reanalysis, which comprises 14 Terabytes of data, are made available for download via a THREDDS (Thematic Real-time Environmental Distributed Data Services) web service to facilitate user geospatial or temporal sub-setting.\nThe THREDDS catalog URLs and example filenames available here, for the respective collections, are:\n\t- 12 minute snapshots of the Doppio domain 2009-2015:\nhttps://tds.marine.rutgers.edu/thredds/roms/snaildel/catalog.html?dataset=snaildel_doppio_history\n\t- 12 minute snapshots of the Snaildel domain 2009-2015:\nhttps://tds.marine.rutgers.edu/thredds/roms/snaildel/catalog.html?dataset=snaildel_snaildel_history\n \nGarwood, J. C., H. L. Fuchs, G. P. Gerbi, E. J. Hunter, R. J. Chant and J. L. Wilkin (2022). "Estuarine retention of larvae: Contrasting effects of behavioral responses to turbulence and waves." Limnol. Oceanogr. 67: 992-1005.\nHunter, E. J., H. L. Fuchs, J. L. Wilkin, G. P. Gerbi, R. J. Chant and J. C. Garwood (2022). "ROMSPath v1.0: Offline Particle Tracking for the Regional Ocean Modeling System (ROMS)." Geosci. Model Dev. 15: 4297-4311."]} 

Abstract. Offline particle tracking (OPT) is a widely used tool for theanalysis of data in oceanographic research. Given the output of ahydrodynamic model, OPT can provide answers to a wide variety of researchquestions involving fluid kinematics, zooplankton transport, the dispersionof pollutants, and the fate of chemical tracers, among others. In thispaper, we introduce ROMSPath, an OPT model designed to complement theRegional Ocean Modeling System (ROMS). Based on the Lagrangian TRANSport(LTRANS) model (North et al., 2008), ROMSPath is written in Fortran90 and provides advancements in functionality and efficiency compared toLTRANS. First, ROMSPath calculates particle trajectories using the ROMSnative grid, which provides advantages in interpolation, masking, andboundary interaction while improving accuracy. Second, ROMSPath enablessimulated particles to pass between nested ROMS grids, which is anincreasingly popular scheme to simulate the ocean over multiple scales.Third, the ROMSPath vertical turbulence module enables the turbulent(diffusion) time step and advection time step to be specified separately,adding flexibility and improving computational efficiency. Lastly, ROMSPathincludes new infrastructure which enables inputting of auxiliary parameters for addedfunctionality. In particular, Stokes drift can be input and added toparticle advection. Here we describe the details of these updates andperformance improvements.