skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


  • NSF Public Access
  • Search Results
  • Intercomparisons of Tracker v1.1 and four other ocean particle-tracking software packages in the Regional Ocean Modeling System
Title: Intercomparisons of Tracker v1.1 and four other ocean particle-tracking software packages in the Regional Ocean Modeling System
Abstract. Particle tracking is widely utilized to study transport features in a range of physical, chemical, and biological processes in oceanography. In this study, a new offline particle-tracking package, Tracker v1.1, is introduced, and its performance is evaluated in comparison to an online Eulerian dye, one online particle-tracking software package, and three offline particle-tracking software packages in a small, high-resolution model domain and a large coarser model domain. It was found that both particle and dye approaches give similar results across different model resolutions and domains when they were tracking the same water mass, as indicated by similar mean advection pathways and spatial distributions of dye and particles. The flexibility of offline particle tracking and its similarity against online dye and online particle tracking make it a useful tool to complement existing ocean circulation models. The new Tracker was shown to be a reliable particle-tracking package to complement the Regional Ocean Modeling System (ROMS) with the advantages of platform independence and speed improvements, especially in large model domains achieved by the nearest-neighbor search algorithm. Lastly, trade-offs of computational efficiency, modifiability, and ease of use that can influence the choice of which package to use are explored. The main value of the present study is that the different particle and dye tracking codes were all run on the same model output or within the model that generated the output. This allows some measure of intercomparison between the different tracking schemes, and we conclude that all choices that make each tracking package unique do not necessarily lead to very different results.  more » « less
Award ID(s):
2122420
PAR ID:
10558994
Author(s) / Creator(s):
;
Publisher / Repository:
Copernicus Publications
Date Published:
Journal Name:
Geoscientific Model Development
Volume:
17
Issue:
8
ISSN:
1991-9603
Page Range / eLocation ID:
3341 to 3356
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; (, Geoscientific Model Development)
    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. 
    more » « less
  2. ; ; ; ; ; ; ; ; ; ; et al (, Journal of Instrumentation)
    The LHCb upgrade represents a major change of the experiment. The detectors have been almost completely renewed to allow running at an instantaneous luminosity five times larger than that of the previous running periods. Readout of all detectors into an all-software trigger is central to the new design, facilitating the reconstruction of events at the maximum LHC interaction rate, and their selection in real time. The experiment's tracking system has been completely upgraded with a new pixel vertex detector, a silicon tracker upstream of the dipole magnet and three scintillating fibre tracking stations downstream of the magnet. The whole photon detection system of the RICH detectors has been renewed and the readout electronics of the calorimeter and muon systems have been fully overhauled. The first stage of the all-software trigger is implemented on a GPU farm. The output of the trigger provides a combination of totally reconstructed physics objects, such as tracks and vertices, ready for final analysis, and of entire events which need further offline reprocessing. This scheme required a complete revision of the computing model and rewriting of the experiment's software. 
    more » « less
  3. ; ; ; ; ; ; ; ; (, Journal of Advances in Modeling Earth Systems)
    Abstract Water Mass Transformation (WMT) theory provides conceptual tools that in principle enable innovative analyses of numerical ocean models; in practice, however, these methods can be challenging to implement and interpret, and therefore remain under‐utilized. Our aim is to demonstrate the feasibility of diagnosing all terms in the water mass budget and to exemplify their usefulness for scientific inquiry and model development by quantitatively relating water mass changes, overturning circulations, boundary fluxes, and interior mixing. We begin with a pedagogical derivation of key results of classical WMT theory. We then describe best practices for diagnosing each of the water mass budget terms from the output of Finite‐Volume Generalized Vertical Coordinate (FV‐GVC) ocean models, including the identification of a non‐negligible remainder term as the spurious numerical mixing due to advection scheme discretization errors. We illustrate key aspects of the methodology through the analysis of a polygonal region of the Greater Baltic Sea in a regional demonstration simulation using the Modular Ocean Model v6 (MOM6). We verify the convergence of our WMT diagnostics by brute‐force, comparing time‐averaged (“offline”) diagnostics on various vertical grids to timestep‐averaged (“online”) diagnostics on the native model grid. Finally, we briefly describe a stack of xarray‐enabled Python packages for evaluating WMT budgets in FV‐GVC models (culminating in the newxwmbpackage), which is intended to be model‐agnostic and available for community use and development. 
    more » « less
  4. ; ; ; ; ; (, SEANOE)
    {"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."]} 
    more » « less
  5. ; ; (, PLOS ONE)
    Zhang, Yuji (Ed.)
    In recent years, United States federal funding agencies, including the National Institutes of Health (NIH) and the National Science Foundation (NSF), have implemented public access policies to make research supported by funding from these federal agencies freely available to the public. Enforcement is primarily through annual and final reports submitted to these funding agencies, where all peer-reviewed publications must be registered through the appropriate mechanism as required by the specific federal funding agency. Unreported and/or incorrectly reported papers can result in delayed acceptance of annual and final reports and even funding delays for current and new research grants. So, it’s important to make sure every peer-reviewed publication is reported properly and in a timely manner. For large collaborative research efforts, the tracking and proper registration of peer-reviewed publications along with generation of accurate annual and final reports can create a large administrative burden. With large collaborative teams, it is easy for these administrative tasks to be overlooked, forgotten, or lost in the shuffle. In order to help with this reporting burden, we have developed the Academic Tracker software package, implemented in the Python 3 programming language and supporting Linux, Windows, and Mac operating systems. Academic Tracker helps with publication tracking and reporting by comprehensively searching major peer-reviewed publication tracking web portals, including PubMed, Crossref, ORCID, and Google Scholar, given a list of authors. Academic Tracker provides highly customizable reporting templates so information about the resulting publications is easily transformed into appropriate formats for tracking and reporting purposes. The source code and extensive documentation is hosted on GitHub ( https://moseleybioinformaticslab.github.io/academic_tracker/ ) and is also available on the Python Package Index ( https://pypi.org/project/academic_tracker ) for easy installation. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email