Particles in the Coastal Ocean

Particle Tracking Utilities

There are a variety of ways to track particles. These utilities provide powerful method to query various web-served databases in order to extract particular portions of the data.

Our Community Particle Tracking Code Repository

An electronic archive contains particle tracking codes currently in development and in use in several coastal environments. It is therefore both an archive to support current research as well as an archive of computational products that has been used in published research projects. In all cases the code is provided for experimentation with the caveat that there is still work to be done. The code archive resides in a GitHub account (a web-based hosting service for software development that uses the Git revision control system). The GitHub account is: https://github.com/Particles-in-the-Coastal-Ocean. In the repository, we include:

Other Particle Tracking Code Repositories

Alternatively, there are other implementations of particle tracking algorithms available in the coastal oceanographic community. We provide a list of algorithms that is not meant to be complete. We separate the algorithms into two categories: 1) code run offline using available model results and 2) web-based particle tracking that does not require any execution by the user (point and click). Many of the web-based routines are now being shared and applied in multiple regions of the globe.

Example Offline Particle Tracking Packages

The Larval TRANSport Lagrangian model is an offline particle-tracking model that uses stored predictions of a 3D hydrodynamic model, specifically the Regional Ocean Modeling System (ROMS). Although LTRANS was built to simulate larvae, it has been adapted to simulate passive particles and other planktonic organisms. LTRANS is written in Fortran 90 and is designed to track the trajectories of particles in three dimensions using a 4th order Runge-Kutta scheme for advection and random displacement to account for vertical turbulence.

Ariane is an offline computational tool (Fortran 90/95) to calculate 3D streamlines from the output velocity field of a finite difference circulation model such as OPA-NEMO, ROMS, or Symphonie.

Paegan Transport is a web service build on a Python library that provides a common data model and methods for particle tracking. It was originally developed as a 3D web-based larval fish and invertebrate transport model connected to ROMS circulation fields for the northeast Pacific. It can be used with any Data Access Protocol (DAP) accessible circulation dataset formatted using the network Common Data Format for Climate and Forecast (NetCDF CF).

PartTracker is a particle tracking research tool currently being developed in MatlabTM which is designed to be used with both unstructured and structured model grids and has previously been applied to outputs from SELFE (Semi -implicit Eulerian-Lagrangian Finite- Element model) for the purposes of assessing wastewater and larval dispersal. PartTracker applies the time adaptive composite 4th-5th order Runge-Kutta (RK45) numerical scheme to ensure required minimum standards of accuracy are achieved for individual particle paths. The application of the RK45 approach ensures consistency in particle path accuracy across hydrodynamically complex domains and a range of user defined time steps with the time adaptive aspect of the approach reducing computational overheads in hydrodynamically simple flows by allowing for long time steps. (Knight et al, 2009)

WebDrogue is a beta-release Java graphical user interface used to obtain drift predictions from user-specified points in the model domain and can be installed under MS-Windows and Linux. The drift trajectories are computed using circulation derived from the tides, the seasonal mean circulation, wind-driven circulation, and a surface-wind drift. (Hannah, et al.2000)

In order to determine the source of particle arriving at one location, particle tracks can be run backwards to determine a probable source, then forward to determine the robustness of the results given a prescribed randomness. This is described in Isobe, et al, 2009, for example, where it is applied to the East China Sea.

ICTHYOP was developed to study how physical factors (e.g., currents, water temperature) and biological factors (e.g., egg buoyancy, larva growth) affect the dynamics of fish eggs and larvae. It gathers physicians and biologists together around a common tool, easily available and user-friendly.

OILTRANS is an off-line particle model of oil transport and weathering. Formulations for the dominant oil fate processes of spreading, advection, diffusion, evaporation, emulsification and dispersion have been encoded, providing the model with the ability to accurately predict the horizontal movement of surface oil slick, the vertical entrainment of oil into the water column and the mass balance of spilled oil. (Berry et al, 2012)

A community of models for coastal sediment transport is under development. Some notes on this project are provided here where there is a list of existing models.

The Connectivity Modeling System is a community multiscale modeling system, based on a stochastic Lagrangian framework. It was developed by Claire Paris at the Rosenstiel School of Marine and Atmospheric Science to study complex larval migrations and give probability estimates of population connectivity. In addition, the CMS can also provide Lagrangian descriptions of oceanic phenomena (advection, dispersion, retention) and can be used in a broad range of applications, from the dispersion and fate of pollutants to marine spatial conservation.

JLAB is an open source oceanographic data and analysis software for MATLAB users where there is specific packages for floats and drifters. It also contains a nice compilation of the Global Drifter Program data in the form of mat files.

Example Web-Based Particle Tracking Routines

Product that tracks the Monterey Bay flows off California.

Product that tracks flow in large Northwest Atlantic ROMS/HYCOM grid.

Visualization tool for a surface ocean drift forecast. (Otero et al, 2015)

Connie2 is an online tool for marine scientists and managers to investigate patterns of marine spatial connectivity. It has been applied in areas such as larval dispersion and recruitment studies, and the development of scenarios and risk assessments for contaminant dispersion.

Ocean Surface Current Simulator by W. James Ingraham, Jr. of NOAA's Alaska Fisheries Science Center is described as "a research tool that allows oceanographers and fisheries scientists to perform retrospective analyses of daily ocean surface currents anywhere in a 90-km ocean-wide grid from Baja California to China and from 10N to the Bering Strait."

Northeast Fisheries Science Center provides a utility to track particles through local ocean model fields. Some hindcast and some forecast. Includes drifter tracks to test against.