LTRANS
Description ~ Code ~ User's Guide ~ Forum ~ Publications ~ Workshop
Description ~ Code ~ User's Guide ~ Forum ~ Publications ~ Workshop
| This web site hosts the Larval TRANSport Lagrangian model (LTRANS) open source code, User's guide, and associated implementation and post-processing routines. This page is linked to the Chesapeake Community Modeling Program web page where other open source models can be found. |
LTRANS Model Description ---------------------------------------------------------| The Larval TRANSport Lagrangian model (LTRANS) is an off-line particle-tracking model that runs with the stored predictions of a 3D hydrodynamic model, specifically the Regional Ocean Modeling System (ROMS). Although LTRANS was built to simulate oyster larvae, it can easily be 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. It includes a 4th order Runge-Kutta scheme for particle advection and a random displacement model for vertical turbulent particle motion. Reflective boundary conditions, larval behavior, and settlement routines are also included. A brief description of the LTRANS particle-tracking model can be found here (68 KB .pdf). For more information on LTRANS and the application of LTRANS to oyster larvae transport, see a summary web page with animations, the publication North et al. (2008), and the LTRANS User's Guide. Please cite North et al. (2008) when referring to LTRANS. LTRANS was built by Elizabeth North and Zachary Schlag of University of Maryland Center for Environmental Science Horn Point Laboratory. Funding was provided by the National Science Foundation Biological Oceanography Program**, Maryland Department of Natural Resources, NOAA Chesapeake Bay Studies, NOAA Maryland Sea Grant College Program, and NOAA-funded UMCP Advanced Study Institute for the Environment. |
LTRANS Code ----------------------------------------------------------------------------| LTRANS v.1 Open Source Code. We would appreciate knowing who is using LTRANS. If you would like to share this information with us, please send us your name, contact information, and a brief description of how you plan to use LTRANS to LTRANS@hpl.umces.edu. To refer to LTRANS in a peer-reviewed publication, please cite the publication(s) listed in the Description section above. |
| x License file. This license was based on the ROMS license. Please note that this license applies to all sections of LTRANS except those listed in the 'External Dependencies and Programs' section below. x |
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| x LTRANS v.1 Code. This zip file contains the LTRANS code, license, and User's Guide. Section II of the LTRANS User's Guide contains instructions for setting up and running LTRANS in Linux and Windows environments. Before using LTRANS, please read the External Dependencies and Programs section below. This version of LTRANS is parameterized to run with the input files that are available in the LTRANS Example Input Files section below. x |
| External Dependencies and Programs. LTRANS requires NetCDF libraries and uses the following programs to calculate random numbers (Mersenne Twister) and fit tension splines (TSPACK). Because LTRANS reads-in ROMS-generated NetCDF (.nc) files, it requires that the appropriate NetCDF libraries be installed on your computer (see files and links below). Also, please note that although the Mersenne Twister and TSPACK programs are included in the LTRANS in the Random_module.f90 and Tension_module.f90, respectively, they do not share the same license file as LTRANS. Please review and respect their permissions (links and instructions provided below). |
| x Windows Visual Fortran NetCDF libraries. These NetCDF files that are compatible with Visual Fortran were downloaded from the Unidata NetCDF Binaries Website. The NetCDF 90 files were downloaded from Building the F90 API for Windows for the Intel ifort compiler website. The VF-NetCDF.zip folder contains README.txt that describes where to place the enclosed files. If these files do not work, you may have to build your own by following the instructions at the UCAR Unidata NetCDF website. x |
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| x Linux NetCDF libraries. Linux users will likely have to build their own Fortran 90 libraries using the source code/binaries that are available on the UCAR Unidata NetCDF website. x |
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| x Mersenne Twister random number generator. This program was recoded into F90 and included in the Random_module.f90 in LTRANS. See the Mersenne Twister Home Page for more information about this open source program. If you plan to use this program in LTRANS, please send an email to: m-mat @ math.sci.hiroshima-u.ac.jp (remove space) to inform the developers as a courtesy. x |
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| x TSPACK: tension spline curve-fitting package. This program (ACM TOMS Algorithm 716) was created by Robert J. Renka and is used in LTRANS as part of the water column profile interpolation technique. The original TSPACK code can be found at the link to the left and is copyrighted by the Association for Computing Machinery (ACM). With the permission of Dr. Renka and ACM, TSPACK was modified for use in LTRANS by removing unused code and call variables and updating it to Fortran 90. The modified version of TSPACK is included in the LTRANS source code in the Tension Spline Module (tension_module.f90). If you would like to use LTRANS with the modified TSPACK software, please read and respect the ACM Software Copyright and License Agreement. For noncommercial use, ACM grants "a royalty-free, nonexclusive right to execute, copy, modify and distribute both the binary and source code solely for academic, research and other similar noncommercial uses" subject to the conditions noted in the license agreement. Note that if you plan commercial use of LTRANS with the modified TSPACK software, you must contact ACM at permissions@acm.org to arrange an appropriate license. It may require payment of a license fee for commerical use. x |
| LTRANS Example Input Files. These files can be used to test LTRANS. They include examples of particle and habitat location input files (.csv) and ROMS files (.nc) that are needed to run LTRANS. Many thanks to Ming Li and Liejun Zhong for sharing the ROMS .nc files. (The LTRANS code above is configured to run with these input files). Note: please download the y95hdr_182.nc and y95hdr_183.nc files between the hours of 5 pm and 6 am Eastern Standard Time because of their large size. |
| x Initial particle locations and habitat polygon input files needed for initializing LTRANS. The habitat polygon input files are only required when the settlement module is turned on. x |
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| x ROMS grid (for LTRANS input). Please see READ ME file. x |
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| ROMS predictions (for LTRANS input). Please see READ ME file. |
| LTRANS Utilities. The following programs were developed to run LTRANS or visualize LTRANS model output. Unless specified otherwise within the program code, these open source programs are considered part of LTRANS and fall under the LTRANS license. Many thanks to LTRANS users who have made these contributions! If you would like to share a LTRANS utility or your modifications/additions to LTRANS source code, please send them to LTRANS@hpl.umces.edu. |
| x Surfer/Scripter code for visualizing LTRANS output developed by E. W. North. The .zip file includes the program and associated .bln files. Here are example animations of LTRANS model output using the code and example input files provided above: whole Bay (2.8 MB), close up (2.5 MB). Surfer is a Windows program for contouring and 3D surface mapping. Scripter is an object oriented scripting language (Active X Automation) that comes with, and automates, Surfer. Information on Surfer is available here and a free demo is available here. Please note that the demo version will not allow export so it is likely that you will not be able to use the demo version to create .gif files for animations. x |
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| x A Matlab M-file contributed by Yong Kim. It makes a 3D plot of the model bathymetry (from .nc input file) and particle locations from LTRANS .csv output files. See an example .gif animation here. x |
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LTRANS User's Guide ----------------------------------------------------------------------------
Please send comments or suggestions regarding the User's Guide to LTRANS@hpl.umces.edu.
Schlag, Z. R., E. W. North, and K. A. Smith. 2008. Larval TRANSport Lagrangian model
(LTRANS) User’s Guide. University of Maryland Center for Environmental Science, Horn Point Laboratory. Cambridge, MD. 146 pp. (739 KB .pdf)
Discussion Forum ----------------------------------------------------------------------------------
We started a discussion forum topic in the ROMS/TOMS Ocean Modeling Discussion Forum under ROMS/TOMS Applications > User Applications > LTRANS. Here is the link to the topic. If you have questions about LTRANS, please post them at this site and Elizabeth North, Zachary Schlag, or other LTRANS Users will answer them.
LTRANS Publications ----------------------------------------------------------------------------
If you use LTRANS, please send citations and .pdfs of your publications based on LTRANS to LTRANS@hpl.umces.edu. We would like to add your citations to this list.
North, E. W., R. R. Hood, S.-Y. Chao, and L. P. Sanford. 2006. Using a random displacement model to simulate turbulent particle motion in a baroclinic frontal zone: a new implementation scheme and model performance tests. Journal of Marine Systems 60: 365-380 (request .pdf).
North, E. W., Z. Schlag, R. R. Hood, L. Zhong, M. Li, and T. Gross. 2006. Modeling dispersal of Crassostrea ariakensis oyster larvae in Chesapeake Bay. Final Report to Maryland Department of Natural Resources, July 31, 2006. 55 p. (request .pdf)
North, E. W., Z. Schlag, R. R. Hood, M. Li, L. Zhong, T. Gross, and V. S. Kennedy. 2008. Vertical swimming behavior influences the dispersal of simulated oyster larvae in a coupled particle-tracking and hydrodynamic model of Chesapeake Bay. Marine Ecology Progress Series 359: 99-115 (request .pdf).
Schlag, Z., E. W. North, and K. Smith. 2008. Larval TRANSport Lagrangian model (LTRANS) User’s Guide. University of Maryland Center for Environmental Science, Horn Point Laboratory. Cambridge, MD. 146 pp. (739 KB .pdf)
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LTRANS Workshop ------------------------------------------------------------------------------The first LTRANS workshop was held on July 17-18, 2008 at University of Maryland Center for Environmental Science (UMCES) Horn Point Laboratory. The workshop was hosted by LTRANS developers and sponsored by UMCES Horn Point Laboratory and Chesapeake Research Consortium (many thanks!). A beta version of LTRANS was presented and tested by workshop participants. LTRANS was successfully run with the following compilers: ifort, pathscale, Visual Fortran, and g95. The v.1 LTRANS code posted on this website includes the suggestions and fixes recommended by workshop participants. Many thanks for their hard work and input!
Presentations during the first day of the workshop were recorded and will be posted on this website in September, 2008. Information for workshop participants is located here: Workshop Participants Page.
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