Chesapeake Community Modeling Program

CCMP Newsletter | October 2014

Volume 7, Issue 2


Hello!  Please enjoy this latest edition of the CCMP Newsletter. As always, please contact Dave Jasinski if you have any questions or comments.



1. CCMP News in brief
2. Open Source on the March
3. Featured Model: CH3D
4. Featured Modeler: Richard Tian

1. CCMP News in Brief

New Chesapeake Focus Research Group Chair

Dr. Raleigh Hood
Raleigh Hood

Raleigh Hood is the new chair of the Community Surface Dynamics Modeling System (CSDMS) Chesapeake Focus Research Group (CFRG). He takes the reigns from CCMP sub-committee member Carl Freidrichs who has been the Chair since shortly after the CFRG’s first meeting in April of 2009. It is the goal of the CFRG to foster collaboration between the CFRG and the CCMP. Along those lines, the CCMP is in the initial stages of planning a joint CFRG and CCMP to take place in the summer of 2015. Stay tuned for more information as it becomes available. In the meantime, thanks to Carl for his work as past chair and best of luck to Raleigh!

Climate Change, Marsh Erosion and the Chesapeake Bay TMDL - Carl Cerco and Lewis Linker

Rising sea level in Chesapeake Bay is inexorable. One environmental effect associated with sea level rise is marsh erosion. Marsh erosion can impact water quality in two fashions. The first is the effect on light attenuation and biogeochemistry associated with eroded materials released to the water column. The second, often overlooked, effect is the loss of marsh function. Beneficial marsh functions include retention and burial of suspended solids, nutrient uptake and sequestration, and nitrogen removal through denitrification. Loss of these functions has the potential to affect the living resource based Chesapeake water quality standards.

New work is now underway on Climate Change, Marsh Erosion and the Chesapeake Bay TMDL which will examine the potential impact of marsh loss through a two-phase program. Phase 1 is an estimate of marsh loss and transition due to sea level rise. Phase I will look at the fundamental process of inundation when the rate of sea level rise exceeds the rate at which marshes accrete particulate material. Loss also occurs through physical processes when wave energy dissipated on the shore is enhanced by higher mean sea level. Another potential for loss occurs when increased salinity, associated with higher sea level, impacts vegetation adapted to a different salinity regime. Projected marsh loss will be estimated through several approaches. The first is to investigate existing projections which may have been conducted for other purposes e.g. flood insurance or shoreline protection. The second approach will investigate the use of predictive modeling e.g. the SLAMM (Sea Level Affecting Marshes Model). SLAMM simulates the dominant processes involved in wetland conversions and shoreline modifications during long-term sea level rise. Using these approaches the volumes and rates of material loss will be calculated and the estimated associated sediment and nutrient loads will be applied to the CBP TMDL models in Phase II.

The second phase of quantifying effects of marsh loss on water quality and the TMDL will involve multiple model activities and will interface with the CBP 2017 Midpoint Assessment activity of estimating the impact of sea level rise and marsh loss on the Chesapeake TMDL. Basic algorithms to describe marsh function with relation to water quality will be developed. These algorithms will include, at least, solids removal and burial, nutrient removal and burial, denitrification, and respiration. Algorithms will be developed for two or three marsh types, determined by salinity classification. The algorithms will be based on published investigations in Chesapeake Bay and elsewhere. To augment the modeling work the Chesapeake Bay Program Office is looking for opportunities to expand the work through additional research and field work in Chesapeake marshes.

2. Open Source on the March

Open Source Bash and the Shellshock bug

BASHThe open source software program Bash was developed in the pre-internet days back in 1987. Since then, it has been one of the most important programs in developing the internet we know today. The importance of Bash speaks to the importance of Open source software. However, a recently discovered bug highlights a flaw in the in the open source model.

Bash was developed by Brian Fox, a high school drop out and open source pioneer. Bash is a UNIX shell utility. It allows applications to interact with an operating system. If you’ve ever uploaded a document on the internet, Bash played a key role in allowing the webserver to interact with your computer. Bash has been incorporated into the Mac and any other computer running Linux. Not bad for code originating in 1987. In 1992, Bash development was taken over by Chet Ramey of Case Western University. 1992 may have also been the year that Chet unwittingly wrote a bug into the code. This bug, dubbed “Shellshock”, has recently been exploited by hackers to remotely control unprotected computers. And this highlights a potential flaw of the open source model – lack of oversight for security. This bug went undetected for over two decades simply because no protocol was in place to look for it.

Over its lifetime, Bash has been hacked and modified by thousands of programmers, and if any bugs affecting its performance were discovered, they were fixed. However, no one was in charge of a security audit and the bug lay dormant. This is perhaps not surprising as the code was written before the current internet age. The purpose for which the bug has been exploited didn’t even exist. A similar long dormant bug called Heartbleed was discovered earlier this year. While the power of the open source model is obvious, this incident suggests that a security audit should be a part of open source programming efforts.

Computer Programming at Khan Academy

Khan AcademyMost people with school age kids and access to the internet are more than likely familiar with the online tutoring page Khan Academy. Here, students can learn about subjects ranging from algebra to biology to art history. Khan Academy has recently added computer programming to its list of tutorials. In contrast to the other tutorial subjects which are passive lectures, in the programming tutorials, students actually write and test code. And, in a nod to the open source community, students can share and reuse code written by other students. All lessons are taught using Javascript as the programming language which seems like a decent choice as it shares characteristics with many other object oriented languages. You can check it out at

New NSF Coastal SEES grant will assist managers and stakeholders in choosing policy options for managing oysters.

Coastal SEES Collaborative Research: Integrating stakeholder objectives with natural system models to promote sustainable natural resource policy.

Elizabeth NorthAchieving effective management for most natural resource is challenged by multiple and often competing objectives, a restricted set of policy options, and substantial uncertainty in how well policy options will achieve the objectives. Natural resource management decisions are often based on ad hoc and informal approaches that frequently fail to achieve the desired outcomes. Yet, managers require policies that permit continued use of natural resources while ensuring that future generations will have access to similar resources, all while maintaining other benefits or ecosystem services that the resource provides. Given these challenges, formal approaches are needed that will assist managers and stakeholders in choosing policy options that have a high likelihood of achieving social, ecological, and economic goals.

This new National Science Foundation award to Elizabeth North (and her collaborators Jeff Cornwell, Raleigh Hood, Tom Miller, Mike Wilberg, Lisa Wainger and Troy Hartley) will use a collaborative process involving scientists, managers and stakeholders to build an integrated model that combines quantitative representations of the Chesapeake Bay circulation and biogeochemistry along with the diverse aspects of oyster life history, and the ecosystem services that oysters provide including harvest and water quality. The overall goal of this research is to improve sustainability of natural resource management by 1) developing a quantitative description of a coupled natural human system that allows assessment of the likelihood that policies, if adopted, will achieve stated objectives, 2) integrating stakeholder objectives and values in the creation of this natural system model, and 3) advancing methods for stakeholder participation in natural resource policy development by studying attitudes, perceptions and group dynamics throughout the collaborative modeling process.

3. Featured Model: CH3D

CB_CH3DOur Featured Model for this edition is CH3D – Curvilinear-grid Hydrodynamics model in three dimensions. The original CH3D was developed by Dr. Y. Peter Sheng in 1986 when he was at the Aeronautical Research Associates of Princeton, Inc. Dr. Sheng is now a Professor at the Department of Civil and Coastal Engineering at the University of Florida. CH3D is written in FORTRAN and the latest version has been optimized for running on a parallel computer.

In 1998, Dr. Sheng worked with the U.S. Army Corps of Engineers at the Waterways Experiment Station (WES) to use CH3D to model the circulation of Chesapeake Bay. WES modified CH3D to work on a z-grid as apposed to the original sigma-grid. This CH3D-WES version is the hydrodynamic model currently used by the Bay Program today. Dr. Sheng has continued to modify the CH3D model and has coupled it to wave models, a three dimensional sediment transport model, a three dimensional water quality mode, a light model and a seagrass model. This suite of coupled models is an integrated modeling system called CH3D-IMS. CH3D-WES is in the public domain, however, the most recent version of CH3D is not. Information on the CH3D webpage ( suggests that there is interest in turning CH3D into a “Community Model”.

4. Featured Modeler: Richard Tian

Richard Tian Chesapeake Bay Program Office
410 Severn Avenue
Suite 109
Annapolis, MD 21403

B.A., 1986, Shandong College of Oceanography
M.S., 1988, University of Bordeaux
Ph.D., 1991, University of Bordeaux


Richard Tian has devoted most of his career to marine ecosystem and water quality modeling. The scientific scope of his research ranges from biogeochemical cycles, through nutrient dynamics, primary and secondary production up to fish larvae. Sewage discharge and its impact on water quality parameters and ecosystem function has been a major topic in Richard’s work. He has authored or co-authored over 30 papers in peer-reviewed journals.

At Harvard University, Richard was the lead scientist in developing the Generalized Biological Model (GBM), which consists of 7 functional groups covering suspended detritus, nutrient dynamics, and primary and secondary production. At the University of Massachusetts Dartmouth, he improved this model, coupled it with the Finite-Volume Coastal Ocean Model (FVCOM), and extended it to include fish larvae with a Lagrangian individual-based population dynamics model (IBM). The coupled package was also applied to the Gulf of Maine and Georges Bank. Richard has also coupled the HydroQual RCA model to FVCOM and applied the system to Boston Harbor, Massachusetts Bay and other regions for environmental monitoring, assessment and mitigation analysis.

In addition, Richard has worked on the development and application of coupled physical-biological models with data assimilation and parameter estimation in the Gulf of St. Lawrence and the Labrador Sea, and he has worked on modeling the impacts of industrial discharge and pollution on biogeochemical cycles in the Mediterranean Sea.

At present, Richard is the lead modeler at the Chesapeake Bay Program in charge of running the CH3D, the estuarine circulation model discussed in our Featured Model segment.

Chesapeake Community Model Program
Chesapeake Research Consortium
Edgewater, MD

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