ccrmwiki - User contributions [en]

Mesh generation

2015-09-28T20:02:48Z

Benk:

==Grid generation tool==
We recommend [http://www.aquaveo.com/sms SMS] for grid generation.

==Bathymetric Data==
If you require 'approximate' bathymetry for your area, this can be obtained from the SRTM 15 and 30 meter data sets, available here:

http://topex.ucsd.edu/WWW_html/srtm30_plus.html

Regional specific bathymetry data at 30m resolution in an xyz format is available here:

http://topex.ucsd.edu/cgi-bin/get_srtm30.cgi

Note that this data is of variable quality and may be inaccurate for your region, so please check the quality of the data against available charts and preferentially use local data if available.

==Beware of CFL number==

You may be familiar with the CFL restriction associated with explicit (mode-splitting) models; the CFL number, defined as

CFL=(|u|+sqrt(g*h))*dt/dx

must be <1 for given dx,dt in such models. Here h is the local water depth, and u is the flow velocity. Note that the sqrt() term is related to surface wave celerity.

Being an implicit model using Eulerian-Lagrangian method (ELM), SCHISM has a somewhat opposite requirement: CFL>0.4 (you may be able to get away with CFL>0.2 in some applications like tsunami). Therefore care must be taken in the grid generation
process; otherwise numerical diffusion in ELM would ruin your results, which may manifest itself in the form of either noise or dissipation.

With [http://ccrm.vims.edu/w/index.php/ACE_tools xmgredit5], you can very easily visualize CFL for the entire grid. Note, however, that CFL number is undefined when h<0. In these shallow regions, we should use |u| alone and neglect the wave celerity term (sqrt(g*h)). E.g., if we estimate |u| ~ 1m/s, with a time step of 100s, the max. dx in regions of h<0 should be 250m; with dt=50s, dx_max=125m.

'''Viz CFL number in xmgredit5'''
<UL>
<LI>xmgredit5 -belel -1.e-10 hgrid.gr3 (note: '-belel -1.e-10' is used mainly to increase precision for lat/lon grid. Note: if your hgrid.gr3 is in lat/lon, you need to first project it, as the grid size dx in lat/lon is not in meters)
<LI>since the CFL inside ACE is calculated without u, we should impose a min depth of 0.1 (so that sqrt(g*h)>=1m/s); you can do this by: 
Edit-->Edit over grid/regions-->Evaluate, and then in the dialogue box, type depth=max(depth,0.1). (Note that the Evaluate function is also very useful for generation of other .gr3 files needed by SCHISM)
<LI>Special-->Dimensionless numbers, and then in the right half of the dialogue box, type in dt, Warning value (say 0.4), Unacceptable value (say 0.4) and depress 'Display filled' button. The color will appear in the main window, with red indicating good CFL, and green for bad CFL. You may also 'Display Courant number' but this may take a while to refresh, and so you may want to zoom into a small region first.
<LI>revise your grid accordingly
</UL>

Remember, if you have to reduce the time step for some reason, you may have to refine grid because of CFL. It's wise to plan for a smallest dt you expect to use for a system, and design your grid according to this dt. This issue is closely related to the [http://ccrm.vims.edu/w/index.php/Convergence_study_with_SCHISM convergence property of SCHISM].

In tsunami simulations, dt has to be small due to small wavelength, and you can bypass the CFL condition by turning off advection in deeper depths as the advection is negligible there. You also need to make sure that each wavelength is resolved by at least 20 grid points.

==Grid near wetting and drying==

It's important to have the grid follow the initial shoreline. Reasonable grid transition should be done from shoreline to dryland. Use comaprable or finer grid resolution in the dryland that is expected to be wetted, and then transition to coarser resolution beyond (to account for rare inunation).

Simulating wetting and drying well with SCHISM requires some effort; read more [http://ccrm.vims.edu/w/index.php/Simulating_wetting_and_drying_with_SCHISM here].

'''IMPORTANT:''' in grid generation, make sure channels are resolved by at least 2 ''alway wet'' nodes, to allow flow to pass thru. Failure to do so may lead to noisy flow field.

==Barotropic simulation==

Grid quality requirement is relatively lax for barotropic simulations. Besides the considerations above, you mainly need to use appropriate resolution based on physics (e.g., generally coarser resolution in deeper depths and finer resolution for shallow depths). Remember: you are on unstructured grid territory, and so you are free to resolve features as you wish!

Another commonly asked question is the max. element skewness. SCHISM, in either barotropic or baroclinic configuration, can tolerate elements as skew as 20! (skewness is defined as the ratio between the max. side and the equivalent radius)

==Baroclinic simulation==

The transport process is influenced by your choice of grid, and so grid for baroclinic simulations needs some attention. For example, the channels should be gridded as quasi-structured grid ('Patches' in SMS). 

The Courant number condition for transport may need to be accounted for during gridgen, especially if you use TVD scheme. In SCHISM, the time steps used for momentum and transport can be different, with the latter being usually smaller (the model will automatically calculate the transport step for you and do sub-cycling). The Courant number condition for the transport equations is:

Cu=c*|u|*dtb/dx<1 
where c=1 for upwind and c<1 for TVD; dtb is the transport time step.

Therefore especially for TVD schemes, you should avoid excessively refining areas that expect high flow. Fortunately, there are tools to help you identify 'choke' regions. Here is a [http://ccrm.vims.edu/yinglong/wiki_files/SaltIntrusionwithSELFE-Oct2011.pdf document] on how to do a good salt intrusion study with SCHISM's TVD scheme.

Mesh generation

2015-09-28T20:02:05Z

Benk:

==Grid generation tool==
We recommend [http://www.aquaveo.com/sms SMS] for grid generation.

==Bathymetric Data==
If you require 'approximate' bathymetry for your area, this can be obtained from the SRTM 15 and 30 meter data sets, available here:

[http://topex.ucsd.edu/WWW_html/srtm30_plus.html]

Regional specific bathymetry data at 30m resolution in an xyz format is available here:

[http://topex.ucsd.edu/cgi-bin/get_srtm30.cgi]

Note that this data is of variable quality and may be inaccurate for your region, so please check the quality of the data against available charts and preferentially use local data if available.

==Beware of CFL number==

You may be familiar with the CFL restriction associated with explicit (mode-splitting) models; the CFL number, defined as

CFL=(|u|+sqrt(g*h))*dt/dx

must be <1 for given dx,dt in such models. Here h is the local water depth, and u is the flow velocity. Note that the sqrt() term is related to surface wave celerity.

Being an implicit model using Eulerian-Lagrangian method (ELM), SCHISM has a somewhat opposite requirement: CFL>0.4 (you may be able to get away with CFL>0.2 in some applications like tsunami). Therefore care must be taken in the grid generation
process; otherwise numerical diffusion in ELM would ruin your results, which may manifest itself in the form of either noise or dissipation.

With [http://ccrm.vims.edu/w/index.php/ACE_tools xmgredit5], you can very easily visualize CFL for the entire grid. Note, however, that CFL number is undefined when h<0. In these shallow regions, we should use |u| alone and neglect the wave celerity term (sqrt(g*h)). E.g., if we estimate |u| ~ 1m/s, with a time step of 100s, the max. dx in regions of h<0 should be 250m; with dt=50s, dx_max=125m.

'''Viz CFL number in xmgredit5'''
<UL>
<LI>xmgredit5 -belel -1.e-10 hgrid.gr3 (note: '-belel -1.e-10' is used mainly to increase precision for lat/lon grid. Note: if your hgrid.gr3 is in lat/lon, you need to first project it, as the grid size dx in lat/lon is not in meters)
<LI>since the CFL inside ACE is calculated without u, we should impose a min depth of 0.1 (so that sqrt(g*h)>=1m/s); you can do this by: 
Edit-->Edit over grid/regions-->Evaluate, and then in the dialogue box, type depth=max(depth,0.1). (Note that the Evaluate function is also very useful for generation of other .gr3 files needed by SCHISM)
<LI>Special-->Dimensionless numbers, and then in the right half of the dialogue box, type in dt, Warning value (say 0.4), Unacceptable value (say 0.4) and depress 'Display filled' button. The color will appear in the main window, with red indicating good CFL, and green for bad CFL. You may also 'Display Courant number' but this may take a while to refresh, and so you may want to zoom into a small region first.
<LI>revise your grid accordingly
</UL>

Remember, if you have to reduce the time step for some reason, you may have to refine grid because of CFL. It's wise to plan for a smallest dt you expect to use for a system, and design your grid according to this dt. This issue is closely related to the [http://ccrm.vims.edu/w/index.php/Convergence_study_with_SCHISM convergence property of SCHISM].

In tsunami simulations, dt has to be small due to small wavelength, and you can bypass the CFL condition by turning off advection in deeper depths as the advection is negligible there. You also need to make sure that each wavelength is resolved by at least 20 grid points.

==Grid near wetting and drying==

It's important to have the grid follow the initial shoreline. Reasonable grid transition should be done from shoreline to dryland. Use comaprable or finer grid resolution in the dryland that is expected to be wetted, and then transition to coarser resolution beyond (to account for rare inunation).

Simulating wetting and drying well with SCHISM requires some effort; read more [http://ccrm.vims.edu/w/index.php/Simulating_wetting_and_drying_with_SCHISM here].

'''IMPORTANT:''' in grid generation, make sure channels are resolved by at least 2 ''alway wet'' nodes, to allow flow to pass thru. Failure to do so may lead to noisy flow field.

==Barotropic simulation==

Grid quality requirement is relatively lax for barotropic simulations. Besides the considerations above, you mainly need to use appropriate resolution based on physics (e.g., generally coarser resolution in deeper depths and finer resolution for shallow depths). Remember: you are on unstructured grid territory, and so you are free to resolve features as you wish!

Another commonly asked question is the max. element skewness. SCHISM, in either barotropic or baroclinic configuration, can tolerate elements as skew as 20! (skewness is defined as the ratio between the max. side and the equivalent radius)

==Baroclinic simulation==

The transport process is influenced by your choice of grid, and so grid for baroclinic simulations needs some attention. For example, the channels should be gridded as quasi-structured grid ('Patches' in SMS). 

The Courant number condition for transport may need to be accounted for during gridgen, especially if you use TVD scheme. In SCHISM, the time steps used for momentum and transport can be different, with the latter being usually smaller (the model will automatically calculate the transport step for you and do sub-cycling). The Courant number condition for the transport equations is:

Cu=c*|u|*dtb/dx<1 
where c=1 for upwind and c<1 for TVD; dtb is the transport time step.

Therefore especially for TVD schemes, you should avoid excessively refining areas that expect high flow. Fortunately, there are tools to help you identify 'choke' regions. Here is a [http://ccrm.vims.edu/yinglong/wiki_files/SaltIntrusionwithSELFE-Oct2011.pdf document] on how to do a good salt intrusion study with SCHISM's TVD scheme.

Sharing your tools

2014-03-24T00:59:38Z

Benk: /* Matlab wrapper scripts */

We encourage all users to share useful scripts/tools with the whole community. Please also include a short description to go with your scripts.
If you cannot upload your files due to either type or size restriction, please send them to yjzhang@vims.edu.

Below are user-supplied utility scripts:

=Matlab wrapper scripts =
Author: Ben Knight 
Contact: Ben.Knight@cawthron.org.nz 
Purpose: wrapper for the Matlab viz tool 
Type: matlab 
Links: [http://ccrm.vims.edu/yinglong/wiki_files/matlab_Knight_March2014.zip].

=Pre-processing script=
Author: Li Jian 
Contact: 
Purpose: Script to convert Gambit grid format (.neu) to .gr3 
Type: 
Link: [http://ccrm.vims.edu/yinglong/wiki_files/LiJian_June2011.zip]

Simulating wetting and drying with SELFE

2013-01-23T20:26:07Z

Benk:

SELFE's wetting and drying capability has been carefully benchmarked and verified. There are 2 options: inunfl=0 as a 'light-weight' inundation scheme (you'd always start with this option), and a 'fine-scale' inundation scheme (inunfl=1), which requires some care. In particular, since extrapolation is used with inunfl=1, you'd make sure that the grid is reasonably resolved in the wetting and drying regions. This scheme may also require a smaller time step to very accurately capture the inundation process.

The wetting and drying process is inherently nonlinear and challenging, and below are some tips.

==Bottom friction in shallow areas==

A critical parameter in shallow area is the bottom friction. Note that the bottom friction parameterizations are very different between 2D and 3D model, and so you cannot use same input. For details please read [http://ccrm.vims.edu/yinglong/wiki_files/Report-ChezyFlow-Sept2011.pdf this article].

From a physical point of view, the 2D and 3D models behave very differently. Consider a straight channel with variable depths, with flow coming from deeper part and going into shallower part. Fig. 1 shows the side views of 2D and 3D velocities.

[[File:WetDry-2Dvs3D.PNG|thumb|center|Fig. 1 Side view of channel flow for (a) 2D and (b) 3D cases. Volume conservation dictates larger velocities in shallow areas. Note that strong shear is possible in 3D model.]]

In 2D model, the velocity is depth-averaged and vertical shear is not represented. Strong friction merely translates into reduced velocity. In 3D model however, a large friction will lead to strong shear, although the depth integrated velocity value matches that from the 2D model. This problem is exacerbated by the use of terrain-following coordinates. This is because the log-drag formula, when bfric=1 is used, is:

Cd=[log(dz_b/z_0)/k]^-2

where z_0 is bottom roughness and dz_b is the bottom cell thickness. In shallow areas, dz_b~z_0 which leads to unrealistically large Cd. Note that Z-layer models do not have this problem as dz_b is not small there. A classical pathological velocity field obtained with SELFE is seen in Fig. 2. This problem is especially obvious when a large dt is used, as in the case of Fig. 2.

[[File:WetDry-issue-SELFE.PNG|thumb|center|Fig. 2 Noisy velocity field in shallow areas in SELFE 3D]]

From a grid generation point of view, you'd make sure that channels are not 'blocked', i.e., with at least 2 ''always-wet'' nodes.

Numerically, there is a quick fix to this problem by reducing Cd used in SELFE 3D. When using bfric=1, set a reasonable Cdmax=0.006, and in some tricky regions (e.g. with large acceleration or rapid bathymetric variations), you may need to further reduce Cd locally. If you used bfric=1, you can do so by simply setting the local ?roughness? to a negative value (i.e. telling the code the value is not roughness but Cd!); we found -0.0025 to -0.001 usually works well.

Applications and case studies

2012-10-09T20:08:18Z

Benk: /* Aquaculture and coastal pollutants modelling (New Zealand) */

==Columbia River estuary and plume==
'''Research Team''' 
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton 

'''Projection description''' 
Columbia River estuary and plume circulation presents a formidable challenge for hydrodynamic models due to the interaction between strong tides, meteorological forcing, high river discharge, and strong stratification. SELFE was originally developed to address these challenges and some details can be found in the SELFE paper.

The SELFE-enabled virtual Columbia River is a skill-assessed 4D (space-time) simulation environment that offers multiple representations of circulation processes, variability and change across river-to-shelf scales. Circulation includes water levels, salinity, temperature, and velocities. 

[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site'''] 

'''Related publications''' 
<UL>
<LI>Burla, M., Baptista, A.M. Zhang, Y.L., and Frolov, S. (2010) Seasonal and inter-annual variability of the Columbia River plume: a perspective enabled by multi-year simulation databases. Journal of Geophysical Research: special issue on NSF RISE project, 115, C00B16.
<LI>Frolov, S., Baptista, A.M., Zhang, Y.L., and Seaton, C. (2009) Estimation of Ecologically Significant Circulation Features of the Columbia River Estuary and Plume Using a Reduced-Dimension Kalman Filter. Continental Shelf Research, 29(2), 456-466.
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (accepted). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research.
<LI>Zhang, Y.-L. and Baptista, A.M. (2008) "SELFE: A semi-implicit Eulerian-Lagrangian finite-element model for cross-scale ocean circulation", Ocean Modelling, 21(3-4), 71-96.
</UL>

'''Sample images''' 

Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]] 

==DWR==

==SURA==

'''Research Team''' 
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang 
OHSU: Joseph Zhang 

'''Projection description''' 

SELFE is being used in an IOOS sponsored super-regional testbed for coastal inundation, led by Dr. Rick Luettich (UNC). The testbed focuses on two coastal regions that are prone to inundation hazard: Gulf of Mexico and Gulf of Maine. 

[http://testbed.sura.org/node/554 '''Project web site'''] 
'''Related publications''' 
<UL>
<LI> Teng, Y.C., Wang, H.V., Zhang, Y., Roland, A. (to be submitted) The effect of bottom boundary layer dynamics on the forerunner simulation during Hurricane Ike in the Gulf of Mexico.
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (in press) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research.
<LI>Cho, K.H. Wang, H.V., Shen, J., Valle-Levinson, A. and Teng, Y.C. (2012) A modeling study on the response of the Chesapeake Bay to Hurricane Events of Floyd and Isabel. Ocean Modeling, vol. 49-50, pp. 22-46.
</UL>
'''Sample images''' 
Fig. 2 shows an example application of the fully coupled SELFE-WWM and a simple sediment model to hurricane Ike (2008) in Gulf of Mexico. The full results are being published (Teng et al. 2012).
[[File:SURA-Ike-YC.jpg|thumb|center|Fig. 2 Domain used to simulate hurricane Ike in Gulf of Mexico. The comparison plot shows the primary surge and forerunner simulated with different physical formulations (c/o Y.C. Teng)]]
 

==Xavier's group==

==Portuguese coastal systems==

There are 3 related projects for this system.

<OL>
<LI> ''A nowcast-forecast system for for Portuguese coastal systems'' 
'''Research Team''' 

LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes 
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton 

'''Project description''' 

The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and
the American institution will provide the innovative nowcast-forecast technology. 

[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']

<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' 
'''Research Team''' 

LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin 
'''Project description''' 

Tidal inlets are among the most dynamic environments along the world coastlines while social-economic activities are there concentrated. These problems are particularly relevant in Portugal due to its extensive coastline and the existence of many tidal inlets of social, environmental and economic importance. In the perspective of a sustainable development, it is essential to understand and to be able to predict the long-term evolution of these systems. To achieve these goals, one of the most promising avenues is the development of morphodynamic models, which consist of a set of modules to simulate tidal hydrodynamics, wave propagation, sediment transport and bottom evolution. This project aims at contributing to the advance of an existing morphodynamic modeling system (MORSYS2D) that is under development at the host institution (LNEC). 

[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)''
'''Research Team''' 
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes 
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner 

'''Project description''' 
This proposal aims to integrate complementary research strengths at the two institutions to improve and validate a sophisticated ecological modeling system for operational forecasting of ecosystem dynamics based on grid computing resources. The Portuguese partner will provide the ecological model and the expertise on grid-enabling of numerical models. The American partner will provide the expertise on parallel computing and the benchmark for validation and inter-model comparison. 
[[File:model-ecoselfe.jpg|thumb|center|Fig. 3 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]] 

[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']
</OL>

 

==Tsunami==
'''Research Team''' 
OHSU & VIMS: Joseph Zhang 
DOGAMI: George Priest, Rob Witter, Laura Stimely 
GeoCanada: Kelin Wang 
Oregon State Univ: Chris Goldfinger 

'''Projection description''' 

SELFE has been certified by National Tsunami Hazard Program (NTHMP) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].
It has been used to generate official inundation maps for the state of Oregon, spearheaded by OR Department of Geology ad Mineral Industries [http://www.oregongeology.org/sub/default.htm (DOGAMI)], under the auspice of NTHMP. 

'''Sample images''' 
Fig. 4 is a sample inundation map for Cannon Beach OR.
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]
 

'''Related publications''' 
<UL>
<LI>Witter, R.C, Zhang, Y., Wang, K., Goldfinger, C., Priest, G.R., Allan, J.C. (in press) Coseismic slip on the Cascadia megathrust implied by tsunami deposits in an Oregon lake. Journal of Geophysical Research-Solid Earth.
<LI>Witter, R.C., Jaffe, B., Zhang, Y. and Priest, G.R. (2011) Reconstructing hydrodynamic flow parameters of the 1700 tsunami at Cannon Beach, Oregon, USA., Natural Hazards, DOI 10.1007/s11069-011-9912-7.
<LI>Zhang, Y., Witter, R.W. and Priest, G.P. (2011) Tsunami-Tide Interaction in 1964 Prince William Sound Tsunami, Ocean Modelling, 40, 246-259.
<LI>Priest, G.R., Goldfinger, C., Wang, K., Witter, R.C., Zhang, Y., Baptista, A.M. (2010) Confidence levels for tsunami-inundation limits in northern Oregon inferred from a 10,000-year history of great earthquakes at the Cascadia subduction zone. Natural Hazards, 54(1), 27-73.
<LI>Zhang, Y.L., and Baptista, A.M. (2008) Benchmarking a new finite-element tsunami model on unstructured grids. Pure and Applied Geophysics: Topical issue on Tsunamis, vol. 165, pp. 2229-2248. pdf .
</UL>

 

==Water Quality in the Chesapeake Bay Region==

'''Research Team'''

Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]

'''Projection description'''

The Chesapeake Bay and the Coastal Bays of the Maryland/Virginia Atlantic shore are highly valuable and productive ecosystems that are increasingly threatened by degraded water quality and loss of habitat due to both anthropogenic and natural disturbances.

In an effort to reverse this trend, federal and state governments have implemented a Total Maximum Daily Load (TMDL) program to control point source and non-point source pollution in each watershed.

In order to quantify these controls and better understand cause and effect relationships, the Virginia Institute of Marine Science is developing numerical hydrodynamic and water quality models and linking them together as a tool for predicting and measuring success of the TMDL effort.

Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:

<OL>
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.
</OL>

Both projects involve coupling SELFE and ICM (Integrated Compartment Model).

'''Sample images'''

Fig. 5 shows some sample results.
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]

 

==Aquaculture and coastal pollutants modelling (New Zealand)==

'''Research Team''' 
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight 
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley 

'''Application description''' 
Aquaculture and other coastal developments in New Zealand have the potential to place increasing pressures on coastal environments. The Cawthron Institute and MetOcean Solutions Limited have been collaborating to produce open-source community models for coastal environments around New Zealand to aid in coastal effects assessments. We are presently utilising and building upon SELFE community modelling tools associated with Lagrangian and Eularian transport for a range of coastal transport applications (e.g. faecal indicator bacteria, nutrients, oil spills). 
We have a number of collaborative projects under-way, but are currently working towards simplifying the set up and analysis of tracers for modelling a range of chemical and biological constituents in aquaculture and coastal discharge assessments. 

'''Sample images''' 

Fig. 6 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]

Applications and case studies

2012-10-08T23:31:06Z

Benk: /* Aquaculture and coastal pollutants modelling */

==Columbia River estuary and plume==
'''Research Team''' 
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton 

'''Projection description''' 
Columbia River estuary and plume circulation presents a formidable challenge for hydrodynamic models due to the interaction between strong tides, meteorological forcing, high river discharge, and strong stratification. SELFE was originally developed to address these challenges and some details can be found in the SELFE paper.

The SELFE-enabled virtual Columbia River is a skill-assessed 4D (space-time) simulation environment that offers multiple representations of circulation processes, variability and change across river-to-shelf scales. Circulation includes water levels, salinity, temperature, and velocities. 

'''Project web site'''
[http://www.stccmop.org/datamart/virtualcolumbiariver] 

'''Related publications''' 
<UL>
<LI>Burla, M., Baptista, A.M. Zhang, Y.L., and Frolov, S. (2010) Seasonal and inter-annual variability of the Columbia River plume: a perspective enabled by multi-year simulation databases. Journal of Geophysical Research: special issue on NSF RISE project, 115, C00B16.
<LI>Frolov, S., Baptista, A.M., Zhang, Y.L., and Seaton, C. (2009) Estimation of Ecologically Significant Circulation Features of the Columbia River Estuary and Plume Using a Reduced-Dimension Kalman Filter. Continental Shelf Research, 29(2), 456-466.
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (accepted). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research.
<LI>Zhang, Y.-L. and Baptista, A.M. (2008) "SELFE: A semi-implicit Eulerian-Lagrangian finite-element model for cross-scale ocean circulation", Ocean Modelling, 21(3-4), 71-96.
</UL>

'''Sample images''' 

Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]] 

==DWR==

==SURA==

'''Research Team''' 
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang 
OHSU: Joseph Zhang 

'''Projection description''' 

SELFE is being used in an IOOS sponsored super-regional testbed for coastal inundation, led by Dr. Rick Luettich (UNC). The testbed focuses on two coastal regions that are prone to inundation hazard: Gulf of Mexico and Gulf of Maine. 

'''Project web site'''
[http://testbed.sura.org/node/554] 
'''Related publications''' 
<UL>
<LI> Teng, Y.C., Wang, H.V., Zhang, Y., Roland, A. (to be submitted) The effect of bottom boundary layer dynamics on the forerunner simulation during Hurricane Ike in the Gulf of Mexico.
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (in press) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research.
<LI>Cho, K.H. Wang, H.V., Shen, J., Valle-Levinson, A. and Teng, Y.C. (2012) A modeling study on the response of the Chesapeake Bay to Hurricane Events of Floyd and Isabel. Ocean Modeling, vol. 49-50, pp. 22-46.
</UL>
'''Sample images''' 
Fig. 2 shows an example application of the fully coupled SELFE-WWM and a simple sediment model to hurricane Ike (2008) in Gulf of Mexico. The full results are being published (Teng et al. 2012).
[[File:SURA-Ike-YC.jpg|thumb|center|Fig. 2 Domain used to simulate hurricane Ike in Gulf of Mexico. The comparison plot shows the primary surge and forerunner simulated with different physical formulations (c/o Y.C. Teng)]]
 

==Xavier's group==

==Portuguese coastal systems==

There are 3 related projects for this system.

<OL>
<LI> ''A nowcast-forecast system for for Portuguese coastal systems'' 
'''Research Team''' 

LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes 
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton 

'''Project description''' 

The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and
the American institution will provide the innovative nowcast-forecast technology. 

'''Project web site'''
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast]

<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' 
'''Research Team''' 

LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin 
'''Project description''' 

Tidal inlets are among the most dynamic environments along the world coastlines while social-economic activities are there concentrated. These problems are particularly relevant in Portugal due to its extensive coastline and the existence of many tidal inlets of social, environmental and economic importance. In the perspective of a sustainable development, it is essential to understand and to be able to predict the long-term evolution of these systems. To achieve these goals, one of the most promising avenues is the development of morphodynamic models, which consist of a set of modules to simulate tidal hydrodynamics, wave propagation, sediment transport and bottom evolution. This project aims at contributing to the advance of an existing morphodynamic modeling system (MORSYS2D) that is under development at the host institution (LNEC). 

'''Project web site'''[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie]
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)''
'''Research Team''' 
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes 
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner 

'''Project description''' 
This proposal aims to integrate complementary research strengths at the two institutions to improve and validate a sophisticated ecological modeling system for operational forecasting of ecosystem dynamics based on grid computing resources. The Portuguese partner will provide the ecological model and the expertise on grid-enabling of numerical models. The American partner will provide the expertise on parallel computing and the benchmark for validation and inter-model comparison. 
[[File:model-ecoselfe.jpg|thumb|center|Fig. 3 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]] 

'''Project web site'''
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem]
</OL>

 

==Tsunami==
'''Research Team''' 
OHSU & VIMS: Joseph Zhang 
DOGAMI: George Priest, Rob Witter, Laura Stimely 
GeoCanada: Kelin Wang 
Oregon State Univ: Chris Goldfinger 

'''Projection description''' 

SELFE has been certified by National Tsunami Hazard Program (NTHMP) as a tsunmai inundation model, after passing various benchmarks stipulated by NOAA [http://nctr.pmel.noaa.gov/benchmark/].
It has been used to generate official inundation maps for the state of Oregon, spearheaded by OR Department of Geology ad Mineral Industries (DOGAMI) [http://www.oregongeology.org/sub/default.htm], under the auspice of NTHMP. 

'''Sample images''' 
Fig. 4 is a sample inundation map for Cannon Beach OR.
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]
 

'''Related publications''' 
<UL>
<LI>Witter, R.C, Zhang, Y., Wang, K., Goldfinger, C., Priest, G.R., Allan, J.C. (in press) Coseismic slip on the Cascadia megathrust implied by tsunami deposits in an Oregon lake. Journal of Geophysical Research-Solid Earth.
<LI>Witter, R.C., Jaffe, B., Zhang, Y. and Priest, G.R. (2011) Reconstructing hydrodynamic flow parameters of the 1700 tsunami at Cannon Beach, Oregon, USA., Natural Hazards, DOI 10.1007/s11069-011-9912-7.
<LI>Zhang, Y., Witter, R.W. and Priest, G.P. (2011) Tsunami-Tide Interaction in 1964 Prince William Sound Tsunami, Ocean Modelling, 40, 246-259.
<LI>Priest, G.R., Goldfinger, C., Wang, K., Witter, R.C., Zhang, Y., Baptista, A.M. (2010) Confidence levels for tsunami-inundation limits in northern Oregon inferred from a 10,000-year history of great earthquakes at the Cascadia subduction zone. Natural Hazards, 54(1), 27-73.
<LI>Zhang, Y.L., and Baptista, A.M. (2008) Benchmarking a new finite-element tsunami model on unstructured grids. Pure and Applied Geophysics: Topical issue on Tsunamis, vol. 165, pp. 2229-2248. pdf .
</UL>

 

==Water Quality in the Chesapeake Bay Region==

'''Research Team'''

Virginia Institute of Marine Science: Junzheng Zhu and Harry Wang [http://www.vims.edu/people/wang_hv/index.php]

'''Projection description'''

The Chesapeake Bay and the Coastal Bays of the Maryland/Virginia Atlantic shore are highly valuable and productive ecosystems that are increasingly threatened by degraded water quality and loss of habitat due to both anthropogenic and natural disturbances.

In an effort to reverse this trend, federal and state governments have implemented a Total Maximum Daily Load (TMDL) program to control point source and non-point source pollution in each watershed.

In order to quantify these controls and better understand cause and effect relationships, the Virginia Institute of Marine Science is developing numerical hydrodynamic and water quality models and linking them together as a tool for predicting and measuring success of the TMDL effort.

Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:

<OL>
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.
</OL>

Both projects involve coupling SELFE and ICM (Integrated Compartment Model).

'''Sample images'''

Fig. 5 shows some sample results.
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]

 

==Aquaculture and coastal pollutants modelling==

'''Research Team''' 
Cawthron Institute [http://www.cawthron.org.nz]: Ben Knight 
MetOcean Solutions Limited [http://www.metocean.co.nz/]: Brett Beamsley 

'''Application description''' 
Aquaculture and other coastal developments in New Zealand have the potential to place increasing pressures on coastal environments. The Cawthron Institute and MetOcean Solutions Limited have been collaborating to produce open-source community models for coastal environments around New Zealand to aid in coastal effects assessments. We are presently utilising and building upon SELFE community modelling tools associated with, lagrangian and eularian transport for a range of coastal transport applications (e.g. faecal indicator bacteria, nutrients, oil spills). 
We have a number of collaborative projects under-way, but are currently working towards simplifying the set up and analysis of tracers for modelling a range of chemical and biological constituents in aquaculture and coastal discharge assessments. 

'''Sample images''' 

Fig. 6 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]

Applications and case studies

2012-10-08T23:30:09Z

Benk: /* Aquaculture and coastal pollutants modelling */

==Columbia River estuary and plume==
'''Research Team''' 
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton 

'''Projection description''' 
Columbia River estuary and plume circulation presents a formidable challenge for hydrodynamic models due to the interaction between strong tides, meteorological forcing, high river discharge, and strong stratification. SELFE was originally developed to address these challenges and some details can be found in the SELFE paper.

The SELFE-enabled virtual Columbia River is a skill-assessed 4D (space-time) simulation environment that offers multiple representations of circulation processes, variability and change across river-to-shelf scales. Circulation includes water levels, salinity, temperature, and velocities. 

'''Project web site'''
[http://www.stccmop.org/datamart/virtualcolumbiariver] 

'''Related publications''' 
<UL>
<LI>Burla, M., Baptista, A.M. Zhang, Y.L., and Frolov, S. (2010) Seasonal and inter-annual variability of the Columbia River plume: a perspective enabled by multi-year simulation databases. Journal of Geophysical Research: special issue on NSF RISE project, 115, C00B16.
<LI>Frolov, S., Baptista, A.M., Zhang, Y.L., and Seaton, C. (2009) Estimation of Ecologically Significant Circulation Features of the Columbia River Estuary and Plume Using a Reduced-Dimension Kalman Filter. Continental Shelf Research, 29(2), 456-466.
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (accepted). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research.
<LI>Zhang, Y.-L. and Baptista, A.M. (2008) "SELFE: A semi-implicit Eulerian-Lagrangian finite-element model for cross-scale ocean circulation", Ocean Modelling, 21(3-4), 71-96.
</UL>

'''Sample images''' 

Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]] 

==DWR==

==SURA==

'''Research Team''' 
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang 
OHSU: Joseph Zhang 

'''Projection description''' 

SELFE is being used in an IOOS sponsored super-regional testbed for coastal inundation, led by Dr. Rick Luettich (UNC). The testbed focuses on two coastal regions that are prone to inundation hazard: Gulf of Mexico and Gulf of Maine. 

'''Project web site'''
[http://testbed.sura.org/node/554] 
'''Related publications''' 
<UL>
<LI> Teng, Y.C., Wang, H.V., Zhang, Y., Roland, A. (to be submitted) The effect of bottom boundary layer dynamics on the forerunner simulation during Hurricane Ike in the Gulf of Mexico.
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (in press) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research.
<LI>Cho, K.H. Wang, H.V., Shen, J., Valle-Levinson, A. and Teng, Y.C. (2012) A modeling study on the response of the Chesapeake Bay to Hurricane Events of Floyd and Isabel. Ocean Modeling, vol. 49-50, pp. 22-46.
</UL>
'''Sample images''' 
Fig. 2 shows an example application of the fully coupled SELFE-WWM and a simple sediment model to hurricane Ike (2008) in Gulf of Mexico. The full results are being published (Teng et al. 2012).
[[File:SURA-Ike-YC.jpg|thumb|center|Fig. 2 Domain used to simulate hurricane Ike in Gulf of Mexico. The comparison plot shows the primary surge and forerunner simulated with different physical formulations (c/o Y.C. Teng)]]
 

==Xavier's group==

==Portuguese coastal systems==

There are 3 related projects for this system.

<OL>
<LI> ''A nowcast-forecast system for for Portuguese coastal systems'' 
'''Research Team''' 

LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes 
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton 

'''Project description''' 

The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and
the American institution will provide the innovative nowcast-forecast technology. 

'''Project web site'''
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast]

<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' 
'''Research Team''' 

LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin 
'''Project description''' 

Tidal inlets are among the most dynamic environments along the world coastlines while social-economic activities are there concentrated. These problems are particularly relevant in Portugal due to its extensive coastline and the existence of many tidal inlets of social, environmental and economic importance. In the perspective of a sustainable development, it is essential to understand and to be able to predict the long-term evolution of these systems. To achieve these goals, one of the most promising avenues is the development of morphodynamic models, which consist of a set of modules to simulate tidal hydrodynamics, wave propagation, sediment transport and bottom evolution. This project aims at contributing to the advance of an existing morphodynamic modeling system (MORSYS2D) that is under development at the host institution (LNEC). 

'''Project web site'''[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie]
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)''
'''Research Team''' 
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes 
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner 

'''Project description''' 
This proposal aims to integrate complementary research strengths at the two institutions to improve and validate a sophisticated ecological modeling system for operational forecasting of ecosystem dynamics based on grid computing resources. The Portuguese partner will provide the ecological model and the expertise on grid-enabling of numerical models. The American partner will provide the expertise on parallel computing and the benchmark for validation and inter-model comparison. 
[[File:model-ecoselfe.jpg|thumb|center|Fig. 3 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]] 

'''Project web site'''
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem]
</OL>

 

==Tsunami==
'''Research Team''' 
OHSU & VIMS: Joseph Zhang 
DOGAMI: George Priest, Rob Witter, Laura Stimely 
GeoCanada: Kelin Wang 
Oregon State Univ: Chris Goldfinger 

'''Projection description''' 

SELFE has been certified by National Tsunami Hazard Program (NTHMP) as a tsunmai inundation model, after passing various benchmarks stipulated by NOAA [http://nctr.pmel.noaa.gov/benchmark/].
It has been used to generate official inundation maps for the state of Oregon, spearheaded by OR Department of Geology ad Mineral Industries (DOGAMI) [http://www.oregongeology.org/sub/default.htm], under the auspice of NTHMP. 

'''Sample images''' 
Fig. 4 is a sample inundation map for Cannon Beach OR.
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]
 

'''Related publications''' 
<UL>
<LI>Witter, R.C, Zhang, Y., Wang, K., Goldfinger, C., Priest, G.R., Allan, J.C. (in press) Coseismic slip on the Cascadia megathrust implied by tsunami deposits in an Oregon lake. Journal of Geophysical Research-Solid Earth.
<LI>Witter, R.C., Jaffe, B., Zhang, Y. and Priest, G.R. (2011) Reconstructing hydrodynamic flow parameters of the 1700 tsunami at Cannon Beach, Oregon, USA., Natural Hazards, DOI 10.1007/s11069-011-9912-7.
<LI>Zhang, Y., Witter, R.W. and Priest, G.P. (2011) Tsunami-Tide Interaction in 1964 Prince William Sound Tsunami, Ocean Modelling, 40, 246-259.
<LI>Priest, G.R., Goldfinger, C., Wang, K., Witter, R.C., Zhang, Y., Baptista, A.M. (2010) Confidence levels for tsunami-inundation limits in northern Oregon inferred from a 10,000-year history of great earthquakes at the Cascadia subduction zone. Natural Hazards, 54(1), 27-73.
<LI>Zhang, Y.L., and Baptista, A.M. (2008) Benchmarking a new finite-element tsunami model on unstructured grids. Pure and Applied Geophysics: Topical issue on Tsunamis, vol. 165, pp. 2229-2248. pdf .
</UL>

 

==Water Quality in the Chesapeake Bay Region==

'''Research Team'''

Virginia Institute of Marine Science: Junzheng Zhu and Harry Wang [http://www.vims.edu/people/wang_hv/index.php]

'''Projection description'''

The Chesapeake Bay and the Coastal Bays of the Maryland/Virginia Atlantic shore are highly valuable and productive ecosystems that are increasingly threatened by degraded water quality and loss of habitat due to both anthropogenic and natural disturbances.

In an effort to reverse this trend, federal and state governments have implemented a Total Maximum Daily Load (TMDL) program to control point source and non-point source pollution in each watershed.

In order to quantify these controls and better understand cause and effect relationships, the Virginia Institute of Marine Science is developing numerical hydrodynamic and water quality models and linking them together as a tool for predicting and measuring success of the TMDL effort.

Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:

<OL>
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.
</OL>

Both projects involve coupling SELFE and ICM (Integrated Compartment Model).

'''Sample images'''

Fig. 5 shows some sample results.
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]

 

==Aquaculture and coastal pollutants modelling==

'''Research Team''' 
Cawthron Institute [http://www.cawthron.org.nz]: Ben Knight 
MetOcean Solutions Limited [http://www.metocean.co.nz/]: Brett Beamsley 

'''Application description''' 
Aquaculture and other coastal developments in New Zealand have the potential to place increasing pressures on coastal environments. The Cawthron Institute and MetOcean Solutions Limited have been collaborating to produce open-source community models for coastal environments around New Zealand to aid in coastal effects assessments. We are presently utilising and building upon SELFE community modelling tools associated with, lagrangian and eularian transport for a range of coastal transport applications (e.g. faecal indicator bacteria, nutrients, oil spills). 
We have a number of collaborative projects under-way, but are currently working towards simplifying the set up and analysis of tracers for modelling a range of chemical and biological constituents in aquaculture and coastal discharge assessments. 

'''Sample images''' 

Fig. 6 shows SELFE Matlab GUI (currently under development) showing bathymetric map of the Marlborough Sounds, New Zealand.
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]

Applications and case studies

2012-10-08T23:22:12Z

Benk:

==Columbia River estuary and plume==
'''Research Team''' 
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton 

'''Projection description''' 
Columbia River estuary and plume circulation presents a formidable challenge for hydrodynamic models due to the interaction between strong tides, meteorological forcing, high river discharge, and strong stratification. SELFE was originally developed to address these challenges and some details can be found in the SELFE paper.

The SELFE-enabled virtual Columbia River is a skill-assessed 4D (space-time) simulation environment that offers multiple representations of circulation processes, variability and change across river-to-shelf scales. Circulation includes water levels, salinity, temperature, and velocities. 

'''Project web site'''
[http://www.stccmop.org/datamart/virtualcolumbiariver] 

'''Related publications''' 
<UL>
<LI>Burla, M., Baptista, A.M. Zhang, Y.L., and Frolov, S. (2010) Seasonal and inter-annual variability of the Columbia River plume: a perspective enabled by multi-year simulation databases. Journal of Geophysical Research: special issue on NSF RISE project, 115, C00B16.
<LI>Frolov, S., Baptista, A.M., Zhang, Y.L., and Seaton, C. (2009) Estimation of Ecologically Significant Circulation Features of the Columbia River Estuary and Plume Using a Reduced-Dimension Kalman Filter. Continental Shelf Research, 29(2), 456-466.
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (accepted). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research.
<LI>Zhang, Y.-L. and Baptista, A.M. (2008) "SELFE: A semi-implicit Eulerian-Lagrangian finite-element model for cross-scale ocean circulation", Ocean Modelling, 21(3-4), 71-96.
</UL>

'''Sample images''' 

Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]] 

==DWR==

==SURA==

'''Research Team''' 
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang 
OHSU: Joseph Zhang 

'''Projection description''' 

SELFE is being used in an IOOS sponsored super-regional testbed for coastal inundation, led by Dr. Rick Luettich (UNC). The testbed focuses on two coastal regions that are prone to inundation hazard: Gulf of Mexico and Gulf of Maine. 

'''Project web site'''
[http://testbed.sura.org/node/554] 
'''Related publications''' 
<UL>
<LI> Teng, Y.C., Wang, H.V., Zhang, Y., Roland, A. (to be submitted) The effect of bottom boundary layer dynamics on the forerunner simulation during Hurricane Ike in the Gulf of Mexico.
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (in press) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research.
<LI>Cho, K.H. Wang, H.V., Shen, J., Valle-Levinson, A. and Teng, Y.C. (2012) A modeling study on the response of the Chesapeake Bay to Hurricane Events of Floyd and Isabel. Ocean Modeling, vol. 49-50, pp. 22-46.
</UL>
'''Sample images''' 
Fig. 2 shows an example application of the fully coupled SELFE-WWM and a simple sediment model to hurricane Ike (2008) in Gulf of Mexico. The full results are being published (Teng et al. 2012).
[[File:SURA-Ike-YC.jpg|thumb|center|Fig. 2 Domain used to simulate hurricane Ike in Gulf of Mexico. The comparison plot shows the primary surge and forerunner simulated with different physical formulations (c/o Y.C. Teng)]]
 

==Xavier's group==

==Portuguese coastal systems==

There are 3 related projects for this system.

<OL>
<LI> ''A nowcast-forecast system for for Portuguese coastal systems'' 
'''Research Team''' 

LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes 
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton 

'''Project description''' 

The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and
the American institution will provide the innovative nowcast-forecast technology. 

'''Project web site'''
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast]

<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' 
'''Research Team''' 

LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin 
'''Project description''' 

Tidal inlets are among the most dynamic environments along the world coastlines while social-economic activities are there concentrated. These problems are particularly relevant in Portugal due to its extensive coastline and the existence of many tidal inlets of social, environmental and economic importance. In the perspective of a sustainable development, it is essential to understand and to be able to predict the long-term evolution of these systems. To achieve these goals, one of the most promising avenues is the development of morphodynamic models, which consist of a set of modules to simulate tidal hydrodynamics, wave propagation, sediment transport and bottom evolution. This project aims at contributing to the advance of an existing morphodynamic modeling system (MORSYS2D) that is under development at the host institution (LNEC). 

'''Project web site'''[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie]
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)''
'''Research Team''' 
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes 
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner 

'''Project description''' 
This proposal aims to integrate complementary research strengths at the two institutions to improve and validate a sophisticated ecological modeling system for operational forecasting of ecosystem dynamics based on grid computing resources. The Portuguese partner will provide the ecological model and the expertise on grid-enabling of numerical models. The American partner will provide the expertise on parallel computing and the benchmark for validation and inter-model comparison. 
[[File:model-ecoselfe.jpg|thumb|center|Fig. 3 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]] 

'''Project web site'''
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem]
</OL>

 

==Tsunami==
'''Research Team''' 
OHSU & VIMS: Joseph Zhang 
DOGAMI: George Priest, Rob Witter, Laura Stimely 
GeoCanada: Kelin Wang 
Oregon State Univ: Chris Goldfinger 

'''Projection description''' 

SELFE has been certified by National Tsunami Hazard Program (NTHMP) as a tsunmai inundation model, after passing various benchmarks stipulated by NOAA [http://nctr.pmel.noaa.gov/benchmark/].
It has been used to generate official inundation maps for the state of Oregon, spearheaded by OR Department of Geology ad Mineral Industries (DOGAMI) [http://www.oregongeology.org/sub/default.htm], under the auspice of NTHMP. 

'''Sample images''' 
Fig. 4 is a sample inundation map for Cannon Beach OR.
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]
 

'''Related publications''' 
<UL>
<LI>Witter, R.C, Zhang, Y., Wang, K., Goldfinger, C., Priest, G.R., Allan, J.C. (in press) Coseismic slip on the Cascadia megathrust implied by tsunami deposits in an Oregon lake. Journal of Geophysical Research-Solid Earth.
<LI>Witter, R.C., Jaffe, B., Zhang, Y. and Priest, G.R. (2011) Reconstructing hydrodynamic flow parameters of the 1700 tsunami at Cannon Beach, Oregon, USA., Natural Hazards, DOI 10.1007/s11069-011-9912-7.
<LI>Zhang, Y., Witter, R.W. and Priest, G.P. (2011) Tsunami-Tide Interaction in 1964 Prince William Sound Tsunami, Ocean Modelling, 40, 246-259.
<LI>Priest, G.R., Goldfinger, C., Wang, K., Witter, R.C., Zhang, Y., Baptista, A.M. (2010) Confidence levels for tsunami-inundation limits in northern Oregon inferred from a 10,000-year history of great earthquakes at the Cascadia subduction zone. Natural Hazards, 54(1), 27-73.
<LI>Zhang, Y.L., and Baptista, A.M. (2008) Benchmarking a new finite-element tsunami model on unstructured grids. Pure and Applied Geophysics: Topical issue on Tsunamis, vol. 165, pp. 2229-2248. pdf .
</UL>

 

==Water Quality in the Chesapeake Bay Region==

'''Research Team'''

Virginia Institute of Marine Science: Junzheng Zhu and Harry Wang [http://www.vims.edu/people/wang_hv/index.php]

'''Projection description'''

The Chesapeake Bay and the Coastal Bays of the Maryland/Virginia Atlantic shore are highly valuable and productive ecosystems that are increasingly threatened by degraded water quality and loss of habitat due to both anthropogenic and natural disturbances.

In an effort to reverse this trend, federal and state governments have implemented a Total Maximum Daily Load (TMDL) program to control point source and non-point source pollution in each watershed.

In order to quantify these controls and better understand cause and effect relationships, the Virginia Institute of Marine Science is developing numerical hydrodynamic and water quality models and linking them together as a tool for predicting and measuring success of the TMDL effort.

Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:

<OL>
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.
</OL>

Both projects involve coupling SELFE and ICM (Integrated Compartment Model).

'''Sample images'''

Fig. 5 shows some sample results.
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]

 

==Aquaculture and coastal pollutants modelling==

'''Research Team''' 
Cawthron Institute [http://www.cawthron.org.nz]: Ben Knight 
MetOcean Solutions Limited [http://www.metocean.co.nz/]: Brett Beamsley 

'''Application description''' 
Aquaculture and other coastal developments in New Zealand have the potential to place increasing pressures on coastal environments. The Cawthron Institute and MetOcean Solutions Limited have been collaborating to produce open-source community models for coastal environments around New Zealand to aid in accurate and transparent effects assessments, utilising and building upon SELFE community modelling tools. 
We have a number of collaborative projects under-way, but are currently working towards simplifying the set up and analysis of tracers for modelling a range of chemical and biological constituents in aquaculture and coastal discharge assessments. 

'''Sample images''' 

Fig. 6 shows SELFE Matlab GUI (currently under development) showing bathymetric map of the Marlborough Sounds, New Zealand.
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]

File:SELFE GUI.PNG

2012-10-08T21:21:56Z

Benk: Example of Selfe GUI currently under development.

Example of Selfe GUI currently under development.