http://ccrm.vims.edu/w/api.php?action=feedcontributions&feedformat=atom&user=Kliccrmwiki - User contributions [en]2026-05-07T07:59:46ZUser contributionsMediaWiki 1.31.1http://ccrm.vims.edu/w/index.php?title=Harmonic_analysis&diff=808Harmonic analysis2014-12-12T19:18:41Z<p>Kli: /* Output files */</p>
<hr />
<div>==Purpose==<br />
Harmonic analysis capabilities were introduced in SELFE, version 2.0ha, by Dr. André Fortunato, using the routines of ADCIRC. These routines were developed by R.A. Luettich and J.J. Westerink, who are hereby acknowledged, and were used with written permission by R.A. Luettich. The present document describes the modifications done in SELFE and provides a user’s guide to these capabilities.<br />
<br />
==Capabilities==<br />
ADCIRC performs 4 types of harmonic analyses:<br />
<OL><br />
<LI>Elevations at specified stations<br />
<LI>Depth-averaged velocities at specified stations<br />
<LI>Elevations at all nodes<br />
<LI>Depth-averaged velocities at all nodes<br />
</OL><br />
<br />
In SELFE, harmonic analysis at specified stations was not implemented. Option 3 (elevations at all nodes) was fully implemented. The code associated with option 4 was included and commented out. Because the version of SELFE in which harmonic analysis was originally implemented did not explicitly compute depth-averaged velocities, these values are not available. However, the user can easily uncomment the correspond lines, providing that the necessary variables (UHA and VHA) are computed. This way, the user can easily perform harmonic analysis for any 2D array, defined at the nodes, called UHA or VHA. This feature can be used for instance to perform harmonic analysis for depth-averaged velocities (that will have to be computed), surface velocities, concentrations, etc.<br />
<br />
==Input files==<br />
Performing harmonic analysis requires the changing the following files:<br />
<UL><br />
<LI>Makefile: the flag USE_HA must be set to yes<br />
<LI>param.in: the flag iharind must be included and set to 1<br />
<LI>harm.in: the file harm.in must be created with the following format (text adapted from the ADCIRC user’s manual):<br />
</UL><br />
<br />
where:<br />
<UL><br />
<LI>NFREQ = number of frequencies included in harmonic analysis of model results.<br />
</UL><br />
<br />
for k=1 to NFREQ<br />
<UL><br />
<LI>NAMEFR(k) = an alphanumeric descriptor (i.e. the constituent name) whose length must be <= 16 characters<br />
<LI>HAFREQ(k), HAFF(k), HAFACE(k) = frequency (rad/s), nodal factor, equilibrium argument (degrees)<br />
</UL><br />
end k loop<br />
<UL><br />
<LI>THAS, THAF, NHAINC, FMV = the number of days after which data starts to be harmonically analysed, the number of days after which data ceases to be harmonically analysed, the number of time steps at which information is harmonically analysed (information every NHAINC time steps after THAS is used in harmonic analysis), fraction of the harmonic analysis period (extending back from the end of the harmonic analysis period) to use for comparing the water elevation and velocity means and variances from the raw model time series with corresponding means and variances of a time series resynthesized from the harmonic constituents. This comparison is helpful for identifying numerical instabilities and for determining how complete the harmonic analysis was. Examples: FMV = 0. - do not compute any means and vars. FMV = 0.1 - compute means and vars. over final 10% of period used in harmonic analysis. FMV = 1.0 - compute means and vars. over entire period used in harmonic analysis.<br />
<LI>NHAGE, NHAGV = flags that indicate whether or not harmonic analysis is performed: NHAGE= 0 no harmonic analysis is performed for global elevations; NHAGE = 1 harmonic analysis is performed for global elevations (output on harme.53); NHAGV = 0 no harmonic analysis is performed for global velocities; NHAGV = 1 harmonic analysis is performed for global velocities (output on harmv.54).<br />
</UL><br />
<br />
==Output files==<br />
Results, in the form of amplitudes and phases at every node and for every frequency, are provided in the files harme.53 (for elevations) and harmv.54 (for whatever variable is introduced in UHA and VHA). The file format for harme.53 is the following (text adapted from the ADCIRC user’s manual):<br />
<br />
<UL><br />
NFREQ – see definition above<br />
</UL><br />
for k = 1,NFREQ<br />
<UL><br />
HAFREQ(k), HAFF(k), HAFACE(k), NAMEFR(k) – see definitions above<br />
</UL><br />
end k loop<br />
<br />
NP – number of nodes<br /><br />
for k=1,NP<br />
<UL><br />
k<br />
</UL><br />
for j=1,NFREQ<br />
<UL><br />
EMAGT(k,j), PHASEDE(k,j) = Elevation amplitude and phase (in deg) for constituent j at node k.<br />
</UL><br />
end j loop<br /><br />
end k loop<br />
<br />
The file format for harmv.54 is similar, but with four variables per line in the last loop (amplitudes and phases for the two analysed variables).<br />
<br />
Harmonic analysis output files are written for each processor on the directory outputs. They can be combined using the auxiliary program combine_outHA.f. combine_outHA should be run in the directory above outputs, where the SELFE run was performed. It assumes the local harme.53xxxx files are located in the directory outputs, together with the local_to_global_xxxx files, and writes a single harme.53 for the global grid in the directory where it is run. The harme.53 file can be transformed into a tct file (which is read by xmvis) using the program ad2tct.f.<br />
<br />
==List of global variables==<br />
Note: input and output variables (described above) are listed in italic:<br />
<UL><br />
<LI>ELAV(:) (real)<br />
<LI>ELVA(:) (real)<br />
<LI>''FMV''(real)<br />
<LI>''HAFACE''(:) (real)<br />
<LI>''HAFF''(:) (real)<br />
<LI>''HAFREQ''(:) (real)<br />
<LI>ICHA (integer)<br />
<LI>IHABEG (integer)<br />
<LI>IHOTSTP (integer)<br />
<LI>IHARIND (integer)<br />
<LI>ITHAF (integer)<br />
<LI>ITHAS (integer)<br />
<LI>ITMV (integer)<br />
<LI>''NAMEFR'' (:)(character)<br />
<LI>''NFREQ'' (integer)<br />
<LI>''NHAGE'' (integer)<br />
<LI>''NHAGV'' (integer)<br />
<LI>''NHAINC'' (integer)<br />
<LI>NTSTEPS (integer)<br />
<LI>''THAF'' (real)<br />
<LI>''THAS'' (real)<br />
<LI>TIMEBEG (real)<br />
<LI>XVELAV (:)(real)<br />
<LI>XVELVA (:)(real)<br />
<LI>YVELAV (:)(real)<br />
<LI>YVELVA (:)(real)<br />
</UL><br />
<br />
<br />
==Example: M2 amplitude in the eastern Atlantic==<br />
<br />
[[File:HA eg.jpg|thumb|left|Fig. 1 M2 amplitude simulated with SELFE and harmonically analyzed during the run, for the eastern Atlantic]]</div>Klihttp://ccrm.vims.edu/w/index.php?title=Parallel_output:_time_and_processor_blocks&diff=659Parallel output: time and processor blocks2013-05-05T11:35:43Z<p>Kli: </p>
<hr />
<div>SELFE binary state output is emitted in a directory called /outputs. This directory must exist or you will get an immediate warning from the model. Depending on your MPI configuration, the /outputs directory may exist in a central location (this is more common) or each processor may have an instance in which case you need to collect together the contents into a central location.<br />
<br />
An example file name is 9_0000_elev.61. More generally, the file name is:<br />
[time_block]_[processor_no]_[variable_name].[fortran_unit]<br />
<br />
; Variable name <br />
The variable name is transparent and covered in the documentation. <br />
<br />
; Time block<br />
The time blocks start from 1 and are sequential. The model buffers and writes data occasionally. Every ihfskip time steps it opens a new time block. For instance, if the time step is 120 seconds and ihfskip = 10080 each block will be 14 days long. <br />
# "Neat" time lengths that will make meaningful analysis (e.g. 14 days) are usually easiest later when you postprocess.<br />
# Some of the output post-processing scripts will run a lot better if the length of your simulation is an even multiple of ihfskip. This can be done by altering ihfskip or the simulation length -- at the risk of lengthening the simulation a bit, the latter often produces a neater result.<br />
# If your simulation length is not an even multiple of the time block length, the last time block will be truncated on the last block. This will cause some minor errors and warnings in the post-processing tools. In addition, if you then restart the run it is best to repeat and overwrite the truncated block -- the post-processing tools do not work well with blocks that grow and shrink in the middle of the run.<br />
# Even if the output blocks match the end of the simulation very neatly, the model (at the time of writing) will open a new block that will be unused. This is useful for the autocombine_MPI_elfe.pl, as the latter always waits until a new block to come out before starting to combine the previous block (and so it'd hang if the last block were not written out).<br />
<br />
; Processor number<br />
The mpi_processor number starts at 0 and represents the mpi processor id from the task that wrote the output. If your processor writes to a shared directory, the files for different processors will be collocated, but since clusters are not always set up the same way and each process is writing locally this isn't always the case. The per-processor outputs are usually gathered into a global binary. The scripts that do this are called combine_output*.f90 (a simple perl script autocombine_MPI_elfe.pl exsits to combine all available outputs transparently). Once you are done, you will have a binary file called something like 9_elev.61. The time block and the variable name remain. There is no utility for gathering the outputs in time, instead most post-processing tools are able to work with multiple files.<br />
<br />
; Combine outputs of side-centered variables<br />
Outputs for barotropic pressure gradient force (bpgr.65) and Wave forces (wafo.67) are currently located in side centers. To combine this variables, a ".gr3" type file named "sidecenters.gr3" is needed. "sidecenters.gr3" can be generated by these steps:<br />
# Run model with ipre = 0 (inside param.in), then a build point file "sidecenters.bp" will be generated.<br />
# Triangulate "sidecenters.bp" with xmgredit5 or Aquaeo SMS (SMS is recommended, as xmgredit5 may get very ugly triangulated result sometimes) to generate a ".gr3" file.<br />
# Put "sidecenters.gr3" inside your work directory and use the perl script autocombine_MPI_elfe.pl to combine the outputs. 4. visualize the combined outputs with xmvis6.<br />
The triangulated file "sidecenters.gr3" with xmgredt5 or SMS will get residual elements outside the mesh domain. It's not necessary to remove the extra elements for combining and visulizing, but a cleaner triangulated "sidecenters.gr3" is good for better visualization.</div>Klihttp://ccrm.vims.edu/w/index.php?title=Parallel_output:_time_and_processor_blocks&diff=658Parallel output: time and processor blocks2013-05-05T11:35:05Z<p>Kli: </p>
<hr />
<div>SELFE binary state output is emitted in a directory called /outputs. This directory must exist or you will get an immediate warning from the model. Depending on your MPI configuration, the /outputs directory may exist in a central location (this is more common) or each processor may have an instance in which case you need to collect together the contents into a central location.<br />
<br />
An example file name is 9_0000_elev.61. More generally, the file name is:<br />
[time_block]_[processor_no]_[variable_name].[fortran_unit]<br />
<br />
; Variable name <br />
The variable name is transparent and covered in the documentation. <br />
<br />
; Time block<br />
The time blocks start from 1 and are sequential. The model buffers and writes data occasionally. Every ihfskip time steps it opens a new time block. For instance, if the time step is 120 seconds and ihfskip = 10080 each block will be 14 days long. <br />
# "Neat" time lengths that will make meaningful analysis (e.g. 14 days) are usually easiest later when you postprocess.<br />
# Some of the output post-processing scripts will run a lot better if the length of your simulation is an even multiple of ihfskip. This can be done by altering ihfskip or the simulation length -- at the risk of lengthening the simulation a bit, the latter often produces a neater result.<br />
# If your simulation length is not an even multiple of the time block length, the last time block will be truncated on the last block. This will cause some minor errors and warnings in the post-processing tools. In addition, if you then restart the run it is best to repeat and overwrite the truncated block -- the post-processing tools do not work well with blocks that grow and shrink in the middle of the run.<br />
# Even if the output blocks match the end of the simulation very neatly, the model (at the time of writing) will open a new block that will be unused. This is useful for the autocombine_MPI_elfe.pl, as the latter always waits until a new block to come out before starting to combine the previous block (and so it'd hang if the last block were not written out).<br />
<br />
; Processor number<br />
The mpi_processor number starts at 0 and represents the mpi processor id from the task that wrote the output. If your processor writes to a shared directory, the files for different processors will be collocated, but since clusters are not always set up the same way and each process is writing locally this isn't always the case. The per-processor outputs are usually gathered into a global binary. The scripts that do this are called combine_output*.f90 (a simple perl script autocombine_MPI_elfe.pl exsits to combine all available outputs transparently). Once you are done, you will have a binary file called something like 9_elev.61. The time block and the variable name remain. There is no utility for gathering the outputs in time, instead most post-processing tools are able to work with multiple files.<br />
<br />
<br />
; Combine outputs of side-centered variables<br />
Outputs for barotropic pressure gradient force (bpgr.65) and Wave forces (wafo.67) are currently located in side centers. To combine this variables, a .gr3 type file named "sidecenters.gr3" is needed. "sidecenters.gr3" can be generated by these steps:<br />
# Run model with ipre = 0 (inside param.in), then a build point file "sidecenters.bp" will be generated.<br />
# Triangulate "sidecenters.bp" with xmgredit5 or Aquaeo SMS (SMS is recommended, as xmgredit5 may get very ugly triangulated result sometimes) to generate a ".gr3" file.<br />
# Put "sidecenters.gr3" inside your work directory and use the perl script autocombine_MPI_elfe.pl to combine the outputs. 4. visualize the combined outputs with xmvis6.<br />
The triangulated file "sidecenters.gr3" with xmgredt5 or SMS will get residual elements outside the mesh domain. It's not necessary to remove the extra elements for combining and visulizing, but a cleaner triangulated "sidecenters.gr3" is good for better visualization.</div>Klihttp://ccrm.vims.edu/w/index.php?title=File:Xynthia_flooding.png&diff=549File:Xynthia flooding.png2012-11-07T09:04:05Z<p>Kli: Kli uploaded a new version of &quot;File:Xynthia flooding.png&quot;: Can't refresh the new version of the picture</p>
<hr />
<div>Simulation Water depth in North of La Rochelle during Xynthia</div>Klihttp://ccrm.vims.edu/w/index.php?title=File:Xynthia_flooding.png&diff=548File:Xynthia flooding.png2012-11-06T16:38:27Z<p>Kli: Kli uploaded a new version of &quot;File:Xynthia flooding.png&quot;: Reverted to version as of 16:34, 6 November 2012</p>
<hr />
<div>Simulation Water depth in North of La Rochelle during Xynthia</div>Klihttp://ccrm.vims.edu/w/index.php?title=File:Xynthia_flooding.png&diff=547File:Xynthia flooding.png2012-11-06T16:37:45Z<p>Kli: Kli uploaded a new version of &quot;File:Xynthia flooding.png&quot;: Reverted to version as of 16:04, 6 November 2012</p>
<hr />
<div>Simulation Water depth in North of La Rochelle during Xynthia</div>Klihttp://ccrm.vims.edu/w/index.php?title=File:Xynthia_flooding.png&diff=546File:Xynthia flooding.png2012-11-06T16:34:56Z<p>Kli: Kli uploaded a new version of &quot;File:Xynthia flooding.png&quot;: Cropped blanks.</p>
<hr />
<div>Simulation Water depth in North of La Rochelle during Xynthia</div>Klihttp://ccrm.vims.edu/w/index.php?title=File:Xynthia_flooding.png&diff=545File:Xynthia flooding.png2012-11-06T16:04:27Z<p>Kli: Kli uploaded a new version of &quot;File:Xynthia flooding.png&quot;: Improved result in flooding.</p>
<hr />
<div>Simulation Water depth in North of La Rochelle during Xynthia</div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=502SELFE case studies2012-10-19T11:05:02Z<p>Kli: /* Marine Submersion (Xynthia Storm Surge) */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>Burla, M., Baptista, A.M. Zhang, Y., 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. <br />
<LI>Frolov, S., Baptista, A.M., Zhang, Y., 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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research, 28(19) 2644-2659. <br />
<LI>Zhang, Y. 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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Marine Submersion (Xynthia Storm Surge)==<br />
'''Research Team'''<br/><br />
DPL: Xavier Bertin, Kai Li, Aron Roland, Nicolas Bruneau, Jean-François Breilh et al.<br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WWM coupled model was applied in the research. And a highly refined flooding multiscale grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocean Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 3 shows the simulated water depth in North of La Rochelle during Xynthia of preliminary result.<br />
[[File:Xynthia flooding.png|thumb|center|Fig. 3 Simulated water depth in North of La Rochelle during Xynthia (red line: observed flooding boundary]]<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 4 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 5 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 5 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
[http://www.oregongeology.org/tsuclearinghouse/pubs-technical.htm '''Related web site''']<br><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<LI>Witter, R.C, Zhang, Y., Wang, K., Goldfinger, C., Priest, G.R., Allan, J.C. (2012) Coseismic slip on the Cascadia megathrust implied by tsunami deposits in an Oregon lake. Journal of Geophysical Research-Solid Earth, 117, B10303, doi:10.1029/2012JB009404. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 6 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 6 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 7 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 7 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=501SELFE case studies2012-10-19T11:00:59Z<p>Kli: /* Marine Submersion (Xynthia Strom Surge) */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>Burla, M., Baptista, A.M. Zhang, Y., 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. <br />
<LI>Frolov, S., Baptista, A.M., Zhang, Y., 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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research, 28(19) 2644-2659. <br />
<LI>Zhang, Y. 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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Marine Submersion (Xynthia Storm Surge)==<br />
'''Research Team'''<br/><br />
DPL: Xavier Bertin, Kai Li, Aron Roland, Nicolas Bruneau, Jean-François Breilh et al.<br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WWM coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocean Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 3 shows the simulated water depth in North of La Rochelle during Xynthia of preliminary result.<br />
[[File:Xynthia flooding.png|thumb|center|Fig. 3 Simulated water depth in North of La Rochelle during Xynthia (red line: observed flooding boundary]]<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 4 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 5 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 5 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
[http://www.oregongeology.org/tsuclearinghouse/pubs-technical.htm '''Related web site''']<br><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<LI>Witter, R.C, Zhang, Y., Wang, K., Goldfinger, C., Priest, G.R., Allan, J.C. (2012) Coseismic slip on the Cascadia megathrust implied by tsunami deposits in an Oregon lake. Journal of Geophysical Research-Solid Earth, 117, B10303, doi:10.1029/2012JB009404. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 6 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 6 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 7 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 7 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=500SELFE case studies2012-10-18T21:21:07Z<p>Kli: /* Marine Submersion (Xynthia Strom Surge) */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>Burla, M., Baptista, A.M. Zhang, Y., 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. <br />
<LI>Frolov, S., Baptista, A.M., Zhang, Y., 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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research, 28(19) 2644-2659. <br />
<LI>Zhang, Y. 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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Marine Submersion (Xynthia Strom Surge)==<br />
'''Research Team'''<br/><br />
DPL: Xavier Bertin, Kai Li, Aron Roland, Nicolas Bruneau, Jean-François Breilh et al.<br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WWM coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocean Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 3 shows the simulated water depth in North of La Rochelle during Xynthia of preliminary result.<br />
[[File:Xynthia flooding.png|thumb|center|Fig. 3 Simulated water depth in North of La Rochelle during Xynthia (red line: observed flooding boundary]]<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 4 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 5 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 5 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
[http://www.oregongeology.org/tsuclearinghouse/pubs-technical.htm '''Related web site''']<br><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<LI>Witter, R.C, Zhang, Y., Wang, K., Goldfinger, C., Priest, G.R., Allan, J.C. (2012) Coseismic slip on the Cascadia megathrust implied by tsunami deposits in an Oregon lake. Journal of Geophysical Research-Solid Earth, 117, B10303, doi:10.1029/2012JB009404. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 6 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 6 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 7 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 7 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=499SELFE case studies2012-10-18T21:19:15Z<p>Kli: /* Marine Submersion (Xynthia Strom Surge)*/</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>Burla, M., Baptista, A.M. Zhang, Y., 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. <br />
<LI>Frolov, S., Baptista, A.M., Zhang, Y., 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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research, 28(19) 2644-2659. <br />
<LI>Zhang, Y. 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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Marine Submersion (Xynthia Strom Surge)==<br />
'''Research Team'''<br/><br />
DPL: Xavier Bertin, Kai Li, Aron Roland, Nicolas Bruneau, Jean-François Breilh et al.<br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WWM coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocean Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 3 Simulation Water depth in North of La Rochelle during Xynthia<br />
[[File:Xynthia flooding.png|thumb|center|Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia (red line: observed flooding boundary]]<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 4 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 5 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 5 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
[http://www.oregongeology.org/tsuclearinghouse/pubs-technical.htm '''Related web site''']<br><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<LI>Witter, R.C, Zhang, Y., Wang, K., Goldfinger, C., Priest, G.R., Allan, J.C. (2012) Coseismic slip on the Cascadia megathrust implied by tsunami deposits in an Oregon lake. Journal of Geophysical Research-Solid Earth, 117, B10303, doi:10.1029/2012JB009404. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 6 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 6 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 7 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 7 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=495SELFE case studies2012-10-18T16:36:12Z<p>Kli: /* Xavier's group */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>Burla, M., Baptista, A.M. Zhang, Y., 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. <br />
<LI>Frolov, S., Baptista, A.M., Zhang, Y., 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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research, 28(19) 2644-2659. <br />
<LI>Zhang, Y. 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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WWM coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocean Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 3 Flooding grid of Xynthia with bathymetry<br />
[[File:Flooding grid lr.jpg|thumb|center|Fig. 3 Flooding grid of Xynthia with bathymetry]]<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 4 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 5 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 5 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
[http://www.oregongeology.org/tsuclearinghouse/pubs-technical.htm '''Related web site''']<br><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 6 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 6 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 7 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 7 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=File:Flooding_grid_lr.jpg&diff=494File:Flooding grid lr.jpg2012-10-18T16:34:54Z<p>Kli: Flooding Grid of Xynthia</p>
<hr />
<div>Flooding Grid of Xynthia</div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=493SELFE case studies2012-10-18T16:28:39Z<p>Kli: </p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>Burla, M., Baptista, A.M. Zhang, Y., 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. <br />
<LI>Frolov, S., Baptista, A.M., Zhang, Y., 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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research, 28(19) 2644-2659. <br />
<LI>Zhang, Y. 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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WWM coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocean Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia.<br />
[[File:Xynthia flooding.png|thumb|center|Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia]]<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 4 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 5 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 5 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
[http://www.oregongeology.org/tsuclearinghouse/pubs-technical.htm '''Related web site''']<br><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 6 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 6 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 7 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 7 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=492SELFE case studies2012-10-18T16:28:10Z<p>Kli: </p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>Burla, M., Baptista, A.M. Zhang, Y., 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. <br />
<LI>Frolov, S., Baptista, A.M., Zhang, Y., 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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research, 28(19) 2644-2659. <br />
<LI>Zhang, Y. 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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WWM coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocean Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia.<br />
[[File:Xynthia flooding.png|thumb|center|Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia]]<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 4 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 5 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 5 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
[http://www.oregongeology.org/tsuclearinghouse/pubs-technical.htm '''Related web site''']<br><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 6 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 6 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 7 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=491SELFE case studies2012-10-18T16:26:21Z<p>Kli: </p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>Burla, M., Baptista, A.M. Zhang, Y., 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. <br />
<LI>Frolov, S., Baptista, A.M., Zhang, Y., 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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research, 28(19) 2644-2659. <br />
<LI>Zhang, Y. 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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WWM coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocean Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia.<br />
[[File:Xynthia flooding.png|thumb|center|Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia]]<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 4 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 5 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
[http://www.oregongeology.org/tsuclearinghouse/pubs-technical.htm '''Related web site''']<br><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 6 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 7 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=490SELFE case studies2012-10-18T16:25:42Z<p>Kli: /* Tsunami */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>Burla, M., Baptista, A.M. Zhang, Y., 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. <br />
<LI>Frolov, S., Baptista, A.M., Zhang, Y., 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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research, 28(19) 2644-2659. <br />
<LI>Zhang, Y. 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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WWM coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocean Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia.<br />
[[File:Xynthia flooding.png|thumb|center|Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia]]<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 4 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 5 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
[http://www.oregongeology.org/tsuclearinghouse/pubs-technical.htm '''Related web site''']<br><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 5 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 6 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=489SELFE case studies2012-10-18T16:25:23Z<p>Kli: /* Portuguese coastal systems */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>Burla, M., Baptista, A.M. Zhang, Y., 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. <br />
<LI>Frolov, S., Baptista, A.M., Zhang, Y., 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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research, 28(19) 2644-2659. <br />
<LI>Zhang, Y. 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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WWM coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocean Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia.<br />
[[File:Xynthia flooding.png|thumb|center|Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia]]<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 4 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 4 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
[http://www.oregongeology.org/tsuclearinghouse/pubs-technical.htm '''Related web site''']<br><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 5 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 6 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=488SELFE case studies2012-10-18T16:24:59Z<p>Kli: /* Xavier's group */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>Burla, M., Baptista, A.M. Zhang, Y., 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. <br />
<LI>Frolov, S., Baptista, A.M., Zhang, Y., 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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research, 28(19) 2644-2659. <br />
<LI>Zhang, Y. 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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WWM coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocean Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia.<br />
[[File:Xynthia flooding.png|thumb|center|Fig. 3 Simulated Water depth in North of La Rochelle during Xynthia]]<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 3 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 4 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
[http://www.oregongeology.org/tsuclearinghouse/pubs-technical.htm '''Related web site''']<br><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 5 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 6 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=481SELFE case studies2012-10-18T09:46:00Z<p>Kli: /* Xavier's group */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<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. <br />
<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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (accepted). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research.<br />
<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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WWM coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocen Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 3 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 4 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 5 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 6 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=480SELFE case studies2012-10-18T09:42:03Z<p>Kli: /* Xavier's group */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<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. <br />
<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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (accepted). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research.<br />
<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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WaveWatchIII coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocen Modelling'', 42:16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 3 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 4 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 5 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 6 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=479SELFE case studies2012-10-18T09:41:29Z<p>Kli: /* Xavier's group */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<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. <br />
<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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (accepted). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research.<br />
<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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WaveWatchIII coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., (2011) [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocen Modelling'', 42: 16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 3 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 4 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 5 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 6 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=SELFE_case_studies&diff=478SELFE case studies2012-10-18T09:40:04Z<p>Kli: /* Xavier's group */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<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. <br />
<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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (accepted). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research.<br />
<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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br/><br />
'''Projection description'''<br/><br />
In February 2010, the storm Xynthia hit the central part of the Bay of Biscay severely. The storm surge locally exceeded 1.5m (Bertin et al., 2011) and peaked at the same time as a high spring tide, causing the flooding of large areas of the low-lying coast. Analysis results show the wave processes are important in the storm surge. The 2DH SELFE with WaveWatchIII coupled model was applied in the research. And a highly refined flooding grid was developed to catch the pysical processes of flooding.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., 2011. [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocen Modelling'', 42: 16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 3 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 4 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 5 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 6 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=Applications_and_case_studies&diff=465Applications and case studies2012-10-16T21:44:44Z<p>Kli: /* Xavier's group */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<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. <br />
<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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (accepted). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research.<br />
<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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br/><br />
'''Projection description'''<br/><br />
Storm Xynthia hit center of Biscay seriously in February, 2010. Loss of life and damages are mainly caused by the accompanied inundation of the storm surge. Research show that wave induced processes are important in the storm surge. SELFE with WWM coupled was used in hindcast of the storm surge.<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., 2011. [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocen Modelling'', 42: 16-30.<br />
<br/><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 3 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 4 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 5 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 6 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=Applications_and_case_studies&diff=464Applications and case studies2012-10-16T21:41:51Z<p>Kli: /* Xavier's group */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<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. <br />
<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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (accepted). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research.<br />
<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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<LI>Roland, A., Zhang, Y., Wang, H.V., Meng, Y., Teng, Y., Maderich, V., Brovchenko, I., Dutour-Sikiric, M. and Zanke, U. (2012) A fully coupled wave-current model on unstructured grids, Journal of Geophysical Research- Oceans, 117,C00J33,doi:10.1029/2012JC007952.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL: <br/><br />
<br />
'''Projection description'''<br/><br />
Storm Xynthia hit center of Biscay seriously in February, 2010. Loss of life and damages are mainly caused by the accompanied inundation of the storm surge. Research show that wave induced processes are important in the storm surge. SELFE with WWM coupled was used in hindcast of the storm surge.<br />
<br/><br />
<br />
'''Sample images'''<br/><br />
<br />
<br />
'''Related publications'''<br><br />
*Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., 2011. [http://www.sciencedirect.com/science/article/pii/S1463500311001776 Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay]. ''Ocen Modelling'', 42: 16-30.<br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 3 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 4 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 5 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 6 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=File:Xynthia_flooding.png&diff=463File:Xynthia flooding.png2012-10-16T21:26:47Z<p>Kli: Simulation Water depth in North of La Rochelle during Xynthia</p>
<hr />
<div>Simulation Water depth in North of La Rochelle during Xynthia</div>Klihttp://ccrm.vims.edu/w/index.php?title=Applications_and_case_studies&diff=456Applications and case studies2012-10-16T16:48:56Z<p>Kli: /* Xavier's group */</p>
<hr />
<div>==Columbia River estuary and plume==<br />
'''Research Team'''<br/><br />
OHSU: Antonio Baptista, Joseph Zhang, Nate Hyde, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Projection description'''<br/><br />
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.<br />
<br />
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. <br/><br />
<br />
<br />
<br />
[http://www.stccmop.org/datamart/virtualcolumbiariver '''Project web site''']<br/><br />
<br />
<br />
'''Related publications'''<br><br />
<UL><br />
<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. <br />
<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. <br />
<LI>Frolov, S., A.M. Baptista, M. Wilkin, (accepted). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory, Continental Shelf Research.<br />
<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. <br />
</UL><br />
<br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 1 shows the Columbia River plume in 3D view forecasted by SELFE.<br />
[[File:Virtual-CR.png|thumb|center|Fig. 1 3D view of the Columbia River plume]]<br/><br />
<br />
==DWR==<br />
<br />
<br />
==SURA==<br />
<br />
'''Research Team'''<br/><br />
VIMS: Harry Wang, Yi-Cheng Teng, Yan-qiu Meng, Joseph Zhang<br/><br />
OHSU: Joseph Zhang<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
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.<br/><br />
<br />
<br />
<br />
[http://testbed.sura.org/node/554 '''Project web site''']<br><br />
'''Related publications'''<br><br />
<UL><br />
<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.<br />
<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.<br />
<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.<br />
</UL><br />
'''Sample images'''<br/><br />
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).<br />
[[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)]]<br />
<br/><br />
<br />
==Xavier's group==<br />
'''Research Team'''<br/><br />
DPL:<br/><br />
<br />
'''Projection description'''<br/><br />
<br/><br />
<br />
<br />
'''Related publications'''<br><br />
Bertin, X., Bruneau, N., Breilh, J., Fortunato, A. and Karpytchev, M., 2011. Importance of wave age and resonance in storm surges: The case Xynthia, Bay of Biscay. Ocen Modelling, 42: 16-30.<br />
<br />
==Portuguese coastal systems==<br />
<br />
There are 3 related projects for this system.<br />
<br />
<OL><br />
<LI> ''A nowcast-forecast system for for Portuguese coastal systems''<br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues, Alberto Azevedo, João Palha Fernandes<br/><br />
OHSU: António Melo Baptista, Joseph Zhang, Bill Howe, Paul J. Turner, Charles Seaton<br/><br />
<br />
'''Project description'''<br/><br />
<br />
The goal of this project is to integrate complementary research strengths at the two institutions towards the development of a nowcast-forecast system for <br />
water quality prediction in estuarine and coastal waters. The Portuguese partners will provide the water quality models and <br />
the American institution will provide the innovative nowcast-forecast technology.<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/nowcast '''Project web site''']<br />
<br />
<LI>''Improvement of a morphodynamic model applied to tidal inlet environments'' <br/><br />
'''Research Team'''<br/><br />
<br />
LNEC: André Fortunato, Anabela Oliveira, Xavier Bertin<br/><br />
'''Project description'''<br/><br />
<br />
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). <br/><br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/immatie '''Project web site''']<br />
<LI>''Towards operational forecasting of ecosystem dynamics: Benchmarking and Grid-enabling of an ecological model (BGEM)'' <br />
'''Research Team'''<br/><br />
LNEC: Anabela Oliveira, André Fortunato, Marta Rodrigues and João Palha Fernandes<br/><br />
CMOP: António Melo Baptista, Joseph Zhang, Bill Howe, Charles Seaton, Paul J. Turner<br/><br />
<br />
<br />
'''Project description'''<br/><br />
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.<br/><br />
[[File:model-ecoselfe.jpg|thumb|center|Fig. 3 An overview of the ecological model ECOSELFE (Rodrigues, 2008)]]<br/><br />
<br />
<br />
[http://www.lnec.pt/organization/dha/nec/estudos_id/bgem '''Project web site''']<br />
</OL><br />
<br />
<br/><br />
<br />
==Tsunami==<br />
'''Research Team'''<br/><br />
OHSU & VIMS: Joseph Zhang<br/><br />
DOGAMI: George Priest, Rob Witter, Laura Stimely<br/><br />
GeoCanada: Kelin Wang<br/><br />
Oregon State Univ: Chris Goldfinger<br/><br />
<br />
<br />
'''Projection description'''<br/><br />
<br />
SELFE has been certified by National Tsunami Hazard Program (NTHMP, 2012) as a tsunmai inundation model, after passing various benchmarks stipulated by [http://nctr.pmel.noaa.gov/benchmark/ NOAA/PMEL].<br />
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. <br/><br />
<br />
'''Sample images'''<br/><br />
Fig. 4 is a sample inundation map for Cannon Beach OR.<br />
[[File:CannonBeachMap-draft.jpg|thumb|center|Fig. 4 Tsunami hazard map for Cannon Beach OR, generated from SELFE (c/o DOGAMI)]]<br />
<br/><br />
<br />
'''Related publications'''<br><br />
<UL><br />
<LI>NTHMP (2012) Proceedings and results of the 2011 NTHMP model benchmarking workshop. Boulder: US Depart. of Commerce/NOAA/NTHMP, NOAA Special<br />
Report 436p.<br />
<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.<br />
<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. <br />
<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.<br />
<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. <br />
<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 . <br />
</UL><br />
<br />
<br/><br />
<br />
==Water Quality in the Chesapeake Bay Region==<br />
<br />
'''Research Team'''<br />
<br />
Virginia Institute of Marine Science: Junzheng Zhu and [http://www.vims.edu/people/wang_hv/index.php Harry Wang]<br />
<br />
'''Projection description'''<br />
<br />
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.<br />
<br />
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.<br />
<br />
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.<br />
<br />
<br />
Virginia Institute of Marine Science is involved in two TMDL projects in the Chesapeake Bay region:<br />
<br />
<OL><br />
<LI>TMDL scenario development and implementation for the Maryland and Virginia Coastal Bays system.<br />
<LI>Impact on localized water quality resulting from allocation of nutrient loads to dredged material contaminant facilities in Baltimore Harbor.<br />
</OL><br />
<br />
Both projects involve coupling SELFE and ICM (Integrated Compartment Model). <br />
<br />
'''Sample images'''<br />
<br />
Fig. 5 shows some sample results.<br />
[[File:MDcoast-image.jpg|thumb|center|Fig. 5 SELFE-ICM for Maryland coast and bay]]<br />
<br />
<br/><br />
<br />
==Aquaculture and coastal pollutants modelling (New Zealand)==<br />
<br />
'''Research Team'''<br/><br />
[http://www.cawthron.org.nz Cawthron Institute]: Ben Knight<br/><br />
[http://www.metocean.co.nz/ MetOcean Solutions Limited]: Brett Beamsley<br/><br />
<br />
'''Application description'''<br/><br />
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).<br/><br/><br />
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.<br/> <br />
<br />
'''Sample images'''<br/><br />
<br />
Fig. 6 shows SELFE Matlab GUI (currently under development) with a bathymetric map of the Marlborough Sounds, New Zealand.<br />
[[File:SELFE_GUI.PNG|thumb|center|Fig. 6 SELFE Matlab GUI showing bathymetric map of the Marlborough Sounds, New Zealand]]<br/></div>Klihttp://ccrm.vims.edu/w/index.php?title=Talk:Atmospheric_forcing&diff=454Talk:Atmospheric forcing2012-10-16T14:30:03Z<p>Kli: Created page with "== Format of NetCDF atmospheric forcing files == Are the sflux_air files in SELFE intended to be in a compatible format with "[http://cf-pcmdi.llnl.gov/documents/cf-convention..."</p>
<hr />
<div>== Format of NetCDF atmospheric forcing files ==<br />
Are the sflux_air files in SELFE intended to be in a compatible format with "[http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.0/cf-conventions.html NetCDF Climate and Forecast (CF) Metadata Convention 1.0]"? If it is, why not provide the link to it for detailed documentation. --[[User:Kli|Kli]] ([[User talk:Kli|talk]]) 10:30, 16 October 2012 (EDT)</div>Klihttp://ccrm.vims.edu/w/index.php?title=Visualization&diff=453Visualization2012-10-16T12:41:11Z<p>Kli: </p>
<hr />
<div>Right now there are two main tools for viz:<br />
<br />
<UL><br />
<LI>ACE tools: see [http://ccrm.vims.edu/w/index.php/ACE_tools]<br />
<LI>Matlab: see [http://www.stccmop.org/CORIE/modeling/selfe/vis_matlab.html]<br />
</UL><br />
<br />
We recommend you use ACE tools for daily research, and matlab and other tools for publications.<br />
<br />
== Gallery ==<br />
* [[Images with Matlab]]<br />
* [[Animations with Matlab]]</div>Klihttp://ccrm.vims.edu/w/index.php?title=User:Kli&diff=368User:Kli2012-09-27T13:24:10Z<p>Kli: Created page with "李凯(Kai Li)"</p>
<hr />
<div>李凯(Kai Li)</div>Kli