Labs WMT ROMSLIte WaveForcing

==Introduction to Regional Ocean Modeling - Wave Forcing==
This lab has been designed and developed by Courtney Harris, Julia Moriarty, and Danielle Tarpley Virginia Institute of Marine Sciences, Gloucester Point, VA 
with assistance of Irina Overeem, CSDMS, University of Colorado, CO
Classroom organization
This is the third lab in a mini series to introduce a Web-Based version of the Regional Ocean Modeling System (ROMS) for inexperienced users. ROMS is a three-dimensional hydrodynamic ocean model (see Haidvogel et al. 2008; myroms.org). ROMS solves the conservation of mass and three-dimensional momentum equations and includes transport equations for temperature and salinity. The version implemented here also accounts for suspended sediment transport and deposition, following Warner et al. (2008). Here we present a basic configuration of ROMS in the framework of the Web Modeling Tool (WMT). This series of labs is designed for inexperienced modelers to gain some experience with running a numerical model, changing model inputs, and analyzing model output. The example provided looks at the influence of a river plume on the hydrodynamics and sediment transport within an idealized continental shelf. 
This lab focuses on the impact of waves on sediment deposition on the continental shelf. 
This lab will likely take ~ 3hours to complete in the classroom. 
If you have never used the Web Modeling Tool, learn how to use it here. The WMT allows you to set up simulations, but once you are ready to run them, you will need an account on the CSDMS supercomputer to submit your job.
More information on getting an account can be found here HPCC Access. Note that getting permission for access takes a few days after your application. 
Learning objectives
Skills
* familiarize with a basic configuration of the Regional Ocean Modeling System
* hands-on experience with visualizing NetCDF output with Matlab or Panoply.
Technical learning objectives: learn about
* how to describe waves
* wave orbital velocities and current affects bed shear stresses
* the effects of waves on fluvial deposition
Lab Notes
>> Open a new browser window and open the Web Modeling Tool here and select the ROMS project
>> This WMT project is unique in that there is only a single driver, ROMS-Lite. It is a pre-compiled implementation of the larger ROMS system specially configured to the river plume case for teaching use. 
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The numerical experiment has been designed to use idealized inputs (see Lessons 1 and 2), including constant wave energy (steady and uniform waves). The standard wave inputs for the WMT ROMS-Lite are a significant wave height of 2 m, and a wave period of 10 s. The waves are propogating toward shore (direction from which the waves are traveling is set at 1.6 radians measured clockwise from geographic North; nautical convention). Currents in the model vary in response to the river plume entering the shelf, but are generally directed alongshore in response to a larger-scale southward flowing current. Together, the modeled waves and currents affect estimates of bed shear stresses, as well as sediment transport and deposition on the shelf. 
Waves
Energetic waves and currents may increase bed stress, resuspending sediments. Waves are characterized by their wave height, period, length and direction (see the graphic). The "waves" here are surface gravity waves that have wave periods of about 6 - 10 seconds in many coastal oceans. They are the waves you see on the beach. For more information about waves, see Chapter 1, "Waves" of the book "Waves, Tides, and Shallow Water Processes" by the Open University Press (1999).
The ROMS model does not resolve these wave oscillations, but does account for the added stress that they cause on the seabed. 
Important definitions include: 
* Significant wave height (Hs): the mean wave height of the highest third of the waves 
* Wave period: the amount of time it takes for one wave length to pass a given location
* Dominant wave period: the period associated with the waves containing the most energy in a wave spectrum
* Dominant wave direction: the direction associated with the waves containing the most energy in a wave spectrum (typically the direction from which the waves are traveling).
* Wave orbitals: the circular or elliptical motion that water parcels make under a passing waves
* Wave orbital velocity: the velocity of water as it moves due to passing waves (often used to refer to orbital motions near the seabed)
* Wave base: the water depth beneath which passing waves no longer influence water movement 
Currents are described by their velocity, which includes a speed and a direction.
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Various methods have been used to estimate bed stresses based on hydrodynamic conditions (i.e. waves and currents). For the river plume model run with ROMS-Lite, bed stresses are estimated using the method in Madsen (1994), which uses a two-layer bottom boundary layer formulation. In the output, ROMS provides estimates of the wave-induced, current-induced, and combined maximum wave-and-current-induced bed stresses. Sediment may be resuspended when this combined bed stress exceeds a critical threshold for motion (i.e. the critical shear stress; see Lesson 2). 
 How do you expect large vs. small waves to affect sediment deposition on a continental shelf?
>> Run the base case configuration. It is purposely configured to be short and fast (it takes only a few minutes to run). Download the zip file with your simulation output from the run status window 
The ocean_riverplume2.nc file contains all of the important model output in a NetCDF file. 
 Plot the current-induced and wave-induced bed stresses. Do waves or currents dominate the bed stress? Does your answer depend on what part of the shelf you are looking at? Why?
 Plot the sediment bed deposit. Over what water depths can the waves and/or currents suspended riverine sediments from the seabed? How does your answer vary for the different classes of sediment?
>> Now, re-run the model changing the significant wave height to 0.1 m and the dominant waver period to 1 s. Download the zip file with your simulation output from the run status window 
 Plot the current-induced and wave-induced bed stresses and the sediment bed deposit. How do your answers to the first two questions answers change? How does the sediment deposit change in this new “low wave” model run, compared to the base case model run?
 What does this tell us about the effect of storms vs. quiescent periods on sediment transport and deposition? How about sheltered lagoons vs. energetic beach faces?
References
* Grant, W.D. and Madsen, O.S., 1979. Combined wave and current interaction with a rough bottom. Journal of Geophysical Research, 84(C4) 1797-1808.
* Haidvogel, D.B., H.G. Arango, K. Hedstrom, A. Beckmann, P. Malanotte-Rizzoli, and A.F. Shchepetkin, 2000: Model evaluation experiments in the North Atlantic Basin: Simulations in nonlinear terrain-following coordinates, Dyn. Atmos. Oceans, 32, 239-281.
* Madsen, O.S. Spectral Wave-Current Bottom Boundary Layer Flows. In Proceedings of the 24th International Conference on Coastal Engineering, Kobe, Japan, 23–28 October 1994; American Society of Civil Engineers: Reston, VA, USA, 1994; pp. 384–398.
* Nardin, W., Mariotti, G., Edmonds, E., Guercio,R., Fagherazzi, S., 2013. Growth of river mouth bars in sheltered bays in teh presence of frontal waves. Journal of Geophysical research, Earth Surface, 118, 872-886, doi:10.1002/jgrf.20057.
* Warner, Sherwood, Signell, Harris, and Arango, 2008. Development of a three-dimensional, regional, coupled wave, current, and sediment-transport model. Computers & Geosciences.
* Wiberg, P.L., and Sherwood, C.R., 2008. Calculating wave-generated bottom orbital velocities from surface-wave parameters. Computers & Geosciences. 34, 1243-1262. 
* More information on the ROMS Sediment transport model