Labs WMT ROMSLIte RiverForcing

==Introduction to Regional Ocean Modeling - River Forcing-flood and drought conditions==
This lab has been designed and developed by Courtney Harris, Julia Moriarty, Danielle Tarpley, Virginia Institute of Marine Sciences, Gloucester Point, VA 
with assistance of Irina Overeem, CSDMS, University of Colorado, CO
Classroom organization
This lab is the fourth in a mini series of introduction to 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 fourth lab will compare the effect of river flood conditions with low river water or drought conditions.
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
* compare simulation output for several configurations of the Regional Ocean Modeling System
* hands-on experience with visualizing NetCDF output with Matlab or Panoply.
Topical learning objectives
* learn about the impact of river conditions on the nearshore environment
* explore river flood deposition versus drought conditions deposition
Lab Notes
>> Open a new browser window and open the Web Modeling Tool here and select the ROMS project
>> A set of matlab files to can be used for data plotting, with . 
You are now familiar with the basic river plume numerical experiment. Sofar, we have kept river discharge constant over the duration of the simulation at 1500 m3/sec. In these experiments we will drastically increase and reduce river discharge and sediment concentration in different simulations and investigate the effects of fluvial forcing on the plume and nearshore deposition. 
>> Set up a configuration for a river in flood, the discharge at 2000 m3/sec, but maintain the base-case sediment concentration. We will run the river flood for 96 hours (this simulation still takes only a few minutes to run). Download the zip file with your new "river flood" simulation output from the run status window. Similarly, set up a configuration for a river with very small discharge, 200 m3/sec, while maintainting the base case concentration. Download the zip file with your new "river flood" simulation output from the run status window. 
The ocean_riverplume2.nc file has bundled all important output. Recall that the tracer quantities, like salinity and suspended sediment concentration, can be plotted as a 2D plot of eta-rho (x-axis) and xhi_rho (y-axis). But you can also plot cross-sections by plotting xhi-rho on the x-axis and s-rho on the y-axis.
 Make two animations of the river salinity with depth near the river mouth. How far out offshore do the respective freshwater plumes of a river in flood and a river at drought conditions still affect the ocean conditions? 
 In the low river discharge or drought scenario, does much more sediment transport with alongshore currents occur? If yes, based on what parameter did you get to your answer?
>> Set up an additional WMT ROMS-Lite simulation for the river flood conditions, i.e. 2000 m3/sec, but now also increase the suspended sediment concentrations by 300%. Run this simulation and download the output. Total bed thickness can not be directly plotted from the netcdf file, it is the sum of the thicknesses of each of the sediment classes. You can download a zipped archive with Matlab routines to do this instead.
 Use the matlab routines to plot the total deposited bed thickness for the river flood conditions with high sediment concentration. 
References and More information
* Much more information on ROMS community help pages 
* Yao, H.W., Leonardi,N., Li,J., Fagherazzi, S., 2016. Sediment transport in a surface advected estuarine plume. Continental Shelf Research 116, 122-135.