User Guide 010
Initial Condition The salinity initial condition is specified from within the Salinity tab of the CMS-Flow Model Control window (see Figure 2 74. Two options are available for the initial condition: (1) a constant value, or (2) a user-specified dataset. The CMS card used to specify the salinity initial condition is described in Table 2 68.
table 2-66
Note: • For some applications, using a constant value for the initial condition may be lead to a long spin-up time for salinity. The spin-up time is the time it takes for the salinity to reach a quasi equilibrium or in other words the time it takes for the effects of the initial condition to disap-pear. A better approach is to use a spatially-varying user-specified da-taset. The dataset may be obtained from a previous simulation or manually created based on user judgment.
Boundary Conditions The salinity boundary conditions are setup in the CMS-Flow Boundary Conditions window (see figure below). Currently, the CMS only supports a single salinity time series boundary condition. In this boundary condition, a constant salinity is assigned along the whole boundary. The value is interpolated in time from a user specified time series. The salinity must be specified at ALL open boundary conditions. The user specified salinity is only applied for inflow conditions. When the flow is directed outward of the computational domain, a zero-gradient boundary condition is applied.
figure 2-71
The CMS card used to turn on or off the salinity transport is described in Table 2 68.
table 2-67
Notes: • The salinity must be specified at all open boundary conditions. In addition the input time series at each boundary must be at least as long as the simulation duration. • The salinity is NOT used to update the water density or viscosity during the simulation. The CMS uses a constant water density and viscosity. Therefore density gradients are ignored in the momentum equations. • Turning on the salinity transport increases the computational time because an additional transport equation needs to be solved.
Advanced Settings To Be Completed
Step-By-Step Salinity Transport Application for Matagorda Bay, TX Matagorda Bay is the largest estuarine bay on the coast of Texas and is connected to the Gulf of Mexico and the Gulf Intracoastal Waterway (GIWW) through Matagorda Ship Channel (MSC), a federally-maintained inlet, and Pass Cavallo, a natural inlet just downdrift from the MSC (Figure 2 72).
figure 2-72
In application of the CMS to Matagorda Bay, a telescoping grid was devel-oped to discretized the bay and the offshore. The computational domain extends approximately 80 km alongshore and 20 km offshore, and the seaward boundary of the domain reaches to the 25-m isobath. Figure 2 72shows the telescoping grid with 70,000 ocean cells, bathymetric fea-tures of Matagorda Bay, and the adjoining nearshore area. The CMS grid permits fine resolution in areas of high interest such as jetties and chan-nels. The implicit solver of the CMS, with a large time step of 15 minutes, was employed for the simulation.
Freshwater discharges into the bay come from a number of streams along the coast. The Colorado and the Lavaca Rivers provide most of the inflows. However, “the freshwater discharge is typically less than 10 percent of the daily tidal exchange” in the bay (Kraus et al. 2006). The bay entrance is protected by dual jetties from ocean waves. Momentum transfer, diffusive process and spatial distributions of salinity in the system are mostly controlled by wind, tide, and freshwater inflows. CMS-Flow is driven by time-dependent water surface elevation at the off-shore open boundary, wind forcing over the air-sea interface, and freshwater inflows from rivers and tributaries. Time varying salinity values at BI are also specified along the open boundaries with the water surface elevation and the river boundaries with the freshwater inflows. The initial salinity field is specified to the entire CMS domain as well. 5. CMS-Flow setup: The CMS hydrodynamic input files for Matagorda Bay are required and prepared by the SMS shown in Figure 2 73.
figure 2-73
After opening “MB_rev11_flow_1A.cmcards” in the SMS, choose CMS-Flow | Model Control, click on Salinity, and select Calculate salinity (Figure 2 74). A default time step equal to the hydrodynamic time step has been specified. In this case, 900 sec is used for the salinity calculation.
6. Salinity initial condition: Because of the large spatial variability of salinity in a coastal system, it usually requires long spin-up periods for a salinity simulation to reach to the present salinity distribution, which could range from a few days to weeks. To shorten the spin-up time, an accurate initial condition for the salinity field should be specified. There are two options to assign the initial salinity condition in CMS-Flow: 7. A global initial salinity: Specify a constant initial value for the entire model domain. The salinity value can be specified by checking the Global concentration (ppt) under the Initial condition (Figure 2 74). If this option is applied, it is best to define an average representative salinity for the entire domain. 8. Spatially varying initial salinity: Generate a spatially varying initial salinity field by choosing the Spatially varied toggle under the Initial condition (Figure 2 74). Clicking the Create Dataset and assigning a value under the Default concentration (ppt) in the pop-up window will generate a new dataset with a constant initial salinity value. Clicking OK to close this window and then clicking OK, to close the CMS-FLOW Model Control window, will cause the dataset, Salinity Initial Concentration, to appear in the CMS-Flow data tree, as shown in Figure 2 75a. Highlight the dataset to specify different salinity values in the CMS domain in the same way to modify other datasets such as D50 or Hard Bottom.
figure 2-74
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The dataset for a spatially varying initial salinity can also be generated by using the Data Calculator tool in the Data menu (Demirbilek et al. 2007). For an existing dataset, click the Select Dataset under the Spatially varied toggle and then select the dataset for the initial salinity that already exists (Figure 2 75b). Based on the historical survey data, initial salinity is assigned in the da-taset, Salinity Initial Concentration, for the Matagorda Bay system. The salinity varies from 21.0 ppt near the mouth of the Lavaca River to 33.0 ppt at the offshore open boundary (Figure 2 76).
figure 2-76
9. Salinity boundary conditions: To calculate salinity transport, salinity values at CMS-Flow boundaries need to be specified. Salinity may be specified at two boundary types in the CMS: water surface elevation (WSE) boundary (WSE-forcing boundary) (Figure 2 77a) and freshwater inflow boundary (Flow rate-forcing boundary) (Figure 2 77b). 10. WSE-forcing boundary: Using the Select Cellstring tool and clicking/ highlighting, the cellstring of water surface elevation boundary can be specified as shown in Figure 2 77a. Selecting CMS-Flow | Assign BC will open the CMS-Flow Boundary Conditions window (Figure 2 77). A time series of salinity can be assigned along the WSE-Forcing boundary by clicking the Curve undefined under Salinity on the left hand side of the dialog. 11. The time series is specified either by clicking the Import button to read a salinity boundary input file in xys format (Figure 2 78) (Aquaveo 2010), or by entering time and salinity values manually in two separate data columns, or by importing salinity data from an opened Excel file by using Copy/Paste.
figure 2-77
figure 2-78
figure 2-79
The salinity and water surface elevation measurements at Pass Cavallo and the NOAA Corpus Christi Gage were assigned to the offshore boundary. The 12-day time series of salinity data (November-December 2005) is shown for the WSE-forcing boundary in Figure 2 79. Salinity at this location varies between 31.5 and 33.0 ppt and shows apparent influence of the ocean during the period.
12. ii) Flow rate-forcing boundary: Following the same steps as specifying WSE-forcing boundary, salinity values at freshwater inflow boundaries can be assigned together with flow specifications.
13. The Colorado River, the Lavaca River, and the Garcitas Creek are fresh water sources that flow into Matagorda Bay and flow measurements are available at three USGS gages. A zero salinity value is assigned at the Flow rate-forcing boundaries. The CMS’ capability in conducting the depth-averaged salinity calculation in Matagorda Bay was demonstrated. The CMS simulations represent the salinity transport in Matagorda Bay to a level useful for comparison be-tween engineering alternatives, and to understand the temporal variation and spatial distribution of salinity and the interaction between tides, freshwater inflows and meteorological conditions in the bay.