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== Post-Processing Coastal Modeling System Simulations: Part 1, Calculating Volumetric Change ==
{{DISPLAYTITLE:Post-Processing Coastal Modeling System Simulations: Part 1, Calculating Volumetric Change}}
<p style="margin:0; background:#2580a2; font-size:20px; font-weight:bold; border:1px solid #a3bfb1; text-align:left; color:#FFF; padding:0.2em 0.4em;">CIRP-WN-10-1</p>


<div style="text-align:left">'''''by Julie D. Rosati, Tanya M. Beck, and Alejandro Sanchez'''''</div>
<div style="text-align:left">'''''by Julie D. Rosati, Tanya M. Beck, and Alejandro Sanchez'''''</div><br/>  
<br/>  


'''PURPOSE:''' :  This Coastal and Hydraulics Engineering Technical Note (CHETN) is the first in a series that presents methods for analyzing output from Coastal Modeling System (CMS) simulations.  Part 1 discusses calculation of volumetric change using results of a 1-year CMS simulation for Shark River Inlet, New Jersey.
__TOC__


'''CITATION''':
==PURPOSE==
    ''Rosati, J.D., Beck, T.M., and Sanchez, A., 2010, Post-Processing Coastal Modeling System Simulations, Part 1, Calculating Sand Transport Rates,Coastal and Hydraulics Engineering Technical Note ERDC/CHL CHETN-XX-XX, Vicksburg, MS: U.S. Army Engineer Research and Development Center,http://chl.erdc.usace.army.mil/chetn.''
This Coastal and Hydraulics Engineering Technical Note (CHETN) is the first in a series that presents methods for analyzing output from Coastal Modeling System (CMS) simulations.  Part 1 discusses calculation of volumetric change using results of a 1-year CMS simulation for Shark River Inlet, New Jersey.  


'''INTRODUCTION:'''  The Coastal Modeling System (CMS) is an integrated wave, current, sediment transport, and morphology change numerical model within the Surface Water Modeling System (SMS) (Buttolph et al. 2006, Lin et al. 2008, CIRP 2010, and Wu et al. 2010).  The CMS is designed for practical engineering calculations in the coastal zone, including coastal inlets, inlet structures such as jetties, and navigation channels.  Processes calculated within the CMS include tidal forcing, wind, wave-driven currents, and the resulting sediment transport and morphology change. Three sediment transport models are available to calculate the transport due to bed and suspended loads, and resulting morphology change. Wave and structure calculations include reflection, diffraction, refraction, transmission, runup, and overtopping. The CMS calculates coastal and inlet processes and the resulting morphology change for simulation periods ranging from hours to months up to a year (e.g., Beck and Kraus 2010).
==CITATION==
  ''Rosati, J.D., Beck, T.M., and Sanchez, A., 2010, Post-Processing Coastal Modeling System <br> Simulations, Part 1, Calculating Volumetric Change,Coastal and Hydraulics Engineering<br> Wiki-Technical Note CHL/CIRP-WN-10-1, Vicksburg, MS: U.S. Army Engineer Research and Development<br> Center, http://cirp.usace.army.mil/wiki/Publications:CIRP-WN-10-1.''


The analyses discussed herein present methods to analyze CMS output for volumetric change within a defined polygon such as a section of a navigation channel or a morphologic feature such as an ebb shoal.  The step-by-step procedure is applied to CMS output from a study at Shark River Inlet, New Jersey (Beck and Kraus 2010).  CMS output files applied herein are available for download: [[http://cirp.usace.army.mil/wiki/Applications]] .
==INTRODUCTION==
The Coastal Modeling System (CMS) is an integrated wave, current, sediment transport, and morphology change numerical model within the Surface Water Modeling System (SMS) (Buttolph et al. 2006, Lin et al. 2008, CIRP 2010, and Wu et al. 2010).  The CMS is designed for practical engineering calculations in the coastal zone, including coastal inlets, inlet structures such as jetties, and navigation channels.  Processes calculated within the CMS include tidal forcing, wind, wave-driven currents, and the resulting sediment transport and morphology change.  Three sediment transport models are available to calculate the transport due to bed and suspended loads, and resulting morphology change.  Wave and structure calculations include reflection, diffraction, refraction, transmission, runup, and overtopping. The CMS calculates coastal and inlet processes and the resulting morphology change for simulation periods ranging from hours to months up to a year (e.g., Beck and Kraus 2010).   


'''OVERVIEW OF SHARK RIVER INLET SIMULATION:'''  The Shark River Inlet calculations were conducted for a 1-year simulation to determine future conditions of the navigation channel under different channel and structural configurations.  The model was first calibrated for hydrodynamics, and then for sediment transport and morphology change through comparison of pre- and post-dredging bathymetric surveys (conducted by the Corps of Engineers, New York District).  For the Shark River application discussed herein, the total load non-equilibrium sediment transport model with Lund-CIRP transport equations were applied and used with the bed change equation to calculate the morphology change.  Simulation results were both calibrated and validated based on short-term measurements of channel infilling, following the frequent 3-4 month channel surveys, and with model simulations extending to a year of calculations.  The model was forced with the Sandy Hook NOAA tide gauge for water levels and currents, and offshore waves from Wave Information Study (WIS) Station 129 for 1994 were applied for wave-current interaction.
The analyses discussed herein present methods to analyze CMS output for volumetric change within a defined polygon such as a section of a navigation channel or a morphologic feature such as an ebb shoal.  The step-by-step procedure is applied to CMS output from a study at Shark River Inlet, New Jersey (Beck and Kraus 2010).  CMS output files applied herein are available for download: [[Media: SRI.zip|Shark River Inlet Files]].  


'''CALCULATING VOLUME CHANGE:'''  Calculating volume change is necessary for determining rates of channel infilling, inlet shoal evolution, and on a more basic level understanding sand pathways and formulating sand budgets. In the CMS, volume change can be calculated for any polygon defined by feature arcs in the SMS. The following section presents a step-by-step method for calculating volumetric change using the Shark River Inlet simulation files.
==OVERVIEW OF SHARK RIVER INLET SIMULATION==
The Shark River Inlet calculations were conducted for a 1-year simulation to determine future conditions of the navigation channel under different channel and structural configurations.  The model was first calibrated for hydrodynamics, and then for sediment transport and morphology change through comparison of pre- and post-dredging bathymetric surveys (conducted by the Corps of Engineers, New York District). For the Shark River application discussed herein, the total load non-equilibrium sediment transport model with Lund-CIRP transport equations were applied and used with the bed change equation to calculate the morphology change. Simulation results were both calibrated and validated based on short-term measurements of channel infilling, following the frequent 3-4 month channel surveys, and with model simulations extending to a year of calculations.  The model was forced with the Sandy Hook NOAA tide gauge for water levels and currents, and offshore waves from Wave Information Study (WIS) Station 129 for 1994 were applied for wave-current interaction.


'''Loading Files and Setting Projection:''' Download the Shark River Inlet calculation file SRI.zip from: [[http://cirp.usace.army.mil/wiki/Applications]]. Unzip the files in a directory on your PC.
==CALCULATING VOLUME CHANGE==
Calculating volume change is necessary for determining rates of channel infilling, inlet shoal evolution, and on a more basic level understanding sand pathways and formulating sand budgets. In the CMS, volume change can be calculated for any polygon defined by feature arcs in the SMS. The following section presents a step-by-step method for calculating volumetric change using the Shark River Inlet simulation files.


Load the file Shark River Inlet.cmcards into SMS by dragging it into the SMS or by clicking ''File | Open | Shark River Inlet.cmcards''. The solution file should load in automatically as shown in Figure 1.  Once you have loaded the solution file, zoom in to show the channel region (Figure 2).
===Loading Files and Setting Projection===
Download the Shark River Inlet calculation file SRI.zip from: [[Media: SRI.zip|Shark River Inlet Files]]. Unzip the files in a directory on your PC.


Load the file Shark River Inlet.cmcards into SMS by dragging it into the SMS or by clicking ''File | Open | Shark River Inlet.cmcards''. The solution file should load in automatically as shown in Figure 1a.  Once you have loaded the solution file, zoom in to show the channel region (Figure 1b).


{{Image|Figure1.png|150px|'''a. Zoomed-out view of Shark River Inlet grid.'''}}
[[File:JFigure1a.png|thumb|right|Figure 1a. CMS grid, zoom-out showing study area.]]
[[File:JFigure1b.png|thumb|right|Figure 1b. CMS grid, zoom-in showing 1-year morphology change calculation.]]


{{Image|Figure2.png|150px|'''b. Zoom-in of calculated morphology change after 1 year simulation.
CMS makes calculations in metric units, so to make sure the volumetric change is interpreted properly in SMS, you need to check that your projection is in meters by clicking the top toolbar under Edit – Projection (Figure 2).
Figure 1. CMS calculations for Shark River Inlet, NJ.'''}}


{{Image|Figure3.png|150px|'''Figure 3. Files for the CMS-Flow salinity simulation.'''}}
[[File:JFigure2.png|thumb|right|Figure 2. Setting the horizontal and vertical projection to meters.]]


{{Image|Figure4.png|150px|'''Figure 4. Setting up the salinity calculation.'''}}
===Defining a polygon for volumetric change===
To begin defining the polygon in which we will calculate volume change, you will define a transect or ''Feature Arc'' in SMS and convert this arc or a set of arcs into a polygon. To start, in the project explorer to the left of the SMS window, Right-click on the default coverage and select ''Type | Generic | Observation'' (Figure 3).


{{Image|Figure5.png|150px|'''Figure 5. Specifying spatially varied initial salinity.'''}}
[[File:JFigure3.png|thumb|right|Figure 3. Changing the default coverage to ''Type-Generic-Observation''.]]


{{Image|Figure6.png|150px|'''Figure 6. CMS-Flow data tree.'''}}
Next, zoom into the area of interest and create a Feature Arc. Make sure you are in the Map module by clicking on the Map Module Tool or by clicking on Map Data. The Map Module toolbar should become available in the SMS window. Click on the Create Feature Arc tool (Figure 4).  


{{Image|Figure7.png|150px|'''Figure 7. Salinity boundary types in the CMS.'''}}
[[File:JFigure4.png|thumb|right|Figure 4. Selecting ''Map Module'' (left) and ''Feature Arc'' (right).]]


{{Image|Figure8.png|150px|'''Figure 8. Salinity specifications along the WSE-forcing boundary.'''}}
A polygon can be created with the Feature Arc tool that delineates the area of interest. For this example, a Feature Arc delineating the inlet navigation channel from the landward bend in the channel (west) out seaward to the 5.5 m contour is chosen to document the channel infilling rate (Figure 5).  


{{Image|Figure9.png|150px|'''Figure 9. Salinity boundary input from a xys file.'''}}
[[File:JFigure5.png|thumb|right|Figure 5. Creating a ''Feature Arc'' to delineate a portion of the inlet navigation channel.]]


{{Image|Figure10.png|150px|'''Figure 10. Salinity and current distributions during (a) the flood current and (b) the ebb current.'''}}
To select the Feature Arc, click on the ''Select Feature Arc tool'' [[File:SelectFeatureArc.png]] and click on the Feature Arc.  Next we will convert the Feature Arc into a polygon. With the Feature Arc selected, click on ''Feature Objects | Build Polygons'' (Figure 6).


{{Image|Figure11.png|150px|'''Figure 11. CMS computational domain and data collection locations.'''}}
[[File:JFigure6.png|thumb|right|Figure 6. Converting a ''Feature Arc'' into a polygon.]]


{{Image|Figure12.png|150px|'''Figure 12. Salinity and velocity sampling stations (URS 2010).'''}}
Select the Polygon by clicking on the ''Select Feature Polygon tool'' [[image:SelectFeaturePolygon.png|30px]] (Figure 7). Note that Morphology_Change is selected in the left file tree structure and the final time step is selected in the Time steps window.  The area of the polygon is shown at the bottom of the SMS window.


{{Image|Figure13.png|150px|'''Figure 13. Salinity comparisons between measurements and CMS calculations (URS 2010).'''}}
[[File:JFigure7.png|thumb|right|Figure 7. Select ''Feature Polygon'' with channel polygon selected.]]


'''MODEL ASSUMPTIONS:''' CMS-Flow is presently capable of 2D salinity computations in both the explicit and implicit solvers. 3D representation of salinity in the CMS, discussed herein, is being tested.  The simulation of salinity can often require a 3D solution due to the presence of vertical salinity gradients that can significantly influence flow. It is therefore important to understand the limitations of 2D salinity simulations, and apply them only when the assumptions inherent in 2D simulations are valid. Typically, 2D salinity calculations are valid when the salinity is well mixed over the water column. These conditions are usually met for shallow bays with open exchanges to the ocean or gulf, dominant tidal signals, and sufficient wind energy to provide the vertical mixing. Also, the assumption of sufficient energy to mix over the water column is valid under storm conditions, even for deeper water bodies. Finally, when the exchange with the open sea is restricted by an inlet, the tidal range is an important indicator of vertical mixing conditions. For low tide ranges, significant vertical stratification can occur, even in shallow bays and estuaries, especially when the winds are calm. Pritchard (1955) and Cameron and Pritchard (1963) have classified estuaries using stratification and salinity distribution as the governing criteria, and these classifications can be used for guidance in applying the 2D simulations.
===Calculate Volume Change===
To integrate volume change within the defined polygon at the time step selected, click on ''Feature Objects | Select/Delete Data'', and in the window that pops up, choose ''Inside polygon(s)''for the Data Domain, then ''OK'' (Figure 8).  SMS will calculate statistics about the selected cells within the polygon and summarize these in the bottom portion of the window. Note that the calculation represents the area and cumulative volume change associated with the selected cells that are in contact with the polygon; this area will most likely be slightly different than the polygon area that was calculated in Figure 7. The net volumetric change for the example channel polygon shown in Figure 8 is approximately 22,000 cu m.


The lateral mixing for salinity in the CMS Flow model is the same as the lateral mixing in the momentum equations.   
[[File:JFigure8.png|thumb|right|Figure 8.  Calculating volume change associated with selected cells.]]


'''SALINITY MODELING AT HUMBOLDT BAY, CA:''' In this section, the salinity modeling is described to demonstrate the CMS capability at Humboldt Bay, CA.
===Interpretation of Results===
With the polygon selected in the main SMS window, scroll through selected time steps of interest (bottom left window) and note the volume for each one in a spreadsheet.  Figure 9 shows volumetric change for the Shark River Inlet channel and ebb shoal through time.  The channel polygon in Figure 9 was selected to match the channel survey data available from the New York District, so that calculated infilling could be compared to measurements.  Calculations show a large initial infilling during the first 0.25 year, followed by a slightly scouring period, and once again increasing during 0.75-1 year.  The greater rates of volume change in the first quarter (Jan – Mar) and last quarter (Oct-Dec) of the year illustrate the influence of storms in transporting larger sand volumes into the channel during these periods.  In contrast, the ebb shoal increases in volume continually during this period of time, indicating that it is likely not yet in equilibrium.  We would expect that the ebb shoal’s rate of growth would decrease for longer simulation periods over multiple years.


Humboldt Bay is a natural multi-basin, bar-built, coastal lagoon located along the rugged North Coast of California. The bay entrance is protected by dual rubble-mound jetties from the high-energy waves at the Northeast Pacific coast (Figure 1). Wave-induced long-shore current, nearshore wave breaking, and wave-dependent mixing have a significant contribution to momentum transfer in the water column, diffusive process and spatial distributions of salinity (Moon 2005). Tides and wind are the primary forcing to drive hydrodynamics and salinity transport inside the bay.
[[File:JFigure9.png|thumb|right|Figure 9. Calculation of Shark River Inlet channel infilling and ebb shoal growth.]]


In application of the CMS to Humboldt Bay, a quadtree grid system was developed to discretize the bay and the offshore. The computational domain extends approximately 25 km alongshore and 20 km offshore, and the seaward boundary of the domain reaches to the 300 m isobath. Figure 2 shows the quadtree grid with 43,000 ocean cells and bathymetric features of Humboldt Bay, and adjoining nearshore and continental shelf. The CMS grid permits fine resolution in areas of high interest such as jetties, channels, and the bay. The implicit solver of the CMS with a large time step of 10 minutes was employed for the simulation. The implicit version of CMS typically reduces the computation time by more than 50% as compared ot the explicit version.
For comparison, Figure 10 shows the measured (surveyed) volume change in the channel for this same region of the channel (from the bridge out to the -5.5 m Mean Low Water elevation contour; modified from Figure 16 of Beck and Kraus, 2010). The measured channel infilling shows ~ 18,000 cu m in the first year, comparable to the calculated channel infilling shown in Figure 9. In recent years, shoaling has increased to 30,000-40,000 cu m/year, and the New York District must dredge the channel quarterly to maintain navigability.


CMS-Flow is driven by time-dependent water surface elevation at the offshore open boundaries, wind forcing over the surface boundary, and freshwater inflows from rivers and tributaries. Time varying salinity values are specified along the open boundaries and with the freshwater inflows. The initial salinity field needs to be specified to the entire CMS domain as well.
[[File:JFigure10.png|thumb|right|Figure 10.  Measured channel infilling at Shark River Inlet based on post-1999 survey data (from bridge out to -5.5 m MLW contour; modified from Figure 16 of Beck and Kraus, 2010).]]


'''1. CMS-Flow setup:''' The CMS hydrodynamic input files for Humboldt Bay, CA are required to be generated and prepared by the SMS shown in Figure 3:
==CONCLUSIONS==
This CHETN is Part 1 of a series discussing post-processing of Coastal Modeling System (CMS) simulations. Herein we present a step-by-step method for calculating volume change within defined polygons. With this method, the time history of volume change for defined polygons can be calculated within SMS.  Output files used in the examples are provided for download from the CIRP wiki (http://cirp.usace.army.mil/wiki/Applications).


After opening “HB_Flow.cmcards” in the SMS, choose CMS-Flow | Model Control, click on the Salinity, and select the Calculate salinity (Figure 4). A time step of greater than (integer multiplier) or equal to the hydrodynamic time step should be specified. In this case, the Transport rate under the Time steps is set to 600 sec (equal to the hydrodynamic time step) for the salinity calculation.


'''2. Salinity initial condition:''' Because of the large salinity range 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:
==ADDITIONAL INFORMATION==
This CHETN was prepared as part of the Coastal Inlets Research Program (CIRP) under the Inlet Engineering Toolbox work unit, and was written by Dr. Julie Dean Rosati (Julie.D.Rosati@usace.army.mil), Ms. Tanya Beck (Tanya.M.Beck@usace.army.mil), and Mr. Alejandro Sanchez (Alejandro.Sanchez@usace.army.mil ) of the U.S. Army Engineer Research and Development Center (ERDC), Coastal and Hydraulics Laboratory (CHL). The Shark River Inlet application used to illustrate the method was part of a study conducted for the USACE District, New York.  Ms. Irene Watts, New England District, reviewed this CHETN. This CHETN should be cited as follows:


'''i) A global initial salinity:''' Specify a constant initial value for the entire model domain. Figure 4 shows the example of using a constant 33.5 ppt as the global initial salinity value for the Humboldt Bay model.
Rosati, J.D., Beck, T.M., and Sanchez, A., 2010. Post-Processing Coastal Modeling System Simulations: Part 1, Calculating Sand Transport Rates. Coastal and Hydraulics Engineering Technical Note ERDC/CHL CHETN-XX-XX. Vicksburg, MS: U.S. Army Engineer Research and Development Center. http://chl.erdc.usace.army.mil/chetn.


'''ii) Spatially varying initial salinity:''' Generate a spatially varying initial salinity field by choosing the Spatially varied toggle under the Initial condition (Figure 5). 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, the dataset, Salinity Initial Concentration, will appear in the CMS-Flow data tree as shown in Figure 6a. 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.


The dataset for a spatially varying initial salinity can also be generated by using Data Calculator tool in the Data menu (Demirbilek et al. 2008). For an existing dataset, click the Select Dataset under the Spatially varied and then select the dataset for the initial salinity that already exists (Figure 6b). 


'''3. Salinity boundary conditions:''' Salinity conditions need to be specified at CMS-Flow boundaries. Two salinity boundary types are available in the CMS: water surface elevation (WSE) boundary (WSE-forcing boundary) and freshwater inflow boundary (Flow rate-forcing boundary) (Figure 7).
==REFERENCES==
*Beck, T.M., and Kraus, N.C.  2010. Shark River Inlet, New Jersey, Entrance Shoaling: Report 2, Analysis with Coastal Modeling System. Coastal and Hydraulics Laboratory Technical Report 10-4. Vicksburg, MS: U.S. Army Engineer Research and Development Center, U.S.A.


'''i) 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 7a. Selecting CMS-Flow | Assign BC will open the CMS-Flow Boundary Conditions window (Figure 8). 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.
*Buttolph, A.M., Reed, C.W., Kraus, N.C., Ono, N., Larson, M., Carmenen, B., Hanson, H., Wamsley, T., and Zundel, A.K. 2006. Two-dimensional depth-averaged circulation model CMS-M2D: Version 3.0, Report 2: Sand transport and morphology change. Coastal and Hydraulics Laboratory Technical Report ERDC/CHL TR-06-9. Vicksburg, MS: U.S. Army Engineer Research and Development Center, U.S.A.
The time series is specified either by clicking the Import button to read a salinity boundary input file in xys format (Figure 9) (Aquaveo 2010) or by manually entering time and salinity values in two separate data columns or by importing salinity data from an opened Excel file by Copy/Paste.


Because the WSE-forcing boundary of the Humboldt Bay grid is located outside the bay in open coast, salinity measurements at Trinidad Bay, approximately 18 km north of the CMS domain by CeNCOOS at Humboldt State University (2010), were assigned to the CMS-Flow open boundary. A 30-day time series of the salinity data is shown for the WSE-forcing boundary in Figure 8. Salinity at this location varies between 30.5 and 33.5 ppt that show apparent influence of the ocean on salinity variations during the period.
*Coastal Inlets Research Program (CIRP), 2010.  CIRP wiki – CMS. http://cirp.usace.army.mil/wiki/CMS , last updated 28 July 2010, accessed 16 August 2010.


'''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.  
*Lin, L., Demirbilek, Z., Mase, H., Zheng, J., and Yamada, F. 2008. CMS-Wave: A nearshore spectral wave processes model for coastal inlets and navigation projects. Coastal and Hydraulics Laboratory Technical Report ERDC/CHL TR-08-13, Vicksburg, MS: U.S. Army Engineer Research and Development Center, U.S.A.


Only a few rivers and creeks flow into Humboldt Bay and no stream measurements are available. Although small, there are seasonal variations in freshwater inflows to the bay. Relatively large amount of land runoffs flows into the bay during the rainy season in northern California from October to April. For demonstration purpose in this CMS application, 10 ppt was assigned for a constant river flow in the Elk River (Figure 7). A non-zero salinity value is given here considering that the location of the Flow rate-forcing cellstring is within the intertidal zone.
*Wu, W., Zhang, M., and Sanchez, A. 2010. An implicit 2-D shallow water flow model on unstructured quadtree rectangular mesh. J. Coastal Res., in press.


'''SIMULATION RESULTS:''' For the Humboldt Bay demonstration, the CMS-Flow simulation was conducted for a 30 day winter period (December 2007). Depth-averaged current and salinity fields near the bay entrance channel were retrieved from two snapshots of the CMS results at Day 19 of the simulation, corresponding to the flood and ebb currents, respectively (Figure 10).  
*Zundel, A. K., 2000. Surface-water modeling system reference manual. Brigham Young University, Environmental Modeling Research Laboratory, Provo, UT.


The current speed is between 1 and 2 m/sec at the Humboldt Bay entrance during the flood and ebb tides. The bay is dominated by relatively high salinity water and low salinity water fills the downstream reach of the Elk River, consistent with the salinity specifications along the WSE-forcing and the Flow rate-forcing boundaries.  Figure 10 shows that high salinity ocean water is brought into the bay by the flood current. A salt front near the mouth of the Elk River indicates that intrusion of freshwater plume into the bay. The plume is pushed upstream of the river by strong flood current passing by to the Arcata Bay and extends further into Humboldt Bay during the ebb tidal cycle.
[[category:publication]]
 
'''SALINITY TRANSPORT MODELING AT WHITE DITCH AREA, LA:''' Located southeast of New Orleans on the coast of Louisiana, the White Ditch area has been experiencing the shortage of fresh water, sediments and nutrients from the Mississippi River, and saltwater intrusion due to sea level rise and storms. As a result, extensive wetland loss and degradation of tidal marshes have occurred in the area through the years. A hydrodynamic and salinity modeling analysis was conducted by URS (2010) to evaluate alternative designs for a fresh water diversion from the Mississippi River to the project area.
 
CMS-Flow was developed for the White Ditch project. The model domain extends about 60 km along the NW-SE directions and about 30 km along the SW-NE direction, and includes the Mississippi River levees, the Mississippi River-Gulf Outlet (MRGO) channel, and other features (Figure 11). The size of the CMS grid cells ranges from 24 to 600 m with the fine grid along the White Ditch (Mississippi River) and the coarse grid in the Gulf of Mexico.
 
The CMS was driven by the tide data downloaded from U.S. Geological Survey (USGS) station (7374527) (Figure 11), Northeast Bay Gardene near Point-A-LA-Hache, LA (http://waterdata.usgs.gov/nwis). Rainfall data were obtained from the NOAA Port Sulfer Station (167471) and from a Belle Chasse station. Daily evaporation data were not available at the project area. Evaporation rates specified in the CMS were based on a study conducted by Cooke et al. (2008). Freshwater flows were measured from the Caernarvon Diversion and the Mississippi River. The New Orleans District, USACE, manages the Caernarvon Freshwater Diversion Project and provided daily flow information for the study.
 
The salinity data for the CMS were collected on a field survey conducted from 20 July through 23 July, 2009 by URS. The sampling stations are shown in Figure 12. Flow velocity, temperature, salinity and turbidity were collected periodically between 21 and 23 July, 2009 at the primary stations (N1, N2, N3, S1, S2, and S3). Less frequent flow velocity, temperature and salinity measurements were collected at the secondary locations (Oak River Channel, N4, N5, N6, S4, S5, S6, S7, S8, S9, S10, and S11).
 
Statistical analysis of the salinity data was performed to compute the median, maximum and minimum salinity at each station. The time-averaged salinity values over the last four days of the CMS simulation corresponding to the time period of the measurements by URS (2010), were compared with the measurements (Figure 13).
 
The time- and depth-averaged salinity in this wetland area ranges from about 3 to 10 ppt. The variability of salinity is less than 1 ppt at the landward stations (Points 33-35) and can reach as high as more than 3 ppt at the seaward stations (Point 36) over the 4-day survey period. The salinity data show a general trend in the survey area. Salinity is relatively high at the southeast corner of the CMS domain in nearshore waters of the Gulf of Mexico, and decreases towards the northwest. High salinity also occurs along the east bank of the Mississippi River and decreases to the northeast of the CMS domain. The general trend indicates that significant sources of freshwater in the White Ditch area are from the Caernarvon Diversion. CMS-Flow tends to underestimate the salinity at some stations, but overall the CMS results show good agreement between measurements and calculated salinity, and well represent the spatial pattern and temporally averaged salinity levels.
'''CONCLUSIONS:''' The depth-averaged salinity calculation procedure by the CMS was demonstrated in this technical note. The Humboldt Bay example shows that the procedures to set up the CMS for salinity calculation are straightforward and user-friendly. The White Ditch example provides an estuarine application of salinity calculations and verification for the CMS results, which well reproduce the spatial salinity distributions in the wetland area. Due to lack of measurements such as rainfall and evaporation, detailed bathymetry and salinity data, some assumptions were made for the study. Further improvement can be made as more data are collected in the future.
 
'''ADDITIONAL INFORMATION:'''  This CHETN was prepared and funded under the Coastal Inlet Research Program (CIRP) and was written by Dr. Honghai Li (Honghai.Li@usace.army.mil, voice: 601-634-2840, fax: 601-634-3080) of the U.S. Army Engineer Research and Development Center (ERDC), Coastal and Hydraulics Laboratory (CHL), Dr. Christopher W. Reed (Chris_Reed@URSCorp.com) of URS Corporation, and Mitchell E. Brown (Mitchell.E.Brown@usace.army.mil) of ERDC, CHL. Alejandro Sanchez of CIRP provided hydrodynamic model information for the Humboldt Bay example. The CIRP Program Manager, Dr. Julie D. Rosati (Julie.D.Rosati@usace.army.mil), the assistant Program Manager, Dr. Nicholas C. Kraus, the Chief of the Coastal Engineering Branch at CHL, Dr. Jeffrey P. Waters, and Dr. Lihwa Lin, the Coastal Engineering Branch, reviewed this CHETN. Files for the example may be obtained by contacting the author. This CHETN should be cited as follows:
 
Li, H., C. W. Reed, and M. E. Brown. 2010. Salinity Calculations in the Coastal Modeling System. Coastal and Hydraulics Engineering Technical Note ERDC/CHL CHETN-IV-XX. Vicksburg, MS: U.S. Army Engineer Research and Development Center. An electronic copy of this CHETN is available from http://chl.erdc.usace.army.mil/chetn or http://cirp.usace.army.mil/pubs/chetns.html.
 
'''REFERENCES'''
 
Aquaveo. 2010. SMS: XY Series Files (*.xys). http://www.xmswiki.com/xms/SMS:XY_Series_Files_(*.xys).
 
Buttolph, A. M., C. W. Reed, N. C. Kraus, N. Ono, M. Larson, B. Camenen, H. Hanson, T. Wamsley, and A.
K. Zundel, A. K. 2006. Two-dimensional depth-averaged circulation model CMS-M2D: Version 3.0, Report 2, sediment transport and morphology change. Coastal and Hydraulics Laboratory Technical Report ERDC/CHL-TR-06-7. Vicksburg, MS: U.S. Army Engineer Research and Development Center. 
 
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Lin, L., Z. Demirbilek, H. Mase, J. Zheng, and F. Yamada. 2008. CMS-Wave: A nearshore spectral wave processes model for coastal inlets and navigation projects. Coastal and Hydraulics Laboratory Technical Report ERDC/CHL-TR-08-13. Vicksburg, MS: U.S. Army Engineer Research and Development Center. 
 
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Latest revision as of 20:44, 25 August 2020

CIRP-WN-10-1

by Julie D. Rosati, Tanya M. Beck, and Alejandro Sanchez


PURPOSE

This Coastal and Hydraulics Engineering Technical Note (CHETN) is the first in a series that presents methods for analyzing output from Coastal Modeling System (CMS) simulations. Part 1 discusses calculation of volumetric change using results of a 1-year CMS simulation for Shark River Inlet, New Jersey.

CITATION

 Rosati, J.D., Beck, T.M., and Sanchez, A., 2010, Post-Processing Coastal Modeling System 
 Simulations, Part 1, Calculating Volumetric Change,Coastal and Hydraulics Engineering
 Wiki-Technical Note CHL/CIRP-WN-10-1, Vicksburg, MS: U.S. Army Engineer Research and Development
 Center, http://cirp.usace.army.mil/wiki/Publications:CIRP-WN-10-1.

INTRODUCTION

The Coastal Modeling System (CMS) is an integrated wave, current, sediment transport, and morphology change numerical model within the Surface Water Modeling System (SMS) (Buttolph et al. 2006, Lin et al. 2008, CIRP 2010, and Wu et al. 2010). The CMS is designed for practical engineering calculations in the coastal zone, including coastal inlets, inlet structures such as jetties, and navigation channels. Processes calculated within the CMS include tidal forcing, wind, wave-driven currents, and the resulting sediment transport and morphology change. Three sediment transport models are available to calculate the transport due to bed and suspended loads, and resulting morphology change. Wave and structure calculations include reflection, diffraction, refraction, transmission, runup, and overtopping. The CMS calculates coastal and inlet processes and the resulting morphology change for simulation periods ranging from hours to months up to a year (e.g., Beck and Kraus 2010).

The analyses discussed herein present methods to analyze CMS output for volumetric change within a defined polygon such as a section of a navigation channel or a morphologic feature such as an ebb shoal. The step-by-step procedure is applied to CMS output from a study at Shark River Inlet, New Jersey (Beck and Kraus 2010). CMS output files applied herein are available for download: Shark River Inlet Files.

OVERVIEW OF SHARK RIVER INLET SIMULATION

The Shark River Inlet calculations were conducted for a 1-year simulation to determine future conditions of the navigation channel under different channel and structural configurations. The model was first calibrated for hydrodynamics, and then for sediment transport and morphology change through comparison of pre- and post-dredging bathymetric surveys (conducted by the Corps of Engineers, New York District). For the Shark River application discussed herein, the total load non-equilibrium sediment transport model with Lund-CIRP transport equations were applied and used with the bed change equation to calculate the morphology change. Simulation results were both calibrated and validated based on short-term measurements of channel infilling, following the frequent 3-4 month channel surveys, and with model simulations extending to a year of calculations. The model was forced with the Sandy Hook NOAA tide gauge for water levels and currents, and offshore waves from Wave Information Study (WIS) Station 129 for 1994 were applied for wave-current interaction.

CALCULATING VOLUME CHANGE

Calculating volume change is necessary for determining rates of channel infilling, inlet shoal evolution, and on a more basic level understanding sand pathways and formulating sand budgets. In the CMS, volume change can be calculated for any polygon defined by feature arcs in the SMS. The following section presents a step-by-step method for calculating volumetric change using the Shark River Inlet simulation files.

Loading Files and Setting Projection

Download the Shark River Inlet calculation file SRI.zip from: Shark River Inlet Files. Unzip the files in a directory on your PC.

Load the file Shark River Inlet.cmcards into SMS by dragging it into the SMS or by clicking File | Open | Shark River Inlet.cmcards. The solution file should load in automatically as shown in Figure 1a. Once you have loaded the solution file, zoom in to show the channel region (Figure 1b).

Figure 1a. CMS grid, zoom-out showing study area.
Figure 1b. CMS grid, zoom-in showing 1-year morphology change calculation.

CMS makes calculations in metric units, so to make sure the volumetric change is interpreted properly in SMS, you need to check that your projection is in meters by clicking the top toolbar under Edit – Projection (Figure 2).

Figure 2. Setting the horizontal and vertical projection to meters.

Defining a polygon for volumetric change

To begin defining the polygon in which we will calculate volume change, you will define a transect or Feature Arc in SMS and convert this arc or a set of arcs into a polygon. To start, in the project explorer to the left of the SMS window, Right-click on the default coverage and select Type | Generic | Observation (Figure 3).

Figure 3. Changing the default coverage to Type-Generic-Observation.

Next, zoom into the area of interest and create a Feature Arc. Make sure you are in the Map module by clicking on the Map Module Tool or by clicking on Map Data. The Map Module toolbar should become available in the SMS window. Click on the Create Feature Arc tool (Figure 4).

Figure 4. Selecting Map Module (left) and Feature Arc (right).

A polygon can be created with the Feature Arc tool that delineates the area of interest. For this example, a Feature Arc delineating the inlet navigation channel from the landward bend in the channel (west) out seaward to the 5.5 m contour is chosen to document the channel infilling rate (Figure 5).

Figure 5. Creating a Feature Arc to delineate a portion of the inlet navigation channel.

To select the Feature Arc, click on the Select Feature Arc tool SelectFeatureArc.png and click on the Feature Arc. Next we will convert the Feature Arc into a polygon. With the Feature Arc selected, click on Feature Objects | Build Polygons (Figure 6).

Figure 6. Converting a Feature Arc into a polygon.

Select the Polygon by clicking on the Select Feature Polygon tool SelectFeaturePolygon.png (Figure 7). Note that Morphology_Change is selected in the left file tree structure and the final time step is selected in the Time steps window. The area of the polygon is shown at the bottom of the SMS window.

Figure 7. Select Feature Polygon with channel polygon selected.

Calculate Volume Change

To integrate volume change within the defined polygon at the time step selected, click on Feature Objects | Select/Delete Data, and in the window that pops up, choose Inside polygon(s)for the Data Domain, then OK (Figure 8). SMS will calculate statistics about the selected cells within the polygon and summarize these in the bottom portion of the window. Note that the calculation represents the area and cumulative volume change associated with the selected cells that are in contact with the polygon; this area will most likely be slightly different than the polygon area that was calculated in Figure 7. The net volumetric change for the example channel polygon shown in Figure 8 is approximately 22,000 cu m.

Figure 8. Calculating volume change associated with selected cells.

Interpretation of Results

With the polygon selected in the main SMS window, scroll through selected time steps of interest (bottom left window) and note the volume for each one in a spreadsheet. Figure 9 shows volumetric change for the Shark River Inlet channel and ebb shoal through time. The channel polygon in Figure 9 was selected to match the channel survey data available from the New York District, so that calculated infilling could be compared to measurements. Calculations show a large initial infilling during the first 0.25 year, followed by a slightly scouring period, and once again increasing during 0.75-1 year. The greater rates of volume change in the first quarter (Jan – Mar) and last quarter (Oct-Dec) of the year illustrate the influence of storms in transporting larger sand volumes into the channel during these periods. In contrast, the ebb shoal increases in volume continually during this period of time, indicating that it is likely not yet in equilibrium. We would expect that the ebb shoal’s rate of growth would decrease for longer simulation periods over multiple years.

Figure 9. Calculation of Shark River Inlet channel infilling and ebb shoal growth.

For comparison, Figure 10 shows the measured (surveyed) volume change in the channel for this same region of the channel (from the bridge out to the -5.5 m Mean Low Water elevation contour; modified from Figure 16 of Beck and Kraus, 2010). The measured channel infilling shows ~ 18,000 cu m in the first year, comparable to the calculated channel infilling shown in Figure 9. In recent years, shoaling has increased to 30,000-40,000 cu m/year, and the New York District must dredge the channel quarterly to maintain navigability.

Figure 10. Measured channel infilling at Shark River Inlet based on post-1999 survey data (from bridge out to -5.5 m MLW contour; modified from Figure 16 of Beck and Kraus, 2010).

CONCLUSIONS

This CHETN is Part 1 of a series discussing post-processing of Coastal Modeling System (CMS) simulations. Herein we present a step-by-step method for calculating volume change within defined polygons. With this method, the time history of volume change for defined polygons can be calculated within SMS. Output files used in the examples are provided for download from the CIRP wiki (http://cirp.usace.army.mil/wiki/Applications).


ADDITIONAL INFORMATION

This CHETN was prepared as part of the Coastal Inlets Research Program (CIRP) under the Inlet Engineering Toolbox work unit, and was written by Dr. Julie Dean Rosati (Julie.D.Rosati@usace.army.mil), Ms. Tanya Beck (Tanya.M.Beck@usace.army.mil), and Mr. Alejandro Sanchez (Alejandro.Sanchez@usace.army.mil ) of the U.S. Army Engineer Research and Development Center (ERDC), Coastal and Hydraulics Laboratory (CHL). The Shark River Inlet application used to illustrate the method was part of a study conducted for the USACE District, New York. Ms. Irene Watts, New England District, reviewed this CHETN. This CHETN should be cited as follows:

Rosati, J.D., Beck, T.M., and Sanchez, A., 2010. Post-Processing Coastal Modeling System Simulations: Part 1, Calculating Sand Transport Rates. Coastal and Hydraulics Engineering Technical Note ERDC/CHL CHETN-XX-XX. Vicksburg, MS: U.S. Army Engineer Research and Development Center. http://chl.erdc.usace.army.mil/chetn.


REFERENCES

  • Beck, T.M., and Kraus, N.C. 2010. Shark River Inlet, New Jersey, Entrance Shoaling: Report 2, Analysis with Coastal Modeling System. Coastal and Hydraulics Laboratory Technical Report 10-4. Vicksburg, MS: U.S. Army Engineer Research and Development Center, U.S.A.
  • Buttolph, A.M., Reed, C.W., Kraus, N.C., Ono, N., Larson, M., Carmenen, B., Hanson, H., Wamsley, T., and Zundel, A.K. 2006. Two-dimensional depth-averaged circulation model CMS-M2D: Version 3.0, Report 2: Sand transport and morphology change. Coastal and Hydraulics Laboratory Technical Report ERDC/CHL TR-06-9. Vicksburg, MS: U.S. Army Engineer Research and Development Center, U.S.A.
  • Lin, L., Demirbilek, Z., Mase, H., Zheng, J., and Yamada, F. 2008. CMS-Wave: A nearshore spectral wave processes model for coastal inlets and navigation projects. Coastal and Hydraulics Laboratory Technical Report ERDC/CHL TR-08-13, Vicksburg, MS: U.S. Army Engineer Research and Development Center, U.S.A.
  • Wu, W., Zhang, M., and Sanchez, A. 2010. An implicit 2-D shallow water flow model on unstructured quadtree rectangular mesh. J. Coastal Res., in press.
  • Zundel, A. K., 2000. Surface-water modeling system reference manual. Brigham Young University, Environmental Modeling Research Laboratory, Provo, UT.
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