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U.S. GEOLOGICAL SURVEY
Scientific Investigations Report 2007–5173

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Using The Model

SPOOM simulates pond volume, salinity, and temperature for Alviso ponds A9–A17 using historical data collected during 7 years with variable start and end dates. The model gives the user many options to make it a versatile management tool. There are six worksheets (Main, Weirs, Rainfall, Pumping, ScrewGates, ComboGates) in which the user can specify parameters to customize the pond simulation.

On the Main worksheet (fig. 13), the user can:

• Select a vertical datum system for pond elevations, NGVD 29 or NAVD 88.
• Select a unit system for initial pond elevations and output (metric or inch-pound).
• Select a water year for simulation on the Main worksheet from a pull-down menu that lists the annual percent of normal precipitation and temperature, relative to the annual averages from the 7 water years or select a custom rainfall water year.
• Select start and end dates of the simulation period.
• Select to simulate temperature or not (choosing not to simulate temperature will reduce the simulation run time).
• Specify the initial pond water-surface elevations (relative to the chosen datum and unit systems), and pond temperatures (in degrees Celsius).
• Define which ponds are connected hydraulically and how they are connected.
• Specify pond management criteria: minimum and maximum water-surface elevations and salinities.

On the Weirs worksheet (fig. 14), the user can:

• Specify the use of weirs for discharge periods to sloughs from ponds A14, A16, A17.
• Specify total weir length, in feet or meters.
• Specify elevation of the weir crest, in feet or meters, NGVD29 or NAVD88.
• Specify weir height, in feet or meters.
• Specify the number of weir boxes.

On the Rainfall worksheet (fig. 15), the user can:

• Enter a user-defined rainfall series in column C, in millimeters.

On the Pumping worksheet (fig. 16), the user can:

• Specify the daily pumping rate from pond A13 to pond A14, in gallons per day.
• Specify the daily pumping rate from pond A13 to pond A15, in gallons per day.
• Specify the daily pumping rate from pond A8 to pond A11, in gallons per day and salinity in pond A8.

On the ScrewGates worksheet (fig. 17), the user can:

• Enter the percent of the culvert flow area, if it is less than 100 percent, for any culvert connecting two ponds in the pond system.

On the ComboGates worksheet (fig. 18), the user can:

• Specify daily directional culvert flow for ponds with slough connections: None, Inflow, Outflow, or Bidirectional, when ‘Custom’ is selected in pond-to-slough connection dropdown lists on the Main worksheet

The Main worksheet includes a table for the user to define which ponds flow to one another and under what conditions. The table is set up with ‘flow from’ on the vertical axis and ‘flow to’ on the horizontal axis. Entries on the axes include ponds A9–A17 and the surrounding sloughs. Water bodies that are not adjacent to one another and, therefore, that cannot have flow between them are shown blocked out in black.

Within the table, there are two types of connections: slough-to-pond and pond-to-pond. Each has a different set of inputs to define its connection. Figure 19 shows an example, highlighted in yellow, of an input for a culvert connecting a slough and a pond: flow is from Alviso Slough to pond A9. The first line describes the flow direction of the culvert. A pull-down menu is exposed when a cell is selected to allow the user to choose the flow direction from a list. The list entries include ‘Inflow’, ‘Outflow’, ‘Bidirectional’, ‘Custom’, or ‘None’. If there is no connecting culvert or the culvert is closed in both flow directions, ‘None’ is selected; if the culvert flows from the slough to the pond, ‘Inflow’ is selected; and if the culvert flows from the pond to the slough, ‘Outflow’ is selected. For the case of muted tidal flow when the culvert is capable of inflow and outflow, ‘Bidirectional’ is selected. Some simulations will require a change in culvert flow regime within the simulation period. In this case, ‘Custom’ is selected and the flow directions are specified in the ComboGates worksheet as daily values. The second line describes (1) the number of culverts and (2) the diameter of the culvert(s), in inches. A pull-down menu is exposed when each of these cells are selected. Entries in the quantity cell pull-down menu are 1 and 2, and in the diameter cell pull-down menu are 36 and 48 inches. These cells also can be left blank when the flow direction is selected as ‘None’. The third and fourth lines intentionally are left blank.

Winter inflow restrictions are required by the ISP to minimize entrainment of salmonids from December 1 to May 31. It specifies that ponds A9 and A15 are closed to tidal inflow and the intake-outlet circulation of pond A16 and A17 are reversed. Pond A14 must be closed to tidal inflow from December 1 to April 30 and can be open to bidirectional tidal flow during the month of May to maintain salinity levels. To specify the ISP or other inflow restrictions, flow directions can be specified on the Main worksheet or on the ComboGates worksheet if ‘Custom’ is selected in the first line of the slough to pond entry on the Main worksheet (fig. 19). The ComboGates worksheet allows the user to define multiple tidal flow controls for each pond during a simulation period. On the ComboGates worksheet, flow direction (None, Inflow, Outflow, or Bidirectional) is selected for each day of the simulation period from a pull-down list given in each cell. ISP inflow restrictions are specified in the original SPOOM ComboGates worksheet.

The second type of connection is pond-to-pond, as shown highlighted in yellow in figure 20: flow is from pond A9 to pond A10. The first line defines whether the pond is connected and the kind of connection. The five possible entries for this line are ‘New’, ‘Existing’, ‘None’, ‘Siphon’, or ‘Pump’ and are specified by the user from a pull-down list when a cell is selected. ‘New’ and ‘Existing’ refer to when the culverts were constructed: for the ISP or prior the ISP. ‘None’ is selected for ponds without a connecting culvert. ‘Siphon’ is selected for the siphon between ponds A15 and A16 and ‘Pump’ is selected for the pumping connections between ponds A13 and A14, ponds A13 and A15. In addition to specifying ‘Pump’ on the Main worksheet, pumping rates must be entered in the Pumping worksheet. The second line is similar to the slough-to-pond case with pull-down lists for quantity and diameter of the connecting culverts. The third and fourth lines refer to the management guidelines of the ‘flow from’ pond, as specified by the model user. The third line indicates the minimum and maximum water level, relative to the chosen datum and unit system, and the fourth line indicates the minimum and maximum salinity. If the calculated pond depth or salinity is outside the specified ranges on a given day, the Results page will alert the user by showing the depth or salinity cell filled in red.

The Weirs worksheet allows the user to specify weir box operation for discharge ponds A14, A16 and A17. The flow direction of these ponds can vary during the simulation period, as specified in the ComboGates worksheet, and will not always be outflow. For example, A14 is allowed to have bidirectional flow during May, and A16 is an outflow pond only when A17 is an inflow pond, and vice versa. As a result, the ponds with weir use specified as ‘yes’ will not simulate weir flow if the ponds are inflow or bidirectional. The model assumes the weir boards are removed during these periods. The Weir worksheet also allows the user to specify weir lengths, heights, and crest elevations. Inputs must be consistent with the unit system and vertical datum specified by the user on the main worksheet.

The ScrewGates worksheet allows the user to specify screw gate operations for each of the pond-to-pond connections. If a screw gate is less than fully open, the value of the percentage of area open to flow is entered for each day. If the screw gate is open fully, the cell remains empty.

To initiate a model run, the user chooses the base water year, the start and end dates of the simulation, and ‘yes’ or ‘no’ to model temperature, and then clicks the ‘Calculate’ button on the Main worksheet. Once the simulation is complete, the figures on the Charts worksheet are updated, as are the individual pond results worksheets that list daily outputs of depth, salinity, and temperature, and the Flows worksheet. Daily pond depths and salinities that are not within the ranges of the management guidelines specified by the model user in the Main worksheet are highlighted in red in the individual pond results worksheets.

Example of Using the Model

Application of the model is demonstrated by the following example: The ISP indicates that A14 is a tidal outflow pond during the month of August, although there may be instances when it must be closed, such as for low dissolved-oxygen concentrations. A prediction of the water-surface elevation and salinity at the end of the month and the difference between the open and closed scenarios would be useful information for pond managers. In this example, two simulations will be made for pond A14: (1) normal tidal outflow conditions and (2) no tidal outflow. The results will be compared to determine how outflow affects water level, salinity, and temperature in pond A14.

Initial conditions for the two simulations were determined by starting the simulation at the beginning of the water year to allow the model to become insensitive to the specified initial conditions and to allow for the influence of winter flow controls on the ponds. The water year used for these simulations is 1993. This year was chosen because of its relatively normal precipitation and temperature (105 percent of normal precipitation and 102 percent of normal temperature).

The model was set up to operate the ponds under the ISP. In the Main worksheet, pond connections were defined and the slough flow directions were selected as ‘Custom’ to have more control over the system during winter. Vertical datum ‘NGVD 29’ and unit measurement ‘inch-pound’ were selected. Weir use was set to ‘no’ for ponds A14, A16, and A17. Therefore, pond outflows were controlled by culverts only. The ScrewGates worksheet was modified to block flow between A9 and A14, A11 and A12, A13 and A14, and A14 and A15 (set to zero). In the ComboGates worksheet, ponds without connections to their adjacent sloughs were defined as ‘None’ (ponds A10–A12). Connections between Alviso Slough and A9, and Coyote Creek and A17 were selected as ‘Inflow’. Connections between Coyote Creek and A14, and Artesian Slough and A16 were selected as ‘Outflow’. The ComboGates worksheet was set up for the winter flow control periods. Circulation of ponds A16 and A17 was reversed and ponds A9 and A14 were selected as ‘None’ from December 1 to April 30. During the month of May, pond A14 was defined as ‘Bidirectional’ while the other winter-flow controls remained the same. The resulting temperatures, salinities, and water-surface elevations on July 31 were entered as the initial conditions on the Main worksheet for the two simulations.

Normal tidal outflow conditions in pond A14 were simulated from August 1 to September 1. No changes were made to the pond management setup previously described. Results of simulated water-surface elevation and volume show a spring-neap cycle with more water in the pond during the neap period than during the spring period (fig. 21). The mean salinity and temperature for the month are given in table 4.

The simulation period was run again with the Coyote Creek and pond A14 daily connection selected as ‘None’ in the ComboGates worksheet. All other pond connections and initial conditions were left unchanged. With no water leaving pond A14 and water continuing to flow in from pond A11, the pond water volume and water-surface elevation increased (fig. 21). Salinities were, on average, 8.7-percent higher with no outflow, and temperatures varied only a small amount (table 4). The increased salinity did not exceed the maximum allowable discharge salinity (40) to the sloughs.

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