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When computing a transient simulation with an emergency pump shutdown, no matter what surge protection I try to put in place, it does not seem to help with negative pressures.
Take a close look at the profile of your system. If you're pumping over a hill and the boundary conditions on either end of the system are lower, than it may not be possible to maintain a positive pressure, so long as the pump(s) remain off. Basically when the pump turns off and the HGL drops, even if you had multiple tanks along the pipeline, they may help protect the system at first, but will eventually drain out and cause the HGL to drop to low levels. This can cause vapor pocket formation. When vapor pockets collapse, they can cause severe pressure spikes (or "upsurges").
If you only have air valves as protection, it's important to note that they can only limit the pressure from dropping below zero in the immediate vicinity of the air valve. Pressure can still become subatmospheric some distance to either side of the air valve. There are a number of factors that come into play, including the physical topology and angle of the surge wave as it approaches the air valve location. In some cases, other protective measures may be necessary, such as a tank or pump flywheel (increased inertia). Another factor to consider is what happens when air is released back out of the air valves. If a controlled air release does not occur (such as with a triple acting air valve or smaller outflow orifice diameter with a double acting air valve) then the adjacent water columns can rejoin too quickly, causing a severe upsurge, which can reflect and combine with other waves, causing severe a downsurge.
The best way to visualize and understand if this is happening is to animate a profile path of the area in question. In your transient solver Calculation Options, make sure you have selected "True" for "Generate Animation data", then open the Profile of "Hydraulic Grade and Air/Vapor Volume" for a profile covering the area of interest. Click the play button at the top or move the time bar to animate the transient simulation and get a better understanding of exactly what's happening. You may notice an air or vapor pocket forming (top graph) and later collapsing with subsequent severe surges forming, reflecting and interacting with each other.
You may need to consider how long the pumps will be off and size the surge protection device(s) based on that. You can use the "variable speed" transient pump type to simulate the pump turning off and then back on, or consider two runs (one for shutdown and the other for start up). For example, if the pump is shut down for 10 minutes the surge protection device would need to mitigate the transient wave for at least that long. In the case of a surge tank (hydropneumatic tank) the tank will need to be sized appropriately for the water to supply the demands and dampen the transient wave for at least the minimum time the pump is off. There may be concerns with how fast any trapped air is released upon startup.