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If the "Drag Vortices" radio button is selected, as it should be when the applet starts, then you can move vortices simply by dragging them with the mouse. It's usually easiest to do this when the animation has stopped, which it does automatically whenever you click on the vortex pane. To start it up again, simply turn the "Running" checkbox back on.
The other two radio buttons allow you to add and remove vortices. If the "Add Vortices" radio button is selected, then clicking on the vortex pane will create a new vortex, which you can then position if you haven't let go of the mouse yet. If the "Remove Vortices" radio button is selected, then clicking on a vortex removes it.
The numerical method used for simulation is very accurate when the vortices are spaced reasonably far apart, at least one-third the distance between grid points in the vortex pane. When the vortices get closer together than that, the method becomes inaccurate. In particular, it does strange things if vortices are placed right on top of each other. So don't do that.