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The iPhone includes a built-in vibrating motor for silently notifying the user of new events. This is controlled by the MeCCA framework, which is a private C++ framework used for low-level communications with various devices including audio, Bluetooth, and other hardware. Daniel Peebles has written a low-level vibration example, which can be wrapped into an application or called as a standalone binary.
To vibrate the iPhone, create an instance of the MeCCA_Vibrator C++ class. The prototype for this class looks like this: