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There might be pins that don't have an internal diode available and so always require an external diode for these I/O standards.
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For some device families, internal PCI clamping diodes are available on only certain pins. For example, Stratix II has them only on column I/O pins. For Cyclone III, however, the device handbook on the page 7-14 I mentioned says, "Cyclone III devices provide an optional PCI-clamp diode enabled input and output for
each I/O pin" (emphasis added).
Even though the internal diode is available on all Cyclone III I/O pins, you might not be able to use it. I have had to turn it off on dual-purpose pins being used for both user I/O and Active Serial configuration if I placed an input-only or bidirectional signal on those pins. Turning off the PCI clamping diode results in the warning in the original post for I/O standards that require inputs to be clamped.
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