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Tsu would be the difference in the routing and propagation delays between the the clock and data plus the actual setup up time that would be required?
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Hopefully someone will correct me if I'm wrong but I think Quartus looks after the internal setup time of the register itself so you can forget about it (i.e. assume it's zero)
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So by placing a Tsu constraint it is actually affecting the routing delays to the register pins?
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Pretty much yes - Quartus is placing logic and routing connections in a way that will try and meet those timing requirements - setting the requirement doesn't guarantee that Quartus will meet the timing constraints but it does make it try and at least tell you if it can't.
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As quartus does not know when the clock or data wil arrive at the input pins. Does quartus try and match the propagation and rounting delays of the clock and data inputs (or any input pin for that matter), or could one input pin have a completely different delay from the nexy?
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The clock should be routed along dedicated global clock paths internally with powerful buffers so that it can reach all parts of the chip with very little skew. Quaruts doesn't try and match the routing delays between clock and data - it just tries to meet your setup requirement. What happens externally is part of your analysis to calulate what those setup times should be. If, for example, your data has a long windy track on the PCB and a much greater delay than the clock then this will mean that you need to set a smaller setup time in Quartus.
Really to work out your setup times you need to know the clock to output time of the transmitting device, the routing delay (time of flight) and the clock period. You could have a decent guess at your PCB routing delays - they might be pretty small unless you have long tracks - have an interweb search engine search for signal transmission speeds in PCBS (or something similar) - it depends on the dielectric material (e.g. FR4) of the PCB mind. It's been a while since I've done this sort of thing so I can't give you a figure off the top of my head.
Good luck
batfink