Freezing partion layout exactly in Cyclone III (not LS)

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Put the logic in its own hierarchy, make it a design partition and set it to Post-Fit. When you get a build with good timing, right-click and export the partition as a .qxp. Then add that to your project instead of the source HDL for that hierarchy. (Continue to keep it as a post-fit partition). That was brief, but there should be lots of posts/documentation on partitions.

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Great info sharing.