I'm going to put in my 2¢ worth of input just because I'm bored. I have a lot of years of wasted time playing with defraggers and have learned that when dealing with the various popular file systems for Unix derivatives it's generally a waste of time. If you have modified and replaced so much data that it's actually causing a performance problem, there is a faster and safer alternative that won't overheat your drive (I have to assume we're discussing electro-mechanical spinners), or rely on the quality of the tool which sometimes proves to be not so great when working with many Terabytes, and may cause data loss.
I find it much more efficient to copy the data to a different drive, reformat the fragmented drive, then copy the data back. This is generally much faster, and gets mostly similar results. This also produces less wear to the actuator parts and less internal heat.
IMHO it's much better to use the copy method if you REALLY need to reduce data fragmentation.
If it's a system drive, a backup & restore can accomplish the same thing.
