How to find duplicate 3d points?

I have a large data file of upto 1 million x,y,z coordinates of
points. I want to identify which points are within 0.01 mm from each
other. I can compare the distance from each point to every other
point , but this takes 1 million * 1 million operations, or forever!

Any quick way to do it, perhaps by inserting just the integer portion
of the coordinates into an array, and checking if the integer has
already been defined before inserting a new point?
.

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