In general, everything is too small. I don't know if it's due to shrinkage or something else but holes are too small and a simple part like a cube will be smaller than desired. It's not steps/mm as that is very accurate. I think it's a combination of many factors including ringing, play/backlash, belts that can stretch, and shrinkage due to cooling. In addition I beleive that sometimes there is a pulling affect when laying down a "thread". Especially seen on first layer when there is bad adhesion to the bed that makes circles and other shapes deformed into a smaller shape then desired.
Like illuminarti says, nozzle diameter is taken into account. You can see this if you slice a 10mm cube with nozzle set to .4mm. If you look at the gcode it's very simple to see the movements are 9.6mm which takes into account the .2mm radius of the nozzle on each side of the cube.
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illuminarti 18
Cura does allow you to specify the nozzle diameter that you are using, and takes that diameter into account when planning the toolpaths that it uses.
Nonetheless, overall parts diameters are going to end up slightly off, due to both mechanical imperfections and variability, and the fact that plastic contracts as it cools.
The effects depend on the particular model geometry, so typically you have to adjust the model on a case-by-case basis.
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