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You can add multiple materials to a part, but what's its use if you can't apply both at the same time? For example I need a M16 nut in stainless steel 304 and a M16 nut in brass in the same assembly. If I change the material for one nut, the other changes as well.
Do I need a separate part file for the same geometry/different material parts? Or is there another solution?
I would say most people do use separate files for different materials as they really are a different part. If you were trying to procure these parts from a vendor each would likely have its own part number, but I understand every company has their own numbering scheme and documentation methods.
Family tables are likely one good reason to have multiple materials assigned. You could assign the various materials to the family table generic and then the instances could select whichever material they need from there.
We did have one occasion to try to make the material flexible to allow users to change that value. This was a strange situation where the vendor had the same part number for two different materials. (Which really made us uneassy and I think they eventually created a second number) I just did a quick test and at least with our BOM setup they do show up as separate BOM items.
Most of my standard hardware items are in family tables which are created by type of hardware and material. Since our common vendors have different part numbers for an 18-8ph, 316 or steel part, we also have them as different part numbers internally. Create one family table and then copy it and change the material and part numbers and the second family is done. One of the things I did was create a full range of sizes in the family tables. For bolts, we went from 1/4 to 1-1/2 in diameter and 3/8 to 6 in length. Very easy for the designer to swap out for a new length if they need it.