1. Core section shall have strong clamps - mechanical clamping should be proper.
2. Design clearances between primary & secondary winding, phase to phase clearances, & phase to earth clearances should be proper.
3. Now a days, foil type Copper winding is used in place of wire / Copper flats for windings. They reduces the eddy current forces , lowers the short circuit levels, & reduces the I2R Copper load losses. We have tried this successfully in one of the applications.
4. Design the transformer with little higher %Z imedence value, within limits of Techno commercial aspects.
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Exploring the Science of Electricity
these methods allow for a continuous dead short, with the heat dissipation contained by the design to safe levels.
On high current units, a short can cause heating, and if there is no fusing, varnish softening, and the mechanical forces due to the short can cause wire migration and turn to turn shorting, which can increase heating even more. So the correct fusing is also required. In the case of deliberate over-fusing, by someone who pushes the envelope, there is the imbedded thermal fuse. These open at high temperature and interrupt current flow. Some types re-close when the temperature drops, and some do not, as some equipment should not be repowered without some inspection and analysis.
Your question is a little ambiguous to me. If you meant, how do you protect a transformer from a short circuit when assembling a circuit using the transformer? Then other people here have already answered this question. Depending on how one scales the circuit, the fuse or circuit breaker can be placed on the input or output side of the transformer. Each approach has their own advantages and drawbacks. Be cause of this some designs put protection devices on both sides.
If you meant, how do you prevent the windings of a transformer from shorting out when assembling the transformer itself? The short answer is maintain wire insulation integrity. In spinning the coils make sure that you don't exceed the recommended tension strength stated by the wire manufacturer. This not only prevents the wire from snapping but prevents cracking of the enamel, Kapton or Formvar insulation used on the magnet wire. Also a hidden specification is to not exceed the bend radius of the wire. (a.k.a. be careful of sharp corners ) A common technique to isolate primary and secondary coils of E block transformers is to wind each coil on separate bobbins.
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"Don't disturb my circles." translation of Archimedes last words