In the early phase its about the aerodynamic design, not the physical hardware prototype. Once the design is validated via independent verification and validation via a committee, the general design config is frozen. ie airframe how much load can take, things like that I guess.
Next is you start realising the various engineering parts for the prototype building since you are not 3D printing it as a whole. So the prototype jet hardware is sort of combination of thousands of parts, right ? There you start first doing this cfd study on those smaller parts individually, everything is defined including the tiny fasteners of which engineering drawing is made. Many of those airframe parts are needed to be designed with specific tolerance level in mind, so the mfg company can test it to confirm and prove the same.
Hence at first you need detailed engg design of entire airframe variety of sections like cockpit fuselage wings elevator rudder stabilizer everything, then go by each subsystem based. Material choice is up to the design committee and the manufacturing agency (HAL or its vendors) will be qualifying the said parts as specified per the engg design team via testing under strict QA. This QA will be prepared by the engg design team, which is usually outsourced by ADA to a reputed Aero engg firm.
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