Yes, like my ELS, a fundamental rule for 1 PPR threading is that the spindle must not change under threading load. ?Normally that's not a lot anyway with a few thou per pass.? And my ELS does do minor compensation for Z axis motion if the spindle changes speed but of course nothing is detected for a full turn.
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More wondering if there is a difference if feed hold is hit and if then the spindle speed is changed.
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LinuxCNC with the index and quadrature does much better.
I am using LinuxCNC for threading because of the issue you have mentioned. With Mach3 I was getting incorrect pitch on the first 2 turns because of the load slowing down the motor. LinuxCNC does a beautiful job. you can hold the chuck to slow the lathe and it keeps cutting perfectly. I have a 70mm disc with 60 slots, one deeper with two slotted photo interrupter to pick up the two pulses