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I have tried looking into the printer firmware to see how the Acceleration setting affects the machine movement. From what I could tell, Acceleration seemed to be implemented differently depending on what firmware I looked at and was also affected by what the settings used on the printer were. I didn't look any further because writing different rules for every different firmware seemed like too much trouble. Maybe someone that knows more about this would know if most firmware uses the same calculations.
I suspect that the acceleration setting will not make a lot of difference to the time that the print takes. They haven't seemed to make a difference on the small prints that I have done printing with slow speeds. If you were printing larger prints at faster speeds that had long paths where the nozzle had time to accelerate and decelerate then I suspect you would notice a bigger difference with the time.
I have found that the biggest error between the predicted time and the actual time has been the time the machine spends processing the instructions. When printing a model that has a lot of short movements that need to be sent to the printer and they need to be processed and calculated by the printer, I have noticed the printer will pause for a fraction of a second. It is not long enough to see a difference in the printers movements, but it is noticeable enough to hear. I suspect that on cheaper printers this would cause a bigger error than the acceleration.
If someone can find out how the acceleration settings are calculated by the printer and what G-code command can be used to get the acceleration settings out of the printer, I would be really interested in knowing more about this.