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MCF8329EVM: Not able to start without using Motor Studio

Part Number: MCF8329EVM

Tool/software:

Hi

I have the EVM unit connected to my motor. I am able to set it up via Motor Studio and get it running to 100% speed. I have followed a previous video posted by yourselves: MCF8329EVM_Getting_started. I have to clear a Fault flag from power up to get things started but then I can control speed using the pot. I program the EEPROM with all registers. I unplug the USB lead and power cycle the EVM board (pot is set to 100%) and the motor fails to start, An FAULT is triggered. I plug the Motor Studio back in and I have to reload my config to Motor Studio and clear teh flags before the motor will start again.

How do I make the driver run without Motor Studio? 

Each time I reconnect it looks like the sense limit is changed back to 60% from my 80% level.

I have also tried disconnecting all I2C lines before power cycle to ensure controller MCU not adjusting the 8329.

Thanks