With the proper loading caps, the PT7C4311WEX accuracy is better, but not as good as I'd like.
The solution is to set the calibration register. The mechanism for doing so is to set the FT bit in the config register and then measure the frequency on the output pin (which on the Hydra is not connected) with a GPS-locked frequency counter to see how far away from 512 Hz it is. From that, it's possible to work out the correction factor to apply at startup.
The Hydra EVSE doesn't really have enough space left for more features, but it does have enough space to poke the calibration value in to the RTC. Storing the calibration value in EEPROM in the controller is a safer place than in the RTC chip, since the contents of the RTC are lost when the battery dies (or is changed).
A special sketch can be loaded to turn on the test frequency output for measurement. Once the calibration value is determined, it can be written into EEPROM with avrdude. If you set the EESAVE fuse, then this value will be stored permanently across code updates.
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