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From your question we assume that you are trying to develop an efficient battery
operated application using the AVR Device for which you need the Source code and tools.
Unfortunately I do not have the ready-made application note for the AVR device
mentioned in the request. However, it can be implemented using any AVR microcontroller with A/D converter, PWM output and enough program memory to store the desired charging algorithm.
You can refer the following documents to have a general idea for implementing battery operated applications along with source code and schematics: