Questions regarding how to configure the various clocks on SAM D5x/E5x are a frequent topic on the SAM forum.
Many developers get by just fine using the Microchip/Atmel "Start" tool to configure clocking for their project. However, just as many seem to want to go beyond what the tool can offer; it can be somewhat uncooperative at times. This project is targeted at the latter group.
The header (sam_clock.h) and source (sam_clock.c) files provide a set of API functions to configure most of the clock facilities available on SAM D5x/E5x. Both files are reasonably well commented throughout so I won't go into details here, but the API documentation should be read in conjunction with the relevant sections of the data sheet. Not all hardware features are implemented (sam_clock.h has a list), and of those which are implemented, not all combinations have been tested.
An example code fragment of how the API might be used on the SAME54-XplainedPro board is provided for reference purposes. It's not a complete example, but should be enough to get started.
The source code is provided As-Is, with no warranty or guarantee whatsoever that it will work, let alone compile (I use the Gnu Arm Embedded Toolchain, for reference). Use it entirely at your own risk. A two-clause BSD license applies.
Please direct feedback/questions to the forum, or to email@example.com.
Steve (scdoubleu on the forum).