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How does the adp1046 keep zero crossing.

Right now we are testing HB LLC converter based on adp1046 CPU.

We had observed spikes on the secondary side while adp1046 changes frequency to keep needed output voltage.

While frequency is steady spikes absent.  We consider that the periodical zero crossing failure causes spikes.

The question is how does CPU follow the actual zero crossing during control process?

How important is the digital filters adjustment in GUI (currently we are in default  setting)?

Thanks