What I do:
I define node as a new board position. So I increment the node counter each time I enter Search() or Quiesce().
Also I increment the node counter each time I try a illegal makemove, because although is illegal, is a new position which is rejected, like it would be if a cut off.
I think this system is similar to increment node count each time makemove() is call.
FS
How to determine NPS
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