Why does atomicity practice fail?

The most common reason atomicity practice fails: Treating atomicity as a binary — either a note is 'atomic' or it is not — and then freezing when you cannot determine which side of the line your note falls on. This perfectionism is the most common way people abandon their note-taking practice entirely. The question is never 'is this note perfectly atomic?' The question is 'is this note more atomic than the one I would have written last month?' If yes, your practice is working.

The fix: Write three versions of the same idea at three different granularities: (1) A rough capture — the idea as it first occurs to you, messy and unstructured. (2) A first atomic attempt — one idea, one title, one container. (3) A refined atom — precise title, sourced claim, explicit link to at least one other note. Then write a brief reflection: what changed between each version? What did the act of refining teach you about the idea itself? Save all three versions. This is not a cleanup exercise — it is a record of your decomposition skill improving in real time.

The underlying principle is straightforward: The goal is not perfect decomposition but steadily improving your ability to decompose.