Not atoms.
From Hickey’s History of Clojure paper:
“ Taking on the design and implementation of an STM was a lot to add atop designing a programming language. In practice, the STM is rarely needed or used. It is quite common for Clojure programs to use only atoms for state, and even then only one or a handful of atoms in an entire program. But when a program needs coordinated state it really needs it, and without the STM I did not think Clojure would be fully practical.”
https://dl.acm.org/doi/pdf/10.1145/3386321
Atoms do an atomic compare and swap. It’s not the same thing.
That said, I have never used a ref, nor seen one in use outside of a demo blogpost.
For example, when it comes to concurrent access to a map the Clojure community generally forces a dichotomy, either stick a standard Clojure map in an atom and get fully atomic semantics at the expense of serial write performance or use a Java ConcurrentMap at the expense of inter-key atomicity (or do a more gnarly atom around a map itself containing atoms which gets quite messy quite fast).
Such a stark tradeoff doesn't need to exist! In theory STM gives you exactly the granularity you need where you can access the keys that you need atomicity for and only those keys together while allowing concurrent writes to anything else that doesn't touch those keys (this is exactly how e.g. the stm-containers library for Haskell works that's linked elsewhere).