An atomic transaction is an indivisible and irreducible series of database operations such that either all occur, or nothing occurs. A guarantee of atomicity prevents updates to the database occurring only partially, which can cause greater problems than rejecting the whole series outright.
In cryptocurrency this translates to a trustless exchange. Komodo's Barterdex is an atomic swap protocol that is blockchain agnostic and allows traders to swap tokens atomically across blockchains while remaining in control of their privatekeys.
 Not to be confused with a Lightning Network (LN) off chain atomic swap which does not guarantee the above.