What is an Atom?
An atom is originally an unsplittable unit. In Atom.apex, we refer it as a piece of business logic that gets executed even when governor limits are reached.
Usually when we reach the governor limits(heap size, cpu time, query, ...), it is because we are repeating a resource-consuming action. Everything works when there is reasonable repetition. But the unexpected data may cause the repetition count to grow out of control. By then, the governor limits are reached, exceptions are thrown, business logic is aborted and you are left in a mess(especially when you interact with external services).
What we have dreamed is that if the governor limits are reached, Salesforce does not throw exceptions directly, and instead it will schedule our remaining logic to the next available time spot to continue.
Sadly this has always been a dream and Salesforce aborts your execution brutally in this case(roll back your transaction as well, which is a good thing).
This is how we got our inspiration. We want to split our business logic into steps, so that each step can be executed sequentially and if resources are running out, we have a chance to save our progress and then continue the remaining steps.
We call the whole process an Atom, which means that your business logic is guaranteed to be executed even if some governor limits are reached, so that it will not be broken.