Usually the naming of the layers depend on the architectural approach:
The traditional layering is presentation / business logic / data access layer.
Another popular variant is Fowler’s presentation / domain logic / data source layer.
More recent architectures were inspired by the (data neutral) hexagonal architecture and use a more concentric idioms, ...
What the user assumes the inputs - trial options - are […]
Don't allow the user to make such assumptions. With more that a handful of options, the user will guaranteed get some of them wrong.
Instead, let the user give each combination of options they want to use a descriptive name before starting a simulation. Then the user can recall that set of options ...