Prototype Implementations

AtomsBase provides two prototype implementations of AbstractSystem{D} that are exported:

• FlexibleSystem
• FastSystem

and are briefly discussed in more detail in the remainder of this page.

Struct-of-Arrays vs. Array-of-Structs

The "struct-of-arrays" (SoA) vs. "array-of-structs" (AoS) is a common design dilemma in representations of systems of particles. AtomsBase is deliberately designed to be agnostic to how a concrete implementation chooses to structure its data. Some specific notes regarding how implementations might differ for these two paradigms are included below.

A way to think about this broadly is that the difference amounts to the ordering of function calls. For example, to get the position of a single particle in an AoS implementation, the explicit function chaining would be position(getindex(sys)) (i.e. extract the single struct representing the particle of interest and query its position), while for SoA, one should prefer an implementation like getindex(position(sys)) (extract the array of positions, then index into it for a single particle). The beauty of an abstract interface in Julia is that these details can be, in large part, abstracted away through method dispatch such that the end user sees the same expected behavior irrespective of how things are implemented "under the hood".

Struct of Arrays / FastSystem

The file fast_system.jl contains an implementation of AtomsBase based on the struct-of-arrays approach. All species data is stored as plain arrays, but for convenience indexing of individual atoms is supported by a light-weight AtomView. See the implementation files as well as the tests for how these can be used.

Atoms and FlexibleSystem

A flexible implementation of the interface is provided by the FlexibleSystem and the Atom structs for representing atomic systems.These are discussed in detail in the tutorial.