Move atom mapping section to multiple calculations paper

[fjclark]

Proposed Change

This is a small change - move the atom mapping section in the simulation protocol section to the second paper (where this paper assumes that we are dealing with minor changes and mapping is trivial).

This is a trivial change which I am happy to make unless there are any objections to restructuring like this.

Proposed Authors and Reviewers

Please volunteer (before the end of January) to author/ review and state when you're available. Authors, please say roughly when you plan to contribute the changes (no later than the end of May).

Proposed author: I'm happy to do this in early January
Proposed reviewer: Maybe @ppxasjsm can confirm that this is sensible and briefly check?