Prepare simulated annealing refactoring

Prepare simulated annealing refactoring

Prepare simulated annealing refactoring by moving variable declarations
to where they are first used, rename a non-descriptive integer `i`, use
a const reference to the inputrec where possible, replace a gmx_fatal
by an assert, and replace a switch / case construct by an if / else.

This is pure refactoring, no change in functionality, but will make
follow-up changes significantly easier to review.