Adjust benchmark to more recent changes

[Samuel-amap]

Recreating the benchmark locally (or a near-equivalent) currently has issues with variables' names having changed.

to_initialize(leaf) returns (photosynthesis = (:aPPFD,), energy_balance = (:Ra_SW_f,)), and some variables in the models are initialised to -Inf. After the simulation has run, some NaN values have propagated here and there. A few adjustments need to be made to obtain a correct output.