[Feature]: Equilibrium growth for equilibrium calculations

[k-doering-NOAA]

Imported from redmine, Issue #70928
Opened by @RickMethot on 2019-11-05
Status when imported: Under Review

benchmark calculations should be able to recalculate growth from averaged parameters rather than calculating average length from the range of years.

per Andre Punt comment at CAPAM

Code development logic below:

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To achieve density-dependence, need to put biology calcs in a loop.
First stage code development steps:
create averaged MG parms
create biology-at-age from those parameters and store in styr-1 if in time_series, or styr-3 for benchmark

Second stage
put equil calcs in a loop
do the first stage calcs
loop 1 is with F=0; store store resultant equil quantities (SSB and SmryBio, etc. ) for use in density-dependent calcs
loop 2 with specified F; store resultant equil quantities; update biology-at-age
loop 3+: adjust Density-dependent parameters, including spawner-recruitment; update resultant equil quants; update biology-at-age; repeat
The calculations without density-dependence are easier because it only involves the first stage calcs.
Also, to gain some speed, the 3*Amax extra ages in equil_calcs might be made conditional such that it only occurs in the last iteration.
For styr-1, this could be invoked using this existing option:
0/1 to use steepness in initial equ recruitment calculation

[k-doering-NOAA]

comment from @RickMethot on 2020-02-28:
per Andre Punt

[Rick-Methot-NOAA]

in addition to equilibrium, it would be extraordinarily informative if density-dependent parameters could also be active in the benchmark calculations. Note that density-dependent parameters are active in the forecast in existing code.
@puntae