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rwildermuth / atlantisom

Forked from Atlantis operating model 10/20/2020. Generates data sets from Atlantis scenarios. Modifications for functionality with old (pre-Dec 2015) Atlantis code base.
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Biomass for invert pools #4

Closed rwildermuth closed 3 years ago

rwildermuth commented 3 years ago

Hi @sgaichas, this relates to Issue #3, since I have to first convert invertebrate pool nitrogen to biomass before feeding into the survey functions. Looking at the calc_biomass_age() function, at line 70, the weight of an individual is calculated as the product of total N times a conversion factor 'bio_conv', then scaled to the whole box by multiplying by the number of fish, etc.

At line 50 'bio_conv' is calculated with a denominator of 1e9, but in the Atlantis manual when they're talking about length/weight conversion (Part 1, pg 150), they have a denominator of 1000. This leads to some questions:

rwildermuth commented 3 years ago

I think I answered the first part, since calc_biomass_age() reports back in tonnes and the text on page 150 of the manual is for grams, so 'bio_conv' just does that conversion ahead of time.

I'm still not sure how to deal with the biomass pools, unless I just need to use that conversion and the biomass across entire boxes for some groups is still very small.