Timestep benthic prey with fish #24
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Rather than updating benthic prey biomass early in compute_tendencies, we now return benthic prey biomass tendency along with the fish biomass tendencies. There is one kludge in process.compute_total_tendency() to address: I changed the dimension of total_tendency from "fish" to "group", so there are now indices for zooplankton and benthic_prey. When computing the tendency for fish, though, we use some terms that still have dimension "fish", so we need to convert the index space somehow. (Currently, I'm taking advantage of the single zooplankton class to just set fish_i = i - 1 but that isn't a long-term solution.)
test_init_tendency_arrays() was failing because I updated the size of arrays with dimension "group"; test_update_benthic_prey() was failing because I removed the _update_benthic_biomass() function from interface.py
Also, I added hooks for comparing multiple tests and updated the yaml file with results from test_loc3.m
in compute_total_tendency(), we are looping through member_obj_list instead of fish_list, so we can access biomass[i,:] directly instead of relying on biomass.sel(group=...)
compute_tracer_tendency() takes an additional argument named first_fish_id, which is the index of the first fish in the group dimension. When looping over enumerate(member_obj_link), i is the index of the object in the group dimension so i - first_fish_id is the index into the fish dimension.
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I addressed the concerns in the first post: c73da71 removes the kludge, and I was able to regenerate matlab solutions with the updated initial conditions. Differences in biomass after one year (in the first column):
@matt-long this is ready for review / merging - I'm happy to respond to comments here or we can schedule a code walk-through if you prefer |
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Rather than update biomass for benthic prey inside
compute_tendencies(), that function now returns a tendency term for the benthic prey biomass.Testing: I hard-coded the initial benthic prey biomass to
2.098534303641961e-03, which was the biomass in the shallowest column at the end of the first time step. When comparing to matlab results, thebenthic_preybiomass is off by a full timestep, but everything else looks good:Still a draft because there is one kludgy line where I assume a single zooplankton when mapping fish indices from
groupdimension tofishdimension. Also, for the actual commit I used 2e-3 for initial benthic prey biomass, and I haven't generated new baselines from matlab yet.