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add ability to homogenize the seed pool #181

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ckoven opened this issue Jan 26, 2017 · 4 comments · Fixed by #184
Closed

add ability to homogenize the seed pool #181

ckoven opened this issue Jan 26, 2017 · 4 comments · Fixed by #184
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@ckoven
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ckoven commented Jan 26, 2017

On call today, in discussion of possible ways to understand the nature of the competitive exclusion that dominates PFT dynamics of FATES, one proposal was to try cutting the reproduction-recruitment feedback to decouple recruitment rates from overstory survivorship. that way we can better understand the relative magnitude of competitive exclusion that occurs over an individuals' life from the overall exclusion that occurs. There are (at least) two ways of doing that: (1) seed rain, which already exists in the model, or (2) just homogenize the seed production so that each PFT produces seed mass of every existing PFT in equal proportions. A possible advantage of option 2 is that it is carbon-conservative, whereas option 1 clearly isn't. Option 2 is essentially how they do it in LPJml-FIT (combined wit an arbitrarily large number of PFTs). Anyway it would be nice to play around with this idea, not necessarily as a long-term solution, but to allow us to do some of these experiments to understand the conditions under which exclusion does or does not occur in the model.
@rgknox
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rgknox commented Jan 26, 2017

One thing to consider is that eventually we may want to investigate spatial migration of PFTs, ie grid-to-grid over long-time scales. This type of behavior would be influenced by cross-grid seed rain and how prevalent a PFT is in neighboring cells. How we make decisions vis-a-vis 1/2 would impact this type of dynamic.

@ckoven
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ckoven commented Jan 26, 2017

@rgknox good point, but I see that as a pretty different issue, as it starts to get into island biogeography type population/metapopulation issues. suggest tabling that for now until we really start to deal with seed dispersal. anyway, what i am proposing is a switch that will default be off for the time being so will not necessarily conflict with whatever we do for seed dispersal.

@rosiealice
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rosiealice commented Jan 26, 2017 via email

@ckoven
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ckoven commented Jan 27, 2017

if anyone's interested in playing with this, i pushed up a version that does it on a new branch, https://github.com/ckoven/ed-clm/tree/homogenize_seeds aka commit ac46e0f .

@ckoven ckoven mentioned this issue Feb 10, 2017
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bandre-ucar added a commit that referenced this issue Mar 10, 2017
@bandre-ucar
new mortality and canopy/understory diagnostics and option for seed h…
4ccb9ef 
…omogenization

Merge branch 'new_mort_diagnostics'

added a bunch of new diagnostics and also a mode to prevent
competitive exclusion.

the new diagnostics cover:

* canopy vs. understory resolved population numbers, mortality, growth
  increment, GPP, and respiration fluxes so as to see what's going on
  in the understory separately from what's going on in the canopy

* now tracking cohort termination (due to both numerical truncation
  but more importantly also when cohorts' storage pools go negative)
  as a sixth mortality term, which has been occurring all along, but
  was not being tracked as a mortality term, and turns out to be
  important to the population budget

* now tracking recruitment, so that we can ensure conservation of
  individuals as dn/dt = recruitment - sum of all mortality terms

* redefined the canopy_area_by_patch_age diagnostic to use
  cohort-level rather than patch-level canopy area (since patch-level
  canopy area saturates at the patch area, whereas cohort-level canopy
  area doesn't so that the ratio of canopy_area_by_patch_age /
  patch_area_by_age becomes a useful metric of that space from
  pre-closure through multiple canopy levels

* the seed homogenization is default off but if set to be on prevents
  competitive exclusion, like seed rain, but without requiring a
  non-balanced carbon budget.

Fixes: #181

User interface changes?: No

Code review: Requesting @rosiealice and @rgknox review.

Testing:

  rgknox / ckoven

    Test suite: ed suite on lawrencium-lr3
    Test baseline: a5dc8da
    Test namelist changes:
    Test answer changes: bit for bit

    Test summary: all PASS

andre:

    Test suite: ed - yellowstone gnu, intel, pgi
                ed - hobart nag
    Test baseline: b0bceb0
    Test namelist changes: none?
    Test answer changes: bit for bit

    Test suite: clm_short - yellowstone gnu, intel, pgi
    Test baseline: clm4_5_12_r195
    Test namelist changes: none
    Test answer changes: bit for bit
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new mortality and canopy/understory diagnostics and option for seed homogenization
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@rgknox @ckoven @rosiealice