temperature criteria for preventing recruitment?

[rgknox]

WIth PR #737, we introduce a new filter on recruitment. If the temperature of vegetation is at or below freezing, we cancel the recruitment process and return all mass to the germinated seed pool. This is a nice start, but here are a few specifics to keep in mind:

1. We are only performing this filter when hydro is on
2. The temperature diagnostic we are using is:
   a) instantaneous, which is really not ideal because we aren't using local times, so depending on your longitude, you could be using the temperature at midnight or the temperature at noon, or somewhere in between
   b) the vegetation temperature for patch 1. This is also not ideal, the temperature should be associated with the direct environment of the potential recruit. But I held off on making it the current patch in light of issue "a", and the need for a completely new time averaged diagnostic.

We can improve this temperature threshold. Any suggestions?

The "vegetation temperature" we get from CLM & ELM is for the whole patch, which includes vegetation of all sizes. My sense is that maybe upper layer soil temperature is more relevant for new recruits... but maybe not? Also, note that the vegetation heat balance algorithm may or may not take into account the heat capacity of the woody biomass, depending on the HLM and the parameterizations used.

It seems resonable to move this filter to outside of hydro and be applicable to non-hydro simulations, right?

There are different time averages we can perform as well. We could use the average temperature for the last 24 hours (coming soon), or an exponential moving average with any frequency (1 day, 2 day, 5 day?).

Should this filter have similarities with cold phenology filters?

I think @adamhb is planning to introduce a time-averaged temperature filter along with a set of other changes, but I'm not sure on the timeline there.

@adamhb @mariuslam @lmkueppers @JunyanDing @xuchongang @pnlfang

[rosiealice]

Hi @rgknox. Thanks for this. I agree with most of your suggestions, specifically

1. It would make sense to turn off recruitment when soil is frozen for all versions of FATES

2. I think we should probably be using soil and not vegetation temperature because the soil is where the seeds are doing their thing and because it has better implicit time averaging.

3. While 'soil is unfrozen' is maybe a good minimum criteria for establishment, it probably really needs soil to be a little warmer than that.
   In one of his many papers on this subject, Christian Korner mentions 5C at the observed limit for plant growth and 2C as the absolute limit for cell expansion ('Growth at low temperature' paragraph) https://www.sciencedirect.com/science/article/pii/S1369526615000540?casa_token=zGv6FCd-AMIAAAAA:6x57JeIdyIsizzwSl6-ts6U95DlbQVj5ojmMVC3_SrK79GBNSJEbQ2fBXkNZFNqRuNxIna_o8w

I guess my only concern is that there might be some threshold type behaviour that could be prevented with a general 'temperature limitation' scalar on recruitment. Maybe that will be part of @adamhb 's updates but I think it's still a sensible minimum condition.

[adamhb]

Hi Rosie and all, The recruitment code that I've been bringing in from the offline tree recruitment scheme doesn't actually deal with temperature at all because the initial focus has been on the tropics. Therefore, this would be a good thing to add in addition to the code that I'm bringing in. The patch-level time averages I have added are light at the forest floor and “soil moisture deficit days” (similar to GDDs) at ~6 cm depth. In my new recruitment scheme, light at the forest floor is used to calcuate seedling mortality rates from light stress and seedling to sapling transition rates. Soil moisture deficit days are used to calculate seedling mortality rates from moisture stress. The timeline for me fully adding the code into FATES is by the end of December. This had to get pushed back a little due to paper deadlines and the need to get fieldwork done before the snow-free season ended here. Sorry for the delay! I looked back at some code that Chonggang added to FATES. With the code that Chonggang previously added <https://github.com/NGEET/fates/blob/master/biogeochem/EDPhysiologyMod.F90#L1783> to FATES (without hydro), seed germination doesn't occur if a cold status flag is switched on (the same status used to guide the phenology of cold deciduous trees I believe). Therefore, there shouldn't be any carbon available for recruitment for these "cold" timesteps, right? If so, then I suppose one question is whether or not this temperature-sensitive germination function is sufficiently capturing the dynamics we're trying to capture? I think these phenology flags do incorporate some time averaging right Ryan (albeit not at the patch or cohort level with the new functionality you added)? If Chonggang's code is not sufficient, then perhaps a temperature-based recruitment limitation could be implemented similarly to his code (i.e. as a "go" or "no go"), but with the logic more specific to soil or vegetation temperature like what Rosie/Ryan were suggesting. I haven't read / thought much about exactly what temperature limitations to recruitment are honestly, but these prior suggestions sound reasonable to me. If it was set up as a simple boolean (stopping or allowing recruitment) this should be pretty easy to fit together with the code I'm putting in currently which deals more with determining seedling moratlity rates and seedling to sapling recruitment rates as a function of light and soil mositure. Adam

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On Thu, Nov 25, 2021 at 2:33 AM Rosie Fisher ***@***.***> wrote: Hi @rgknox <https://github.com/rgknox>. Thanks for this. I agree with most of your suggestions, specifically 1. It would make sense to turn off recruitment when soil is frozen for all versions of FATES 2. I think we should probably be using soil and not vegetation temperature because the soil is where the seeds are doing their thing and because it has better implicit time averaging. 3. While 'soil is unfrozen' is maybe a good minimum criteria for establishment, it probably really needs soil to be a little warmer than that. In one of his many papers on this subject, Christian Korner mentions 5C at the observed limit for plant growth and 2C as the absolute limit for cell expansion ('Growth at low temperature' paragraph) https://www.sciencedirect.com/science/article/pii/S1369526615000540?casa_token=zGv6FCd-AMIAAAAA:6x57JeIdyIsizzwSl6-ts6U95DlbQVj5ojmMVC3_SrK79GBNSJEbQ2fBXkNZFNqRuNxIna_o8w I guess my only concern is that there might be some threshold type behaviour that could be prevented with a general 'temperature limitation' scalar on recruitment. Maybe that will be part of @adamhb <https://github.com/adamhb> 's updates but I think it's still a sensible minimum condition. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#813 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGBXLIPTRETEOSZIQDJ5RNDUNYGGDANCNFSM5IHP3KFQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Adam Hanbury-Brown PhD Student Energy and Resources Group UC Berkeley