Grass and woody biomass

[rosiealice]

So, my first go at trying a grass-only simulation (for this workshop in Ft Collins) revealed that even with woody=0, there is still a non-zero non-trivial amount of woody biomass (didn't get to equilibrium, but >1kg/m2). Looking at the allocation code, there isn't actually a filter for woody. Instead , on line 597 of https://github.com/NGEET/fates/blob/master/biogeochem/EDPhysiologyMod.F90 , 'vs' is set to 1, if dbh>max_dbh, meaning that we currrently get fat woody grasses?

I think the solution is just to force:
if(EDPftvarcon_inst%woody(currentCohort%pft)==0)then
va = 1.0_r8; vs = 0.0_r8
endif

I tested this and it does reduce equilibrated bdead to <10g/m2 (the residual being from initialization I think). One thing that confused me is that my first fix, or setting EDPftvarcon_inst%allom_agb1 to 0 had barely any impact.

Does anyone object to this fix, or have an alternative grass allometry path we should take? @jkshuman @lmkueppers @ckoven @rgknox ?

[jkshuman]

@rosiealice Please confirm the line you want to put this at, but, I think it is in the area of line 957. Seems reasonable to me. Nice find (though weird).

[rgknox]

One thing I saw that might also need addressing: at the end of Growth_Derivatives(), in EDPhysiologyMod,F90, we set the dbh and height derivatives off of dbdeaddt (which is always 0 with the new logic). Now, I know grass doesn't have dbh, but I'm just curious how this will impact the model.
Still looking through this..

[rgknox]

I guess the assumption is that grasses have a "ghost" dbh and wood density; and that allows leaf biomass, and that the size is constant? @rosiealice, are grasses supposed to grow in size following some allometry, or are they just expected to spread (or something else)?

[lmkueppers]

Not sure what does happen, but it seems to me that what should happen is that there should be some allometry. Grasses can shade each other, and do have characteristic heights and spreading habits. But I don't know enough about grasses to know what the equivalent to "dbh" should be (all things allometry for trees are tied to dbh, just as all things allometry for grass are tied to ?...). We could ask a grass expert on this model comparison project...

…

On 9/25/17 1:58 PM, Ryan Knox wrote: I guess the assumption is that grasses have a "ghost" dbh and wood density; and that allows leaf biomass, and that the size is constant? @rosiealice <https://github.com/rosiealice>, are grasses supposed to grow in size following some allometry, or are they just expected to spread (or something else)? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#277 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASpkpYVZZEjfT-9bMCY6vwdhqd6uP9eaks5smBPvgaJpZM4PiEjs>.

-- Lara M. Kueppers Assistant Professor, Energy & Resources Group, UC Berkeley Faculty Scientist, Climate and Ecosystem Sciences Division, Berkeley Lab Assistant Research Scientist, Sierra Nevada Research Institute, UC Merced 510.486.5813 o.

[alistairrogers]

Alan Knapp (Colorado State University) would be my go-to U.S. grass expert. A From: lmkueppers [mailto:notifications@github.com] Sent: Monday, September 25, 2017 5:12 PM To: NGEET/fates <fates@noreply.github.com> Cc: Subscribed <subscribed@noreply.github.com> Subject: Re: [NGEET/fates] Grass and woody biomass (#277) Not sure what does happen, but it seems to me that what should happen is that there should be some allometry. Grasses can shade each other, and do have characteristic heights and spreading habits. But I don't know enough about grasses to know what the equivalent to "dbh" should be (all things allometry for trees are tied to dbh, just as all things allometry for grass are tied to ?...). We could ask a grass expert on this model comparison project...

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On 9/25/17 1:58 PM, Ryan Knox wrote: I guess the assumption is that grasses have a "ghost" dbh and wood density; and that allows leaf biomass, and that the size is constant? @rosiealice <https://github.com/rosiealice>, are grasses supposed to grow in size following some allometry, or are they just expected to spread (or something else)? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#277 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASpkpYVZZEjfT-9bMCY6vwdhqd6uP9eaks5smBPvgaJpZM4PiEjs>.

-- Lara M. Kueppers Assistant Professor, Energy & Resources Group, UC Berkeley Faculty Scientist, Climate and Ecosystem Sciences Division, Berkeley Lab Assistant Research Scientist, Sierra Nevada Research Institute, UC Merced 510.486.5813 o. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#277 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ANTfrXnpMntG__1XZsYrL917H0Jw3km4ks5smBc9gaJpZM4PiEjs>.

[bpbond]

One go-to reference for this is the LTER book (co-edited by Alan Knapp) "Principles and Standards for Measuring Primary Production".

Nice find (though weird).

No kidding!

[lmkueppers]

The folks running the intercomparison that is motivating these grass simulations work at Konza and have degrees/postdocs with Alan/Melinda/Yiqi, so I'll see what they say since I don't have the book in hand.

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On 9/25/17 2:26 PM, Ben Bond-Lamberty wrote: One go-to reference for this is the LTER book (co-edited by Alan Knapp) "Principles and Standards for Measuring Primary Production". — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#277 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASpkpcvRCm4oGb_x_PnkjOrtinfYRV6yks5smBqOgaJpZM4PiEjs>.

-- Lara M. Kueppers Assistant Professor, Energy & Resources Group, UC Berkeley Faculty Scientist, Climate and Ecosystem Sciences Division, Berkeley Lab Assistant Research Scientist, Sierra Nevada Research Institute, UC Merced 510.486.5813 o.

[rosiealice]

Ah, I think I have realized the error of my ways. There was a bug in my pft file script which caused clone_alloc + seed_alloc to be slightly <1, thus, some carbon was still going to structural while we were at the max_dbh (see #278). Testing the fix now. But yes, @rgknox and @lmkueppers , there is a 'ghost' dbh for grass which at the moment lives on the same allometry as the trees.

@bpbond, does Alan's book contain said descriptions of the allometric relations of grasses and how one might conceptualize the equivalent of 'dbh'? I don't have the book, and I'm probably not going to find it in the NCAR library. (We don't even have a New Phytologist subscription...) but it would be useful to know if there is a canonical grass expansion model out there.

[bpbond]

Hi @rosiealice -

I've just gone through the relevant part (chapter 3) of Fahey & Knapp and no, there's nothing about grass allometry; it's all about biomass harvest. I next turned to Karl Niklas' book and again, zip, zilch, nada on grasses.

Now I was interested :) Google Scholar doesn't yield a lot, but at least a couple publications:

• Oliveras et al. (2013) fit high-altitude grass biomass regressions based on basal area, crown area, and maximum height. R2 values of 0.5-0.8, i.e. significantly lower than most single-stem woody plants.
• Nafus et al. (2015) did something similar for semidesert rangeland grasses; height not significant, and better fits (R2 0.8-0.9) for diameter-based regression.

So, people don't do allometry with grasses very much. At all.

[rosiealice]

Great. Thanks @bpbond! @lmkueppers has been communicating with the people organizing the workshop, who have ideas about leaf area-biomass relationships. Beginning to wonder whether we need a different concept for the grass populations. Maybe we should ignore 'n' and 'dbh' and just use biomass/lai/areal extent relationships instead?

[mdietze]

We encountered a similar problem when my lab started using ED2 to do biofuel work. Tying the allometry to DBH (or 'virtual DBH') doesn't make sense so we switched to height as the basis and were able to calibrate relationships in the field pretty easily. Yes, the R2 are lower

[alistairrogers]

Ben, Did you look at crops? A From: Ben Bond-Lamberty [mailto:notifications@github.com] Sent: Tuesday, September 26, 2017 11:57 AM To: NGEET/fates <fates@noreply.github.com> Cc: Rogers, Alistair <arogers@bnl.gov>; Comment <comment@noreply.github.com> Subject: Re: [NGEET/fates] Grass and woody biomass (#277) Hi @rosiealice<https://github.com/rosiealice> - I've just gone through the relevant part (chapter 3) of Fahey & Knapp and no, there's nothing about grass allometry; it's all about biomass harvest. I next turned to Karl Niklas' book<http://www.press.uchicago.edu/ucp/books/book/chicago/P/bo3629790.html> and again, zip, zilch, nada on grasses. Now I was interested :) Google Scholar doesn't yield a lot, but at least a couple publications: * Oliveras et al. (2013)<http://onlinelibrary.wiley.com/doi/10.1111/aec.12098/full> fit high-altitude grass biomass regressions based on basal area, crown area, and maximum height. R2 values of 0.5-0.8, i.e. significantly lower than most single-stem woody plants. * Nafus et al. (2015)<http://www.sciencedirect.com/science/article/pii/S1550742409500036> did something similar for semidesert rangeland grasses; height not significant, and better fits (R2 0.8-0.9) for diameter-based regression. So, people don't do allometry with grasses very much. At all. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#277 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ANTfrRplLNt600bJQOnb5bVH1Zjb9Dobks5smR7kgaJpZM4PiEjs>.

[bpbond]

@alistairrogers - no, I was just looking for grasses. Could do so.

Based on those two publications and @mdietze 's experience, it does seem like height would be a promising general biomass predictor. I'd be interested to hear a grassland specialist's opinion on this too, though.

[lmkueppers]

I was just coming to the same conclusion myself, ground area-height relationships would give a 'volume' and then there just needs to be info on how densely packed the volume is to affect things like light competition between grasses and biomass. If, for grasses, dbh became a representation of ground area instead, the existing height parameter could stay relevant. Lara

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On 9/26/17 9:03 AM, Michael Dietze wrote: We encountered a similar problem when my lab started using ED2 to do biofuel work. Tying the allometry to DBH (or 'virtual DBH') doesn't make sense so we switched to height as the basis and were able to calibrate relationships in the field pretty easily. Yes, the R2 are lower — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#277 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASpkpafqQl1spgHk2vYSZMwDd3iYVINyks5smSBvgaJpZM4PiEjs>.

-- Lara M. Kueppers Assistant Professor, Energy & Resources Group, UC Berkeley Faculty Scientist, Climate and Ecosystem Sciences Division, Berkeley Lab Assistant Research Scientist, Sierra Nevada Research Institute, UC Merced 510.486.5813 o.

[ckoven]

isnt the bigger issue the crown area allometry and how to adapt ppa to grasses? or are we assumjng stem diamater equals crown diameter?

[lmkueppers]

I think that makes sense - if crown area = "dbh" in this scheme, area can be lost or gained, and needn't equal ground area (i.e., could be. > or < ground area). Alistair's idea about grass crops may be useful if we want to relate to N.

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On 9/26/17 9:14 AM, Charlie Koven wrote: isnt the bigger issue the crown area allometry and how to adapt ppa to grasses? or are we assumjng stem diamater equals crown diameter? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#277 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASpkpbhf2WbljRi1PTiEcYHrceFNktL9ks5smSL5gaJpZM4PiEjs>.

-- Lara M. Kueppers Assistant Professor, Energy & Resources Group, UC Berkeley Faculty Scientist, Climate and Ecosystem Sciences Division, Berkeley Lab Assistant Research Scientist, Sierra Nevada Research Institute, UC Merced 510.486.5813 o.

[aswann]

I dealt with this in ED2.1 a while back. I changed grass height to follow a function of bleaf but still back-calculated a “ghost” dbh because it was needed in other parts of the code. Not the most elegant. Grasses also had a maximum height.

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-Abby

On Sep 26, 2017, at 9:17 AM, rosiealice ***@***.***> wrote: Great. Thanks @bpbond! @lmkueppers has been communicating with the people organizing the workshop, who have ideas about leaf area-biomass relationships. Beginning to wonder whether we need a different concept for the grass populations. Maybe we should ignore 'n' and 'dbh' and just use biomass/lai/areal extent relationships instead? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[rosiealice]

This is still open for so,e reason. Do we still have woody biomass in grasses or can we throw this one on the closed pile?

[ckoven]

So I think there are two separate issues here. One was that grasses were producing coarse (woody) fuels, and the other is the live biomass allocation (which I read this issue to be mostly talking about). #891 fixed the first issue but not the second. If the allometry parameters are such that dead stem carbon is nonzero, then grasses will follow that. So I would suggest we keep this open until we have a PR that addresses actual measured grass allometry parameters (which @XiulinGao is working on) and close it once that is merged.