Add option to use the Johnson & Berry formulation for the response of electron transport to irradiance

[alistairrogers]

Describe the changes

Julien Lamour is leading a manuscript where we have used a multi-biome analysis of light response curves to demonstrate that the Johnson & Berry (2021) (JB) formulation for the response of electron transport to light has a better goodness of fit to gas exchange data than the original Farquhar von Caemmerer and Berry (FvCB) formulation that is currently implemented in FATES. Julien’s work also showed that the JB model could be simplified to a form that resembles a rectangular hyperbola. The goal with this issue to to add a switch to enable use of the simplified JB model formulation in FATES. I’ve attached my recent AGU talk deck so you can see the equations and hopefully follow the logic.

The current FvCB formulation is a non-rectangular hyperbola (NRH). When the convexity parameter (theta_psii) approaches zero the response can be described by a rectangular hyperbola with the same form as the simplified JB formulation. Note that Julien’s work supports the elimination of the convexity parameter and adoption of a RH formulation.

There are four parameters to consider in a RH formulation

Irradiance

Alpha (leaf absorbtance)

I’ve had a noodle around in FATES and it looks like FATES delivers absorbed irradiance (qabs) to the currently implemented NRH FvCB formulation. So we just need to simply the proposed equation to account for irradiance being expressed as absorbed irradiance

Phi (Quantum yield)

Quantum yield is not explicitly called out in FATES but is (1-f)/2. F (fpns) is hard coded (0.15_r8)

Sidebar on f. This could potentially be pulled out into a parameter file and it is dependent on a number of factors, f typically decreases with stress. The default fpns (0.15) is relatively low and is what you might expect to observe in a dark-adapted unstressed leaf. Note other land surface models use much higher values for f (see table 1 in Rogers et al. 2019).

Jmax (FvCB)

Calculated from Jmax25 which is calculated from Vcmax25 using a growth temperature dependent ratio (jvr).

The JB model does not include Jmax but includes a new parameter, the maximum conductance through the cytochrome b6f complex (Vqmax). Julien’s work also presents an equation to convert Jmax to Vqmax (with some assumptions about the irradiance used to estimate Jmax).

What I think needs to happen is the following

Addition of a switch to flip between the existing FvCB formulation and the simplified JB formulation
Addition of an equation to convert PFT specific Jmax to Vqmax (slide 22, with possible simplification)
Addition of the simplified RH JB formulation (slide 13)
It would be nice to tidy up quantum yield and address the f issue but not necessary at this point. We can stay with the FATES default of (1-f)/2

The anticipated net result of this will be to decrease modeled photosynthesis at intermediate irradiance.

Is your request related to a problem?

Rogers_B23L-05_Tuesday3pm.pptx

Alternative options

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Additional context

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[rosiealice]

On the issue with 'f' @alistairrogers might this explain why it has always been so hard to get the model to produce sensible GPP fluxes using the observed (quite high) Vcmax's for high latitude vegetation? That was a big problem in CLM5 and I note that @adrifoster 's calibration of FATES-SP mode returns a quite low vcmax for boreal trees, for example.

[adrifoster]

On the issue with 'f' @alistairrogers might this explain why it has always been so hard to get the model to produce sensible GPP fluxes using the observed (quite high) Vcmax's for high latitude vegetation? That was a big problem in CLM5 and I note that @adrifoster 's calibration of FATES-SP mode returns a quite low vcmax for boreal trees, for example.

yes we really need to bring down GPP in SP mode! Some of the "calibrated" vcmaxes are quite low, and it worries me.

[rosiealice]

So I ran an SP run with f set to 0.35, and just fwiw there is a large impact. I think this should perhaps be a parameter we can modify? (sorry about the massive colorbars, trying to figure out where their size is set in the diagnostics package is eluding me right now).

[JessicaNeedham]

I can make a start implementing these changes. @rgknox guessing it makes sense to add them on top of #1262 ?

[adrifoster]

@rosiealice and @JessicaNeedham yes it would be great to do all this (esp. making f a parameter! (pft-specific?)).

I still haven't re-run my calibration ensembles so it would be really good to get this in before I kick those off.

[alistairrogers]

Hi Rosie, Adrianna,

Yes. high (observed) Vcmax at high latitudes will increase photosynthesis at high irradiance. Increasing f (lowering quantum yield) will reduce photosynthesis at non-saturating irradiance (see fig 6 in my 2019 paper linked above for a visual). Pulling f out as a tunable parameter would be useful but fwiw I don't think it should change with PFT (unless those PFTs differ in stress tolerance). In the long run, I think changing it with stress, would be a better approach perhaps analogous to btran tuning of Vcmax and stomatal slope. Fig 5 in the 2019 paper shows the effect of low temperature on "f" and how much of an outlier the CLM4.5 assumption of f=0.15 is relative to other LSMs, something that is exacerbated at low temperature. Another paper you might want to check out is Xueli's JGR paper where she applied an empirical tweak on quantum yield based on my 2019 paper and reduced GPP at high latitude to better match benchmarks.

It would be very exciting to see this change in FATES.

Alistair

[rosiealice]

How does it change with stress? Does it dynamically adjust or is it more of an adaptation thing (more defence=less light absorption ?) Do we have a good handle on that from observations? Interesting...

[alistairrogers]

I'd say it's an area for research. Stress is one factor, there's a long history of cold stress reducing quantum yield (increasing f) but also high temperature stress. But yes when the products of the dark reactions of photosynthesis can't be used you need to turn down the supply of electrons from the light reactions. Stress that limits photochemistry should be well correlated with increasing f. Of relevance to LSMs photoprotective mechanisms would operate on the scale of hours to a day, photodamage could be days. But overall f=0.15 is optimal and rarely realized in the field.