Looking for some parameters

[bnulzq]

Dear Egor,

I want to check some parameters here. Do you have the following parameters in the simulation output/input (default)?

1. 𝑘_(𝜆_𝐹)/𝑘_𝑃𝐴𝑅: The extinction coefficient of ChlaF/PAR under Beer's law
2. 𝜀_(↑0)(𝜆_𝐹 ): upward escape probability of ChlaF emission at TOC. (Is this SigmaF refers to?)
3. 𝑠_𝐼𝐼 (𝜆_𝐹 )/𝑠_𝐼 (𝜆_𝐹 ): spectral shape function of ChlaF emission of PSII/PSI
4. 𝜙_𝐹𝐼/𝜙_𝐹𝐼𝐼: canopy-level fluorescence quantum yield of PSI/PSII

Thanks,
Zhenqi Luo

[Prikaziuk]

Dear @bnulzq ,

I think we have to ask @Christiaanvandertol for more details at the end of next week.

Preliminary answers are:

1. not quite sure we provide/compute/use those
2. yes, this is sigmaF computed in L425 of SCOPE.m
3. At some point we stopped separating PSI and PSII in SCOPE. The spectra can be found in the input structure optipar.phiI, optipar.phiII separated and optipar.phi together which is currently used
4. canopy.fqe, computed in L427 of SCOPE.m output as canopy_level_FQE column in vegetation.csv

[bnulzq]

Dear @bnulzq ,

I think we have to ask @Christiaanvandertol for more details at the end of next week.

Preliminary answers are:

1. not quite sure we provide/compute/use those
2. yes, this is sigmaF computed in L425 of SCOPE.m
3. At some point we stopped separating PSI and PSII in SCOPE. The spectra can be found in the input structure optipar.phiI, optipar.phiII separated and optipar.phi together which is currently used
4. canopy.fqe, computed in L427 of SCOPE.m output as canopy_level_FQE column in vegetation.csv

[bnulzq]

Thanks for the answering! Today I also discussed with my advisor Dr. Ying Sun @cornell about these questions. We appreciated if Dr. @Christiaanvandertol can help and cooperate with us if possible.

For these questions:

1. The extinction coefficient basically can be calculated using multi-layer simulated PAR and SIF, using the option mSCOPE. I did not run this mode before, so I wonder can I get the vertical profile of the PAR and SIF?
2. From the SCOPE2.0 paper the sigmaF is the fluorescence scattering coefficient, here I just want to confirm that it is the upward escape probability of ChlaF emission (for example at the 740 nm).
3. For the fluorescence partitioning, we found this paper (https://doi.org/10.1016/j.rse.2020.111678) using the v1.7 seems to be able to separate PSI and PSII. And where can I find the optipar.phiI, optipar.phiII and optipar.phiin the input structure that can be used to partition the fluorescence.
4. Is 'canopy_level_FQE' the total fluorescence quantum yield? Again, can I also get the quantum yield of PSII and PSI separately?

[Prikaziuk]

Dear @bnulzq ,

I would like to ask you to explore the code more actively, please. The answers to questions 3 and 4 are complete in the previous comment, including the line numbers of files where the computation takes place.

3. optipar is a matlab structure available in the workspace after SCOPE.m is finished. It is loaded in L177 of SCOPE.m (load([path_input,'fluspect_parameters/', F(3).FileName]);) from "input/fluspect_parameters/Optipar2021_ProspectPRO_CX.mat". For the second part, I think, you answered your question yourself. If you want to compute PSI and PSII separately you can use SCOPEv1.73. I repeat, we do not separate PSI and PSII anymore.
4. I repeat, we do not separate PSI and PSII anymore.

Still struggling with your first two questions, will ask Christiaan. It's possible to compute PAR profile from L429-434 of RTMo.m

rad.Eplu_ = Eplu_; % [nlxnwl double] upward diffuse radiation in the canopy (mW m-2 um-1)
rad.Emin_ = Emin_; % [nlxnwl double] downward diffuse radiation in the canopy (mW m-2 um-1)
rad.Emins_ = Emins_; % [nlxnwl double] downward diffuse radiation in the canopy due to direct solar rad (mW m-2 um-1)
rad.Emind_ = Emind_; % [nlxnwl double] downward diffuse radiation in the canopy due to sky rad (mW m-2 um-1)
rad.Eplus_ = Eplus_; % [nlxnwl double] upward diffuse radiation in the canopy due to direct solar rad (mW m-2 um-1)
rad.Eplud_ = Eplud_; % [nlxnwl double] upward diffuse radiation in the canopy due to sky rad (mW m-2 um-1)

I'm just thinking there's an easier way. For example, the profiles of APAR are in rad.Rnh_PAR (shaded leaves) and rad.Rnu_PAR (sunlit leaves). If it is not mSCOPE where the canopy has different leaves, the profiles of PAR are close to the profiles of APAR.

[peiqiyang]

Hello Zhenqi, Let me try to answer your questions. Regarding the extinction coefficients, the question itself is not very clear. Theoretically speaking, extinction coefficients for direct fluxes are structurally dependent. Hence, for directional incoming PAR and directional SIF (as stated in your equation), the ratio is unity as long as the sources of the radiation are at the same location and the directions are the same. However, after considering your recent message, I have a better understanding of your questions. My answer is: The extinction coefficient for incoming PAR (direct radiation) is computed and saved in RTMo as 'k,' which is wavelength-independent. However, for diffuse incoming PAR, the extinction coefficient is wavelength-dependent and is not directly computed in RTMo. Instead, the transmittance is represented by 'tau_dd.' Hence, obtaining 'k' for diffuse PAR is also not difficult. As for SIF, the transmittance of a thin layer is also 'tau_dd.' However, for longer wavelengths, you can find the variable in RTMf. Using the PAR profile to compute the extinction coefficient is acceptable. We do have the profiles as output, as long as you enable the option (at least in SCOPE v1.73). However, using the SIF profile to compute the extinction coefficient is questionable since the difference between layers is contributed by both extinction and emission. Lastly, It is important to note that when you want to obtain the extinction coefficient, you need to specify: a. The original location of the flux (e.g., top of the canopy) b. The target position of the flux c. The type of flux (e.g., direct, diffuse, or mixed) Regarding sigma_F, it is commonly referred to as the directional escape probability in the direction of viewing at 760nm (as mentioned in our 2018 and 2020 RSE papers on SIF scattering). Alternatively, it can be called the upward/directional escape probability of chlorophyll fluorescence (ChaF) emission. However, it is important to note that the scattering coefficient can be considered for any wavelength, either wavelength-integrated or hemispherically integrated. I hope this clarifies your questions. If you have any further inquiries, please let me know. Best regards, Peiqi Zhenqi Luo ***@***.***> 于2023年6月6日周二 12:02写道：

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Dear Egor, I want to check some parameters here. Do you have the following parameters in the simulation output/input (default)? 1. 𝑘_(𝜆_𝐹)/𝑘_𝑃𝐴𝑅: The extinction coefficient under Beer's law 2. 𝜀_(↑0)(𝜆_𝐹 ): upward escape probability of ChlaF emission at TOC. (Is this SigmaF refers to?) 3. 𝑠_𝐼𝐼 (𝜆_𝐹 )/𝑠_𝐼 (𝜆_𝐹 ): spectral shape function of ChlaF emission of PSII/PSI 4. 𝜙_𝐹𝐼/𝜙_𝐹𝐼𝐼: canopy-level fluorescence quantum yield of PSI/PSII Thanks, Zhenqi Luo — Reply to this email directly, view it on GitHub <#46>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC3C7EVWNQ6I2JTUARG66HTXJ2TUXANCNFSM6AAAAAAY32CFPU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[bnulzq]

Hello @peiqiyang and @Prikaziuk,

I hope you are fine and in good health. Firstly, I want to express my gratitude for your informative answers. I'm pleased to inform you that your recommendations proved to be quite effective in my study.

I have further asking based on Dr. Yang's clarification:

1. The extinction coefficient: I think we need the directional flux, so probably the 'k' in RTMo is what we need (the k_PAR in https://doi.org/10.1111/gcb.16634). Could you help to confirm it? And does SCOPE has similar coefficient for directional ChlaF flux?
   We could also try the profile method to compute the extinction coefficient. For the SIF extinction and emission, I guess we already consider it. Please refer to eq.S23 and eq.S24.
2. sigma_F refers to as the directional escape probability of and the output is related to its wavelength in SCOPE. So is this corresponding to 𝜀_(↑0)(𝜆_𝐹) (The upward escape probability of ChlaF emission for an infinitesimally thin leaf layer at TOC) or f^(esc) (The directional fluorescence escape probability from TOC), as in the Table S1.b in our paper?
3. & 4: It seems like we can separate the PSI and PSII in v1.73, I will try that later.

Apologize for my late response during my travel back to China this week. Thank you once again for your assistance, and I plan to visit Beijing Normal University during 23-26 June for several days. Look forward to meeting with you in Beijing if available at that time for further discussion and cooperation. Your support is highly appreciated.

Zhenqi