This scenario asks you to recreate the photosynthesis module (Chapter 8 of the documentation) as it was programmed and defined in CLM/CTSM 4.0 and iteratively update it to match CLM 4.5. It will not be an exact match however, because a few terms require many other parts of CLM to be run, which is out of scope for this scenario. For reference, the photosynthesis module’s code can be found here.
Extract equations from Chapter 8 of CLM/CTSM 4.0, relating to photosynthesis. There are 28 equations in total to extract.
Extract parameters from Tables 8.1, 8.2, and 8.3, in the CLM/CTSM 4.0 documentation. For parameters that can’t be found in this chapter or easily incorporated (some of which are defined in other parts of the CLM documentation), find reasonable values from the literature instead.
Extract the photosynthesis equations from Chapter 8 of CLM 4.5.
Do a model comparison between the extracted models from Q1, and Q3. This requires each model to be grounded, because there are variables representing the same concepts between CLM 4.0 and 4.5, but have different notations.
Starting with the CLM 4.0 model extracted in Q1, update the equations to match those in CLM 4.5. In particular, include the following specific changes (equation and table numbering refer to CLM 4.5 documentation):
Renaming of the photosynthesis constituent variables
Different values of α in Table 8.1
Addition of the respiration term in Equation 8.2
Change in equation of the PEP carboxylase-limited rate of carboxylation (equation 8.5)
Change in the maximum rate of carboxylation (equation 8.4)
Inclusion of new PFT root distribution parameters (Table 8.3)
Different expression for $V_{cmax}$ (many equations but specifically 8.12)
(Challenge) To ensure the updates in Q5 were done correctly, do a model comparison between the Q5 updated model, and the CLM 4.5 photosynthesis model extracted in Q3.
(Challenge) Calculate the leaf photosynthesis A, for the updated model in Q5, for 10 plant functional types. Choose 5 plant functional types that have parameters in tables 8.1, 8.2, and 8.3, and find parameters for 5 other plant functional types, from the literature.
Scenario 3: Photosynthesis Model
This scenario asks you to recreate the photosynthesis module (Chapter 8 of the documentation) as it was programmed and defined in CLM/CTSM 4.0 and iteratively update it to match CLM 4.5. It will not be an exact match however, because a few terms require many other parts of CLM to be run, which is out of scope for this scenario. For reference, the photosynthesis module’s code can be found here.