Source code for the JAMES paper: Representation of leaf-to-canopy radiative transfer processes improves simulation of far-red solar-induced chlorophyll fluorescence in the Community Land Model version 5. https://doi.org/10.1029/2021MS002747.
Results in the paper were generated by incorporting the code in this repository into the CESM relase cesm2.1.1-rc.05.
Below are descriptions of each file in this repository:
PhotosynthesisMod.F90: leaf level fluorescence and scaling up to canopy level (Kn calibrated with cotton dataset, from van der Tol et al, 2014)
PhotosynthesisMod_droughtfluorescencemodel.F90: Kn calibtrated with drought dataset (from van der Tol et al, 2014)
PhotosynthesisMod_sustainedNPQ.F90: consideres sustained NPQ according to Raczka et al (2019)
SolarAbsorbedType.F90: added variables needed for the modified leaf APAR calculation
SurfaceAlbedoMod.F90: modifications of radiative transfer
SurfaceAlbedoType.F90: add variables and outputs related to radiative transfer
SurfaceRadiationMod.F90: add variables for PAR absorbed by leaves only (not affected by stem/snow); PAR/SR set to be 0.435 instead of 0.5. If coupled with CAM, the default-PAR version should be used.
SurfaceRadiationMod_oriPAR_SR_ratio.F90: The default PAR/SR=0.5 is used when not coupled with CAM (PAR is based on radiative transfer if coupled with CAM).
UrbanAlbedoMod.F90: Account for urban landuints for added variables (ftnn, ftin, refd, refi, refd_gr, refi_gr)
CanopyFluxesMod.F90: add input variables when calling PhotosynthesisTotal (for calculation of canopy scattering)
pftconMod.F90: add Clumping index for each pft as an input
Code in branch "orginal APAR calculation" is for simulation without the correction of snow and stem for leaf APAR estimation
Folder 'input' contains input parameter files with different modifications incorporated. All files have an added variable 'CI_pft' providing clumping index for each PFT.
clm5_params.c171117_CI_Vcmax_Majrt.nc: with all modifications incorporated (added clumping index (CI), changed flnr (for TRY Vcmax), leaf reflecatnce and leaf transmittance)
clm5_params.c171117_CI1.nc: no modifications made (added variable 'CI_pft', with all clumping indices set to 1, i.e., no clumping)
clm5_params.c171117_CI.nc: considered clumping
clm5_params.c171117_CI_Majrt.nc: considered clumping, modified leaf reflectance and transmittance (based on Majasalmi et al, 2019)
clm5_params.c171117_CI_Vcmax.nc: considered clumping, modified flnr (for TRY Vcmax)
clm5_params.c171117_CI1_Vcmax_Majrt.nc: modified flnr (for TRY Vcmax) and leaf refleactance and transmittance, clumping not considered