Project CAMS41 Phase 2
Implementation of Farquhar photosynthesis model in CTESSEL


CTESSEL call tree (version CY43R3)

BLUE : driver (OSM_LSCE/src/CY43R3/surf/offline/driver)
RED : module (OSM_LSCE/src/CY43R3/surf/module)
GREEN : new developments in module (OSM_LSCE/src/CY43R3/surf/module)

CPG1S : grid point calculations

CALLPAR1S : call the subroutines of the physics package

UPDDIAG : interface routine to copy IFS variables to offline code diagnostics buffers

VDFMAIN1S : does the vertical exchange of U,V,SLG,QT by turbulence

SURFEXCDRIVER_CTL : controls the ensemble of routines that prepare the surface exchange coefficients and associated surface quantities needed for the solution of the vertical diffusion equations

VSURF : prepares surface boundary condition for T and Q

COTWORESTRESS : calculates net assimilation of CO2 and canopy conductance with moisture stress response

CCETR : calculates radiative transfer within the canopy

COTWO : calculates net assimilation of CO2 and leaf conductance

SRFCOTWO : does the post-processing of CO2 values

FARQUHAR : calculates photosynthesis following Farquhar model

SUFARQUHAR : initialisation of Farquhar parameters

YOS_AGF : definition of Farquhar parameters


CTESSEL PROFILING

AGSAGF


Optimization at FR-Hes site (3 parameters)

ParameterPriorMinMaxPostDescription
VCMAX_PFT160.035.085.085.0Maximum rate of Rubisco activity-limited carboxylation at 25°C (PFT1)
VCMAX_PFT1950.025.075.026.3Maximum rate of Rubisco activity-limited carboxylation at 25°C (PFT19)
A1_C30.850.800.900.884Empirical constant 'a' involved in the calculation of fvpd (C3 vegetation)
A1_C40.720.670.770.77Empirical constant 'a' involved in the calculation of fvpd (C4 vegetation)
B1_C30.140.090.190.09Empirical constant 'b' involved in the calculation of fvpd (C3 vegetation)
B1_C40.200.150.250.15Empirical constant 'b' involved in the calculation of fvpd (C4 vegetation)

AGS : CTESSEL carbon assimilation
AGF : Farquhar carbon assimilation
PRIORPOSTERIOR

Optimization at FR-Hes site (8 parameters)
Standard composition : PFT1 - 78%, PFT19 - 22%

ParameterPriorMinMaxPostDescription
VCMAX_PFT160.036.084.084.0Maximum rate of Rubisco activity-limited carboxylation at 25°C (PFT1)
VCMAX_PFT1950.030.070.030.3Maximum rate of Rubisco activity-limited carboxylation at 25°C (PFT19)
A1_C30.850.7680.9350.791Empirical constant 'a' involved in the calculation of fvpd (C3 vegetation)
A1_C40.720.6480.7920.792Empirical constant 'a' involved in the calculation of fvpd (C4 vegetation)
B1_C30.140.1260.1540.139Empirical constant 'b' involved in the calculation of fvpd (C3 vegetation)
B1_C40.200.180.220.18Empirical constant 'b' involved in the calculation of fvpd (C4 vegetation)
G0_C30.006250.0050.00750.0068Residual stomatal conductance when irradiance approaches zero (C3 vegetation)
G0_C40.018750.0150.02250.0225Residual stomatal conductance when irradiance approaches zero (C4 vegetation)
GM_C30.40.10.80.1Mesophyll diffusion conductance at 25°C (C3 vegetation)
EVCMAX_C371513572108581585815Activation energy for Vcmax (C3 vegetation)
EVCMAX_C467300538408076080760Activation energy for Vcmax (C4 vegetation)
EJMAX_C349884399075986056330Activation energy for Jmax (C3 vegetation)
EJMAX_C477900623209348093480Activation energy for Jmax (C4 vegetation)
KHUMREL1.00.81.21.2Scaling factor for soil water stress function (virtual parameter)

AGS : CTESSEL carbon assimilation
AGF : Farquhar carbon assimilation
PRIOR POSTERIOR COST-FUNCTION
A1_C3 A1_C4 B1_C3 B1_C4
EVCMAX_C3 EVCMAX_C4 EJMAX_C3 EJMAX_C4
G0_C3 G0_C4 GM_C3 KHUMREL
VCMAX_PFT1 VCMAX_PFT19

Optimization at FR-Hes site (8 parameters)
Altered composition : PFT5 - 100%

ParameterPriorMinMaxPostDescription
VCMAX_PFT550.030.070.067.5Maximum rate of Rubisco activity-limited carboxylation at 25°C (PFT5)
A1_C30.850.7680.9350.935Empirical constant 'a' involved in the calculation of fvpd (C3 vegetation)
B1_C30.140.1260.1540.126Empirical constant 'b' involved in the calculation of fvpd (C3 vegetation)
G0_C30.006250.0050.00750.00739Residual stomatal conductance when irradiance approaches zero (C3 vegetation)
GM_C30.40.10.80.783Mesophyll diffusion conductance at 25°C (C3 vegetation)
EVCMAX_C371513572108581585815Activation energy for Vcmax (C3 vegetation)
EJMAX_C349884399075986043013Activation energy for Jmax (C3 vegetation)
KHUMREL1.00.81.21.2Scaling factor for soil water stress function (virtual parameter)

AGS : CTESSEL carbon assimilation
AGF : Farquhar carbon assimilation
PRIOR POSTERIOR COST-FUNCTION
A1_C3 B1_C3 EVCMAX_C3 EJMAX_C3
G0_C3 GM_C3 KHUMREL VCMAX_PFT5

Tests at the PALS sites


AGS : CTESSEL GPP
AGF : Farquhar GPP

LOCATION and COMPOSITION TIME-SERIES
(daily mean with 15-days running average window,
RMSD vs FluxNet in brackets)
CORELLATION
(daily mean with 15-days running average window,
corellation coefficient in brackets)
ANNUAL CYCLE
(monthly mean)
DIURNAL CYCLE
(May - September, hourly mean)


CTESSEL vs ORCHIDEE PFTs correspondence

CTESSEL ORCHIDEE C3/C4
PFT1 Crops, Mixed Farming PFT13 (C4 crops) C4
PFT2 Short Grass PFT10 (C3 grass) C3
PFT3 Evergreen Needleleaf Trees PFT7 (Boreal Needleleaf Evergreen) C3
PFT4 Deciduous Needleleaf Trees PFT9 (Boreal Needleleaf Deciduous) C3
PFT5 Deciduous Broadleaf Trees PFT6 (Temperate Broadleaf Summergreen) C3
PFT6 Evergreen Broadleaf Trees PFT5 (Temperate Broadleaf Evergreen) C3
PFT7 Tall Grass PFT11 (C4 grass) C4
PFT8 Desert none none
PFT9 Tundra PFT10 (C3 grass) C3
PFT10 Irrigated Crops PFT12 (C3 crops) C3
PFT11 Semidesert PFT11 (C4 grass) C4
PFT12 Ice Caps and Glaciers none none
PFT13 Bogs and Marshes PFT10 (C3 grass) C3
PFT14 Inland Water none none
PFT15 Ocean none none
PFT16 Evergreen Shrubs PFT11 (C4 grass) C4
PFT17 Deciduous Shrubs PFT10 (C3 grass) C3
PFT18 Mixed Forest/woodland PFT6 (Temperate Broadleaf Summergreen) C3
PFT19 Interrupted Forest PFT6 (Temperate Broadleaf Summergreen) C3
PFT20 Water and Land Mixtures none none

FARQUHAR module INPUT VARIABLES

CTESSEL name ORCHIDEE analog Units Description
KIDIA Begin point in arrays
KFDIA End point in arrays
KLON Length of arrays
KVTYPE Vegetation type corresponding to tile
LDLAND True/False Land/sea mask
PTM1 temp_air K Temperature at T-1
? temp_growth ? Growth temperature (equal to t2m_month)
PQM1 qair kg/kg Specific humidity at T-1
? qsurf kg/kg Near surface specific humidity
PAPHM1 pb Pa Pressure at T-1 (to scale to hPa)
PSRFD swdown W/m2 Downward shortwave radiation flux at surface
ZRHO rau kg/m3 Air density
PUWIND u m/s Lowest level wind speed (to pass to COTWORESTRESS)
PVWIND v m/s Lowest level wind speed (to pass to COTWORESTRESS)
? q_cdrag Surface drag coefficient
assim_param umol/m2/s min+max+opt temps, vcmax, vjmax (to define inside)
ZCO2 Ca gCO2/gAir Corrected atmospheric concentration of CO2 at canopy level (to recalc to umol/m2/s)
ZDMAXT? humrel kg/kg Soil moisture stress (recalc to 0-1)
PCVT veget_max 0-1 Maximum vegetation type fraction
PCVT veget 0-1 Vegetation type fraction (to calc from max fraction PCVT?)
PLAI lai m2/m2 Leaf area index
? qsintveg kg/m2 Water on vegetation due to interception
? qsintmax kg/m2 Maximum water on vegetation
? vbeta23 Beta for fraction of wetted foliage that will transpire

FARQUHAR module OUTPUT VARIABLES

CTESSEL name ORCHIDEE analog Units Description
PAGF gpp kgCO2/kgAir*m/s Gross assimilation of CO2
PGSF gsmean m/s Leaf conductance to H2O (cuticular and stomatal)

FARQUHAR module LOCAL PARAMETERS

Name Value Units Description
a1 0.85 Empirical constant involved in the calculation of fvpd
alpha_LL 0.3 mol-e/mol-photon Conversion efficiency of absorbed light into J at strictly limiting light
arJV 2.59 umol-e/umol-CO2 a coefficient of the linear regression (a+bT) defining the Jmax25/Vcmax25 ratio
aSJ 659.7 J/K/mol a coefficient of the linear regression (a+bT) defining the Entropy term for Jmax
aSV 668.39 J/K/mol a coefficient of the linear regression (a+bT) defining the Entropy term for Vcmax
b1 0.14 Empirical constant involved in the calculation of fvpd
brJV -0.035 umol-e/umol-CO2/C b coefficient of the linear regression (a+bT) defining the Jmax25/Vcmax25 ratio
bSJ -0.75 J/K/mol/C b coefficient of the linear regression (a+bT) defining the Entropy term for Jmax
bSV -1.07 J/K/mol/C b coefficient of the linear regression (a+bT) defining the Entropy term for Vcmax
D_gm 437400 J/mol Deactivation energy for gm
D_Jmax 200000 J/mol Deactivation energy for Jmax
D_Vcmax 200000 J/mol Deactivation energy for Vcmax
E_gamma_star 37830 J/mol Activation energy for Γ*
E_gm 49600 J/mol Activation energy for gm
E_Jmax 49884 J/mol Activation energy for Jmax
E_KmC 79430 J/mol Activation energy for KmC
E_KmO 36380 J/mol Activation energy for KmO
E_Rd 46390 J/mol Activation energy for Rd
E_Sco -24460 J/mol Activation energy for Sco
E_Vcmax 71513 J/mol Activation energy for Vcmax
g0 0.00625 mol/(m2 s bar) Residual stomatal conductance when irradiance approaches zero
gamma_star25 42.75 ubar Ci-based CO2 compensation point in the absence of Rd at 25°C
gm25 0.4 mol/(m2 s bar) Mesophyll diffusion conductance at 25°C
h_protons 4 mol/mol Number of protons required to produce one ATP
KmC25 404.9 ubar Michaelis–Menten constant of Rubisco for CO2 at 25°C
KmO25 278400 ubar Michaelis–Menten constant of Rubisco for O2 at 25°C
S_gm 1400 J/K/mol Entropy term for gm
Sco25 2800 bar/bar Relative CO2/O2 specificity factor for Rubisco at 25°C
stress_gm 1 Water stress on gm
stress_gs 1 Water stress on gs
stress_vcmax 1 Water stress on Vcmax
theta 0.7 Convexity factor for response of J to irradiance
tphoto_max 55 C Maximum photosynthesis temperature
tphoto_min -4 C Minimum photosynthesis temperature
Vcmax25 35 ÷ 60 umol/m2/s Maximum rate of Rubisco activity-limited carboxylation at 25°C

Meeting on photosynthesis model developments in the IFS (16 October 2020)

  1. Implementation of the ORCHIDEE photosynthesis scheme in CTESSEL (F. Maignan)
  2. Potential future steps for CTESSEL (P. Peylin)

Bibliography

  1. Yin X., Struik P.C. C3 and C4 photosynthesis models: an overview from the perspective of crop modelling. NJAS-Wageningen Journal of Life Sciences, 57, 27-38, 2009