From d09f85a60fbb1e88f2ecb63d1d1f710bb2c2b19a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 27 May 2026 16:56:15 -0600 Subject: [PATCH 1/8] Updates to Technote section 2.9 Stom. Resistance and Photosynthesis --- .../Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index d739751d7d..2594c9e61b 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -3,12 +3,10 @@ Stomatal Resistance and Photosynthesis ========================================= -Summary of CLM5.0 updates relative to the CLM4.5 ------------------------------------------------------ +History +------- -We describe here the complete photosynthesis and stomatal conductance parameterizations that appear in CLM5.0. Corresponding information for CLM4.5 appeared in the CLM4.5 Technical Note (:ref:`Oleson et al. 2013 `). - -CLM5 includes the following new changes to photosynthesis and stomatal conductance: +We describe here the complete photosynthesis and stomatal conductance parameterizations that appear in CLM6.0. In this version relative to CLM5, we have changed numerous parameter values, but have kept the algorithm unchanged. In CLM5 relative to CLM4.5, this section included the following updates: - Default stomatal conductance calculation uses the Medlyn conductance model @@ -28,7 +26,7 @@ Leaf stomatal resistance, which is needed for the water vapor flux (Chapter :num Stomatal resistance ----------------------- -CLM5 calculates stomatal conductance using the Medlyn stomatal conductance model (:ref:`Medlyn et al. 2011`). Previous versions of CLM calculated leaf stomatal resistance using the Ball-Berry conductance model as described by :ref:`Collatz et al. (1991)` and implemented in global climate models (:ref:`Sellers et al. 1996`). The Medlyn model calculates stomatal conductance (i.e., the inverse of resistance) based on net leaf photosynthesis, the leaf-to-air vapor pressure difference, and the CO\ :sub:`2` concentration at the leaf surface. Leaf stomatal resistance is: +Since CLM5 the model has calculated stomatal conductance using the Medlyn stomatal conductance model (:ref:`Medlyn et al. 2011`). Previous versions of CLM calculated leaf stomatal resistance using the Ball-Berry conductance model as described by :ref:`Collatz et al. (1991)` and implemented in global climate models (:ref:`Sellers et al. 1996`). The Medlyn model calculates stomatal conductance (i.e., the inverse of resistance) based on net leaf photosynthesis, the leaf-to-air vapor pressure difference, and the CO\ :sub:`2` concentration at the leaf surface. Leaf stomatal resistance is: .. math:: :label: 9.1 From 364be79dad7a7e9b854affb504099850ddb46a3c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 May 2026 13:11:43 -0600 Subject: [PATCH 2/8] Insert beta_t in equations where it was missing --- .../CLM50_Tech_Note_Photosynthesis.rst | 4 ++-- .../CLM50_Tech_Note_Plant_Hydraulics.rst | 16 +++++++--------- 2 files changed, 9 insertions(+), 11 deletions(-) diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index 2594c9e61b..e31abbe265 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -112,9 +112,9 @@ The RuBP carboxylase (Rubisco) limited rate of carboxylation :math:`A_{c}` (:mat .. math:: :label: 9.3 - A_{c} =\left\{\begin{array}{l} {\frac{V_{c\max } \left(c_{i} -\Gamma _{*} \right)}{c_{i} +K_{c} \left(1+{o_{i} \mathord{\left/ {\vphantom {o_{i} K_{o} }} \right.} K_{o} } \right)} \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {V_{c\max } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}\qquad \qquad c_{i} -\Gamma _{*} \ge 0. + A_{c} =\left\{\begin{array}{l} {\frac{\beta_{t} V_{c\max } \left(c_{i} -\Gamma _{*} \right)}{c_{i} +K_{c} \left(1+{o_{i} \mathord{\left/ {\vphantom {o_{i} K_{o} }} \right.} K_{o} } \right)} \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {\beta_{t} V_{c\max } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}\qquad \qquad c_{i} -\Gamma _{*} \ge 0. -The maximum rate of carboxylation allowed by the capacity to regenerate RuBP (i.e., the light-limited rate) :math:`A_{j}` (:math:`\mu` \ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is +where :math:`\beta_{t} = \beta_{t,sun}` is the transpiration water stress for sunlit leaves and :math:`\beta_{t} = \beta_{t,sha}` for shaded leaves (Eqs. :eq:`beta_t_sun`, :eq:`beta_t_sha`). The maximum rate of carboxylation allowed by the capacity to regenerate RuBP (i.e., the light-limited rate) :math:`A_{j}` (:math:`\mu` \ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is .. math:: :label: 9.4 diff --git a/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst b/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst index 18a4fe1fdc..db9cb172fc 100644 --- a/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst +++ b/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst @@ -353,12 +353,12 @@ Plant water demand depends on stomatal conductance, which is described in sectio E_{shade} = E_{shade,max} \cdot 2^{-\left(\dfrac{\psi_{shadeleaf}}{p50_e}\right)^{c_k}} .. math:: - :label: 11.203 + :label: beta_t_sun \beta_{t,sun} = \dfrac{g_{s,sun}}{g_{s,sun,\beta_t=1}} .. math:: - :label: 11.204 + :label: beta_t_sha \beta_{t,shade} = \dfrac{g_{s,shade}}{g_{s,shade,\beta_t=1}} @@ -382,9 +382,9 @@ Plant water demand depends on stomatal conductance, which is described in sectio :math:`g_{s,shade}` = stomatal conductance of water corresponding to :math:`E_{shade}` -:math:`g_{s,sun,max}` = stomatal conductance of water corresponding to :math:`E_{sun,max}` +:math:`g_{s,sun,\beta_t=1}` = stomatal conductance of water corresponding to :math:`E_{sun,max}` -:math:`g_{s,shade,max}` = stomatal conductance of water corresponding to :math:`E_{shade,max}` +:math:`g_{s,shade,\beta_t=1}` = stomatal conductance of water corresponding to :math:`E_{shade,max}` .. _Vegetation Water Potential: @@ -574,16 +574,14 @@ Now we compute all the entries for :math:`A` and :math:`b` based on the soil moi We iterate until :math:`b\to 0`, signifying water flux balance through the system. The result is a final set of water potentials ( :math:`\psi_{root}`, :math:`\psi_{xylem}`, :math:`\psi_{shadeleaf}`, :math:`\psi_{sunleaf}`) satisfying non-divergent water flux through the system. The magnitude of the water flux is driven by soil matric potential and unstressed ( :math:`\beta_t=1`) transpiration. -We use the transpiration solution (corresponding to the final solution for :math:`\psi`) to compute stomatal conductance. The stomatal conductance is then used to compute :math:`\beta_t`. +We use the transpiration solution (corresponding to the final solution for :math:`\psi`) to compute stomatal conductance. The stomatal conductance is then used to compute :math:`\beta_t` as in Eqs :eq:`beta_t_sun`, :eq:`beta_t_sha` shown again here: -.. math:: - :label: 11.416 +.. SKIP math labels here, as these equations have been numbered elsewhere +.. math:: \beta_{t,sun} = \dfrac{g_{s,sun}}{g_{s,sun,\beta_t=1}} .. math:: - :label: 11.417 - \beta_{t,shade} = \dfrac{g_{s,shade}}{g_{s,shade,\beta_t=1}} The :math:`\beta_t` values are used in the Photosynthesis module (see section :numref:`Photosynthesis`) to apply water stress. The solution for :math:`\psi` is saved as a new variable (vegetation water potential) and is indicative of plant water status. The soil-to-root fluxes :math:`\left( q_{3,1},q_{3,2},\mbox{...},q_{3,n}\right)` are used as the soil transpiration sink in the Richards' equation subsurface flow equations (see section :numref:`Soil Water`). From fed4dbc9716d573ae7f66903067967a13c29c901 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 May 2026 14:52:20 -0600 Subject: [PATCH 3/8] Mention that PHI_PSII = 1 - f_nps for consistency with the code --- .../tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index e31abbe265..0cb5a37cec 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -144,7 +144,7 @@ where :math:`J_{\max }` is the maximum potential rate of electron transport (:ma I_{PSII} =0.5\Phi _{PSII} (4.6\phi ) -where :math:`\Phi _{PSII}` is the quantum yield of photosystem II, and the term 0.5 arises because one photon is absorbed by each of the two photosystems to move one electron. Parameter values are :math:`\Theta _{PSII}` \ = 0.7 and :math:`\Phi _{PSII}` \ = 0.85. In calculating :math:`A_{j}` (for both C\ :sub:`3` and C\ :sub:`4` plants), :math:`\phi =\phi ^{sun}` for sunlit leaves and :math:`\phi =\phi ^{sha}` for shaded leaves. +where :math:`\Phi _{PSII}` is the quantum yield of photosystem II, and the term 0.5 arises because one photon is absorbed by each of the two photosystems to move one electron. Parameter values are :math:`\Theta _{PSII}` \ = 0.7 and :math:`\Phi _{PSII} = 1 - f_{nps} = 0.85`, where :math:`f_{nps}` is the fraction of light absorbed by non-photosynthetic pigment. In calculating :math:`A_{j}` (for both C\ :sub:`3` and C\ :sub:`4` plants), :math:`\phi =\phi ^{sun}` for sunlit leaves and :math:`\phi =\phi ^{sha}` for shaded leaves. The model uses co-limitation as described by :ref:`Collatz et al. (1991, 1992) `. The actual gross photosynthesis rate, :math:`A`, is given by the smaller root of the equations From d65ff1b60ee776d21bccd2805095049bee160b2c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 May 2026 15:57:50 -0600 Subject: [PATCH 4/8] Show that respiration is multiplied by beta_t (+ some cosmetic changes) --- .../CLM50_Tech_Note_Photosynthesis.rst | 28 +++++++------------ 1 file changed, 10 insertions(+), 18 deletions(-) diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index 0cb5a37cec..14f57f184b 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -10,7 +10,7 @@ We describe here the complete photosynthesis and stomatal conductance parameteri - Default stomatal conductance calculation uses the Medlyn conductance model -- :math:`V_{c,max}` and :math:`J_{max}` at 25 :sup:`\o`\ C: are now prognostic, and predicted via optimality by the LUNA model (Chapter :numref:`rst_Photosynthetic Capacity`) +- :math:`V_{c,max}` and :math:`J_{max}` at 25\ :sup:`\o`\ C: are now prognostic, and predicted via optimality by the LUNA model (Chapter :numref:`rst_Photosynthetic Capacity`) - Leaf N concentration and the fraction of leaf N in Rubisco used to calculate :math:`V_{cmax25}` are determined by the LUNA model (Chapter :numref:`rst_Photosynthetic Capacity`) @@ -103,14 +103,14 @@ Photosynthesis Photosynthesis in C\ :sub:`3` plants is based on the model of :ref:`Farquhar et al. (1980)`. Photosynthesis in C\ :sub:`4` plants is based on the model of :ref:`Collatz et al. (1992)`. :ref:`Bonan et al. (2011)` describe the implementation, modified here. In its simplest form, leaf net photosynthesis after accounting for respiration (:math:`R_{d}` ) is .. math:: - :label: 9.2 + :label: leaf_net_psn A_{n} =\min \left(A_{c} ,A_{j} ,A_{p} \right)-R_{d} . The RuBP carboxylase (Rubisco) limited rate of carboxylation :math:`A_{c}` (:math:`\mu` \ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is .. math:: - :label: 9.3 + :label: rubisco_lim_rate_of_carboxylation A_{c} =\left\{\begin{array}{l} {\frac{\beta_{t} V_{c\max } \left(c_{i} -\Gamma _{*} \right)}{c_{i} +K_{c} \left(1+{o_{i} \mathord{\left/ {\vphantom {o_{i} K_{o} }} \right.} K_{o} } \right)} \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {\beta_{t} V_{c\max } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}\qquad \qquad c_{i} -\Gamma _{*} \ge 0. @@ -153,21 +153,13 @@ The model uses co-limitation as described by :ref:`Collatz et al. (1991, 1992) < \begin{array}{rcl} {\Theta _{cj} A_{i}^{2} -\left(A_{c} +A_{j} \right)A_{i} +A_{c} A_{j} } & {=} & {0} \\ {\Theta _{ip} A^{2} -\left(A_{i} +A_{p} \right)A+A_{i} A_{p} } & {=} & {0} \end{array} . -Values are :math:`\Theta _{cj} =0.98` and :math:`\Theta _{ip} =0.95` for C\ :sub:`3` plants; and :math:`\Theta _{cj} =0.80`\ and :math:`\Theta _{ip} =0.95` for C\ :sub:`4` plants. :math:`A_{i}` is the intermediate co-limited photosynthesis. :math:`A_{n} =A-R_{d}`. +Values are :math:`\Theta _{cj} =0.98` and :math:`\Theta _{ip} =0.95` for C\ :sub:`3` plants; and :math:`\Theta _{cj} =0.80`\ and :math:`\Theta _{ip} =0.95` for C\ :sub:`4` plants. :math:`A_{i}` is the intermediate co-limited photosynthesis. Now we can write Eq. :eq:`leaf_net_psn` as :math:`A_{n} = A - \beta_{t} R_{d}` with :math:`\beta_{t}` as defined in Eq. :eq:`rubisco_lim_rate_of_carboxylation` to account for the effect of water stress on respiration. -The parameters :math:`K_{c}`, :math:`K_{o}`, and :math:`\Gamma` depend on temperature. Values at 25 °C are :math:`K_{c25} ={\rm 4}0{\rm 4}.{\rm 9}\times 10^{-6} P_{atm}`, :math:`K_{o25} =278.4\times 10^{-3} P_{atm}`, and :math:`\Gamma _{25} {\rm =42}.75\times 10^{-6} P_{atm}`. :math:`V_{c\max }`, :math:`J_{\max }`, :math:`T_{p}`, :math:`k_{p}`, and :math:`R_{d}` also vary with temperature. +The parameters :math:`K_{c}`, :math:`K_{o}`, and :math:`\Gamma` depend on temperature. Values at 25°C are :math:`K_{c25} ={\rm 4}0{\rm 4}.{\rm 9}\times 10^{-6} P_{atm}`, :math:`K_{o25} =278.4\times 10^{-3} P_{atm}`, and :math:`\Gamma _{25} {\rm =42}.75\times 10^{-6} P_{atm}`. -:math:`J_{\max 25}` at 25 :sup:`\o`\ C: is calculated by the LUNA model (Chapter :numref:`rst_Photosynthetic Capacity`) +:math:`V_{c\max }`, :math:`J_{\max }`, :math:`T_{p}`, :math:`k_{p}`, and :math:`R_{d}` also vary with temperature. :math:`J_{\max 25}` at 25\ :sup:`\o`\ C is calculated by the LUNA model (Chapter :numref:`rst_Photosynthetic Capacity`). -Parameter values at 25 :sup:`\o`\ C are calculated from :math:`V_{c\max }` \ at 25 -:sup:`\o`\ C:, including: -:math:`T_{p25} =0.167V_{c\max 25}`, and -:math:`R_{d25} =0.015V_{c\max 25}` (C\ :sub:`3`) and -:math:`R_{d25} =0.025V_{c\max 25}` (C\ :sub:`4`). - -For C\ :sub:`4` plants, :math:`k_{p25} =20000\; V_{c\max 25}`. - -However, when the biogeochemistry is active (the default mode), :math:`R_{d25}` is calculated from leaf nitrogen as described in (Chapter :numref:`rst_Plant Respiration`) +Parameter values at 25\ :sup:`\o`\ C are calculated from :math:`V_{c\max }` \ at 25\ :sup:`\o`\ C, including: :math:`T_{p25} =0.167V_{c\max 25}`, :math:`R_{d25} =0.015V_{c\max 25}` (C\ :sub:`3`), and :math:`R_{d25} =0.025V_{c\max 25}` (C\ :sub:`4`). For C\ :sub:`4` plants, :math:`k_{p25} =20000\; V_{c\max 25}`. However, in active biogeochemistry mode (default), :math:`R_{d25}` is calculated from leaf nitrogen (see Chapter :numref:`rst_Plant Respiration`) The parameters :math:`V_{c\max 25}`, :math:`J_{\max 25}`, :math:`T_{p25}`, :math:`k_{p25}`, and :math:`R_{d25}` are scaled over the canopy for sunlit and shaded leaves (section :numref:`Canopy scaling`). In C\ :sub:`3` plants, these are adjusted for leaf temperature, :math:`T_{v}` (K), as: @@ -244,7 +236,7 @@ In the model, acclimation is implemented as in :ref:`Kattge and Knorr (2007) Date: Fri, 29 May 2026 16:37:04 -0600 Subject: [PATCH 5/8] Minor cosmetic changes --- .../CLM50_Tech_Note_Photosynthesis.rst | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index 14f57f184b..e5074f9d21 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -105,7 +105,7 @@ Photosynthesis in C\ :sub:`3` plants is based on the model of :ref:`Farquhar et .. math:: :label: leaf_net_psn - A_{n} =\min \left(A_{c} ,A_{j} ,A_{p} \right)-R_{d} . + A_{n} =\min \left(A_{c} ,A_{j} ,A_{p} \right)-R_{d} The RuBP carboxylase (Rubisco) limited rate of carboxylation :math:`A_{c}` (:math:`\mu` \ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is @@ -126,7 +126,7 @@ The product-limited rate of carboxylation for C\ :sub:`3` plants and the PEP car .. math:: :label: 9.5 - A_{p} =\left\{\begin{array}{l} {3T_{p\qquad } \qquad \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {k_{p} \frac{c_{i} }{P_{atm} } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}. + A_{p} =\left\{\begin{array}{l} {3T_{p\qquad } \qquad \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {k_{p} \frac{c_{i} }{P_{atm} } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\} In these equations, :math:`c_{i}` is the internal leaf CO\ :sub:`2` partial pressure (Pa) and :math:`o_{i} =0.20P_{atm}` is the O\ :sub:`2` partial pressure (Pa). :math:`K_{c}` and :math:`K_{o}` are the Michaelis-Menten constants (Pa) for CO\ :sub:`2` and O\ :sub:`2`. :math:`\Gamma _{*}` (Pa) is the CO\ :sub:`2` compensation point. :math:`V_{c\max }` is the maximum rate of carboxylation (µmol m\ :sup:`-2` s\ :sup:`-1`, Chapter :numref:`rst_Photosynthetic Capacity`) and :math:`J_{x}` is the electron transport rate (µmol m\ :sup:`-2` s\ :sup:`-1`). :math:`T_{p}` is the triose phosphate utilization rate (µmol m\ :sup:`-2` s\ :sup:`-1`), taken as :math:`T_{p} =0.167V_{c\max }` so that :math:`A_{p} =0.5V_{c\max }` for C\ :sub:`3` plants (as in :ref:`Collatz et al. 1992 `). For C\ :sub:`4` plants, the light-limited rate :math:`A_{j}` varies with :math:`\phi` in relation to the quantum efficiency (:math:`\alpha =0.05` mol CO\ :sub:`2` mol\ :sup:`-1` photon). :math:`\phi` is the absorbed photosynthetically active radiation (W m\ :sup:`-2`) (section :numref:`Solar Fluxes`), which is converted to photosynthetic photon flux assuming 4.6 :math:`\mu` \ mol photons per joule. :math:`k_{p}` is the initial slope of C\ :sub:`4` CO\ :sub:`2` response curve. @@ -151,9 +151,11 @@ The model uses co-limitation as described by :ref:`Collatz et al. (1991, 1992) < .. math:: :label: 9.8 - \begin{array}{rcl} {\Theta _{cj} A_{i}^{2} -\left(A_{c} +A_{j} \right)A_{i} +A_{c} A_{j} } & {=} & {0} \\ {\Theta _{ip} A^{2} -\left(A_{i} +A_{p} \right)A+A_{i} A_{p} } & {=} & {0} \end{array} . + \begin{array}{rcl} {\Theta _{cj} A_{i}^{2} -\left(A_{c} +A_{j} \right)A_{i} +A_{c} A_{j} } & {=} & {0} \\ {\Theta _{ip} A^{2} -\left(A_{i} +A_{p} \right)A+A_{i} A_{p} } & {=} & {0} \end{array} -Values are :math:`\Theta _{cj} =0.98` and :math:`\Theta _{ip} =0.95` for C\ :sub:`3` plants; and :math:`\Theta _{cj} =0.80`\ and :math:`\Theta _{ip} =0.95` for C\ :sub:`4` plants. :math:`A_{i}` is the intermediate co-limited photosynthesis. Now we can write Eq. :eq:`leaf_net_psn` as :math:`A_{n} = A - \beta_{t} R_{d}` with :math:`\beta_{t}` as defined in Eq. :eq:`rubisco_lim_rate_of_carboxylation` to account for the effect of water stress on respiration. +Values are :math:`\Theta _{cj} =0.98` and :math:`\Theta _{ip} =0.95` for C\ :sub:`3` plants; and :math:`\Theta _{cj} =0.80`\ and :math:`\Theta _{ip} =0.95` for C\ :sub:`4` plants. :math:`A_{i}` is the intermediate co-limited photosynthesis. + +Now we write Eq. :eq:`leaf_net_psn` as :math:`A_{n} = A - \beta_{t} R_{d}` with :math:`\beta_{t}` as defined in Eq. :eq:`rubisco_lim_rate_of_carboxylation` to account for the effect of water stress on respiration. The parameters :math:`K_{c}`, :math:`K_{o}`, and :math:`\Gamma` depend on temperature. Values at 25°C are :math:`K_{c25} ={\rm 4}0{\rm 4}.{\rm 9}\times 10^{-6} P_{atm}`, :math:`K_{o25} =278.4\times 10^{-3} P_{atm}`, and :math:`\Gamma _{25} {\rm =42}.75\times 10^{-6} P_{atm}`. @@ -178,7 +180,7 @@ and .. math:: :label: 9.11 - f_{H} \left(T_{v} \right)=\frac{1+\exp \left(\frac{298.15\Delta S-\Delta H_{d} }{298.15\times 0.001R_{gas} } \right)}{1+\exp \left(\frac{\Delta ST_{v} -\Delta H_{d} }{0.001R_{gas} T_{v} } \right)} . + f_{H} \left(T_{v} \right)=\frac{1+\exp \left(\frac{298.15\Delta S-\Delta H_{d} }{298.15\times 0.001R_{gas} } \right)}{1+\exp \left(\frac{\Delta ST_{v} -\Delta H_{d} }{0.001R_{gas} T_{v} } \right)} :numref:`Table Temperature dependence parameters for C3 photosynthesis` lists parameter values for :math:`\Delta H_{a}` and :math:`\Delta H_{d}`. :math:`\Delta S` is calculated separately for :math:`V_{c\max }` and :math:`J_{max }` to allow for temperature acclimation of photosynthesis (see equation :eq:`9.16`), and :math:`\Delta S` is 490 J mol :sup:`-1` K :sup:`-1` for :math:`R_d` (:ref:`Bonan et al. 2011`, :ref:`Lombardozzi et al. 2015`). Because :math:`T_{p}` as implemented here varies with :math:`V_{c\max }`, :math:`T_{p}` uses the same temperature parameters as :math:`V_{c\max}`. For C\ :sub:`4` plants, @@ -241,7 +243,7 @@ The effect is to cause the temperature optimum of :math:`V_{c\max }` and :math:` .. math:: :label: 9.16 - J_{\max 25} /V_{c\max 25} =2.59-0.035(T_{10} -T_{f} ). + J_{\max 25} /V_{c\max 25} =2.59-0.035(T_{10} -T_{f} ) In these acclimation functions, :math:`T_{10}` is the 10-day mean air temperature (K) and :math:`T_{f}` is the freezing point of water (K). For lack of data, :math:`T_{p}` acclimates similar to :math:`V_{c\max }`. Acclimation is restricted over the temperature range :math:`T_{10} -T_{f} \ge` 11°C and :math:`T_{10} -T_{f} \le` 35°C. @@ -315,7 +317,7 @@ In terms of conductance with :math:`g_{s} =1/r_{s}` and :math:`g_{b} =1/r_{b}` .. math:: :label: 9.36 - e_{s} =\frac{e_{a} g_{b} +e_{i} g_{s} }{g_{b} +g_{s} } . + e_{s} =\frac{e_{a} g_{b} +e_{i} g_{s} }{g_{b} +g_{s} } Substitution of equation :eq:`9.36` into equation :eq:`9.1` gives an expression for the stomatal resistance (:math:`r_{s}`) as a function of photosynthesis (:math:`A_{n}` ) From 138cfc75996255f4f06826bd1b7ef0ce17e01e1b Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 May 2026 17:54:03 -0600 Subject: [PATCH 6/8] Parameter value updates in sections 2.9.1 to 2.9.3 --- .../CLM50_Tech_Note_Photosynthesis.rst | 108 +++++++++--------- 1 file changed, 55 insertions(+), 53 deletions(-) diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index e5074f9d21..740c8a5ad1 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -33,9 +33,9 @@ Since CLM5 the model has calculated stomatal conductance using the Medlyn stomat \frac{1}{r_{s} } =g_{s} = g_{o} + 1.6(1 + \frac{g_{1} }{\sqrt{D_{s}}}) \frac{A_{n} }{{c_{s} \mathord{\left/ {\vphantom {c_{s} P_{atm} }} \right.} P_{atm} } } -where :math:`r_{s}` is leaf stomatal resistance (s m\ :sup:`2` :math:`\mu`\ mol\ :sup:`-1`), :math:`g_{o}` is the minimum stomatal conductance (:math:`\mu` mol m :sup:`-2` s\ :sup:`-1`), :math:`A_{n}` is leaf net photosynthesis (:math:`\mu`\ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`), :math:`c_{s}` is the CO\ :sub:`2` partial pressure at the leaf surface (Pa), :math:`P_{atm}` is the atmospheric pressure (Pa), and :math:`D_{s}=(e_{i}-e{_s})/1000` is the leaf-to-air vapor pressure difference at the leaf surface (kPa) where :math:`e_{i}` is the saturation vapor pressure (Pa) evaluated at the leaf temperature :math:`T_{v}`, and :math:`e_{s}` is the vapor pressure at the leaf surface (Pa). :math:`g_{1}` is a plant functional type dependent parameter (:numref:`Table Plant functional type (PFT) stomatal conductance parameters`) and is the same as those used in the CABLE model (:ref:`de Kauwe et al. 2015 `). +where :math:`r_{s}` is leaf stomatal resistance (s m\ :sup:`2` :math:`\mu`\ mol\ :sup:`-1`), :math:`A_{n}` is leaf net photosynthesis (:math:`\mu`\ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`), :math:`c_{s}` is the CO\ :sub:`2` partial pressure at the leaf surface (Pa), :math:`P_{atm}` is the atmospheric pressure (Pa), and :math:`D_{s}=(e_{i}-e{_s})/1000` is the leaf-to-air vapor pressure difference at the leaf surface (kPa) where :math:`e_{i}` is the saturation vapor pressure (Pa) evaluated at the leaf temperature :math:`T_{v}`, and :math:`e_{s}` is the vapor pressure at the leaf surface (Pa). :math:`g_{o}` is plant functional type (pft)-dependent minimum stomatal conductance (:math:`\mu` mol m :sup:`-2` s\ :sup:`-1`) and :math:`g_{1}` is a pft-dependent parameter (:numref:`Table Plant functional type (PFT) stomatal conductance parameters`) with same values originally as in the CABLE model (:ref:`de Kauwe et al. 2015 `) but most values have been replaced in CLM6. -The value for :math:`g_{o}=100` :math:`\mu` mol m :sup:`-2` s\ :sup:`-1` for C\ :sub:`3` and C\ :sub:`4` plants. Photosynthesis is calculated for sunlit (:math:`A^{sun}`) and shaded (:math:`A^{sha}`) leaves to give :math:`r_{s}^{sun}` and :math:`r_{s}^{sha}`. Additionally, soil water influences stomatal resistance through plant hydraulic stress, detailed in the :ref:`rst_Plant Hydraulics` chapter. +Photosynthesis is calculated for sunlit (:math:`A^{sun}`) and shaded (:math:`A^{sha}`) leaves to give :math:`r_{s}^{sun}` and :math:`r_{s}^{sha}`. Additionally, soil water influences stomatal resistance through plant hydraulic stress, detailed in the :ref:`rst_Plant Hydraulics` chapter. Resistance is converted from units of s m\ :sup:`2` :math:`\mu` mol\ :sup:`-1` to s m\ :sup:`-1` as: 1 s m\ :sup:`-1` = :math:`1\times 10^{-9} R_{gas} \frac{\theta _{atm} }{P_{atm} }` :math:`\mu` mol\ :sup:`-1` m\ :sup:`2` s, where :math:`R_{gas}` is the universal gas constant (J K\ :sup:`-1` kmol\ :sup:`-1`) (:numref:`Table Physical constants`) and :math:`\theta _{atm}` is the atmospheric potential temperature (K). @@ -43,57 +43,59 @@ Resistance is converted from units of s m\ :sup:`2` :math:`\mu` mol\ :sup:`-1` t .. table:: Plant functional type (PFT) stomatal conductance parameters. - +----------------------------------+-------------------+ - | PFT | g\ :sub:`1` | - +==================================+===================+ - | NET Temperate | 2.35 | - +----------------------------------+-------------------+ - | NET Boreal | 2.35 | - +----------------------------------+-------------------+ - | NDT Boreal | 2.35 | - +----------------------------------+-------------------+ - | BET Tropical | 4.12 | - +----------------------------------+-------------------+ - | BET temperate | 4.12 | - +----------------------------------+-------------------+ - | BDT tropical | 4.45 | - +----------------------------------+-------------------+ - | BDT temperate | 4.45 | - +----------------------------------+-------------------+ - | BDT boreal | 4.45 | - +----------------------------------+-------------------+ - | BES temperate | 4.70 | - +----------------------------------+-------------------+ - | BDS temperate | 4.70 | - +----------------------------------+-------------------+ - | BDS boreal | 4.70 | - +----------------------------------+-------------------+ - | C\ :sub:`3` arctic grass | 2.22 | - +----------------------------------+-------------------+ - | C\ :sub:`3` grass | 5.25 | - +----------------------------------+-------------------+ - | C\ :sub:`4` grass | 1.62 | - +----------------------------------+-------------------+ - | Temperate Corn | 1.79 | - +----------------------------------+-------------------+ - | Spring Wheat | 5.79 | - +----------------------------------+-------------------+ - | Temperate Soybean | 5.79 | - +----------------------------------+-------------------+ - | Cotton | 5.79 | - +----------------------------------+-------------------+ - | Rice | 5.79 | - +----------------------------------+-------------------+ - | Sugarcane | 1.79 | - +----------------------------------+-------------------+ - | Tropical Corn | 1.79 | - +----------------------------------+-------------------+ - | Tropical Soybean | 5.79 | - +----------------------------------+-------------------+ - | Miscanthus | 1.79 | - +----------------------------------+-------------------+ - | Switchgrass | 1.79 | - +----------------------------------+-------------------+ + +----------------------------------+-------------+------------------+ + | PFT | g\ :sub:`o` | g\ :sub:`1` | + +==================================+=============+==================+ + | NET Temperate | 110.93 | 2.35 | + +----------------------------------+-------------+------------------+ + | NET Boreal | 12500 | 2.57 | + +----------------------------------+-------------+------------------+ + | NDT Boreal | 1.00 | 2.09 | + +----------------------------------+-------------+------------------+ + | BET Tropical | 1733.21 | 3.50 | + +----------------------------------+-------------+------------------+ + | BET temperate | 102.24 | 4.12 | + +----------------------------------+-------------+------------------+ + | BDT tropical | 97.56 | 2.85 | + +----------------------------------+-------------+------------------+ + | BDT temperate | 100.40 | 4.45 | + +----------------------------------+-------------+------------------+ + | BDT boreal | 99.73 | 5.05 | + +----------------------------------+-------------+------------------+ + | BES temperate | 100.00 | 4.38 | + +----------------------------------+-------------+------------------+ + | BDS temperate | 100.00 | 4.70 | + +----------------------------------+-------------+------------------+ + | BDS boreal | 100.00 | 4.70 | + +----------------------------------+-------------+------------------+ + | C\ :sub:`3` arctic grass | 100.00 | 3.78 | + +----------------------------------+-------------+------------------+ + | C\ :sub:`3` grass | 5063.54 | 8.32 | + +----------------------------------+-------------+------------------+ + | C\ :sub:`4` grass | 100.00 | 1.62 | + +----------------------------------+-------------+------------------+ + | C\ :sub:`3` crop | 5063.54 | 9.17 | + +----------------------------------+-------------+------------------+ + | Temperate Corn | 100.00 | 1.79 | + +----------------------------------+-------------+------------------+ + | Spring Wheat | 100.00 | 5.79 | + +----------------------------------+-------------+------------------+ + | Temperate Soybean | 100.00 | 5.79 | + +----------------------------------+-------------+------------------+ + | Cotton | 100.00 | 5.79 | + +----------------------------------+-------------+------------------+ + | Rice | 100.00 | 5.79 | + +----------------------------------+-------------+------------------+ + | Sugarcane | 100.00 | 1.79 | + +----------------------------------+-------------+------------------+ + | Tropical Corn | 100.00 | 1.79 | + +----------------------------------+-------------+------------------+ + | Tropical Soybean | 100.00 | 5.79 | + +----------------------------------+-------------+------------------+ + | Miscanthus | 100.00 | 1.79 | + +----------------------------------+-------------+------------------+ + | Switchgrass | 100.00 | 1.79 | + +----------------------------------+-------------+------------------+ .. _Photosynthesis: From f31a11995d888d681c831df08bcb29304e206763 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 May 2026 18:09:09 -0600 Subject: [PATCH 7/8] Replace rounded with exact value for o2_molar_const --- .../tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index 740c8a5ad1..0e26669b31 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -130,7 +130,7 @@ The product-limited rate of carboxylation for C\ :sub:`3` plants and the PEP car A_{p} =\left\{\begin{array}{l} {3T_{p\qquad } \qquad \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {k_{p} \frac{c_{i} }{P_{atm} } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\} -In these equations, :math:`c_{i}` is the internal leaf CO\ :sub:`2` partial pressure (Pa) and :math:`o_{i} =0.20P_{atm}` is the O\ :sub:`2` partial pressure (Pa). :math:`K_{c}` and :math:`K_{o}` are the Michaelis-Menten constants (Pa) for CO\ :sub:`2` and O\ :sub:`2`. :math:`\Gamma _{*}` (Pa) is the CO\ :sub:`2` compensation point. :math:`V_{c\max }` is the maximum rate of carboxylation (µmol m\ :sup:`-2` s\ :sup:`-1`, Chapter :numref:`rst_Photosynthetic Capacity`) and :math:`J_{x}` is the electron transport rate (µmol m\ :sup:`-2` s\ :sup:`-1`). :math:`T_{p}` is the triose phosphate utilization rate (µmol m\ :sup:`-2` s\ :sup:`-1`), taken as :math:`T_{p} =0.167V_{c\max }` so that :math:`A_{p} =0.5V_{c\max }` for C\ :sub:`3` plants (as in :ref:`Collatz et al. 1992 `). For C\ :sub:`4` plants, the light-limited rate :math:`A_{j}` varies with :math:`\phi` in relation to the quantum efficiency (:math:`\alpha =0.05` mol CO\ :sub:`2` mol\ :sup:`-1` photon). :math:`\phi` is the absorbed photosynthetically active radiation (W m\ :sup:`-2`) (section :numref:`Solar Fluxes`), which is converted to photosynthetic photon flux assuming 4.6 :math:`\mu` \ mol photons per joule. :math:`k_{p}` is the initial slope of C\ :sub:`4` CO\ :sub:`2` response curve. +In these equations, :math:`c_{i}` is the internal leaf CO\ :sub:`2` partial pressure (Pa) and :math:`o_{i} =0.209P_{atm}` is the O\ :sub:`2` partial pressure (Pa) (where 0.209 is the value of the atmospheric O\ :sub:`2` molar ratio in mol/mol). :math:`K_{c}` and :math:`K_{o}` are the Michaelis-Menten constants (Pa) for CO\ :sub:`2` and O\ :sub:`2`. :math:`\Gamma _{*}` (Pa) is the CO\ :sub:`2` compensation point. :math:`V_{c\max }` is the maximum rate of carboxylation (µmol m\ :sup:`-2` s\ :sup:`-1`, Chapter :numref:`rst_Photosynthetic Capacity`) and :math:`J_{x}` is the electron transport rate (µmol m\ :sup:`-2` s\ :sup:`-1`). :math:`T_{p}` is the triose phosphate utilization rate (µmol m\ :sup:`-2` s\ :sup:`-1`), taken as :math:`T_{p} =0.167V_{c\max }` so that :math:`A_{p} =0.5V_{c\max }` for C\ :sub:`3` plants (as in :ref:`Collatz et al. 1992 `). For C\ :sub:`4` plants, the light-limited rate :math:`A_{j}` varies with :math:`\phi` in relation to the quantum efficiency (:math:`\alpha =0.05` mol CO\ :sub:`2` mol\ :sup:`-1` photon). :math:`\phi` is the absorbed photosynthetically active radiation (W m\ :sup:`-2`) (section :numref:`Solar Fluxes`), which is converted to photosynthetic photon flux assuming 4.6 :math:`\mu` \ mol photons per joule. :math:`k_{p}` is the initial slope of C\ :sub:`4` CO\ :sub:`2` response curve. For C\ :sub:`3` plants, the electron transport rate depends on the photosynthetically active radiation absorbed by the leaf. A common expression is the smaller of the two roots of the equation From 2f64d0d61491ea58eb75c0e5bcdc72c513f09ec0 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 May 2026 18:36:26 -0600 Subject: [PATCH 8/8] Update some theta parameter values --- .../tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index 0e26669b31..525751dd95 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -155,7 +155,7 @@ The model uses co-limitation as described by :ref:`Collatz et al. (1991, 1992) < \begin{array}{rcl} {\Theta _{cj} A_{i}^{2} -\left(A_{c} +A_{j} \right)A_{i} +A_{c} A_{j} } & {=} & {0} \\ {\Theta _{ip} A^{2} -\left(A_{i} +A_{p} \right)A+A_{i} A_{p} } & {=} & {0} \end{array} -Values are :math:`\Theta _{cj} =0.98` and :math:`\Theta _{ip} =0.95` for C\ :sub:`3` plants; and :math:`\Theta _{cj} =0.80`\ and :math:`\Theta _{ip} =0.95` for C\ :sub:`4` plants. :math:`A_{i}` is the intermediate co-limited photosynthesis. +Values are :math:`\Theta _{cj} =0.9393` and :math:`\Theta _{ip} =0.95` for C\ :sub:`3` plants, :math:`\Theta _{cj} =0.80` and :math:`\Theta _{ip} =0.95` for C\ :sub:`4` plants, and :math:`\Theta _{cj} =0.98` for C\ :sub:`3` non-generic crops. :math:`A_{i}` is the intermediate co-limited photosynthesis. Now we write Eq. :eq:`leaf_net_psn` as :math:`A_{n} = A - \beta_{t} R_{d}` with :math:`\beta_{t}` as defined in Eq. :eq:`rubisco_lim_rate_of_carboxylation` to account for the effect of water stress on respiration.