From a8ae0baafe4ae0a1266679c47d47e0571f7b8d81 Mon Sep 17 00:00:00 2001 From: Katie Rocci Date: Thu, 28 May 2026 15:59:00 -0600 Subject: [PATCH 1/3] Decomposition tech note updated for CLM6 --- .../CLM4_vertsoil_soilstruct_drawing.png | 3 - .../CLM50_Tech_Note_Decomposition.rst | 264 +++++++----------- .../Decomposition/CLM6_decomp_image.png | 3 + .../Decomposition/MIMICS_Wiring_BW.png | 3 + .../Decomposition/soil_C_pools_CN_century.png | 3 - .../References/CLM50_Tech_Note_References.rst | 16 ++ 6 files changed, 123 insertions(+), 169 deletions(-) delete mode 100644 doc/source/tech_note/Decomposition/CLM4_vertsoil_soilstruct_drawing.png create mode 100644 doc/source/tech_note/Decomposition/CLM6_decomp_image.png create mode 100644 doc/source/tech_note/Decomposition/MIMICS_Wiring_BW.png delete mode 100644 doc/source/tech_note/Decomposition/soil_C_pools_CN_century.png diff --git a/doc/source/tech_note/Decomposition/CLM4_vertsoil_soilstruct_drawing.png b/doc/source/tech_note/Decomposition/CLM4_vertsoil_soilstruct_drawing.png deleted file mode 100644 index 5bbd835f60..0000000000 --- a/doc/source/tech_note/Decomposition/CLM4_vertsoil_soilstruct_drawing.png +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:60e79931915921514486ee7c42f7944b05ec7f3c86885bb9aedc55c0c70732a6 -size 141651 diff --git a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst index bf6d52ee45..fa78d18ea9 100644 --- a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst +++ b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst @@ -3,119 +3,21 @@ Decomposition ================= -Decomposition of fresh litter material into progressively more recalcitrant forms of soil organic matter is represented in CLM is defined as a cascade of :math:`{k}_{tras}` transformations between :math:`{m}_{pool}` decomposing coarse woody debris (CWD), litter, and soil organic matter (SOM) pools, each defined at :math:`{n}_{lev}` vertical levels. CLM allows the user to define, at compile time, between 2 contrasting hypotheses of decomposition as embodied by two separate decomposition submodels: the CLM-CN pool structure used in CLM4.0, or a second pool structure, characterized by slower decomposition rates, based on the fCentury model (Parton et al 1988). In addition, the user can choose, at compile time, whether to allow :math:`{n}_{lev}` to equal 1, as in CLM4.0, or to equal the number of soil levels used for the soil hydrological and thermal calculations (see Section :numref:`Soil Layers` for soil layering). +Decomposition of fresh litter material into progressively longer turnover pools of soil organic matter is represented in CLM as a cascade of transformations between decomposing coarse woody debris (CWD), litter, and soil organic matter (SOM) pools, each defined at :math:`{n}_{lev}` vertical levels. The default soil submodel in CLM6 is comparable to the Century model (Parton et al 1988). -.. _Figure Schematic of decomposition model in CLM: -.. figure:: CLM4_vertsoil_soilstruct_drawing.png - - Schematic of decomposition model in CLM. - -Model is structured to allow different representations of the soil C and N decomposition cascade, as well as a vertically-explicit treatment of soil biogeochemistry. - -For the single-level model structure, the fundamental equation for carbon balance of the decomposing pools is: - -.. math:: - :label: 21.1) - - \frac{\partial C_{i} }{\partial t} =R_{i} +\sum _{j\ne i}\left(i-r_{j} \right)T_{ji} k_{j} C_{j} -k_{i} C_{i} - -where :math:`{C}_{i}` is the carbon content of pool *i*, :math:`{R}_{i}` are the carbon inputs from plant tissues directly to pool *i* (only non-zero for CWD and litter pools), :math:`{k}_{i}` is the decay constant of pool *i*; :math:`{T}_{ji}` is the fraction of carbon directed from pool *j* to pool *i* with fraction :math:`{r}_{j}` lost as a respiration flux along the way. - -Adding the vertical dimension to the decomposing pools changes the balance equation to the following: - -.. math:: - :label: 21.2) - - \begin{array}{l} {\frac{\partial C_{i} (z)}{\partial t} =R_{i} (z)+\sum _{i\ne j}\left(1-r_{j} \right)T_{ji} k_{j} (z)C_{j} (z) -k_{i} (z)C_{i} (z)} \\ {+\frac{\partial }{\partial z} \left(D(z)\frac{\partial C_{i} }{\partial z} \right)+\frac{\partial }{\partial z} \left(A(z)C_{i} \right)} \end{array} - -where :math:`{C}_{i}`\ (z) is now defined at each model level, and in volumetric (gC m\ :sup:`-3`) rather than areal (gC m\ :sup:`-2`) units, along with :math:`{R}_{i}`\ (z) and :math:`{k}_{j}`\ (z). In addition, vertical transport is handled by the last two terms, for diffusive and advective transport. In the base model, advective transport is set to zero, leaving only a diffusive flux with diffusivity *D(z)* defined for all decomposing carbon and nitrogen pools. Further discussion of the vertical distribution of carbon inputs :math:`{R}_{i}`\ (z), vertical turnover times :math:`{k}_{j}`\ (z), and vertical transport *D(z)* is below Discussion of the vertical model and analysis of both decomposition structures is in :ref:`Koven et al. (2013) `. - -.. _Figure Pool structure: - -.. figure:: soil_C_pools_CN_century.png - - Pool structure, transitions, respired fractions (numbers at - end of arrows), and turnover times (numbers in boxes) for the 2 - alternate soil decomposition models included in CLM. - -CLM-CN Pool Structure, Rate Constants and Parameters ---------------------------------------------------------- - -The CLM-CN structure in CLM45 uses three state variables for fresh litter and four state variables for soil organic matter (SOM). The masses of carbon and nitrogen in the live microbial community are not modeled explicitly, but the activity of these organisms is represented by decomposition fluxes transferring mass between the litter and SOM pools, and heterotrophic respiration losses associated with these transformations. The litter and SOM pools in CLM-CN are arranged as a converging cascade (Figure 15.2), derived directly from the implementation in Biome-BGC v4.1.2 (Thornton et al. 2002; Thornton and Rosenbloom, 2005). - -Model parameters are estimated based on a synthesis of microcosm decomposition studies using radio-labeled substrates (Degens and Sparling, 1996; Ladd et al. 1992; Martin et al. 1980; Mary et al. 1993 Saggar et al. 1994; Sørensen, 1981; van Veen et al. 1984). Multiple exponential models are fitted to data from the microcosm studies to estimate exponential decay rates and respiration fractions (Thornton, 1998). The microcosm experiments used for parameterization were all conducted at constant temperature and under moist conditions with relatively high mineral nitrogen concentrations, and so the resulting rate constants are assumed not limited by the availability of water or mineral nitrogen. :numref:`Table Decomposition rate constants` lists the base decomposition rates for each litter and SOM pool, as well as a base rate for physical fragmentation for the coarse woody debris pool (CWD). - -.. _Table Decomposition rate constants: - -.. table:: Decomposition rate constants for litter and SOM pools, C:N ratios, and acceleration parameters for the CLM-CN decomposition pool structure. - - +--------------------------+------------------------------------------------+-----------------------------------------------+---------------+-----------------------------------------+ - | | Biome-BGC | CLM-CN | | | - +==========================+================================================+===============================================+===============+=========================================+ - | | :math:`{k}_{disc1}`\ (d\ :sup:`-1`) | :math:`{k}_{disc2}` (hr\ :sup:`-1`) | *C:N ratio* | Acceleration term (:math:`{a}_{i}`) | - +--------------------------+------------------------------------------------+-----------------------------------------------+---------------+-----------------------------------------+ - | :math:`{k}_{Lit1}` | 0.7 | 0.04892 | - | 1 | - +--------------------------+------------------------------------------------+-----------------------------------------------+---------------+-----------------------------------------+ - | :math:`{k}_{Lit2}` | 0.07 | 0.00302 | - | 1 | - +--------------------------+------------------------------------------------+-----------------------------------------------+---------------+-----------------------------------------+ - | :math:`{k}_{Lit3}` | 0.014 | 0.00059 | - | 1 | - +--------------------------+------------------------------------------------+-----------------------------------------------+---------------+-----------------------------------------+ - | :math:`{k}_{SOM1}` | 0.07 | 0.00302 | 12 | 1 | - +--------------------------+------------------------------------------------+-----------------------------------------------+---------------+-----------------------------------------+ - | :math:`{k}_{SOM2}` | 0.014 | 0.00059 | 12 | 1 | - +--------------------------+------------------------------------------------+-----------------------------------------------+---------------+-----------------------------------------+ - | :math:`{k}_{SOM3}` | 0.0014 | 0.00006 | 10 | 5 | - +--------------------------+------------------------------------------------+-----------------------------------------------+---------------+-----------------------------------------+ - | :math:`{k}_{SOM4}` | 0.0001 | 0.000004 | 10 | 70 | - +--------------------------+------------------------------------------------+-----------------------------------------------+---------------+-----------------------------------------+ - | :math:`{k}_{CWD}` | 0.001 | 0.00004 | - | 1 | - +--------------------------+------------------------------------------------+-----------------------------------------------+---------------+-----------------------------------------+ - -The first column of :numref:`Table Decomposition rate constants` gives the rates as used for the Biome-BGC model, which uses a discrete-time model with a daily timestep. The second column of :numref:`Table Decomposition rate constants` shows the rates transformed for a one-hour discrete timestep typical of CLM-CN. The transformation is based on the conversion of the initial discrete-time value (:math:`{k}_{disc1}` first to a continuous time value (:math:`{k}_{cont}`), then to the new discrete-time value with a different timestep (:math:`{k}_{disc2}`), following Olson (1963): - -.. math:: - :label: ZEqnNum608251 - - k_{cont} =-\log \left(1-k_{disc1} \right) - -.. math:: - :label: ZEqnNum772630 - - k_{disc2} =1-\exp \left(-k_{cont} \frac{\Delta t_{2} }{\Delta t_{1} } \right) - -where :math:`\Delta`\ :math:`{t}_{1}` (s) and :math:`\Delta`\ t\ :sub:`2` (s) are the time steps of the initial and new discrete-time models, respectively. +Century-based Pool Structure, Rate Constants and Parameters +---------------------------------------------------------------- -Respiration fractions are parameterized for decomposition fluxes out of each litter and SOM pool. The respiration fraction (*rf*, unitless) is the fraction of the decomposition carbon flux leaving one of the litter or SOM pools that is released as CO\ :sub:`2` due to heterotrophic respiration. Respiration fractions and exponential decay rates are estimated simultaneously from the results of microcosm decomposition experiments (Thornton, 1998). The same values are used in CLM-CN and Biome-BGC (:numref:`Table Respiration fractions for litter and SOM pools`). +The Century-based decomposition cascade is a first-order decay model. It includes a CWD pool, 3 litter pools, and 3 soil organic matter pools. Pools each have a turnover time and are connected to a number of different pools, as seen in Figure 2.22.1. Soil pools also each have a fixed C:N ratio. Each flux between pools has a respiration fraction that determines the proportion of carbon lost during the flux. -.. _Table Respiration fractions for litter and SOM pools: +.. _Figure Century-based soil model structure: -.. table:: Respiration fractions for litter and SOM pools +.. Figure:: CLM6_decomp_image.png - +---------------------------+-----------------------+ - | Pool | *rf* | - +===========================+=======================+ - | :math:`{rf}_{Lit1}` | 0.39 | - +---------------------------+-----------------------+ - | :math:`{rf}_{Lit2}` | 0.55 | - +---------------------------+-----------------------+ - | :math:`{rf}_{Lit3}` | 0.29 | - +---------------------------+-----------------------+ - | :math:`{rf}_{SOM1}` | 0.28 | - +---------------------------+-----------------------+ - | :math:`{rf}_{SOM2}` | 0.46 | - +---------------------------+-----------------------+ - | :math:`{rf}_{SOM3}` | 0.55 | - +---------------------------+-----------------------+ - | :math:`{rf}_{SOM4}` | :math:`{1.0}^{a}` | - +---------------------------+-----------------------+ + Pool structure, transitions, respired fractions (numbers at end of arrows), and turnover times (numbers in boxes) for the default, Century-based soil model in CLM. -:sup:`a`:math:`{}^{a}` The respiration fraction for pool SOM4 is 1.0 by definition: since there is no pool downstream of SOM4, the entire carbon flux leaving this pool is assumed to be respired as CO\ :sub:`2`. - -Century-based Pool Structure, Rate Constants and Parameters ----------------------------------------------------------------- - -The Century-based decomposition cascade is, like CLM-CN, a first-order decay model; the two structures differ in the number of pools, the connections between those pools, the turnover times of the pools, and the respired fraction during each transition (Figure 15.2). The turnover times are different for the Century-based pool structure, following those described in Parton et al. (1988) (:numref:`Table Turnover times`). +The turnover times for the Century-based pool structure follow those described in Parton et al. (1988) (Table 2.22.1). .. _Table Turnover times: @@ -164,7 +66,7 @@ Likewise, values for the respiration fraction of Century-based structure are in Environmental modifiers on decomposition rate -------------------------------------------------- -These base rates are modified on each timestep by functions of the current soil environment. For the single-level model, there are two rate modifiers, temperature (:math:`{r}_{tsoil}`, unitless) and moisture (:math:`{r}_{water}`, unitless), both of which are calculated using the average environmental conditions of the top five model levels (top 29 cm of soil column). For the vertically-resolved model, two additional environmental modifiers are calculated beyond the temperature and moisture limitations: an oxygen scalar (:math:`{r}_{oxygen}`, unitless), and a depth scalar (:math:`{r}_{depth}`, unitless). +These base rates are modified on each timestep by functions of the current soil environment. There are four rate modifiers: temperature (:math:`{r}_{tsoil}`, unitless), moisture (:math:`{r}_{water}`, unitless), an oxygen scalar (:math:`{r}_{oxygen}`, unitless), and a depth scalar (:math:`{r}_{depth}`, unitless). The Temperature scalar :math:`{r}_{tsoil}` is calculated in CLM using a :math:`{Q}_{10}` approach, with :math:`{Q}_{10} = 1.5`. @@ -182,7 +84,7 @@ The rate scalar for soil water potential (:math:`{r}_{water}`, unitless) is calc r_{water} =\sum _{j=1}^{5}\left\{\begin{array}{l} {0\qquad {\rm for\; }\Psi _{j} <\Psi _{\min } } \\ {\frac{\log \left({\Psi _{\min } \mathord{\left/ {\vphantom {\Psi _{\min } \Psi _{j} }} \right.} \Psi _{j} } \right)}{\log \left({\Psi _{\min } \mathord{\left/ {\vphantom {\Psi _{\min } \Psi _{\max } }} \right.} \Psi _{\max } } \right)} w_{soil,\, j} \qquad {\rm for\; }\Psi _{\min } \le \Psi _{j} \le \Psi _{\max } } \\ {1\qquad {\rm for\; }\Psi _{j} >\Psi _{\max } \qquad \qquad } \end{array}\right\} -where :math:`{\Psi}_{j}` is the soil water potential in layer *j*, :math:`{\Psi}_{min}` is a lower limit for soil water potential control on decomposition rate (in CLM5, this was changed from a default value of -10 MPa used in CLM4.5 and earlier to a default value of -2.5 MPa). :math:`{\Psi}_{max,j}` (MPa) is the soil moisture at which decomposition proceeds at a moisture-unlimited rate. The default value of :math:`{\Psi}_{max,j}` for CLM5 is updated from a saturated value used in CLM4.5 and earlier, to a value nominally at field capacity, with a value of -0.002 MPa For frozen soils, the bulk of the rapid dropoff in decomposition with decreasing temperature is due to the moisture limitation, since matric potential is limited by temperature in the supercooled water formulation of Niu and Yang (2006), +where :math:`{\Psi}_{j}` is the soil water potential in layer *j*, :math:`{\Psi}_{min}` is a lower limit for soil water potential control on decomposition rate. :math:`{\Psi}_{max,j}` (MPa) is the soil moisture at which decomposition proceeds at a moisture-unlimited rate. The default value of :math:`{\Psi}_{max,j}` for CLM6 is -0.002 MPa, nominally at field capacity. For frozen soils, the bulk of the rapid dropoff in decomposition with decreasing temperature is due to the moisture limitation, since matric potential is limited by temperature in the supercooled water formulation of Niu and Yang (2006), .. math:: :label: 21.8) @@ -191,16 +93,16 @@ where :math:`{\Psi}_{j}` is the soil water potential in layer *j*, :math:`{\Psi} An additional frozen decomposition limitation can be specified using a ‘frozen Q\ :sub:`10`' following :ref:`Koven et al. (2011) `, however the default value of this is the same as the unfrozen Q\ :sub:`10` value, and therefore the basic hypothesis is that frozen respiration is limited by liquid water availability, and can be modeled following the same approach as thawed but dry soils. -An additional rate scalar, :math:`{r}_{oxygen}` is enabled when the CH\ :sub:`4` submodel is used (set equal to 1 for the single layer model or when the CH\ :sub:`4` submodel is disabled). This limits decomposition when there is insufficient molecular oxygen to satisfy stoichiometric demand (1 mol O\ :sub:`2` consumed per mol CO\ :sub:`2` produced) from heterotrophic decomposers, and supply from diffusion through soil layers (unsaturated and saturated) or aerenchyma (Chapter 19). A minimum value of :math:`{r}_{oxygen}` is set at 0.2, with the assumption that oxygen within organic tissues can supply the necessary stoichiometric demand at this rate. This value lies between estimates of 0.025–0.1 (Frolking et al. 2001), and 0.35 (Wania et al. 2009); the large range of these estimates poses a large unresolved uncertainty. +An additional rate scalar, :math:`{r}_{oxygen}` is enabled when the CH\ :sub:`4` submodel is used. This limits decomposition when there is insufficient molecular oxygen to satisfy stoichiometric demand (1 mol O\ :sub:`2` consumed per mol CO\ :sub:`2` produced) from heterotrophic decomposers, and supply from diffusion through soil layers (unsaturated and saturated) or aerenchyma (Chapter 19). A minimum value of :math:`{r}_{oxygen}` is set at 0.2, with the assumption that oxygen within organic tissues can supply the necessary stoichiometric demand at this rate. This value lies between estimates of 0.025–0.1 (Frolking et al. 2001), and 0.35 (Wania et al. 2009); the large range of these estimates poses a large unresolved uncertainty. -Lastly, a possible explicit depth dependence, :math:`{r}_{depth}`, (set equal to 1 for the single layer model) can be applied to soil C decomposition rates to account for processes other than temperature, moisture, and anoxia that can limit decomposition. This depth dependence of decomposition was shown by Jenkinson and Coleman (2008) to be an important term in fitting total C and 14C profiles, and implies that unresolved processes, such as priming effects, microscale anoxia, soil mineral surface and/or aggregate stabilization may be important in controlling the fate of carbon at depth :ref:`Koven et al. (2013) `. CLM includes these unresolved depth controls via an exponential decrease in the soil turnover time with depth: +Lastly, a possible explicit depth dependence, :math:`{r}_{depth}`, can be applied to soil C decomposition rates to account for processes other than temperature, moisture, and anoxia that can limit decomposition. This depth dependence of decomposition was shown by Jenkinson and Coleman (2008) to be an important term in fitting total C and 14C profiles, and implies that unresolved processes, such as priming effects, microscale anoxia, soil mineral surface and/or aggregate stabilization may be important in controlling the fate of carbon at depth :ref:`Koven et al. (2013) `. CLM includes these unresolved depth controls via an exponential decrease in the soil turnover time with depth: .. math:: :label: 21.9) r_{depth} =\exp \left(-\frac{z}{z_{\tau } } \right) -where :math:`{z}_{\tau}` is the e-folding depth for decomposition. For CLM4.5, the default value of this was 0.5m. For CLM5, this has been changed to a default value of 10m, which effectively means that intrinsic decomposition rates may proceed as quickly at depth as at the surface. +where :math:`{z}_{\tau}` is the e-folding depth for decomposition. For CLM6, the e-folding depth is 10m, which effectively means that intrinsic decomposition rates may proceed as quickly at depth as at the surface. The combined decomposition rate scalar (:math:`{r}_{total}`,unitless) is: @@ -257,7 +159,7 @@ where :math:`{CS}_{u}` (gC m\ :sup:`-2`) is the initial mass in the upstream poo where :math:`{rf}_{u}` is the respiration fraction for fluxes leaving the upstream pool, :math:`{CN}_{u}` and :math:`{CN}_{d}` are the C:N ratios for upstream and downstream pools, respectively Negative values of :math:`{NF}_{pot\_min,u}`\ :math:`{}_{\rightarrow}`\ :math:`{}_{d}` indicate that the decomposition flux results in a source of new mineral nitrogen, while positive values indicate that the potential decomposition flux results in a sink (demand) for mineral nitrogen. -Following from the general case, potential carbon fluxes leaving individual pools in the decomposition cascade, for the example of the CLM-CN pool structure, are given as: +Following from the general case, potential carbon fluxes leaving individual pools in the decomposition cascade are given as: .. math:: :label: 21.13) @@ -289,51 +191,49 @@ Following from the general case, potential carbon fluxes leaving individual pool CF_{pot,\, SOM3} ={CS_{SOM3} k_{SOM3} r_{total} \mathord{\left/ {\vphantom {CS_{SOM3} k_{SOM3} r_{total} \Delta t}} \right.} \Delta t} +where the factor (1/:math:`\Delta`\ *t*) is included because the rate constant is calculated for the entire timestep (Eqs. and ), but the convention is to express all fluxes on a per-second basis. Potential mineral nitrogen fluxes associated with these decomposition steps are: + .. math:: :label: 21.19) - CF_{pot,\, SOM4} ={CS_{SOM4} k_{SOM4} r_{total} \mathord{\left/ {\vphantom {CS_{SOM4} k_{SOM4} r_{total} \Delta t}} \right.} \Delta t} - -where the factor (1/:math:`\Delta`\ *t*) is included because the rate constant is calculated for the entire timestep (Eqs. and ), but the convention is to express all fluxes on a per-second basis. Potential mineral nitrogen fluxes associated with these decomposition steps are, again for the example of the CLM-CN pool structure (the CENTURY structure will be similar but without the different terminal step): + NF_{pot\_ min,\, Lit1\to SOM1} ={CF_{pot,\, Lit1} \left(1-rf_{Lit1} -\frac{CN_{SOM1} }{CN_{Lit1} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit1} \left(1-rf_{Lit1} -\frac{CN_{SOM1} }{CN_{Lit1} } \right) CN_{SOM1} }} \right.} CN_{SOM1} } .. math:: - :label: ZEqnNum934998 + :label: 21.20) - NF_{pot\_ min,\, Lit1\to SOM1} ={CF_{pot,\, Lit1} \left(1-rf_{Lit1} -\frac{CN_{SOM1} }{CN_{Lit1} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit1} \left(1-rf_{Lit1} -\frac{CN_{SOM1} }{CN_{Lit1} } \right) CN_{SOM1} }} \right.} CN_{SOM1} } + NF_{pot\_ min,\, Lit2\to SOM1} ={CF_{pot,\, Lit2} \left(1-rf_{Lit2} -\frac{CN_{SOM1} }{CN_{Lit2} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit2} \left(1-rf_{Lit2} -\frac{CN_{SOM1} }{CN_{Lit2} } \right) CN_{SOM1} }} \right.} CN_{SOM1} } .. math:: :label: 21.21) - NF_{pot\_ min,\, Lit2\to SOM2} ={CF_{pot,\, Lit2} \left(1-rf_{Lit2} -\frac{CN_{SOM2} }{CN_{Lit2} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit2} \left(1-rf_{Lit2} -\frac{CN_{SOM2} }{CN_{Lit2} } \right) CN_{SOM2} }} \right.} CN_{SOM2} } + NF_{pot\_ min,\, Lit3\to SOM2} ={CF_{pot,\, Lit3} \left(1-rf_{Lit3} -\frac{CN_{SOM2} }{CN_{Lit3} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit3} \left(1-rf_{Lit3} -\frac{CN_{SOM2} }{CN_{Lit3} } \right) CN_{SOM2} }} \right.} CN_{SOM2} } .. math:: :label: 21.22) - NF_{pot\_ min,\, Lit3\to SOM3} ={CF_{pot,\, Lit3} \left(1-rf_{Lit3} -\frac{CN_{SOM3} }{CN_{Lit3} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit3} \left(1-rf_{Lit3} -\frac{CN_{SOM3} }{CN_{Lit3} } \right) CN_{SOM3} }} \right.} CN_{SOM3} } + NF_{pot\_ min,\, SOM1\to SOM2} ={CF_{pot,\, SOM1} \left(1-rf_{SOM1} -\frac{CN_{SOM2} }{CN_{SOM1} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM1} \left(1-rf_{SOM1} -\frac{CN_{SOM2} }{CN_{SOM1} } \right) CN_{SOM2} }} \right.} CN_{SOM2} } .. math:: :label: 21.23) - NF_{pot\_ min,\, SOM1\to SOM2} ={CF_{pot,\, SOM1} \left(1-rf_{SOM1} -\frac{CN_{SOM2} }{CN_{SOM1} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM1} \left(1-rf_{SOM1} -\frac{CN_{SOM2} }{CN_{SOM1} } \right) CN_{SOM2} }} \right.} CN_{SOM2} } + NF_{pot\_ min,\, SOM2\to SOM3} ={CF_{pot,\, SOM2} \left(1-rf_{SOM2} -\frac{CN_{SOM3} }{CN_{SOM2} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM2} \left(1-rf_{SOM2} -\frac{CN_{SOM3} }{CN_{SOM2} } \right) CN_{SOM3} }} \right.} CN_{SOM3} } .. math:: :label: 21.24) - NF_{pot\_ min,\, SOM2\to SOM3} ={CF_{pot,\, SOM2} \left(1-rf_{SOM2} -\frac{CN_{SOM3} }{CN_{SOM2} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM2} \left(1-rf_{SOM2} -\frac{CN_{SOM3} }{CN_{SOM2} } \right) CN_{SOM3} }} \right.} CN_{SOM3} } + NF_{pot\_ min,\, SOM1\to SOM3} ={CF_{pot,\, SOM1} \left(1-rf_{SOM1} -\frac{CN_{SOM3} }{CN_{SOM1} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM3} \left(1-rf_{SOM1} -\frac{CN_{SOM3} }{CN_{SOM1} } \right) CN_{SOM3} }} \right.} CN_{SOM3} } .. math:: :label: 21.25) - NF_{pot\_ min,\, SOM3\to SOM4} ={CF_{pot,\, SOM3} \left(1-rf_{SOM3} -\frac{CN_{SOM4} }{CN_{SOM3} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM3} \left(1-rf_{SOM3} -\frac{CN_{SOM4} }{CN_{SOM3} } \right) CN_{SOM4} }} \right.} CN_{SOM4} } + NF_{pot\_ min,\, SOM2\to SOM1} ={CF_{pot,\, SOM2} \left(1-rf_{SOM2} -\frac{CN_{SOM1} }{CN_{SOM2} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM1} \left(1-rf_{SOM2} -\frac{CN_{SOM1} }{CN_{SOM2} } \right) CN_{SOM1} }} \right.} CN_{SOM1} } .. math:: - :label: ZEqnNum473594 + :label: 21.26) - NF_{pot\_ min,\, SOM4} =-{CF_{pot,\, SOM4} \mathord{\left/ {\vphantom {CF_{pot,\, SOM4} CN_{SOM4} }} \right.} CN_{SOM4} } + NF_{pot\_ min,\, SOM3\to SOM1} ={CF_{pot,\, SOM3} \left(1-rf_{SOM3} -\frac{CN_{SOM1} }{CN_{SOM3} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM1} \left(1-rf_{SOM3} -\frac{CN_{SOM1} }{CN_{SOM3} } \right) CN_{SOM1} }} \right.} CN_{SOM1} } -where the special form of Eq. arises because there is no SOM pool downstream of SOM4 in the converging cascade: all carbon fluxes leaving that pool are assumed to be in the form of respired CO\ :sub:`2`, and all nitrogen fluxes leaving that pool are assumed to be sources of new mineral nitrogen. - -Steps in the decomposition cascade that result in release of new mineral nitrogen (mineralization fluxes) are allowed to proceed at their potential rates, without modification for nitrogen availability. Steps that result in an uptake of mineral nitrogen (immobilization fluxes) are subject to rate limitation, depending on the availability of mineral nitrogen, the total immobilization demand, and the total demand for soil mineral nitrogen to support new plant growth. The potential mineral nitrogen fluxes from Eqs. - are evaluated, summing all the positive fluxes to generate the total potential nitrogen immobilization flux (:math:`{NF}_{immob\_demand}`, gN m\ :sup:`-2` s\ :sup:`-1`), and summing absolute values of all the negative fluxes to generate the total nitrogen mineralization flux (:math:`{NF}_{gross\_nmin}`, gN m\ :sup:`-2` s\ :sup:`-1`). Since :math:`{NF}_{griss\_nmin}` is a source of new mineral nitrogen to the soil mineral nitrogen pool it is not limited by the availability of soil mineral nitrogen, and is therefore an actual as opposed to a potential flux. +Steps in the decomposition cascade that result in release of new mineral nitrogen (mineralization fluxes) are allowed to proceed at their potential rates, without modification for nitrogen availability. Steps that result in an uptake of mineral nitrogen (immobilization fluxes) are subject to rate limitation, depending on the availability of mineral nitrogen, the total immobilization demand, and the total demand for soil mineral nitrogen to support new plant growth. The potential mineral nitrogen fluxes from Eqs. 2.21.19-2.21.26 are evaluated, summing all the positive fluxes to generate the total potential nitrogen immobilization flux (:math:`{NF}_{immob\_demand}`, gN m\ :sup:`-2` s\ :sup:`-1`), and summing absolute values of all the negative fluxes to generate the total nitrogen mineralization flux (:math:`{NF}_{gross\_nmin}`, gN m\ :sup:`-2` s\ :sup:`-1`). Since :math:`{NF}_{gross\_nmin}` is a source of new mineral nitrogen to the soil mineral nitrogen pool it is not limited by the availability of soil mineral nitrogen, and is therefore an actual as opposed to a potential flux. N Competition between plant uptake and soil immobilization fluxes ---------------------------------------------------------------------- @@ -375,7 +275,7 @@ If :math:`{NF}_{total\_demand,j} \Delta t \mathrm{\ge} {NS}_{sminn,j}`, then the The N available to the FUN model for plant uptake (:math:`{NF}_ {plant\_ avail\_ sminn}` (gN m\ :sup:`-2`), which determines both the cost of N uptake, and the absolute limit on the N which is available for acquisition, is calculated as the total mineralized pool minus the actual immobilized flux: .. math:: - :label: 21.311) + :label: 21.31) NF_{plant\_ avail\_ sminn,j} = NS_{sminn,j} - f_{immob\_demand} NF_{immob\_ demand,j} @@ -384,7 +284,7 @@ This treatment of competition for nitrogen as a limiting resource is referred to Final Decomposition Fluxes ------------------------------- -With :math:`{f}_{immob\_demand}` known, final decomposition fluxes can be calculated. Actual carbon fluxes leaving the individual litter and SOM pools, again for the example of the CLM-CN pool structure (the CENTURY structure will be similar but, again without the different terminal step), are calculated as: +With :math:`{f}_{immob\_demand}` known, final decomposition fluxes can be calculated. Actual carbon fluxes leaving the individual litter and SOM pools are calculated as: .. math:: :label: 21.32) @@ -394,12 +294,12 @@ With :math:`{f}_{immob\_demand}` known, final decomposition fluxes can be calcul .. math:: :label: 21.33) - CF_{Lit2} =\left\{\begin{array}{l} {CF_{pot,\, Lit2} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit2\to SOM2} >0} \\ {CF_{pot,\, Lit2} \qquad {\rm for\; }NF_{pot\_ min,\, Lit2\to SOM2} \le 0} \end{array}\right\} + CF_{Lit2} =\left\{\begin{array}{l} {CF_{pot,\, Lit2} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit2\to SOM1} >0} \\ {CF_{pot,\, Lit2} \qquad {\rm for\; }NF_{pot\_ min,\, Lit2\to SOM1} \le 0} \end{array}\right\} .. math:: :label: 21.34) - CF_{Lit3} =\left\{\begin{array}{l} {CF_{pot,\, Lit3} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit3\to SOM3} >0} \\ {CF_{pot,\, Lit3} \qquad {\rm for\; }NF_{pot\_ min,\, Lit3\to SOM3} \le 0} \end{array}\right\} + CF_{Lit3} =\left\{\begin{array}{l} {CF_{pot,\, Lit3} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit3\to SOM2} >0} \\ {CF_{pot,\, Lit3} \qquad {\rm for\; }NF_{pot\_ min,\, Lit3\to SOM2} \le 0} \end{array}\right\} .. math:: :label: 21.35) @@ -414,49 +314,49 @@ With :math:`{f}_{immob\_demand}` known, final decomposition fluxes can be calcul .. math:: :label: 21.37) - CF_{SOM3} =\left\{\begin{array}{l} {CF_{pot,\, SOM3} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM3\to SOM4} >0} \\ {CF_{pot,\, SOM3} \qquad {\rm for\; }NF_{pot\_ min,\, SOM3\to SOM4} \le 0} \end{array}\right\} + CF_{SOM1} =\left\{\begin{array}{l} {CF_{pot,\, SOM1} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM1\to SOM3} >0} \\ {CF_{pot,\, SOM1} \qquad {\rm for\; }NF_{pot\_ min,\, SOM1\to SOM3} \le 0} \end{array}\right\} .. math:: :label: 21.38) - CF_{SOM4} =CF_{pot,\, SOM4} - -Heterotrophic respiration fluxes (losses of carbon as CO\ :sub:`2` to the atmosphere) are: + CF_{SOM2} =\left\{\begin{array}{l} {CF_{pot,\, SOM2} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM2\to SOM1} >0} \\ {CF_{pot,\, SOM2} \qquad {\rm for\; }NF_{pot\_ min,\, SOM2\to SOM1} \le 0} \end{array}\right\} .. math:: :label: 21.39) - CF_{Lit1,\, HR} =CF_{Lit1} rf_{Lit1} + CF_{SOM3} =\left\{\begin{array}{l} {CF_{pot,\, SOM3} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM3\to SOM1} >0} \\ {CF_{pot,\, SOM3} \qquad {\rm for\; }NF_{pot\_ min,\, SOM3\to SOM1} \le 0} \end{array}\right\} + +Heterotrophic respiration fluxes (losses of carbon as CO\ :sub:`2` to the atmosphere) are: .. math:: :label: 21.40) - CF_{Lit2,\, HR} =CF_{Lit2} rf_{Lit2} + CF_{Lit1,\, HR} =CF_{Lit1} rf_{Lit1} .. math:: :label: 21.41) - CF_{Lit3,\, HR} =CF_{Lit3} rf_{Lit3} + CF_{Lit2,\, HR} =CF_{Lit2} rf_{Lit2} .. math:: :label: 21.42) - CF_{SOM1,\, HR} =CF_{SOM1} rf_{SOM1} + CF_{Lit3,\, HR} =CF_{Lit3} rf_{Lit3} .. math:: :label: 21.43) - CF_{SOM2,\, HR} =CF_{SOM2} rf_{SOM2} + CF_{SOM1,\, HR} =CF_{SOM1} rf_{SOM1} .. math:: :label: 21.44) - CF_{SOM3,\, HR} =CF_{SOM3} rf_{SOM3} + CF_{SOM2,\, HR} =CF_{SOM2} rf_{SOM2} .. math:: :label: 21.45) - CF_{SOM4,\, HR} =CF_{SOM4} rf_{SOM4} + CF_{SOM3,\, HR} =CF_{SOM3} rf_{SOM3} Transfers of carbon from upstream to downstream pools in the decomposition cascade are given as: @@ -468,12 +368,12 @@ Transfers of carbon from upstream to downstream pools in the decomposition casca .. math:: :label: 21.47) - CF_{Lit2,\, SOM2} =CF_{Lit2} \left(1-rf_{Lit2} \right) + CF_{Lit2,\, SOM1} =CF_{Lit2} \left(1-rf_{Lit2} \right) .. math:: :label: 21.48) - CF_{Lit3,\, SOM3} =CF_{Lit3} \left(1-rf_{Lit3} \right) + CF_{Lit3,\, SOM2} =CF_{Lit3} \left(1-rf_{Lit3} \right) .. math:: :label: 21.49) @@ -488,76 +388,101 @@ Transfers of carbon from upstream to downstream pools in the decomposition casca .. math:: :label: 21.51) - CF_{SOM3,\, SOM4} =CF_{SOM3} \left(1-rf_{SOM3} \right) - -In accounting for the fluxes of nitrogen between pools in the decomposition cascade and associated fluxes to or from the soil mineral nitrogen pool, the model first calculates a flux of nitrogen from an upstream pool to a downstream pool, then calculates a flux either from the soil mineral nitrogen pool to the downstream pool (immobilization or from the downstream pool to the soil mineral nitrogen pool (mineralization). Transfers of nitrogen from upstream to downstream pools in the decomposition cascade are given as: + CF_{SOM1,\, SOM3} =CF_{SOM1} \left(1-rf_{SOM1} \right) .. math:: :label: 21.52) - NF_{Lit1,\, SOM1} ={CF_{Lit1} \mathord{\left/ {\vphantom {CF_{Lit1} CN_{Lit1} }} \right.} CN_{Lit1} } + CF_{SOM2,\, SOM1} =CF_{SOM2} \left(1-rf_{SOM2} \right) .. math:: :label: 21.53) - NF_{Lit2,\, SOM2} ={CF_{Lit2} \mathord{\left/ {\vphantom {CF_{Lit2} CN_{Lit2} }} \right.} CN_{Lit2} } + CF_{SOM3,\, SOM1} =CF_{SOM3} \left(1-rf_{SOM3} \right) + +In accounting for the fluxes of nitrogen between pools in the decomposition cascade and associated fluxes to or from the soil mineral nitrogen pool, the model first calculates a flux of nitrogen from an upstream pool to a downstream pool, then calculates a flux either from the soil mineral nitrogen pool to the downstream pool (immobilization or from the downstream pool to the soil mineral nitrogen pool (mineralization). Transfers of nitrogen from upstream to downstream pools in the decomposition cascade are given as: .. math:: :label: 21.54) - NF_{Lit3,\, SOM3} ={CF_{Lit3} \mathord{\left/ {\vphantom {CF_{Lit3} CN_{Lit3} }} \right.} CN_{Lit3} } + NF_{Lit1,\, SOM1} ={CF_{Lit1} \mathord{\left/ {\vphantom {CF_{Lit1} CN_{Lit1} }} \right.} CN_{Lit1} } .. math:: :label: 21.55) - NF_{SOM1,\, SOM2} ={CF_{SOM1} \mathord{\left/ {\vphantom {CF_{SOM1} CN_{SOM1} }} \right.} CN_{SOM1} } + NF_{Lit2,\, SOM1} ={CF_{Lit2} \mathord{\left/ {\vphantom {CF_{Lit2} CN_{Lit2} }} \right.} CN_{Lit2} } .. math:: :label: 21.56) - NF_{SOM2,\, SOM3} ={CF_{SOM2} \mathord{\left/ {\vphantom {CF_{SOM2} CN_{SOM2} }} \right.} CN_{SOM2} } + NF_{Lit3,\, SOM2} ={CF_{Lit3} \mathord{\left/ {\vphantom {CF_{Lit3} CN_{Lit3} }} \right.} CN_{Lit3} } .. math:: :label: 21.57) - NF_{SOM3,\, SOM4} ={CF_{SOM3} \mathord{\left/ {\vphantom {CF_{SOM3} CN_{SOM3} }} \right.} CN_{SOM3} } - -Corresponding fluxes to or from the soil mineral nitrogen pool depend on whether the decomposition step is an immobilization flux or a mineralization flux: + NF_{SOM1,\, SOM2} ={CF_{SOM1} \mathord{\left/ {\vphantom {CF_{SOM1} CN_{SOM1} }} \right.} CN_{SOM1} } .. math:: :label: 21.58) - NF_{sminn,\, Lit1\to SOM1} =\left\{\begin{array}{l} {NF_{pot\_ min,\, Lit1\to SOM1} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit1\to SOM1} >0} \\ {NF_{pot\_ min,\, Lit1\to SOM1} \qquad {\rm for\; }NF_{pot\_ min,\, Lit1\to SOM1} \le 0} \end{array}\right\} + NF_{SOM2,\, SOM3} ={CF_{SOM2} \mathord{\left/ {\vphantom {CF_{SOM2} CN_{SOM2} }} \right.} CN_{SOM2} } .. math:: :label: 21.59) - NF_{sminn,\, Lit2\to SOM2} =\left\{\begin{array}{l} {NF_{pot\_ min,\, Lit2\to SOM2} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit2\to SOM2} >0} \\ {NF_{pot\_ min,\, Lit2\to SOM2} \qquad {\rm for\; }NF_{pot\_ min,\, Lit2\to SOM2} \le 0} \end{array}\right\} + NF_{SOM1,\, SOM3} ={CF_{SOM1} \mathord{\left/ {\vphantom {CF_{SOM1} CN_{SOM1} }} \right.} CN_{SOM1} } .. math:: :label: 21.60) - NF_{sminn,\, Lit3\to SOM3} =\left\{\begin{array}{l} {NF_{pot\_ min,\, Lit3\to SOM3} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit3\to SOM3} >0} \\ {NF_{pot\_ min,\, Lit3\to SOM3} \qquad {\rm for\; }NF_{pot\_ min,\, Lit3\to SOM3} \le 0} \end{array}\right\} + NF_{SOM2,\, SOM1} ={CF_{SOM2} \mathord{\left/ {\vphantom {CF_{SOM2} CN_{SOM2} }} \right.} CN_{SOM2} } .. math:: :label: 21.61) - NF_{sminn,SOM1\to SOM2} =\left\{\begin{array}{l} {NF_{pot\_ min,\, SOM1\to SOM2} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM1\to SOM2} >0} \\ {NF_{pot\_ min,\, SOM1\to SOM2} \qquad {\rm for\; }NF_{pot\_ min,\, SOM1\to SOM2} \le 0} \end{array}\right\} + NF_{SOM3,\, SOM1} ={CF_{SOM3} \mathord{\left/ {\vphantom {CF_{SOM3} CN_{SOM3} }} \right.} CN_{SOM3} } + +Corresponding fluxes to or from the soil mineral nitrogen pool depend on whether the decomposition step is an immobilization flux or a mineralization flux: .. math:: :label: 21.62) - NF_{sminn,SOM2\to SOM3} =\left\{\begin{array}{l} {NF_{pot\_ min,\, SOM2\to SOM3} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM2\to SOM3} >0} \\ {NF_{pot\_ min,\, SOM2\to SOM3} \qquad {\rm for\; }NF_{pot\_ min,\, SOM2\to SOM3} \le 0} \end{array}\right\} + NF_{sminn,\, Lit1\to SOM1} =\left\{\begin{array}{l} {NF_{pot\_ min,\, Lit1\to SOM1} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit1\to SOM1} >0} \\ {NF_{pot\_ min,\, Lit1\to SOM1} \qquad {\rm for\; }NF_{pot\_ min,\, Lit1\to SOM1} \le 0} \end{array}\right\} .. math:: :label: 21.63) - NF_{sminn,SOM3\to SOM4} =\left\{\begin{array}{l} {NF_{pot\_ min,\, SOM3\to SOM4} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM3\to SOM4} >0} \\ {NF_{pot\_ min,\, SOM3\to SOM4} \qquad {\rm for\; }NF_{pot\_ min,\, SOM3\to SOM4} \le 0} \end{array}\right\} + NF_{sminn,\, Lit2\to SOM1} =\left\{\begin{array}{l} {NF_{pot\_ min,\, Lit2\to SOM1} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit2\to SOM1} >0} \\ {NF_{pot\_ min,\, Lit2\to SOM1} \qquad {\rm for\; }NF_{pot\_ min,\, Lit2\to SOM1} \le 0} \end{array}\right\} .. math:: :label: 21.64) - NF_{sminn,\, SOM4} =NF_{pot\_ min,\, SOM4} + NF_{sminn,\, Lit3\to SOM2} =\left\{\begin{array}{l} {NF_{pot\_ min,\, Lit3\to SOM2} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit3\to SOM2} >0} \\ {NF_{pot\_ min,\, Lit3\to SOM2} \qquad {\rm for\; }NF_{pot\_ min,\, Lit3\to SOM2} \le 0} \end{array}\right\} + +.. math:: + :label: 21.65) + + NF_{sminn,SOM1\to SOM2} =\left\{\begin{array}{l} {NF_{pot\_ min,\, SOM1\to SOM2} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM1\to SOM2} >0} \\ {NF_{pot\_ min,\, SOM1\to SOM2} \qquad {\rm for\; }NF_{pot\_ min,\, SOM1\to SOM2} \le 0} \end{array}\right\} + +.. math:: + :label: 21.66) + + NF_{sminn,SOM2\to SOM3} =\left\{\begin{array}{l} {NF_{pot\_ min,\, SOM2\to SOM3} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM2\to SOM3} >0} \\ {NF_{pot\_ min,\, SOM2\to SOM3} \qquad {\rm for\; }NF_{pot\_ min,\, SOM2\to SOM3} \le 0} \end{array}\right\} + +.. math:: + :label: 21.67) + + NF_{sminn,SOM1\to SOM3} =\left\{\begin{array}{l} {NF_{pot\_ min,\, SOM1\to SOM3} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM1\to SOM3} >0} \\ {NF_{pot\_ min,\, SOM1\to SOM3} \qquad {\rm for\; }NF_{pot\_ min,\, SOM1\to SOM3} \le 0} \end{array}\right\} + +.. math:: + :label: 21.68) + + NF_{sminn,SOM2\to SOM1} =\left\{\begin{array}{l} {NF_{pot\_ min,\, SOM2\to SOM1} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM2\to SOM1} >0} \\ {NF_{pot\_ min,\, SOM2\to SOM1} \qquad {\rm for\; }NF_{pot\_ min,\, SOM2\to SOM1} \le 0} \end{array}\right\} + +.. math:: + :label: 21.69) + + NF_{sminn,SOM3\to SOM1} =\left\{\begin{array}{l} {NF_{pot\_ min,\, SOM3\to SOM1} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM3\to SOM1} >0} \\ {NF_{pot\_ min,\, SOM3\to SOM1} \qquad {\rm for\; }NF_{pot\_ min,\, SOM3\to SOM1} \le 0} \end{array}\right\} Vertical Distribution and Transport of Decomposing C and N pools --------------------------------------------------------------------- @@ -577,8 +502,21 @@ Because of the coupling between the slowest SOM pools and productivity through N The base acceleration terms for the two decomposition cascades are shown in Tables 15.1 and 15.3. In addition to the base terms, CLM5 also includes a geographic term to the acceleration in order to apply larger values to high-latitude systems, where decomposition rates are particularly slow and thus equilibration can take significantly longer than in temperate or tropical climates. This geographic term takes the form of a logistic equation, where :math:`{a}_{i}` is equal to the product of the base acceleration term and :math:`{a}_{l}` below: .. math:: - :label: 21.65) + :label: 21.70) a_l = 1 + 50 / \left ( 1 + exp \left (-0.1 * (abs(latitude) - 60 ) \right ) \right ) +Alternate soil sub-model: MIMICS +----------------------------------------- +In CLM6, there is a new capability to use the MIcrobial-MIneral Carbon Stabilization (MIMICS) model (:ref:`Wieder et al. 2014 `; :ref:`Wieder et al. 2015b `; :ref:`Kyker-Snowman et al. 2020 `) instead of the Century-like soil model. MIMICS is a microbially-explicit soil biogeochemical model that represents modern understanding about plant and microbial contributions to soil organic matter and mineral stabilization as a protection mechanism for soil organic matter. MIMICS has two litter pools, two microbial pools, and three soil organic matter pools that are connected as in Figure 2.22.9. Details about MIMICS-CN can be found in :ref:`Kyker-Snowman et al. (2020) `. + +.. _Figure MIMICS soil model structure: + +.. Figure:: MIMICS_Wiring_BW.png + + Wiring diagram for MIMICS soil submodel. + +Unlike the Century-like soil model, MIMICS does not use first-order decomposition rates, and as such, has different parameters. MIMICS uses Michaelis-Menten kinetics which are governed by a max decomposition rate (Vmax) and half saturation constant (Km). The carbon flux is further modified by the carbon use efficiency (CUE), which is comparable to the respiration fraction in the default soil submodel. Vmax, Km, and CUE vary for each flux between microbial (MICr, MICk) and substrate pools (LITs, LITm, and SOMa). Both litter and microbial pools can contribute to the physically- and chemically-protected SOM (SOMp and SOMc), with those pools subsequently contributing to the available SOM pool (SOMa), which can be taken up by microbes. Coupling of C and N occurs in the microbial pools in MIMICS, where incoming C and N fluxes are summed and then adjusted by CUE and nitrogen use efficiency (default value = 0.85). If the C:N of the incoming substrates is greater than those of the microbial groups, overflow respiration (and consequently N immobilization) occurs. If the C:N of incoming substrates is less than those of the microbial groups, N mineralization occurs. + +Because MIMICS uses different decomposition than the Century-like model, it requires a longer spin-up time. Currently, MIMICS is being spun up with an Anderson Acceleration method :ref:`(Khatiwala, 2024) `. diff --git a/doc/source/tech_note/Decomposition/CLM6_decomp_image.png b/doc/source/tech_note/Decomposition/CLM6_decomp_image.png new file mode 100644 index 0000000000..b3045d0316 --- /dev/null +++ b/doc/source/tech_note/Decomposition/CLM6_decomp_image.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5d6aaacfee92e2ca50302481a0fb845d8dadf674560ef46180f11145c4bf8297 +size 35362 diff --git a/doc/source/tech_note/Decomposition/MIMICS_Wiring_BW.png b/doc/source/tech_note/Decomposition/MIMICS_Wiring_BW.png new file mode 100644 index 0000000000..62da3c30f5 --- /dev/null +++ b/doc/source/tech_note/Decomposition/MIMICS_Wiring_BW.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4ad019c79f595a1e8f23bd6f5d1200f87ec1a0de6fc61d4811389587b18993ea +size 56418 diff --git a/doc/source/tech_note/Decomposition/soil_C_pools_CN_century.png b/doc/source/tech_note/Decomposition/soil_C_pools_CN_century.png deleted file mode 100644 index abc02ec15a..0000000000 --- a/doc/source/tech_note/Decomposition/soil_C_pools_CN_century.png +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:47635548f549ccf6cd70a57dbcdcdb22d12d306a3aa32b6a708c07baa174ffb8 -size 53905 diff --git a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst index 3aa6be1b71..9ef5457a38 100644 --- a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst +++ b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst @@ -619,6 +619,10 @@ Keller, M., Palace, M., Asner, G.P., Pereira, R., Jr. and Silva, J.N.M., 2004. C Kellner, E., Baird, A.J., Oosterwoud, M., Harrison, K. and Waddington, J.M., 2006. Effect of temperature and atmospheric pressure on methane (CH4) ebullition from near-surface peats. Geophys. Res. Lett. 33. DOI:10.1029/2006GL027509. +.. _Khatiwala2024: + +Khatiwala, S., 2024. Efficient spin-up of Earth System Models using sequence acceleration. Science Advances 10, eadn2839. + .. _Kimballetal1997: Kimball, J.S., Thornton, P.E., White, M.A. and Running, S.W. 1997. Simulating forest productivity and surface-atmosphere exchange in the BOREAS study region. Tree Physiology 17:589-599. @@ -671,6 +675,10 @@ Kucharik, C.J., Foley, J.A., Delire, C., Fisher, V.A., Coe, M.T., Lenters, J.D., Kucharik, C.J., and Brye, K.R. 2003. Integrated BIosphere Simulator (IBIS) yield and nitrate loss predictions for Wisconsin maize receiving varied amounts of nitrogen fertilizer. Journal of Environmental Quality 32: 247–268. +.. _KykerSnowmanetal2020: + +Kyker-Snowman, E., Wieder, W.R., Frey, S.D., Grandy, A.S., 2020. Stoichiometrically coupled carbon and nitrogen cycling in the MIcrobial-MIneral Carbon Stabilization model version 1.0 (MIMICS-CN v1. 0). Geoscientific Model Development 13, 4413-4434. + .. _Laddetal2992: Ladd, J.N., Jocteur-Monrozier, L. and Amato, M., 1992. Carbon turnover and nitrogen transformations in an alfisol and vertisol amended with [U-:math:`{}^{14}`\ C] glucose and [:math:`{}^{15}`\ N] ammonium sulfate. Soil Biology and Biochemistry, 24: 359-371. @@ -1532,10 +1540,18 @@ White, M.A., Thornton, P.E., and Running, S.W. 1997. A continental phenology mod White, M.A., Thornton, P.E., Running, S.W., and Nemani, R.R. 2000. Parameterization and sensitivity analysis of the Biome-BGC terrestrial ecosystem model: net primary production controls. Earth Interactions 4:1-85. +.. _Wiederetal2014: + +Wieder, W., Grandy, A., Kallenbach, C., Bonan, G., 2014. Integrating microbial physiology and physio-chemical principles in soils with the MIcrobial-MIneral Carbon Stabilization (MIMICS) model. Biogeosciences 11, 3899-3917. + .. _Wiederetal2015: Wieder, W. R., Cleveland, C. C., Lawrence, D. M., and Bonan, G. B. 2015. Effects of model structural uncertainty on carbon cycle projections: biological nitrogen fixation as a case study. Environmental Research Letters, 10(4), 044016. +.. _Wiederetal2015b: + +Wieder, W., Grandy, A., Kallenbach, C., Taylor, P., Bonan, G., 2015. Representing life in the Earth system with soil microbial functional traits in the MIMICS model. Geoscientific Model Development 8, 1789-1808. + .. _Williamsetal1996: Williams, M., Rastetter, E.B., Fernandes, D.N., Goulden, M.L., Wofsy, S.C., Shaver, G.R., Melillo, J.M., Munger, J.W., Fan, S.M. and Nadelhoffer, K.J. 1996. Modelling the soil-plant-atmosphere continuum in a Quercus–Acer stand at Harvard Forest: the regulation of stomatal conductance by light, nitrogen and soil/plant hydraulic properties. Plant, Cell & Environment, 19: 911–927. doi:10.1111/j.1365-3040.1996.tb00456.x From 02c7c13f44e231cfe65742935c3cbdfec882b165 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 29 May 2026 09:31:40 -0600 Subject: [PATCH 2/3] Docs: Fix a reference. --- doc/source/tech_note/References/CLM50_Tech_Note_References.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst index 6474d8518b..950882defb 100644 --- a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst +++ b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst @@ -1773,6 +1773,7 @@ Wieder, W. R., Cleveland, C. C., Lawrence, D. M., and Bonan, G. B. 2015. Effects .. _Wiederetal2015b: Wieder, W., Grandy, A., Kallenbach, C., Taylor, P., Bonan, G., 2015. Representing life in the Earth system with soil microbial functional traits in the MIMICS model. Geoscientific Model Development 8, 1789-1808. + .. _Wiederetal2019: Wieder, W.R., Lawrence, D.M., Fisher, R.A., Bonan, G.B., Cheng, S.J., Goodale, C.L., Grandy, A.S., Koven, C.D., Lombardozzi, D.L., Oleson, K.W. and Thomas, R.Q., 2019. Beyond static benchmarking: Using experimental manipulations to evaluate land model assumptions. Global Biogeochemical Cycles, 33(10), 1289-1309. DOI:10.1029/2018GB006141 From a629a550623b2581f03328c39b08b857faa9f6f7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 29 May 2026 10:24:57 -0600 Subject: [PATCH 3/3] Remove deleted figures from list. --- .../Introduction/CLM50_Tech_Note_Introduction.rst | 8 -------- 1 file changed, 8 deletions(-) diff --git a/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst b/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst index 5925c29270..496b93608f 100644 --- a/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst +++ b/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst @@ -55,10 +55,6 @@ P. O. Box 3000, Boulder, Colorado 80307-300 - :numref:`Figure annual phenology cycle` Example of annual phenology cycle for seasonal deciduous. -- :numref:`Figure Schematic of decomposition model in CLM` Schematic of decomposition model in CLM. - -- :numref:`Figure Pool structure` Pool structure, transitions, respired fractions, and turnover times for the 2 alternate soil decomposition models included in CLM. - - :numref:`Figure Methane Schematic` Schematic representation of biological and physical processes integrated in CLM that affect the net CH4 surface flux. - :numref:`Figure Schematic of land cover change` Schematic of land cover change impacts on CLM carbon pools and fluxes. @@ -117,10 +113,6 @@ P. O. Box 3000, Boulder, Colorado 80307-300 - :numref:`Table Allocation and CN ratio parameters` Allocation and carbon:nitrogen ratio parameters -- :numref:`Table Decomposition rate constants` Decomposition rate constants for litter and SOM pools, C:N ratios, and acceleration parameters for the CLM-CN decomposition pool structure. - -- :numref:`Table Respiration fractions for litter and SOM pools` Respiration fractions for litter and SOM pools - - :numref:`Table Turnover times` Turnover times, C:N ratios, and acceleration parameters for the Century-based decomposition cascade. - :numref:`Table Respiration fractions for Century-based structure` Respiration fractions for litter and SOM pools for Century-based structure