Decomposition tech note updated for CLM6#4063
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The build errors should be resolved now. |
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@slevis-lmwg I'm passing the review of this PR off to you. Thanks in advance. |
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@katierocci I made some suggestions for edits based on the updates that I saw in your branch here in the PR. I will come back to your PR again next week to look more carefully at the "built" version of this chapter.
Thank you for all the work that you put into this!
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| 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. |
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| 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. | |
| 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 :numref:`Figure Century-based soil model structure`. 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. |
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| 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). |
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| The turnover times for the Century-based pool structure follow those described in Parton et al. (1988) (Table 2.22.1). | |
| The turnover times for the Century-based pool structure follow those described in :ref:`Parton et al. (1988) <Partonetal1988>` (:numref:`Table Turnover times`). |
| 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\} | ||
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| 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), |
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| 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), | |
| 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 :ref:`Niu and Yang (2006) <NiuYang2006>`, |
| An additional frozen decomposition limitation can be specified using a 'frozen Q\ :sub:`10`' following :ref:`Koven et al. (2011) <Kovenetal2011>`, 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. | ||
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| 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. |
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| 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. | |
| 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 :numref:`rst_Methane Model`). 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 (:ref:`Frolking et al. 2001 <Frolkingetal2001>`), and 0.35 (:ref:`Wania et al. 2009 <Waniaetal2009>`); the large range of these estimates poses a large unresolved uncertainty. |
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| CF_{pot,\, SOM3} ={CS_{SOM3} k_{SOM3} r_{total} \mathord{\left/ {\vphantom {CS_{SOM3} k_{SOM3} r_{total} \Delta t}} \right.} \Delta t} | ||
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| 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: |
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| 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: | |
| where the factor (1/:math:`\Delta`\ *t*) is included because the rate constant is calculated for the entire timestep (Eqs. :eq:`label_here` and :eq:`label_here`), but the convention is to express all fluxes on a per-second basis. Potential mineral nitrogen fluxes associated with these decomposition steps are: |
@katierocci could you fill the equation labels here?
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| .. math:: | ||
| :label: ZEqnNum934998 | ||
| :label: 21.20) |
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@katierocci here and elsewhere it's better to avoid hardwiring equation labels with numbers since the numbers may change over time. Better to come up with a short (two to four word) description of the equation instead.
I'm not suggesting updating all the equations in the chapter, but since you updated a couple, I'm recommending an alternate update for those. Or go back to their earlier labels, which also raises the question:
Do you know whether the equations with changed labels are referenced in other chapters? That possibility favors the argument of returning them to their earlier labels.
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Description of changes
The Decomposition page of the Tech Note has been updated for CLM6 to remove text about the old soil submodel and text has been added for the MIMICS soil submodel. The equations have been updated accordingly.
Specific notes
Contributors other than yourself, if any:
CTSM issues resolved or otherwise addressed, if any:
Requirements before merge: