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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| 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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I looked around a bit and did not find equations for these rate constants, so maybe we remove the eqs. references?
…on.rst Replace hardwired figure number with reference
…on.rst Replace reference and hardwired table number with links
…on.rst Replace hardwired reference with link
…on.rst Replace hardwired chapter number and 2 references with links
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@katierocci here are a few more changes that I was hoping you could confirm before I make them.
| @@ -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: | |||
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@katierocci should this hardwired reference to Tables 15.1 and 15.3 change to the "Turnover times" table (currently 2.22.1)? If so, then change to
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| 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: | |
| The base acceleration terms for the two decomposition cascades are shown in :numref:`Table Turnover times`. 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: |
| 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. | ||
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| 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. |
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Does the reference to Eqs. 2.21.19-2.21.26 actually mean 2.22.14-2.22.21? If so replace with
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| 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. | |
| 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. :eq:`21.19`-:eq:`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. |
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| Alternate soil sub-model: MIMICS | ||
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| In CLM6, there is a new capability to use the MIcrobial-MIneral Carbon Stabilization (MIMICS) model (:ref:`Wieder et al. 2014 <Wiederetal2014>`; :ref:`Wieder et al. 2015b <Wiederetal2015b>`; :ref:`Kyker-Snowman et al. 2020 <KykerSnowmanetal2020>`) 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) <KykerSnowmanetal2020>`. |
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This hardwired figure reference probably needs to change to
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| In CLM6, there is a new capability to use the MIcrobial-MIneral Carbon Stabilization (MIMICS) model (:ref:`Wieder et al. 2014 <Wiederetal2014>`; :ref:`Wieder et al. 2015b <Wiederetal2015b>`; :ref:`Kyker-Snowman et al. 2020 <KykerSnowmanetal2020>`) 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) <KykerSnowmanetal2020>`. | |
| In CLM6, there is a new capability to use the MIcrobial-MIneral Carbon Stabilization (MIMICS) model (:ref:`Wieder et al. 2014 <Wiederetal2014>`; :ref:`Wieder et al. 2015b <Wiederetal2015b>`; :ref:`Kyker-Snowman et al. 2020 <KykerSnowmanetal2020>`) 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 :numref:`Figure MIMICS soil model structure`. Details about MIMICS-CN can be found in :ref:`Kyker-Snowman et al. (2020) <KykerSnowmanetal2020>`. |
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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: