From 8dfb534acc02a5aefef37770a2dd2c0636bc7499 Mon Sep 17 00:00:00 2001 From: Sanketmandwal Date: Wed, 27 May 2026 12:32:16 +0530 Subject: [PATCH 1/2] [185] Update N cycle documentation --- docs/model-structure.md | 53 +++++++++++++++++++---------------------- docs/parameters.md | 13 +++++----- 2 files changed, 30 insertions(+), 36 deletions(-) diff --git a/docs/model-structure.md b/docs/model-structure.md index 80f506c4..002dba5d 100644 --- a/docs/model-structure.md +++ b/docs/model-structure.md @@ -572,42 +572,38 @@ F^N_\text{min} = \sum_j \left( \frac{R_{H\text{j}}}{CN_{\text{j}}} \right) \small j \in \{\text{soil, litter}\} \end{equation*} -### Nitrogen Volatilization $F^N_\text{vol}: (N_\text{min,soil} \rightarrow N_2O)$ +### Nitrogen Volatilization $F^N_\text{vol}: (N_\text{min} \rightarrow N_2O)$ -The simplest way to represent $N_2O$ flux is as a proportion of the mineral N pool $N_\text{min}$ or the N -mineralization rate $F^N_{min}$. For example, CLM-CN and CLM 4.0 represent $N_2O$ flux as a proportion -of $N_\text{min}$ (Thornton et al 2007, Oleson et al. 2010). By contrast, Biome-BGC (Golinkoff et al 2010; Thornton and -Rosenbloom, 2005 and https://github.com/bpbond/Biome-BGC, Golinkoff et al 2010; Thornton and Rosenbloom, 2005) -represents $N_2O$ flux as a proportion of the N mineralization rate. - -The simplest way to represent $N_2O$ flux is as a proportion of the mineral N pool $N_\text{min}$ or the N -mineralization rate $F^N_{min}$. For example, CLM-CN and CLM 4.0 represent $N_2O$ flux as a proportion of $N_\text{min}$ -(Thornton et al 2007, Oleson et al. 2010). By contrast, Biome-BGC (Golinkoff et al 2010; Thornton and Rosenbloom, 2005 -and https://github.com/bpbond/Biome-BGC, Golinkoff et al 2010; Thornton and Rosenbloom, 2005) represents $N_2O$ flux as -a proportion of the N mineralization rate. - -Because we expect $N_2O$ emissions will be dominated by fertilizer N inputs, we will start with the $N_\text{min}$ pool -size approach. This approach also has the advantage of accounting for reduced $N_2O$ flux when N is limiting (Zahele and -Dalmorech 2011). - -A new parameter $K_\text{vol}$ represents the first-order rate constant governing volatilization losses from the soil -mineral nitrogen pool. The realized volatilization flux is proportional to $N_\text{min}$ and depends on temperature and -soil moisture. +$K_\text{vol}$ is the nitrogen volatilization rate constant that determines the maximum rate of N volatilization as a +proportion of available $N_\text{min}$. The realized volatilization flux is proportional to available Nmin through Kvol and depends on temperature and soil moisture. \begin{equation} F^N_\text{vol} = K_\text{vol} \cdot N_\text{min} \cdot D_{\text{temp}} \cdot D_{\text{water},N_\text{vol}} \label{eq:n_vol} \end{equation} +Justification: SIPNET represents $N_2O$ flux as a proportion of the mineral N pool $N_\text{min}$, rather than as a +proportion of the N mineralization rate $F^N_\text{min}$. CLM-CN and CLM 4.0 use an $N_\text{min}$ approach (Thornton et +al. 2007; Oleson et al. 2010), while Biome-BGC represents $N_2O$ flux as a proportion of the N mineralization rate +(Golinkoff et al. 2010; Thornton and Rosenbloom, 2005; https://github.com/bpbond/Biome-BGC). The $N_\text{min}$ +approach accounts for reduced $N_2O$ flux when N is limiting (Zahele and Dalmorech 2011), and fertilizer N inputs are +expected to dominate $N_2O$ emissions. + ### Nitrogen Leaching $F^N_\text{leach}$ \begin{equation} -F^N_\text{leach} = N_\text{min} \cdot F^W_{drainage} \cdot f_{N leach} +F^N_\text{leach} = N_\text{min} \cdot \phi \cdot f_{N leach} \label{eq:n_leach} \end{equation} -Where $f^N_\text{leach}$ is the fraction of $N_{min}$ in soil that is available to be leached, $F^W_{drainage}$ is -drainage. +where: + +\begin{equation} +\phi = \min\left(\frac{F^W_\text{drainage}}{W_\text{WHC}}, 1\right) +\end{equation} + +$f^N_\text{leach}$ is the fraction of $N_\text{min}$ available to be leached, $F^W_\text{drainage}$ is drainage, and +$W_\text{WHC}$ is soil water holding capacity. SIPNET uses one mineral nitrogen pool, $N_\text{min}$; litter and soil mineralization are separate fluxes that both add to this pool. ### Plant Nitrogen Demand $F^{N}_{\text{demand}}$ @@ -911,15 +907,14 @@ Where $T_{\text{env}}$ may be soil or air temperature $(T_\text{soil}$ or $T_\t Because the function is symmetric around $T_\text{opt}$, the parameters $T_{\text{min}}$ and $T_{\text{opt}}$ are provided and $T_{\text{max}}$ is calculated internally as $T_{\text{max}} = 2 \cdot T_{\text{opt}} - T_{\text{min}}$. -#### Exponential Function for Respiration $D_{\text(temp,Q10)}$ +#### Exponential Function for Respiration $D_{\text{temp,Q10}}$ The temperature response of autotrophic $(R_a)$ and heterotrophic $(R_H)$ respiration represented as an exponential relationship using a simplified Arrhenius function. -\begin{equation} +\[ D_{\text{temp,Q10}} = Q_{10}^{\frac{(T-T_\text{opt})}{10}} -\label{eq:Braswell_A18b} -\end{equation} +\] This is from equation (A18) from Braswell, et al. (2005) @@ -939,8 +934,8 @@ four $Q_{10}$ values ranged from 1.4 to 5.8 when SIPNET was calibrated to $CO_2$ ### Moisture dependence functions $D_{water}$ Moisture dependence functions are typically based on soil water content as a fraction of water holding capacity, also -referred to as soil moisture or fractional soil wetness. We will represent this fraction of soil wetness -as $f_\text{WHC}$. +referred to as soil moisture or fractional soil wetness. SIPNET represents this fraction of soil wetness as +$f_\text{WHC}$. #### Soil Water Content Fraction diff --git a/docs/parameters.md b/docs/parameters.md index 41318140..1f559dfe 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -106,7 +106,7 @@ Run-time parameters can change from one run to the next, or when the model is st | $f_{\text{WHC},0}$ | soilWFracInit | Initial soil water fraction | unitless | May exceed 1.0 when modeling flooded conditions; $W_{\text{soil},0} = f_{\text{WHC},0} \cdot W_{\text{WHC}}$ | | $N_{\text{org, litter},0}$ | litterOrgNInit | Initial litter organic nitrogen content | $\text{g N} \cdot \text{m}^{-2}$ | | | $N_{\text{org, soil},0}$ | soilOrgNInit | Initial soil organic nitrogen content | $\text{g N} \cdot \text{m}^{-2}$ | | -| $N_{\text{min, soil},0}$ | mineralNInit | Initial soil mineral nitrogen content | $\text{g N} \cdot \text{m}^{-2}$ | | +| $N_{\text{min},0}$ | mineralNInit | Initial mineral nitrogen content | $\text{g N} \cdot \text{m}^{-2}$ | Single mineral N pool used by soil and litter N fluxes | | $f_{\text{fine root},0}$ | fineRootFrac | Fraction of `plantWoodInit` allocated to initial fine root carbon pool | unitless | | | $f_{\text{coarse root},0}$ | coarseRootFrac | Fraction of `plantWoodInit` allocated to initial coarse root carbon pool | unitless | | | $W_{\text{snow},0}$ | snowInit | Initial snow water equivalent | cm water equivalent | | @@ -200,13 +200,12 @@ Run-time parameters can change from one run to the next, or when the model is st ### Nitrogen Cycle Parameters -Run-time parameters support mineralization, volatilization, leaching, and -pool stoichiometry. +Run-time parameters support mineral nitrogen losses through volatilization and leaching. -| Symbol | Parameter Name | Definition | Units | Notes | -| -------------------- | ------------------- | -------------------------------------------------------------------------------------- | ----------------- | ------------------ | -| $K_\text{vol}$ | nVolatilizationFrac | Fraction of $N_\text{min}$ volatilized per day (modulated by temperature and moisture) | $\text{day}^{-1}$ | \eqref{eq:n_vol} | -| $f^N_{\text{leach}}$ | nLeachingFrac | Leaching coefficient applied to $N_\text{min}$ scaled by drainage | $\text{day}^{-1}$ | \eqref{eq:n_leach} | +| Symbol | Parameter Name | Definition | Units | Notes | +| ---------------------- | -------------------- | ------------------------------------------------------------------------------------------------------------------------------------ | ----------------- | -------------------------------- | +| $K_\text{vol}$ | nVolatilizationFrac | Nitrogen volatilization rate constant that determines the maximum rate of N volatilization as a proportion of available $N_\text{min}$ | $\text{day}^{-1}$ | \eqref{eq:n_vol} | +| $f^N_{\text{leach}}$ | nLeachingFrac | Fraction of $N_\text{min}$ available to be leached, applied after scaling by $\phi = \min(F^W_\text{drainage}/W_\text{WHC}, 1)$ | unitless | \eqref{eq:n_leach} | ### Moisture-Related Parameters From 29743115deb21ffd716d04ad8aacca138d80767b Mon Sep 17 00:00:00 2001 From: Sanketmandwal Date: Thu, 28 May 2026 10:27:24 +0530 Subject: [PATCH 2/2] Changes Made --- docs/model-structure.md | 9 +++++---- docs/parameters.md | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/docs/model-structure.md b/docs/model-structure.md index 002dba5d..b2aa56c7 100644 --- a/docs/model-structure.md +++ b/docs/model-structure.md @@ -575,7 +575,7 @@ F^N_\text{min} = \sum_j \left( \frac{R_{H\text{j}}}{CN_{\text{j}}} \right) ### Nitrogen Volatilization $F^N_\text{vol}: (N_\text{min} \rightarrow N_2O)$ $K_\text{vol}$ is the nitrogen volatilization rate constant that determines the maximum rate of N volatilization as a -proportion of available $N_\text{min}$. The realized volatilization flux is proportional to available Nmin through Kvol and depends on temperature and soil moisture. +proportion of available $N_\text{min}$. The realized volatilization flux is proportional to available $N_\text{min}$, scaled by $K_\text{vol}$ and modified by temperature and soil moisture. \begin{equation} F^N_\text{vol} = K_\text{vol} \cdot N_\text{min} \cdot D_{\text{temp}} \cdot D_{\text{water},N_\text{vol}} @@ -592,7 +592,7 @@ expected to dominate $N_2O$ emissions. ### Nitrogen Leaching $F^N_\text{leach}$ \begin{equation} -F^N_\text{leach} = N_\text{min} \cdot \phi \cdot f_{N leach} +F^N_\text{leach} = N_\text{min} \cdot \phi \cdot f^N_\text{leach} \label{eq:n_leach} \end{equation} @@ -912,9 +912,10 @@ provided and $T_{\text{max}}$ is calculated internally as $T_{\text{max}} = 2 \c The temperature response of autotrophic $(R_a)$ and heterotrophic $(R_H)$ respiration represented as an exponential relationship using a simplified Arrhenius function. -\[ +\begin{equation} D_{\text{temp,Q10}} = Q_{10}^{\frac{(T-T_\text{opt})}{10}} -\] +\label{eq:Braswell_A18b} +\end{equation} This is from equation (A18) from Braswell, et al. (2005) diff --git a/docs/parameters.md b/docs/parameters.md index 1f559dfe..6c250d60 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -205,7 +205,7 @@ Run-time parameters support mineral nitrogen losses through volatilization and l | Symbol | Parameter Name | Definition | Units | Notes | | ---------------------- | -------------------- | ------------------------------------------------------------------------------------------------------------------------------------ | ----------------- | -------------------------------- | | $K_\text{vol}$ | nVolatilizationFrac | Nitrogen volatilization rate constant that determines the maximum rate of N volatilization as a proportion of available $N_\text{min}$ | $\text{day}^{-1}$ | \eqref{eq:n_vol} | -| $f^N_{\text{leach}}$ | nLeachingFrac | Fraction of $N_\text{min}$ available to be leached, applied after scaling by $\phi = \min(F^W_\text{drainage}/W_\text{WHC}, 1)$ | unitless | \eqref{eq:n_leach} | +| $f^N_{\text{leach}}$ | nLeachingFrac | Fraction of $N_\text{min}$ available to be leached, applied after scaling by $\phi = \min(F^W_\text{drainage}/W_\text{WHC}, 1)$ | $\text{day}^{-1}$ | \eqref{eq:n_leach} | ### Moisture-Related Parameters