diff --git a/docs/model-structure.md b/docs/model-structure.md index 5edba756..b4d53614 100644 --- a/docs/model-structure.md +++ b/docs/model-structure.md @@ -99,7 +99,7 @@ $$ The total adjusted gross primary production (GPP) is the product of potential GPP $(\text{GPP}_{\text{pot}})$ and the water stress factor $D_{\text{water,}A}$. -The water stress factor $D_{\text{water,}A}$ is defined in equation \eqref{eq:A16} as the ratio of actual to potential transpiration, and therefore couples GPP to transpiration by reducing GPP. +The water stress factor $D_{\text{water,}A}$ is defined in equation \ref{eq:A16} as the ratio of actual to potential transpiration, and therefore couples GPP to transpiration by reducing GPP. ### Plant Growth @@ -109,32 +109,25 @@ $$ Net primary productivity $(\text{NPP})$ is the total carbon gain of plant biomass. NPP is allocated to plant biomass pools in proportion to their allocation parameters $\alpha_i$. +To make explicit what contributes to autotrophic respiration, we decompose $R_A$ into maintenance and optional growth components: + $$ -\text{NPP}=\sum_{1}^{i} \frac{dC_{\text{plant,}i}}{dt} \tag{2} \label{eq:npp_summ} +R_A = R_\text{leaf} + R_\text{wood} + R_\text{root} +\ R_\text{growth} \tag{1a}\label{eq:ra_components} $$ -$$\small i \in \{\text{leaf, wood, fine root, coarse root}\}$$ +Here, $R_\text{leaf}$ and $R_\text{wood}$ are maintenance respiration terms (Eqs. \ref{eq:A18a}, \ref{eq:A19}); $R_\text{root}$ denotes root maintenance respiration; and $R_\text{growth}$ is an optional growth respiration term. Because these components are part of $R_A$, their costs are subtracted from GPP before calculating NPP and before allocating NPP to plant pools. Note that $\alpha_i$ are specified input parameters and $\sum_i{\alpha_i} = 1$. $$ -dC_{\text{plant,}i} = \text{NPP} \cdot a_i \mathfrak{- - F^C_{\text{harvest,removed,}i}} - F^C_{\text{litter,}i} +\frac{dC_{\text{plant,}i}}{dt} + = \alpha_i \cdot \text{NPP} + - F^C_{\text{harvest,removed,}i} + - F^C_{\text{litter,}i} \tag{Zobitz 3}\label{eq:Z3} $$ -This results in the following constraints: -- In the case of annuals, all biomass is either harvested and removed or added to litter pools. $F^C_{\text{harvest,removed,}i}$ is calculated by \eqref{eq:harvest}. -- In the case of perennials, a fraction of the biomass remains except at the end of the perennial's life. - -$$\mathfrak{ -F^C_{\text{litter,}i} + F^C_{\text{harvest,removed,}i} = -\begin{cases} -1 & \text{annuals} \\ -\leq 1 & \text{perennials} -\end{cases} -}$$ - +Summing \ref{eq:Z3} over all plant pools shows that NPP is partitioned into biomass growth, litter production, and removed harvest. ### Plant Death @@ -180,7 +173,6 @@ $$ Wood maintenance respiration $(R_m)$ depends on the wood carbon content $(C_\text{wood})$, a scaling constant $(k_\text{wood})$, and the temperature sensitivity scaling function $D_{\text{temp,Q10}_v}$. - ### Litter Carbon The change in the litter carbon pool over time is defined by the input of new litter and the loss to decomposition: @@ -350,7 +342,6 @@ $$ \frac{dN_\text{min}}{{dt}} = F^N_\text{litter,min} + F^N_\text{soil,min} + - F^N_\text{fix} + F^N_\text{fert,min} - F^N_\mathrm{vol} - F^N_\text{leach} - @@ -358,7 +349,7 @@ $$ \tag{15}\label{eq:mineral_n_dndt} $$ -Mineralization, fertilization, and fixation add to the mineral nitrogen pool. Losses include mineralization, volatilization, leaching, and plant uptake, described below: +Mineralization and fertilization add to the mineral nitrogen pool. Losses include volatilization, leaching, and plant uptake, described below. Fixed N enters the plant pool directly (Eq. \eqref{eq:n_fix_demand}). ### $\frak{N \ Mineralization \ (F^N_\text{min})}$ @@ -395,29 +386,56 @@ Where $f^N_\text{leach}$ is the fraction of $N_{min}$ in soil that is available ### $\frak{Nitrogen \ Fixation \ F^N_\text{fix}}$ -The rate at which N is fixed is a function of the NPP of the plant and a fixed parameter $K_\text{fix}$, and is modified by temperature. +For N-fixing plants, symbiotic nitrogen fixation is represented as supplying a fraction of plant nitrogen demand, and is inhibited by high soil mineral N. Plant N demand is defined in Eq. \ref{eq:plant_n_demand}. -For nitrogen fixing plants, rates of symbiotic nitrogen fixation are assumed to be driven by plant growth, and also depend on temperature. +The fraction of plant N demand met by biological N fixation is defined as: $$ -F^N_\text{fix} = K_\text{fix} \cdot NPP \cdot D_{\text{temp}} \tag{19}\label{eq:n_fix} +f_\text{fix} = f_{\text{fix,max}} \cdot D_{N_\text{min}} +\tag{19}\label{eq:f_fix} $$ -Nitrogen fixation is represented by adding fixed nitrogen directly to the soil mineral nitrogen pool. This is a reasonable first approximation, consistent with the simplicity of the nitrogen limitation model where limitation only occurs when nitrogen demand exceeds supply. +where: + +- $f_{\text{fix,max}}$ is the maximum fraction of plant N demand that can be met by fixation under low soil N (dimensionless, $0 \le f_{\text{fix,max}} \le 1$), and +- $D_{N_\text{min}}$ represents inhibition of N fixation by soil mineral N (dimensionless, $0 \le D_{N_\text{min}} \le 1$). -For nitrogen-fixing plants, most of the fixed nitrogen is directly used by the plant. It would be more complicated to model this by splitting, which could include splitting the fixed N into soil and plant pools and then meeting a portion of plant N demand with this flux. +We use a simple down-regulation function with increasing soil mineral N: + +$$ +D_{N_\text{min}} = \frac{1}{1 + \frac{N_\text{min}}{K_N}} +\tag{19a}\label{eq:n_fix_supp_demand} +$$ -### $\frak{Plant \ Nitrogen \ Uptake \ F^N_\text{uptake}}$ +where $N_\text{min}$ is the soil mineral N pool (g N m$^{-2}$) and $K_N$ is the amount of mineral N at which fixation is reduced by half (g N m$^{-2}$). + +Nitrogen fixation and soil N uptake are then partitioned from total plant N demand $F^N_\text{demand}$ (Eq. \ref{eq:plant_n_demand}): + +$$ +F^N_\text{fix} = f_\text{fix} \cdot F^N_\text{demand} +\tag{19b}\label{eq:n_fix_demand} +$$ + +$$ +F^N_\text{uptake} = (1 - f_\text{fix}) \cdot F^N_\text{demand} +\tag{19c}\label{eq:n_uptake_demand} +$$ + +Fixed N ($F^N_\text{fix}$) is added directly to the plant N pool via Eq. \ref{eq:plant_n}, while $F^N_\text{uptake}$ is removed from the soil mineral N pool in Eq. \ref{eq:mineral_n_dndt}. If the available soil mineral N is insufficient to supply $F^N_\text{uptake}$, then actual uptake is capped at $N_\text{min}$ and any residual unmet demand contributes to nitrogen limitation as described in Eq. \ref{eq:n_limit}. + +We do not consider free-living nonsymbiotic N fixation, which is approximately two orders of magnitude smaller (less than 2 kg N ha$^{-1}$ yr$^{-1}$, Cleveland et al. 1999) than crop N demand and typical N fertilization rates. + +### $\mathfrak{Plant\ Nitrogen\ Demand\ and\ Uptake\ (F^{N}_{\text{uptake}})}$, $F^{N}_{\text{demand}}$ Plant N demand is the amount of N required to support plant growth. This is calculated as the sum of changes in plant N pools: $$ -F^N_\text{uptake}=\frac{dN_\text{plant}}{dt} = \sum_{i} \frac{dN_{\text{plant,}i}}{dt} \tag{20}\label{eq:plant_n_demand} +F^N_\text{demand}=\frac{dN_\text{plant}}{dt} = \sum_{i} \frac{dN_{\text{plant,}i}}{dt} \tag{20}\label{eq:plant_n_demand} $$ $$\small i \in \{\text{leaf, wood, fine root, coarse root}\}$$ -Each term in the sum is calculated according to equation \eqref{eq:plant_n}. +Each term in the sum is calculated according to equation \ref{eq:plant_n}. Total plant N demand $F^N_\text{demand}$ is then partitioned between fixation and soil N uptake using equations \ref{eq:n_fix_demand} and \ref{eq:n_uptake_demand}. #### $\frak{Nitrogen \ Limitation \ Indicator \ Function \mathfrak{I_{\text{N limit}}}}$ @@ -459,7 +477,7 @@ $$ \tag{Braswell A4}\label{eq:A4} $$ -The term $(1-f_{\text{intercept}})F^W_{\text{precip}}$ is the portion of gross precipitation that reaches the soil (i.e. infiltration from precipitation). Intercepted water (fraction $f_{\text{intercept}}$ of precipitation or canopy‑applied irrigation) is assumed to evaporate the same day and therefore never enters $W_{\text{soil}}$ and does not appear in \eqref{eq:A4}. $F^W_{\text{trans}}$ here is identical to $F^W_{\text{transpiration}}$ used elsewhere. +The term $(1-f_{\text{intercept}})F^W_{\text{precip}}$ is the portion of gross precipitation that reaches the soil (i.e. infiltration from precipitation). Intercepted water (fraction $f_{\text{intercept}}$ of precipitation or canopy‑applied irrigation) is assumed to evaporate the same day and therefore never enters $W_{\text{soil}}$ and does not appear in equation \ref{eq:A4}. ### Drainage @@ -478,7 +496,7 @@ $$ F^W_{\text{precip,soil}} = (1 - f_{\text{intercept}})\,F^W_{\text{precip}} $$ -$F^W_{\text{precip,soil}}$ is added to soil water in equation \eqref{eq:A4}. +$F^W_{\text{precip,soil}}$ is added to soil water in equation \ref{eq:A4}. ### Evapotranspiration @@ -667,7 +685,7 @@ $$ D_{\textrm{till}}(t) = 1 + f_{\textrm{till}}\cdot e^{-t/30} \tag{25}\label{eq:till} $$ -$f_{\textrm{till}}$ is specified in the `events.in` file, and $D_{\textrm{till}}(t)$ is multiplied by the $KC$ term in the calculation of $R_H$ (Eq. \eqref{eq:rh}). +$f_{\textrm{till}}$ is specified in the `events.in` file, and $D_{\textrm{till}}(t)$ is multiplied by the $KC$ term in the calculation of $R_H$ (Eq. \ref{eq:rh}). A value of $f_{\textrm{till}}=0.2$ represents an initial 20% increase that will exponentially decay. The rate of exponential decay is 1/30 days. This rate was chosen such that $D_{\textrm{till}}$ integrates to 30, which is equivalent to DayCent’s 30‑day step function. @@ -681,7 +699,7 @@ $$ A planting event is defined by its emergence date and directly specifies the amount of carbon added to each of four plant carbon pools: leaf, wood, fine root, and coarse root. On the emergence date, the model initializes the plant pools with the amounts of carbon specified in the events file. -Following carbon addition, nitrogen for each pool is computed using the corresponding C:N stoichiometric ratios following equation \eqref{eq:cn_stoich}. +Following carbon addition, nitrogen for each pool is computed using the corresponding C:N stoichiometric ratios following equation \ref{eq:cn_stoich}. ### $\frak{Harvest}$ @@ -706,7 +724,7 @@ $$ F^C_{\text{harvest,litter}} = f_{\text{transfer,above}} \cdot C_{\text{leaf}} + f_{\text{transfer,below}} \cdot C_{\text{root}} \tag{28}\label{eq:harvest} $$ -This amount is then added to the litter flux in equation \eqref{eq:litter_flux}. +This amount is then added to the litter flux in equation \ref{eq:litter_flux}. ### Irrigation @@ -763,6 +781,7 @@ $$ Braswell, Bobby H., William J. Sacks, Ernst Linder, and David S. Schimel. 2005. Estimating Diurnal to Annual Ecosystem Parameters by Synthesis of a Carbon Flux Model with Eddy Covariance Net Ecosystem Exchange Observations. Global Change Biology 11 (2): 335–55. https://doi.org/10.1111/j.1365-2486.2005.00897.x. +Gutschick, V.P., 1981. Evolved strategies in nitrogen acquisition by plants. Am. Nat. 118, 607–637. https://doi.org/10.1086/283858 Libohova, Z., Seybold, C., Wysocki, D., Wills, S., Schoeneberger, P., Williams, C., Lindbo, D., Stott, D. and Owens, P.R., 2018. Reevaluating the effects of soil organic matter and other properties on available water-holding capacity using the National Cooperative Soil Survey Characterization Database. Journal of soil and water conservation, 73(4), pp.411-421. @@ -770,6 +789,8 @@ Manzoni, Stefano, and Amilcare Porporato. 2009. Soil Carbon and Nitrogen Mineral Parton, W. J., E. A. Holland, S. J. Del Grosso, M. D. Hartman, R. E. Martin, A. R. Mosier, D. S. Ojima, and D. S. Schimel. 2001. Generalized Model for NOx and N2O Emissions from Soils. Journal of Geophysical Research: Atmospheres 106 (D15): 17403–19. https://doi.org/10.1029/2001JD900101. +Rastetter, E.B., Vitousek, P.M., Field, C., Shaver, G.R., Herbert, D., Gren, G.I., 2001. Resource optimization and symbiotic nitrogen fixation. Ecosystems 4, 369–388. https://doi.org/10.1007/s10021-001-0018-z + Wang H, Yan Z, Ju X, Song X, Zhang J, Li S and Zhu-Barker X (2023) Quantifying nitrous oxide production rates from nitrification and denitrification under various moisture conditions in agricultural soils: Laboratory study and literature synthesis. Front. Microbiol. 13:1110151. doi: 10.3389/fmicb.2022.1110151 Zobitz, J. M., D. J. P. Moore, W. J. Sacks, R. K. Monson, D. R. Bowling, and D. S. Schimel. 2008. “Integration of Process-Based Soil Respiration Models with Whole-Ecosystem CO2 Measurements.” Ecosystems 11 (2): 250–69. https://doi.org/10.1007/s10021-007-9120-1. diff --git a/docs/parameters.md b/docs/parameters.md index 2e852162..a41d81a5 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -11,76 +11,75 @@ format: # SIPNET Model States and Parameters {#sec-parameters} - -Note: this is a work in progress. - -- Actual parameters used depend on the how the model structure is configured. -- Numbered items are cross-referenced with original documentation. -- "Notation" section is consistent with model equations, some of the mathematical symbols in the tables may either be missing or need to be updated. +Lists SIPNET state variables and tunable parameters, mapping symbols to the +model equations, configuration names, units, and I/O fields. See +[Model Inputs](user-guide/model-inputs.md) and +[Model Outputs](user-guide/model-outputs.md) for file formats. Unless noted, +pools are mass per ground area and rates are mass per area per day. The actual parameter set that is used depends on the configured model structure. For equation references, see the [model structure](model-structure.md) documentation. ## Notation {#sec-notation} ### Variables (Pools, Fluxes, and Parameters) -| **Category** | **Symbol** | **Description** | -|:---------------------------|:-----------|:--------------------------------------------------------| -| **State variables** | | | -| | $C$ | Carbon pool | -| | $N$ | Nitrogen pool | -| | $W$ | Water pool or content | -| | $CN$ | Carbon-to-Nitrogen ratio | -| **Fluxes and rates** | | | -| | $F$ | Generic flux of carbon, nitrogen, or water | -| | $A$ | Photosynthetic assimilation (net photosynthesis) | -| | $R$ | Respiration flux | -| | $ET$ | Evapotranspiration | -| | $GPP$ | Gross Primary Production | -| | $NPP$ | Net Primary Production | -| | $NEE$ | Net Ecosystem Exchange | -| **Environmental drivers** | | | -| | $T$ | Temperature | -| | $VPD$ | Vapor Pressure Deficit | -| | $PAR$ | Photosynthetically Active Radiation | -| | $LAI$ | Leaf Area Index | -| **Parameters** | | | -| | $K$ | Rate constant (e.g., for decomposition or respiration) | -| | $Q_{10}$ | Temperature sensitivity coefficient | -| | $\alpha$ | Fraction of NPP allocated to a plant pool | -| | $f$ | Fraction of a pool or flux other than NPP | -| | $k$ | Scaling factor | -| | $D$ | Dependency or damping function | +| **Category** | **Symbol** | **Description** | +| :------------------------ | :--------- | :----------------------------------------------------- | +| **State variables** | | | +| | $C$ | Carbon pool | +| | $N$ | Nitrogen pool | +| | $W$ | Water pool or content | +| | $CN$ | Carbon-to-Nitrogen ratio | +| **Fluxes and rates** | | | +| | $F$ | Generic flux of carbon, nitrogen, or water | +| | $A$ | Photosynthetic assimilation (net photosynthesis) | +| | $R$ | Respiration flux | +| | $ET$ | Evapotranspiration | +| | $GPP$ | Gross Primary Production | +| | $NPP$ | Net Primary Production | +| | $NEE$ | Net Ecosystem Exchange | +| **Environmental drivers** | | | +| | $T$ | Temperature | +| | $VPD$ | Vapor Pressure Deficit | +| | $PAR$ | Photosynthetically Active Radiation | +| | $LAI$ | Leaf Area Index | +| **Parameters** | | | +| | $K$ | Rate constant (e.g., for decomposition or respiration) | +| | $Q_{10}$ | Temperature sensitivity coefficient | +| | $\alpha$ | Fraction of NPP allocated to a plant pool | +| | $f$ | Fraction of a pool or flux other than NPP | +| | $k$ | Scaling factor | +| | $D$ | Dependency or damping function | ### Subscripts (Temporal, Spatial, or Contextual Identifiers) -|**Category** | **Subscript** | **Description** | -|:---------------------------|:-----------------------|:-------------------------------------------------| -| **Temporal identifiers** | | | -| | $X_0$ | Initial value | -| | $X_t$ | Value at time $t$ | -| | $X_d$ | Daily value or average | -| | $X_\text{avg}$ | Average value (e.g., over a timestep or spatial area) | -| | $X_\text{max}$ | Maximum value (e.g., temperature or rate) | -| | $X_\text{min}$ | Minimum value (e.g., temperature or rate) | -| | $X_\text{opt}$ | Optimal value (e.g., temperature or rate) | -| **Structural components** | | | -| | $X_\text{leaf}$ | Leaf pools or fluxes | -| | $X_\text{wood}$ | Wood pools or fluxes | -| | $X_\text{root}$ | Root pool | -| | $X_\text{fine root}$ | Fine root pool | -| | $X_\text{coarse root}$| Coarse root pool | -| | $X_\text{soil}$ | Soil pools or processes | -| | $X_\text{litter}$ | Litter pools or processes | -| | $X_\text{veg}$ | Vegetation processes (general) | -| **Processes context** | | | -| | $X_\text{resp}$ | Respiration processes | -| | $X_\text{dec}$ | Decomposition processes | -| | $X_\text{vol}$ | Volatilization processes | -| **Chemical / environmental identifiers** | | | -| | $X_\text{org}$ | Organic forms | -| | $X_\text{mineral}$ | Mineral forms | -| | $X_{\text{anaer}}$ | Anaerobic soil conditions | +| **Category** | **Subscript** | **Description** | +| :--------------------------------------- | :--------------------- | :---------------------------------------------------- | +| **Temporal identifiers** | | | +| | $X_0$ | Initial value | +| | $X_t$ | Value at time $t$ | +| | $X_d$ | Daily value or average | +| | $X_\text{avg}$ | Average value (e.g., over a timestep or spatial area) | +| | $X_\text{max}$ | Maximum value (e.g., temperature or rate) | +| | $X_\text{min}$ | Minimum value (e.g., temperature or rate) | +| | $X_\text{opt}$ | Optimal value (e.g., temperature or rate) | +| **Structural components** | | | +| | $X_\text{leaf}$ | Leaf pools or fluxes | +| | $X_\text{wood}$ | Wood pools or fluxes | +| | $X_\text{root}$ | Root pool | +| | $X_\text{fine root}$ | Fine root pool | +| | $X_\text{coarse root}$ | Coarse root pool | +| | $X_\text{soil}$ | Soil pools or processes | +| | $X_\text{litter}$ | Litter pools or processes | +| | $X_\text{veg}$ | Vegetation processes (general) | +| **Processes context** | | | +| | $X_\text{resp}$ | Respiration processes | +| | $X_\text{dec}$ | Decomposition processes | +| | $X_\text{vol}$ | Volatilization processes | +| **Chemical / environmental identifiers** | | | +| | $X_\text{org}$ | Organic forms | +| | $X_\text{mineral}$ | Mineral forms | +| | $X_{\text{anaer}}$ | Anaerobic soil conditions | Subscripts may be used in combination, e.g. $X_{\text{soil,mineral},0}$. @@ -111,7 +110,7 @@ Run-time parameters can change from one run to the next, or when the model is st | 7 | | snowInit | Initial snow water | cm water equiv. | | | | | microbeInit | | | | ---> + + ### Litter Quality Parameters @@ -151,17 +150,17 @@ Run-time parameters can change from one run to the next, or when the model is st ### Phenology-related parameters -| | Symbol | Parameter Name | Definition | Units | notes | -| --- | -------------------- | ---------------- | ----------------------------------------------------------------------- |---------------------------------------------------------|-------------------------------------------------| -| 17 | $D_{\text{on}}$ | leafOnDay | Day of year when leaves appear | day of year | | -| 18 | | gddLeafOn | with gdd-based phenology, gdd threshold for leaf appearance | | | -| 19 | | soilTempLeafOn | with soil temp-based phenology, soil temp threshold for leaf appearance | | | -| 20 | $D_{\text{off}}$ | leafOffDay | Day of year for leaf drop | | | -| 21 | | leafGrowth | additional leaf growth at start of growing season | $\text{g C} \cdot \text{m}^{-2} \text{ ground}$ | | -| 22 | | fracLeafFall | additional fraction of leaves that fall at end of growing season | | | -| 23 | $\alpha_\text{leaf}$ | leafAllocation | fraction of NPP allocated to leaf growth | | | -| 24 | $K_{leaf}$ | leafTurnoverRate | average turnover rate of leaves | $\text{y}^{-1}$ | converted to per-day rate internally | -| | $L_{\text{max}}$ | | Maximum leaf area index obtained | $\text{m}^2 \text{ leaf } \text{m}^{-2} \text{ ground}$ | ? from Braswell et al 2005; can't find in code | +| | Symbol | Parameter Name | Definition | Units | notes | +| --- | -------------------- | ---------------- | ----------------------------------------------------------------------- | ------------------------------------------------------- | ---------------------------------------------- | +| 17 | $D_{\text{on}}$ | leafOnDay | Day of year when leaves appear | day of year | | +| 18 | | gddLeafOn | with gdd-based phenology, gdd threshold for leaf appearance | | | +| 19 | | soilTempLeafOn | with soil temp-based phenology, soil temp threshold for leaf appearance | | | +| 20 | $D_{\text{off}}$ | leafOffDay | Day of year for leaf drop | | | +| 21 | | leafGrowth | additional leaf growth at start of growing season | $\text{g C} \cdot \text{m}^{-2} \text{ ground}$ | | +| 22 | | fracLeafFall | additional fraction of leaves that fall at end of growing season | | | +| 23 | $\alpha_\text{leaf}$ | leafAllocation | fraction of NPP allocated to leaf growth | | | +| 24 | $K_{leaf}$ | leafTurnoverRate | average turnover rate of leaves | $\text{y}^{-1}$ | converted to per-day rate internally | +| | $L_{\text{max}}$ | | Maximum leaf area index obtained | $\text{m}^2 \text{ leaf } \text{m}^{-2} \text{ ground}$ | ? from Braswell et al 2005; can't find in code | ### Allocation parameters @@ -183,7 +182,7 @@ Run-time parameters can change from one run to the next, or when the model is st | --- | --------------------- | ------------------- | ------------------------------------------------------------------------ | ---------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | | 25 | $R_{\text{a,wood},0}$ | baseVegResp | Wood maintenance respiration rate at $0^\circ C$ | g C respired \* g$^{-1}$ plant C \* day$^{-1}$ | read in as per-year rate only counts plant wood C; leaves handled elsewhere (both above and below-ground: assumed for now to have same resp. rate) | | 26 | $Q_{10v}$ | vegRespQ10 | Vegetation respiration Q10 | | Scalar determining effect of temp on veg. resp. | -| 27 | | growthRespFrac | growth resp. as fraction of ($GPP - R_\text{a,wood} - R_\text{a,leaf}$) | | +| 27 | | growthRespFrac | growth respiration as a fraction of recent mean NPP. | | | 28 | | frozenSoilFolREff | amount that foliar resp. is shutdown if soil is frozen | | 0 = full shutdown, 1 = no shutdown | | 29 | | frozenSoilThreshold | soil temperature below which frozenSoilFolREff and frozenSoilEff kick in | °C | | | | | 72 | | baseFineRootResp | base respiration rate of fine roots | $\text{y}^{-1}$ | per year rate | @@ -205,29 +204,15 @@ Run-time parameters can change from one run to the next, or when the model is st - $R_{dec}$: Rate of decomposition $(\text{day}^{-1})$ - $Q_{10dec}$: Temperature coefficient for $R_{dec}$ (unitless) - ### Nitrogen Cycle Parameters - - -- $K_{n,vol}$: Rate constant for volatilization (day-1) -- $f_{N2O_{vol}}$: Fraction of volatilization leading to N2O production -- $R_{min}$: Rate of mineralization (day-1) -- $I_\text{N limit}$: Indicator for nitrogen limitation - - - - +| | Symbol | Parameter Name | Definition | Units | notes | +| --- | -------------------- | ------------------- | -------------------------------------------------------------------------------------------- | ------------ | -------------------------- | +| new | $N_{\text{min},0}$ | mineralNInit | Initial soil mineral nitrogen pool | g N m$^{-2}$ | Initializes $N_\text{min}$ | +| new | $K_\text{vol}$ | nVolatilizationFrac | Fraction of $N_\text{min}$ volatilized per day (modulated by temperature and moisture) | day$^{-1}$ | Eq. (17) | +| new | $f^N_{\text{leach}}$ | nLeachingFrac | Leaching coefficient applied to $N_\text{min}$ scaled by drainage | day$^{-1}$ | Eq. (18) | +| new | $f_{\text{fix,max}}$ | nFixFracMax | Maximum fraction of plant N demand that can be met by biological N fixation under low soil N | fraction | Eq. (19) | +| new | $K_N$ | nFixHalfSatMinN | Mineral N level at which fixation suppression factor $D_{N_\text{min}}$ equals 0.5 | g N m$^{-2}$ | Eq. (19a) | ### Methane parameters @@ -258,7 +243,7 @@ Run-time parameters can change from one run to the next, or when the model is st ### Tree physiological parameters | | Symbol | Parameter Name | Definition | Units | notes | -| --- | ---------------------- | ---------------------- | -------------------------------------- |----------------------|--------------------------------------------------------------------| +| --- | ---------------------- | ---------------------- | -------------------------------------- | -------------------- | ------------------------------------------------------------------ | | 53 | $SLW$ | leafCSpWt | | g C * m^-2 leaf area | | | 54 | $C_{frac}$ | cFracLeaf | | g leaf C * g^-1 leaf | | | 55 | $K_\text{wood}$ | woodTurnoverRate | average turnover rate of woody plant C | $\text{y}^{-1}$ | converted to per-day rate internally; leaf loss handled separately | @@ -305,10 +290,3 @@ Run-time parameters can change from one run to the next, or when the model is st | `GAMMA` | 66 | psychometric constant (Pa/K) | | `E_STAR_SNOW` | 0.6 | approximate saturation vapor pressure at 0°C (kPa) | -## Input Files {#input-files} - -See [Model Inputs](user-guide/model-inputs.md). - -## Outputs - -See [Model Outputs](user-guide/model-outputs.md).