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SIPNET Model States and Parameters {#sec-parameters}

Lists SIPNET state variables and tunable parameters, mapping symbols to the model equations, configuration names, units, and I/O fields. See Model Inputs and Model Outputs 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 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

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

Subscripts may be used in combination, e.g. $X_{\text{soil,mineral},0}$.

Run-time Parameters

Run-time parameters can change from one run to the next, or when the model is stopped and restarted. These include initial state values and parameters related to plant physiology, soil physics, and biogeochemical cycling.

Initial state values

Symbol Parameter Name Definition Units notes
1 $C_{\text{wood},0}$ plantWoodInit Initial wood carbon $\text{g C} \cdot \text{m}^{-2} \text{ ground area}$ above-ground + roots
$C_{\text{wood,storage}}$ Wood carbon storage pool (delta) $\text{g C} \cdot \text{m}^{-2} \text{ ground area}$ Tracks lag between NPP input and allocation output due to 5-day averaging; initialized to 0; can be negative. In code: plantWoodCStorageDelta. Total wood C = $C_{\text{wood}} + C_{\text{wood,storage}}$
2 $LAI_0$ laiInit Initial leaf area m^2 leaves * m^-2 ground area multiply by SLW to get initial plant leaf C: $C_{\text{leaf},0} = LAI_0 \cdot SLW$
3 $C_{\text{litter},0}$ litterInit Initial litter carbon $\text{g C} \cdot \text{m}^{-2} \text{ ground area}$
4 $C_{\text{soil},0}$ soilInit Initial soil carbon $\text{g C} \cdot \text{m}^{-2} \text{ ground area}$
5 $W_{\text{litter},0}$ litterWFracInit unitless fraction of litterWHC
6 $W_{\text{soil},0}$ soilWFracInit unitless fraction of soilWHC
$N_{\text{org, litter},0}$ Initial litter organic nitrogen content g N m$^{-2}$
$N_{\text{org, soil},0}$ Initial soil organic nitrogen content g N m$^{-2}$
$N_{\text{min, soil},0}$ Initial soil mineral nitrogen content g N m$^{-2}$
${CH_4}_{\text{soil},0}$ Initial methane concentration in the soil g C m$^{-2}$
${N_2O}_{\text{soil},0}$ Nitrous oxide concentration in the soil g N m$^{-2}$
$f_{\text{fine root},0}$ fineRootFrac Fraction of plantWoodInit allocated to initial fine root carbon pool
$f_{\text{coarse root},0}$ coarseRootFrac Fraction of plantWoodInit allocated to initial coarse root carbon pool

Stoichiometry Parameters

Symbol Name Description Units Notes
$CN_{\textrm{wood}}$ woodCN Carbon to Nitrogen ratio of wood $CN_{\textrm{coarse root}} = CN_{\textrm{wood}}$
$CN_{\textrm{leaf}}$ leafCN Carbon to Nitrogen ratio of leaves
$CN_{\textrm{fine root}}$ fineRootCN Carbon to Nitrogen ratio of fine roots
$k_\textit{CN}$ kCN Decomposition CN scaling parameter

Photosynthesis parameters

Symbol Parameter Name Definition Units notes
8 $A_{\text{max}}$ aMax Maximum net CO2 assimilation rate $\text{nmol CO}_2 \cdot \text{g}^{-1} \cdot \text{leaf} \cdot \text{s}^{-1}$ assuming max. possible PAR, all intercepted, no temp, water or VPD stress
9 $f_{A_{\text{max},d}}$ aMaxFrac avg. daily aMax as fraction of instantaneous fraction Avg. daily max photosynthesis as fraction of $A_{\text{max}}$
10 $R_\text{leaf,opt}$ baseFolRespFrac basal Foliar maintenance respiration as fraction of $A_{\text{max}}$ fraction
11 $T_{\text{min}}$ psnTMin Minimum temperature at which net photosynthesis occurs $^{\circ}\text{C}$
12 $T_{\text{opt}}$ psnTOpt Optimum temperature at which net photosynthesis occurs $^{\circ}\text{C}$
13 $K_\text{VPD}$ dVpdSlope Slope of VPD–photosynthesis relationship $kPa^{-1}$ dVpd = 1 - dVpdSlope * vpd^dVpdExp
14 $K_{\text{VPD}},{\text{exp}}$ dVpdExp Exponent used to calculate VPD effect on Psn dimensionless dVpd = 1 - dVpdSlope * vpd^dVpdExp
15 $\text{PAR}_{1/2}$ halfSatPar Half saturation point of PAR–photosynthesis relationship $m^{-2}$\ ground area $\cdot$ day$^{-1}$ PAR at which photosynthesis occurs at 1/2 theoretical maximum
16 $k$ attenuation Canopy PAR extinction coefficient

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

Allocation parameters

Symbol Parameter Name Definition Units notes
64 fineRootFrac fraction of wood carbon allocated to fine root
65 coarseRootFrac fraction of wood carbon that is coarse root
66 $\alpha_\text{fine root}$ fineRootAllocation fraction of NPP allocated to fine roots
67 $\alpha_\text{wood}$ woodAllocation fraction of NPP allocated to wood
68 fineRootExudation fraction of GPP from fine roots exuded to the soil1 fraction Pulsing parameters
69 coarseRootExudation fraction of GPP from coarse roots exuded to the soil1 fraction Pulsing parameters

Autotrophic respiration parameters

Symbol Parameter Name Definition Units notes
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 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
73 baseCoarseRootResp base respiration rate of coarse roots $\text{y}^{-1}$ per year rate

Soil respiration parameters

Symbol Parameter Name Definition Units notes
30 $K_\text{litter}$ litterBreakdownRate rate at which litter is converted to soil / respired at 0°C and max soil moisture g C broken down * g^-1 litter C * day^-1 read in as per-year rate
31 $f_{\text{litter}}$ fracLitterRespired of the litter broken down, fraction respired (the rest is transferred to soil pool)
32 $K_{soil}$ baseSoilResp Soil respiration rate at $0 ^{\circ}\text{C}$ and moisture saturated soil g C respired * g$^{-1}$ soil C * day$^{-1}$ read in as per-year rate
new $K_{\text{meth}}$ methOxidationRate Rate of methane oxidation day$^{-1}$
34 $Q_{10s}$ soilRespQ10 Soil respiration Q10 scalar determining effect of temp on soil respiration
39 soilRespMoistEffect scalar determining effect of moisture on soil resp.
new $f_{\textrm{till}}$ tillageEff Effect of tillage on decomposition that exponentially decays over time fraction Per‑event in events.in; 0 = no effect

Nitrogen Cycle Parameters

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)

Moisture-related parameters

Symbol Parameter Name Definition Units notes
40 $f_{\text{trans,avail}}$ waterRemoveFrac fraction of plant available soil water which can be removed in one day by transpiration without water stress occurring
new $f_\text{drain,0}$ waterDrainFrac fraction of plant available soil water which can be removed in one day by drainage $d^{-1}$ default 1 for well drained soils
41 frozenSoilEff fraction of water that is available if soil is frozen (0 = none available, 1 = all still avail.) if frozenSoilEff = 0, then shut down psn. even if WATER_PSN = 0, if soil is frozen (if frozenSoilEff > 0, it has no effect if WATER_PSN = 0)
42 wueConst water use efficiency constant
43 litterWHC litter (evaporative layer) water holding capacity cm
44 soilWHC soil (transpiration layer) water holding capacity cm
45 $f_\text{intercept} immedEvapFrac fraction of rain that is immediately intercepted & evaporated
46 fastFlowFrac fraction of water entering soil that goes directly to drainage
$k_\text{SOM,drain}$
47 snowMelt rate at which snow melts cm water equivavlent per degree Celsius per day
49 rdConst scalar determining amount of aerodynamic resistance
50 rSoilConst1 soil resistance = e^(rSoilConst1 - rSoilConst2 * W1) , where W1 = (litterWater/litterWHC)
51 rSoilConst2 soil resistance = e^(rSoilConst1 - rSoilConst2 * W1) , where W1 = (litterWater/litterWHC)

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
70 $K_\text{fine root}$ fineRootTurnoverRate turnover of fine roots $\text{y}^{-1}$ converted to per-day rate internally
71 $K_\text{coarse root}$ coarseRootTurnoverRate turnover of coarse roots $\text{y}^{-1}$ converted to per-day rate internally

Hard-coded Values

Parameter Value Description
C_WEIGHT 12.0 molecular weight of carbon
MEAN_NPP_DAYS 5 over how many days do we keep the running mean
MEAN_NPP_MAX_ENTRIES MEAN_NPP_DAYS*50 assume that the most pts we can have is two per hour
MEAN_GPP_SOIL_DAYS 5 over how many days do we keep the running mean
MEAN_GPP_SOIL_MAX_ENTRIES MEAN_GPP_SOIL_DAYS*50 assume that the most pts we can have is one per hour
LAMBDA 2501000 latent heat of vaporization (J/kg)
LAMBDA_S 2835000 latent heat of sublimation (J/kg)
RHO 1.3 air density (kg/m^3)
CP 1005. specific heat of air (J/(kg K))
GAMMA 66 psychometric constant (Pa/K)
E_STAR_SNOW 0.6 approximate saturation vapor pressure at 0°C (kPa)

Footnotes

  1. Fine and coarse root exudation are calculated as a fraction of GPP, but the exudates are subtracted from the fine and coarse root pools, respectively. ↩ ↩2