SIPNET Model States and 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¶

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
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

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		fracLitterRespired	of the litter broken down, fraction respired (the rest is transferred to soil pool)
32	$K_{dec}$	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
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.
		baseMicrobeResp
new	$f_{\textrm{till}}$	tillageEff	Effect of tillage on decomposition that exponentially decays over time	fraction	Per‑event in `events.in`; 0 = no effect

$R_{dec}$: Rate of decomposition $(\text{day}^{-1})$
$Q_{10dec}$: Temperature coefficient for $R_{dec}$ (unitless)

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)

Methane parameters¶

$R_{meth}$: Rate of methane production $(\text{day}^{-1})$
$K_{meth}$: Rate constant for methane production under anaerobic conditions $(\text{day}^{-1})$
$K_{methox}$: Rate constant, methane oxidation $(\text{day}^{-1})$

	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

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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)

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	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

	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
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

	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

	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		fracLitterRespired	of the litter broken down, fraction respired (the rest is transferred to soil pool)
32	\(K_{dec}\)	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
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.
		baseMicrobeResp
new	\(f_{\textrm{till}}\)	tillageEff	Effect of tillage on decomposition that exponentially decays over time	fraction	Per‑event in `events.in`; 0 = no effect

	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)

	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)

	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