Third Party Extensions

---

format: html: engine: katex pdf: geometry: margin=0.5in header-includes: - \usepackage{longtable} - \usepackage{amsmath}

Input and Output Parameters (DRAFT)

Note: this is a work in progress draft. Not all parameters listed will be used in the CCMMF formulation of the model. The "Notation" section should be consistent with model equations, some of the mathematical symbols in the tables may not be.

Numbered items are cross-referenced with original documentation.

Table of Contents

• Input and Output Parameters (DRAFT)
  • Table of Contents
  • Notation
    • Variables (Pools, Fluxes, and Parameters)
    • Subscripts (Temporal, Spatial, or Contextual Identifiers)
  • Run-time Parameters
    • Initial state values
    • Litter Quality Parameters
    • Photosynthesis parameters
    • Phenology-related parameters
    • Allocation parameters
    • Autotrophic respiration parameters
    • Soil respiration parameters
    • Nitrogen Cycle Parameters
    • Methane parameters
    • Moisture-related parameters
    • Tree physiological parameters
  • Compile-time parameters
  • Drivers
    • Climate
      • Examples of climate files:
    • Agronomic Events
      • Fertilization Events
      • Tillage Events
      • Planting Events
      • Harvest Events
      • Example of events file:
  • Outputs

Notation

Variables (Pools, Fluxes, and Parameters)

Symbol	Description
$C$	Carbon pool
$N$	Nitrogen pool
$CN$	Carbon-to-Nitrogen ratio
$W$	Water pool or content
$R$	Respiration flux
$A$	Photosynthesis rate (net assimilation)
$T$	Temperature
$K$	Rate constant (e.g., for decomposition or respiration)
$LAI$	Leaf Area Index
$PAR$	Photosynthetically Active Radiation
$GPP$	Gross Primary Production
$NPP$	Net Primary Production
$NEE$	Net Ecosystem Exchange
$VPD$	Vapor Pressure Deficit
$ET$	Evapotranspiration
$Q_{10}$	Temperature sensitivity coefficient
$f$	The fraction of a pool or flux other than NPP
$F$	Flux of carbon, nitrogen, or water
$D$	Dependency or Damping Function
$N$	Nitrogen
$C$	Carbon
$\alpha$	The fraction of NPP allocated to a plant pool
$k$	Scaling factor

Subscripts (Temporal, Spatial, or Contextual Identifiers)

Subscript	Description
$X_0$	Initial value, default value, state at time zero
$X_t$	Value at time $t$
$X_d$	Daily value
$X_\text{max}$	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)
$X_\text{avg}$	Average value (e.g., over a timestep or spatial area)
$X_\text{leaf}$	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)
$X_\text{resp}$	respiration processes
$X_\text{dec}$	decomposition processes
$X_\text{vol}$	volatilization processes
$X_\text{VPD}$	vapor pressure deficit
$X_\text{org}$	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 physiology, 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
	$N_{\text{soil},0}$		Initial soil organic 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

Litter Quality Parameters

	Symbol	Name	Description	Units	Notes
	$CN_{\textrm{litter}}$		Carbon to Nitrogen ratio of litter
	$CN_{\textrm{wood}}$		Carbon to Nitrogen ratio of wood		CN_coarse_root = CN_wood
	$CN_{\textrm{leaf}}$		Carbon to Nitrogen ratio of leaves
	$CN_{\textrm{fine root}}$		Carbon to Nitrogen ratio of fine roots
	$CN_{\textrm{coarse root}}$		Carbon to Nitrogen ratio of coarse roots
	$k_\textit{CN}$		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	fraction per day	read in as per-year rate
	$L_{\text{max}}$		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

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 resp. as fraction of ($GPP - R_\text{a,wood} - R_\text{a,leaf}$)
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
33		baseSoilRespCold	soil respiration at 0°C and max soil moisture when tsoil < coldSoilThreshold	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
35		soilRespQ10Cold	scalar determining effect of temp on soil resp. when tsoil < coldSoilThreshold
36		coldSoilThreshold	temp. at which use baseSoilRespCold and soilRespQ10Cold	°C	Not used if SEASONAL_R_SOIL is 0
37		E0	E0 in Lloyd-Taylor soil respiration function		Not used if LLOYD_TAYLOR is 0
38		T0	T0 in Lloyd-Taylor soil respiration function		Not used if LLOYD_TAYLOR is 0
39		soilRespMoistEffect	scalar determining effect of moisture on soil resp.
		baseMicrobeResp

• $R_{dec}$: 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

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 $(\text{day}^{-1})$

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
48		litWaterDrainRate	rate at which litter rains into lower layer when litter layer fully moisture-saturated	cm water/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)
52		m_ballBerry	slope for the Ball Berry relationship

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	$\text{y}^{-1}$	read in as per-year rate; leaf loss handled separately
70	$K_\text{fine root}$	fineRootTurnoverRate	turnover of fine roots	$\text{y}^{-1}$	per year rate
71	$K_\text{coarse root}$	coarseRootTurnoverRate	turnover of coarse roots	yr^-1	per year rate

Compile-time parameters

Parameter 0	Default	Description
CSV_O	0	output .out file as a CSV file
ALTERNATIVE_TRANS 0	0	do we want to implement alternative transpiration?
BALL_BERRY 0	0	implement a Ball Berry submodel to calculate gs from RH, CO2 and A
PENMAN_MONTEITH_TRANS 0	0	implement a transpiration calculation based on the Penman-Monteith Equation
GROWTH_RESP 0	0	explicitly model growth resp., rather than including with maint. resp.
LLOYD_TAYLOR 0	0	use Lloyd-Taylor model for soil respiration, in which temperature sensitivity decreases at higher temperatures?
SEASONAL_R_SOIL 0 && !LLOYD_TAYLOR	0	use different parameters for soil resp. (baseSoilResp and soilRespQ10) when tsoil < (some threshold)?
WATER_PSN 1	1	does soil moisture affect photosynthesis?
WATER_HRESP 1	1	does soil moisture affect heterotrophic respiration?
DAYCENT_WATER_HRESP 0 && WATER_HRESP	0	use DAYCENT soil moisture function?
MODEL_WATER 1	1	do we model soil water (and ignore soilWetness)?
COMPLEX_WATER 1 && MODEL_WATER	1	do we use a more complex water submodel? (model evaporation as well as transpiration)
LITTER_WATER 0 && (COMPLEX_WATER)	0	do we have a separate litter water layer, used for evaporation?
LITTER_WATER_DRAINAGE 1 && (LITTER_WATER)	0	does water from the top layer drain down into bottom layer even if top layer not overflowing?
SNOW (1 || (COMPLEX_WATER)) && MODEL_WATER	1	keep track of snowpack, rather than assuming all precip. is liquid
GDD 0	0	use GDD to determine leaf growth? (note: mutually exclusive with SOIL_PHENOL)
SOIL_PHENOL 0 && !GDD	0	use soil temp. to determine leaf growth? (note: mutually exclusive with GDD)
LITTER_POOL 0	0	have extra litter pool, in addition to soil c pool
SOIL_MULTIPOOL 0 && !LITTER_POOL	0	do we have a multipool approach to model soils?
NUMBER_SOIL_CARBON_POOLS 3	3	number of pools we want to have. Equal to 1 if SOIL_MULTIPOOL is 0
SOIL_QUALITY 0 && SOIL_MULTIPOOL	0	do we have a soil quality submodel?
MICROBES 0 && !SOIL_MULTIPOOL	0	do we utilize microbes. This will only be an option if SOIL_MULTIPOOL is 0 and MICROBES is 1
STOICHIOMETRY 0 && MICROBES	0	do we utilize stoichometric considerations for the microbial pool?
ROOTS 0	0	do we model root dynamics? If no, roots are part of wood pool. If yes, split into coarse and fine roots
MODIS 0	0	do we use modis FPAR data to constrain GPP?
C_WEIGHT 12.0	12	molecular weight of carbon
MEAN_NPP_DAYS 5	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	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)

Drivers

Climate

For each step of the model, for each location, the following inputs are needed. These are provided in a file named <sitename>.clim with the following columns:

col	parameter	description	units	notes
1	loc	spatial location index		maps to param-spatial file, can be 0 for a single site, as when used by PEcAn
2	year	year of start of this timestep		integer, e.g. 2010
3	day	day of start of this timestep		integer where 1 = Jan 1
4	time	time of start of this timestep	hours after midnight	e.g. noon = 12.0, midnight = 0.0, can be a fraction
5	length	length of this timestep	days	variable-length timesteps allowed, typically not used
6	tair	avg. air temp for this time step	degrees Celsius
7	tsoil	average soil temperature for this time step	degrees Celsius	can be estimated from Tair
8	par	average photosynthetically active radiation (PAR) for this time step	$\text{Einsteins} \cdot m^{-2} \text{ground area} \cdot \text{time step}^{-1}$	input is in Einsteins * m^-2 ground area, summed over entire time step
9	precip	total precip. for this time step	cm	input is in mm; water equivilant - either rain or snow
10	vpd	average vapor pressure deficit	kPa	input is in Pa, can be calculated from air temperature and relative humidity.
11	vpdSoil	average vapor pressure deficit between soil and air	kPa	input is in Pa ; differs from vpd in that saturation vapor pressure is calculated using Tsoil rather than Tair
12	vPress	average vapor pressure in canopy airspace	kPa	input is in Pa
13	wspd	avg. wind speed	m/s
14	soilWetness	fractional soil wetness	unitless (0-1)	$f_\text{WHC}$; Used if MODEL_WATER=0; if MODEL_WATER=1, soil wetness is simulated

Examples of climate files:

Column names are not used, but are:

loc	year day  time length tair tsoil par    precip vpd   vpdSoil vPress wspd   soilWetness

Half-hour time step

0	1998 305  0.00    -1800   1.9000   1.2719   0.0000   0.0000 109.5364  77.5454 726.6196   1.6300   0.0000
0	1998 305  0.50    -1800   1.9000   1.1832   0.0000   0.0000 109.5364  73.1254 726.6196   1.6300   0.0000
0	1998 305  1.00    -1800   2.0300   1.1171   0.0000   0.0000 110.4243  63.9567 732.5092   0.6800   0.0000
0	1998 305  1.50    -1800   2.0300   1.0439   0.0000   0.0000 110.4243  60.3450 732.5092   0.6800   0.0000

Variable time step

0	  1998 305  0.00  0.292 1.5  0.8   0.0000 0.0000 105.8 70.1    711.6  0.9200 0.0000
0	  1998 305  7.00  0.417 3.6  1.8   5.6016 0.0000 125.7 23.5    809.4  1.1270 0.0000
0	  1998 305 17.00  0.583 1.9  1.3   0.0000 0.0000 108.1 75.9    732.7  1.1350 0.0000
0	  1998 306  7.00  0.417 2.2  1.4   2.7104 1.0000 114.1 71.6    741.8  0.9690 0.0000

Agronomic Events

For managed ecosystems, the following inputs are provided in a file named events.in with the following columns:

col	parameter	description	units	notes
1	loc	spatial location index		maps to param-spatial file
2	year	year of start of this timestep		e.g. 2010
3	day	day of start of this timestep	Day of year	1 = Jan 1
4	event_type	type of event		one of plant, harv, till, fert, irrig
5...n	event_param	parameter associated with event		see table below

• Agronomic events are stored in events.in, one event per row
• Events in the file are sorted first by location, and then chronologically
• Events are specified by year and day (no hourly timestamp)
• It is assumed that there is one (or more) records in the climate file for each location/day that appears in the events file
  • We will throw an error if we find an event with no corresponding climate record
• Events are processed with the first climate record that occurs for the relevant location/day as an instantaneous one-time change
  • We may need events with duration later, spec TBD. Tillage is likely in this bucket.
• The effects of an event are applied after fluxes are calculated for the current climate record; they are applied as a delta to one or more state variables, as required

parameter	col	req?	description
amount	5	Y	Amount added (cm/d)
method	6	Y	0=canopy 1=soil 2=flood (placeholder)

Model representation: an irrigation event increases soil moisture. Canopy irrigation also loses some moisture to evaporation.

Specifically:

• amount is listed as cm/d, but as events are specified per-day, this is treated as cm of water added on that day
• For method=soil, this amount of water is added directly to the soilWater state variable
• For method=canopy, a fraction of the irrigation water (determined by input param immedEvapFrac) is added to the flux state variable immedEvap, with the remainder going to soilWater.
• Initial implementation assumes that LITTER_WATER is not on. This might be revisited at a later date.

Notes:

• irrigation could also directly change the soil moisture content rather than adding water as a flux. This could be used to represent an irrigation program that sets a moisture range and turns irrigation on at the low end and off at the high end of the range.

Fertilization Events

parameter	col	req?	description
org-N	5	Y	g N / m2
org-C	6	Y	g C / m2
min-N	7	Y	g N / m2 (NH4+NO3 in one pool model; NH4 in two pool model)
min-N2	8	Y*	g N / m2 (*not unused in one pool model, NO3 in two pool model)

• model representation: increases size of mineral N and litter C and N. Urea-N is assumed to be mineral N or NH4.
• notes: PEcAn will handle conversion from fertilizer amount and type to mass of N and C allocated to different pools

Tillage Events

parameter	col	req?	description
SOM decomposition modifier	5	Y	% increase in $K_{dec}$
litter decomposition modifier	6	Y	% increase in $K_{lit}$

• model representation:
  • increase k for one month, amount proportional to depth
  • transfer litter C and N to soil pool
• notes: could also alter bulk density and other soil properties

Planting Events

parameter	col	req?	description
leaf-C	5	Y	C added to leaf pool (g C / m2)
wood-C	6	Y	C added to above-ground wood pool (g C / m2)
fine-root-C	7	Y	C added to fine root pool (g C / m2)
coarse-root-C	8	Y	C added to coarse root pool (g C / m2)

• model representation:
  • Date of event is the date of emergence, not the date of actual planting
  • Increases size of carbon pools by the amount of each respective parameter
  • $N$ pools are calculated from $CN$ stoichiometric ratios.
• notes: PFT (crop type) is not an input parameter for a planting event because SIPNET only represents a single PFT.

Harvest Events

parameter	col	req?	description
fraction of aboveground biomass removed	5	Y
fraction of belowground biomass removed	6	N	default = 0
fraction of aboveground biomass transferred to litter pool	7	N	default = 1 - removed
fraction of belowground biomass transferred to litter pool	8	N	default = 1 - removed

• model representation:
  • biomass C and N pools are either removed or added to litter
  • for annuals or plants terminated, no biomass remains (col 5 + col 7 = 1 and col 6 + col 8 = 1).
  • for perennials, some biomass may remain (col 5 + col 7 <= 1 and col 6 + col 8 <= 1; remainder is living).
  • root biomass is only removed for root crops

Example of events file:

1  2022  40  irrig  5   1        # 5cm canopy irrigation on day 40
1  2022  40  fert   10 5 0 0     # fertilized with 10 g / m2 NO3-N and 5 g / m2 NH4-N on day 40
1  2022  35  till   0.2 0.3      # tilled on day 35, soil organic matter pool decomposition rate increases by 20% and soil litter pool decomposition rate increases by 30% 
1  2022  50  plant  10 3 2 5     # plant emergence on day 50 with 10/3/2/4 g C / m2, respectively, added to the leaf/wood/fine root/coarse root pools 
1  2022  250 harv   0.1          # harvest 10% of aboveground plant biomass on day 250

Outputs

	Symbol	Parameter Name	Definition	Units
1		loc	spatial location index
2		year	year of start of this timestep
3		day	day of start of this timestep
4		time	time of start of this timestep
5		plantWoodC	carbon in wood	g C/m$^2$
6		plantLeafC	carbon in leaves	g C/m$^2$
7		soil	carbon in mineral soil	g C/m$^2$
8		microbeC	carbon in soil microbes	g C/m$^2$
9		coarseRootC	carbon in coarse roots	g C/m$^2$
10		fineRootC	carbon in fine roots	g C/m$^2$
11		litter	carbon in litter	g C/m$^2$
12		litterWater	moisture in litter layer	cm
13		soilWater	moisture in soil	cm
14	$f_\text{WHC}$	soilWetnessFrac	moisture in soil as fraction
15		snow	snow water	cm
16		npp	net primary production	g C/m$^2$
17		nee	net ecosystem production	g C/m$^2$
18		cumNEE	cumulative nee	g C/m$^2$
19	$GPP$	gpp	gross ecosystem production	g C/m$^2$
20	$R_{A,\text{above}}$	rAboveground	plant respiration above ground	g C/m$^2$
21	$R_H$	rSoil	soil respiration	g C/m$^2$
22	$R_{A\text{, root}}$	rRoot	root respiration	g C/m$^2$
23	$R$	rtot	total respiration	g C/m$^2$
24		fluxestranspiration	transpiration	cm
	$F^N_\text{vol}$	fluxesn2o	Nitrous Oxide flux	g N/m$^2$ / timestep
	$F^C_{\text{CH}_4}$	fluxesch4	Methane Flux	g C/m$^2$ / timestep
	$F^N_\text{vol}$	fluxesn2o	Nitrous Oxide flux	g N/m$^2$ / timestep
	$F^C_{\text{CH}_4}$	fluxesch4	Methane Flux	g C/m$^2$ / timestep