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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.

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
\(N_{\text{org, litter},0}\) 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

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
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
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
  • \(R_{dec}\): 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 \((\text{day}^{-1})\)
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 \(\text{y}^{-1}\) 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

Run-time Options

Configuration settings are applied in the following order of precedence:

  1. Default values built into SIPNET
  2. Values from the configuration file
  3. Command-line arguments

Thus, command-line arguments override settings in the configuration file, and configuration file settings override default values.

Input / Output Options

Option Default Description
input-file sipnet.in Name of input config file
file-name sipnet Prefix of climate and parameter files

Output Flags

Option Default Description
do-main-output on Print time series of all output variables to <file-name>.out
do-single-outputs off Print outputs one variable per file (e.g. <file-name>.NEE)
dump-config on Print final config to <file-name>.config
print-header on Whether to print header row in output files
quiet off Suppress info and warning message

Model Flags

Option Default Description
events on Enable event handling.
gdd on Use growing degree days to determine leaf growth.
growth-resp off Explicitly model growth respiration, rather than including with maintenance respiration.
leaf-water off Calculate leaf pool and evaporate from that pool.
litter-pool off Enable litter pool in addition to single soil carbon pool.
microbes off Enable microbe modeling.
snow on Keep track of snowpack, rather than assuming all precipitation is liquid.
soil-phenol off Use soil temperature to determine leaf growth.
water-hresp on Whether soil moisture affects heterotrophic respiration.

Note the following restrictions on these options: - soil-phenol and gdd may not both be turned on

Command Line Arguments

Command-line arguments can be used to specify run-time options when starting SIPNET. The syntax is as follows:

sipnet [options]

Where [options] can include any of the run-time options listed above. Flags use the syntax --flag to turn them on, or --no-flag to turn them off. Other options are specified by --option value.

See sipnet --help for a full list of available command-line options.

Configuration File Format

SIPNET reads a configuration file that specifies run-time options without using command-line arguments. By default, SIPNET looks for a file named sipnet.in in the current directory. These will be overwritten by command-line arguments if specified.

The configuration file uses a simple key-value format, option = value, with one option per line; comments follow #. Flags are specified as 0 for off and 1 for on.

Example Configuration File

Note that case is ignored for parameter names, as well as dashes and underscores.

# Base filename (used for derived filenames)
FILE_NAME = mysite

# Output options
DO_MAIN_OUTPUT = 1
DO_SINGLE_OUTPUTS = 0
DUMP_CONFIG = 1
PRINT_HEADER = 1
QUIET = 0

# Model options
EVENTS = 1
GDD = 1
GROWTH_RESP = 0
LEAF_WATER = 0
LITTER_POOL = 0
MICROBES = 0
SNOW = 1
SOIL_PHENOL = 0
WATER_HRESP = 1

When DUMP_CONFIG is on, SIPNET will output the final configuration (after applying all settings from defaults, configuration file, and command line) to a file named <file-name>.config.

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)

Input Files

Run Settings

See Run-time Options above.

Multi-site runs, sensitivity tests, and Monte Carlo runs are no longer supported. Typically these analyses are handled using the PEcAn Framework.

Parameters and Initial Conditions

Both initial conditions and parameters are specified in a file named sipnet.param.

The SIPNET parameter file (sipnet.param) specifies model parameters and their properties for each simulation. Each line in the file corresponds to a single parameter and contains five or six space-separated values.

Column Description
Parameter Name Name of the parameter
Value Value of the parameter to use in the model

Example sipnet.param file

Column names are not used, but are:

param_name value

The first lines in sipnet.param could be:

plantWoodInit 110
laiInit 0
litterInit 200
soilInit 7000
litterWFracInit 0.5
soilWFracInit 0.6
snowInit 1
microbeInit 0.5
fineRootFrac 0.2
coarseRootFrac 0.2
aMax 95
aMaxFrac 0.85
...

Climate

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

col parameter description units notes
1 year year of start of this timestep integer, e.g. 2010
2 day day of start of this timestep Day of year 1 = Jan 1
3 time time of start of this timestep hours after midnight e.g. noon = 12.0, midnight = 0.0, can be a fraction
4 length length of this timestep days variable-length timesteps allowed, typically not used
5 tair avg. air temp for this time step degrees Celsius
6 tsoil average soil temperature for this time step degrees Celsius can be estimated from Tair
7 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
8 precip total precip. for this time step cm input is in mm; water equivilant - either rain or snow
9 vpd average vapor pressure deficit kPa input is in Pa, can be calculated from air temperature and relative humidity.
10 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
11 vPress average vapor pressure in canopy airspace kPa input is in Pa
12 wspd avg. wind speed m/s

Note: An older format for this file included location as the first column and soilWetness as the last column. Files with this older format can still be read by sipnet: * SIPNET will print a warning indicating that it is ignoring the obsolete columns * If there is more than one location specified in the file, SIPNET will error and halt

Example sipnet.clim file:

Column names are not used, but are:

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

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

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     1998 305  7.00  0.417 3.6  1.8   5.6016 0.0000 125.7 23.5    809.4  1.1270
0     1998 305 17.00  0.583 1.9  1.3   0.0000 0.0000 108.1 75.9    732.7  1.1350
0     1998 306  7.00  0.417 2.2  1.4   2.7104 1.0000 114.1 71.6    741.8  0.9690

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 year year of start of this timestep e.g. 2010
2 day day of start of this timestep Day of year 1 = Jan 1
3 event_type type of event one of plant, harv, till, fert, irrig
4...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 must be sorted 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 year/day that appears in the events file
  • SIPNET will throw an error if it finds an event with no corresponding climate record
  • Events are processed with the first climate record that occurs for the relevant year/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
  • model representation: increases size of mineral N and litter C and N. Urea-N is assumed to be mineral N.
  • 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.in file:

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% 
2022  40  irrig  5 1          # 5cm canopy irrigation on day 40 applied to soil
2022  40  fert   0 0 10       # fertilized with 10 g / m2 N_min on day 40 of 2022
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 
2022  250 harv   0.1          # harvest 10% of aboveground plant biomass on day 250

Outputs

Model Outputs

The sipnet.out file contains a time series of state variables and fluxes from the simulation.

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

An example output file can be found in tests/smoke/sipnet.out.

Notes: PlantWoodC, PlantLeafC, Soil and Litter in g C/m^2; Water and Snow in cm; SoilWetness is fraction of WHC;
year day time plantWoodC plantLeafC soil microbeC coarseRootC fineRootC litter litterWater soilWater soilWetnessFrac snow npp nee cumNEE gpp rAboveground rSoil rRoot ra rh rtot evapotranspiration fluxestranspiration fPAR
1998 305  0.00  5759.77  1133.88 16000.06     8.00  1919.90  1919.64   400.00    0.500     6.00    0.500     0.00    -0.32     0.74     0.74     0.00    0.164    0.578    0.159    0.324    0.419    0.742 0.00302126   0.0000   0.0000
1998 305  7.00  5759.63  1133.71 16000.08     8.00  1919.77  1919.10   400.00    0.500     5.99    0.500     0.00    -0.30     0.97     1.71     0.22    0.271    0.917    0.251    0.522    0.666    1.188 0.00240544   0.0022   0.5821
1998 305 17.00  5759.16  1133.48 16000.15     8.00  1919.57  1918.37   400.00    0.500     5.99    0.499     0.00    -0.67     1.56     3.27     0.00    0.338    1.219    0.335    0.673    0.884    1.557 0.00662149   0.0000   0.5821

Events output

When event handling is enabled, SIPNET will create a file named events.out.

This file is designed primarily for testing and debugging.
It contains one row for each agronomic event that is processed. Each row lists the year, day, event type, and parameter name/value pairs. The name/value pairs represent the state variables that are directly changed by an event, recording the change (delta) applied to each.

Information in events.out can, in principle, be reconstructed or inferred from events.in and sipnet.out though this may be confounded if simultaneous events affect the same variable.

Still, sipnet.out is the authoritative source for information about system state and evolution in time, including responses to events.

Below is an example events.out, with header enabled for clarity. Note the delimiters: spaces separate columns, commas separate name/value pairs, and = map names with their values (deltas).

year  day  type     param_name=delta[,param_name=delta,...]
2023   65  plant    envi.plantLeafC=3.00,envi.plantWoodC=4.00,envi.fineRootC=5.00,envi.coarseRootC=6.00
2023   70  irrig    envi.soilWater=5.00
2023  200  harv     env.litter=5.46,envi.plantLeafC=-5.93,envi.plantWoodC=-4.75,envi.fineRootC=-3.73,envi.coarseRootC=-3.89
2024   65  plant    envi.plantLeafC=3.00,envi.plantWoodC=5.00,envi.fineRootC=7.00,envi.coarseRootC=9.00
2024   70  irrig    fluxes.immedEvap=2.50,envi.soilWater=2.50
2024  200  harv     env.litter=4.25,envi.plantLeafC=-1.39,envi.plantWoodC=-1.63,envi.fineRootC=-2.52,envi.coarseRootC=-2.97