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 |
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 |
| 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 \((\text{day}^{-1})\)
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 | \(\text{y}^{-1}\) | 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:
- Default values built into SIPNET
- Values from the configuration file
- 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
cmof water added on that day - For method=soil, this amount of water is added directly to the
soilWaterstate variable - For method=canopy, a fraction of the irrigation water (determined by input param
immedEvapFrac) is added to the flux state variableimmedEvap, with the remainder going tosoilWater. - 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