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‎docs/sipnet_inputs_outputs.md

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# SIPNET Input and Output Parameters
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## Table of Contents
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1. [Run-time Parameters](#1-run-time-parameters)
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- [Initial state values](#initial-state-values)
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- [Photosynthesis parameters](#photosynthesis-parameters)
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- [Phenology-related parameters](#phenology-related-parameters)
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- [Autotrophic respiration parameters](#autotrophic-respiration-parameters)
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- [Soil respiration parameters](#soil-respiration-parameters)
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- [Moisture-related parameters](#moisture-related-parameters)
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- [Quality model parameters](#quality-model-parameters)
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2. [Compile-time parameters](#2-compile-time-parameters)
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3. [Climate driver inputs](#3-climate-driver-inputs)
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4. [Outputs](#4-outputs)
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## 1. Run-time Parameters
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Model parameters that can change from one run to the next. These include initializations of state, allocations, and biophysical rate constants.
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### Initial state values
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| | Parameter Name | Definition | Units | notes |
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| :---- | :---- | :---- | :---- | :---- |
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| 1 | plantWoodInit | Initial wood carbon | g C * m^-2 ground area | above-ground + roots |
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| 2 | laiInit | initial leaf area | m^2 leaves * m^-2 ground area | multiply by leafCSpWt to get initial plant leaf C |
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| 3 | litterInit | Initial litter carbon | g C * m^-2 ground area | |
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| 4 | soilInit | Initial soil carbon | g C * m^-2 ground area | |
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| 5 | litterWFracInit | | unitless | fraction of litterWHC |
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| 6 | soilWFracInit | | unitless | fraction of soilWHC |
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| 7 | snowInit | Initial snow water | cm water equiv. | |
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### Photosynthesis parameters
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| | Parameter Name | Definition | Units | notes |
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| :---- | :---- | :---- | :---- | :---- |
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| 8 | aMax | max photosynthesis | nmol CO2 * g^-1 leaf * sec^-1 | assuming max. possible par, all intercepted, no temp, water or vpd stress |
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| 9 | aMaxFrac | avg. daily aMax as fraction of instantaneous | | |
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| 10 | baseFolRespFrac | basal foliage resp. rate | | as % of max. net photosynth. rate |
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| 11 | psnTMin | min temp at which net photosynthesis occurs | °C | |
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| 12 | psnTOpt | optimal temp at which net photosynthesis occurs | °C | |
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| 13 | dVpdSlope | used to calculate VPD effect on Psn | dimensionless | dVpd = 1 - dVpdSlope * vpd^dVpdExp |
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| 14 | dVpdExp | used to calculate VPD effect on Psn | dimensionless | dVpd = 1 - dVpdSlope * vpd^dVpdExp |
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| 15 | halfSatPar | par at which photosynthesis occurs at 1/2 theoretical maximum | Einsteins * m^-2 ground area * day^-1 | |
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| 16 | attenuation | light attenuation coefficient | | |
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### Phenology-related parameters
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| | Parameter Name | Definition | Units | notes |
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| :---- | :---- | :---- | :---- | :---- |
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| 17 | leafOnDay | day when leaves appear | | |
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| 18 | gddLeafOn | with gdd-based phenology, gdd threshold for leaf appearance | | |
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| 19 | soilTempLeafOn | with soil temp-based phenology, soil temp threshold for leaf appearance | | |
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| 20 | leafOffDay | day when leaves disappear | | |
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| 21 | leafGrowth | additional leaf growth at start of growing season | g C * m^-2 ground | |
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| 22 | fracLeafFall | additional fraction of leaves that fall at end of growing season | | |
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| 23 | leafAllocation | fraction of NPP allocated to leaf growth | | |
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| 24 | leafTurnoverRate | average turnover rate of leaves | fraction per day | read in as per-year rate |
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### Autotrophic respiration parameters
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| | Parameter Name | Definition | Units | notes |
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| :---- | :---- | :---- | :---- | :---- |
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| 25 | baseVegResp | vegetation maintenance respiration at 0°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) |
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| 26 | vegRespQ10 | scalar determining effect of temp on veg. resp. | | |
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| 27 | growthRespFrac | growth resp. as fraction of (GPP - woodResp - folResp) | | |
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| 28 | frozenSoilFolREff | amount that foliar resp. is shutdown if soil is frozen | | 0 = full shutdown, 1 = no shutdown |
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| 29 | frozenSoilThreshold | soil temperature below which frozenSoilFolREff and frozenSoilEff kick in | °C | |
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### Soil respiration parameters
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| | Parameter Name | Definition | Units | notes |
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| :---- | :---- | :---- | :---- | :---- |
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| 30 | 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 |
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| 31 | fracLitterRespired | of the litter broken down, fraction respired (the rest is transferred to soil pool) | | |
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| 32 | baseSoilResp | soil respiration at 0°C and max soil moisture | g C respired * g^-1 soil C * day^-1 | read in as per-year rate |
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| 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 |
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| 34 | soilRespQ10 | scalar determining effect of temp on soil resp. | | |
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| 35 | soilRespQ10Cold | scalar determining effect of temp on soil resp. when tsoil < coldSoilThreshold | | |
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| 36 | coldSoilThreshold | temp. at which use baseSoilRespCold and soilRespQ10Cold | °C | Not used if SEASONAL_R_SOIL is 0 |
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| 37 | E0 | E0 in Lloyd-Taylor soil respiration function | | Not used if LLOYD_TAYLOR is 0 |
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| 38 | T0 | T0 in Lloyd-Taylor soil respiration function | | Not used if LLOYD_TAYLOR is 0 |
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| 39 | soilRespMoistEffect | scalar determining effect of moisture on soil resp. | | |
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### Moisture-related parameters
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| | Parameter Name | Definition | Units | notes |
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| :---- | :---- | :---- | :---- | :---- |
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| 40 | waterRemoveFrac | fraction of plant available soil water which can be removed in one day without water stress occurring | | |
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| 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) |
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| 42 | wueConst | water use efficiency constant | | |
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| 43 | litterWHC | litter (evaporative layer) water holding capacity | cm | |
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| 44 | soilWHC | soil (transpiration layer) water holding capacity | cm | |
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| 45 | immedEvapFrac | fraction of rain that is immediately intercepted & evaporated | | |
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| 46 | fastFlowFrac | fraction of water entering soil that goes directly to drainage | | |
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| 47 | snowMelt | rate at which snow melts | cm water equiv./°C/day | |
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| 48 | litWaterDrainRate | rate at which litter water drains into lower layer when litter layer fully moisture-saturated | c m water/day | |
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| 49 | rdConst | scalar determining amount of aerodynamic resistance | | |
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| 50 | rSoilConst1 | | | soil resistance = e^(rSoilConst1 - rSoilConst2 * W1) , where W1 = (litterWater/litterWHC) |
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| 51 | rSoilConst2 | | | soil resistance = e^(rSoilConst1 - rSoilConst2 * W1) , where W1 = (litterWater/litterWHC) |
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| 52 | m_ballBerry | slope for the Ball Berry relationship | | |
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| 53 | leafCSpWt | | g C * m^-2 leaf area | |
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| 54 | cFracLeaf | | g leaf C * g^-1 leaf | |
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| 55 | woodTurnoverRate | average turnover rate of woody plant C | fraction per day | read in as per-year rate; leaf loss handled separately |
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### Quality model parameters
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| | Parameter Name | Definition | Units | notes |
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| :---- | :---- | :---- | :---- | :---- |
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| 56 | qualityLeaf | value for leaf litter quality | | |
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| 57 | qualityWood | value for wood litter quality | | |
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| 58 | efficiency | conversion efficiency of ingested carbon | | |
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| 59 | maxIngestionRate | maximum ingestion rate of the microbe | hr-1 | |
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| 60 | halfSatIngestion | half saturation ingestion rate of microbe | mg C g-1 soil | |
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| 61 | totNitrogen | Percentage nitrogen in soil | | |
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| 62 | microbeNC | microbe N:C ratio | mg N / mg C | |
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| 63 | microbeInit | | mg C / g soil microbe | initial carbon amount |
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| 64 | fineRootFrac | fraction of wood carbon allocated to fine roots | | |
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| 65 | coarseRootFrac | fraction of wood carbon that is coarse roots | | |
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| 66 | fineRootAllocation | fraction of NPP allocated to fine roots | | |
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| 67 | woodAllocation | fraction of NPP allocated to wood | | |
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| 68 | fineRootExudation | fraction of GPP exuded to the soil | | |
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| 69 | coarseRootExudation | fraction of NPP exuded to the soil | | |
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| 70 | fineRootTurnoverRate | turnover of fine roots | per year rate | |
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| 71 | coarseRootTurnoverRate | turnover of coarse roots | per year rate | |
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| 72 | baseFineRootResp | base respiration rate of fine roots | per year rate | |
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| 73 | baseCoarseRootResp | base respiration rate of coarse roots | per year rate | |
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| 74 | fineRootQ10 | Q10 of fine roots | | |
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| 75 | coarseRootQ10 | Q10 of coarse roots | | |
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| 76 | baseMicrobeResp | base respiration rate of microbes | | |
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| 77 | microbeQ10 | Q10 of coarse roots | | |
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| 78 | microbePulseEff | fraction of exudates that microbes immediately use | | |
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## 2. Compile-time parameters
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| CSV_OUTPUT 0 | 0 | output .out file as a CSV file |
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| :---- | :---- | :---- |
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| ALTERNATIVE_TRANS 0 | 0 | do we want to impliment alternative transpiration? |
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| BALL_BERRY 0 | 0 | impliment a Ball Berry submodel to calculate gs from RH, CO2 and A |
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| PENMAN_MONTEITH_TRANS 0 | 0 | impliment a transpiration calculation based on the Penman-Monteith Equation |
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| GROWTH_RESP 0 | 0 | explicitly model growth resp., rather than including with maint. resp. |
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| LLOYD_TAYLOR 0 | 0 | use Lloyd-Taylor model for soil respiration, in which temperature sensitivity decreases at higher temperatures? |
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| SEASONAL_R_SOIL 0 && !LLOYD_TAYLOR | 0 | use different parameters for soil resp. (baseSoilResp and soilRespQ10) when tsoil < (some threshold)? |
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| WATER_PSN 1 | 1 | does soil moisture affect photosynthesis? |
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| WATER_HRESP 1 | 1 | does soil moisture affect heterotrophic respiration? |
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| DAYCENT_WATER_HRESP 0 && WATER_HRESP | 0 | use DAYCENT soil moisture function? |
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| MODEL_WATER 1 | 1 | do we model soil water (and ignore soilWetness)? |
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| COMPLEX_WATER 1 && MODEL_WATER | 1 | do we use a more complex water submodel? (model evaporation as well as transpiration) |
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| LITTER_WATER 0 && (COMPLEX_WATER) | 0 | do we have a separate litter water layer, used for evaporation? |
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| LITTER_WATER_DRAINAGE 1 && (LITTER_WATER) | 0 | does water from the top layer drain down into bottom layer even if top layer not overflowing? |
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| SNOW (1 || (COMPLEX_WATER)) && MODEL_WATER | 1 | keep track of snowpack, rather than assuming all precip. is liquid |
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| GDD 0 | 0 | use GDD to determine leaf growth? (note: mutually exclusive with SOIL_PHENOL) |
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| SOIL_PHENOL 0 && !GDD | 0 | use soil temp. to determine leaf growth? (note: mutually exclusive with GDD) |
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| LITTER_POOL 0 | 0 | have extra litter pool, in addition to soil c pool |
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| SOIL_MULTIPOOL 0 && !LITTER_POOL | 0 | do we have a multipool approach to model soils? |
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| NUMBER_SOIL_CARBON_POOLS 3 | 3 | number of pools we want to have. Equal to 1 if SOIL_MULTIPOOL is 0 |
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| SOIL_QUALITY 0 && SOIL_MULTIPOOL | 0 | do we have a soil quality submodel? |
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| MICROBES 0 && !SOIL_MULTIPOOL | 0 | do we utilize microbes. This will only be an option if SOIL_MULTIPOOL is 0 and MICROBES is 1 |
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| STOICHIOMETRY 0 && MICROBES | 0 | do we utilize stoichometric considerations for the microbial pool? |
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| ROOTS 0 | 0 | do we model root dynamics? |
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| MODIS 0 | 0 | do we use modis FPAR data to constrain GPP? |
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| C_WEIGHT 12.0 | 12 | molecular weight of carbon |
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| MEAN_NPP_DAYS 5 | 5 | over how many days do we keep the running mean |
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| MEAN_NPP_MAX_ENTRIES | MEAN_NPP_DAYS*50 | assume that the most pts we can have is two per hour |
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| MEAN_GPP_SOIL_DAYS 5 | 5 | over how many days do we keep the running mean |
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| MEAN_GPP_SOIL_MAX_ENTRIES | MEAN_GPP_SOIL_DAYS*50 | assume that the most pts we can have is one per hour |
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| LAMBDA | 2501000 | latent heat of vaporization (J/kg) |
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| LAMBDA_S | 2835000 | latent heat of sublimation (J/kg) |
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| RHO | 1.3 | air density (kg/m^3) |
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| CP | 1005. | specific heat of air (J/(kg K)) |
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| GAMMA | 66 | psychometric constant (Pa/K) |
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| E_STAR_SNOW | 0.6 | approximate saturation vapor pressure at 0°C (kPa) |
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## 3. Climate driver inputs
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For each step of the model, for each location, the following inputs are needed.
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| 1 | loc | spatial location index | | maps to param-spatial file |
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| :---- | :---- | :---- | :---- | :---- |
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| 2 | year | year of start of this timestep | | e.g. 2010 |
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| 3 | day | day of start of this timestep | | 1 = Jan 1 |
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| 4 | time | time of start of this timestep | hour fraction | e.g. noon = 12.0, midnight = 0.0 |
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| 5 | length | length of this timestep | days | allow variable-length timesteps |
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| 6 | tair | avg. air temp for this time step | °C | |
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| 7 | tsoil | avg. soil temp for this time step | °C | |
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| 8 | par | average par for this time step | Einsteins * m^-2 ground area * day^-1 | input is in Einsteins * m^-2 ground area, summed over entire time step |
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| 9 | precip | total precip. for this time step | cm water equiv. - either rain or snow | input is in mm |
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| 10 | vpd | average vapor pressure deficit | kPa | input is in Pa |
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| 11 | vpdSoil | average vapor pressure deficit between soil and air | kPa | input is in Pa ; differs from vpd in that saturation vapor pressure calculated using Tsoil rather than Tair |
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| 12 | vPress | average vapor pressure in canopy airspace | kPa | input is in Pa |
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| 13 | wspd | avg. wind speed | m/s | |
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| 14 | soilWetness | fractional soil wetness | fraction of saturation - between 0 and 1 | Not used if MODEL_WATER is 1 |
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## 4. Outputs
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For each step of the model, for each location, the following outputs are generated.
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| | Parameter Name | Definition | Units |
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| :---- | :---- | :---- | :---- |
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| 1 | loc | spatial location index | |
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| 2 | year | year of start of this timestep | |
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| 3 | day | day of start of this timestep | |
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| 4 | time | time of start of this timestep | |
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| 5 | plantWoodC | carbon in wood | g C/m^2 |
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| 6 | plantLeafC | carbon in leaves | g C/m^2 |
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| 7 | soil | carbon in mineral soil | g C/m^2 |
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| 8 | microbeC | carbon in soil microbes | |
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| 9 | coarseRootC | carbon in coarse roots | |
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| 10 | fineRootC | carbon in fine roots | |
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| 11 | litter | carbon in litter | g C/m^2 |
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| 12 | litterWater | moisture in litter layer | cm |
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| 13 | soilWater | moisture in soil | cm |
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| 14 | soilWetnessFrac | moisture in soil as fraction | |
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| 15 | snow | snow water | cm |
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| 16 | npp | net primary production | |
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| 17 | nee | net ecosystem production | |
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| 18 | cumNEE | cumulative nee | |
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| 19 | gpp | gross ecosystem production | |
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| 20 | rAboveground | plant respiration above ground | |
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| 21 | rSoil | soil respiration | |
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| 22 | rRoot | root respiration | |
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| 23 | rtot | total respiration | |
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| 24 | fluxestranspiration | transpiration | |
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