diff --git a/docs/sipnet_inputs_outputs.md b/docs/sipnet_inputs_outputs.md index bf2c414..148605b 100644 --- a/docs/sipnet_inputs_outputs.md +++ b/docs/sipnet_inputs_outputs.md @@ -23,10 +23,10 @@ Model parameters that can change from one run to the next. These include initial | | Parameter Name | Definition | Units | notes | | :---- | :---- | :---- | :---- | :---- | -| 1 | plantWoodInit | Initial wood carbon | g C $\times$ m$^{-2}$ ground area | above-ground + roots | -| 2 | laiInit | initial leaf area | m$^2$ leaves $\times$ m$^{-2}$ ground area | multiply by leafCSpWt to get initial plant leaf C | -| 3 | litterInit | Initial litter carbon | g C $\times$ m$^{-2}$ ground area | | -| 4 | soilInit | Initial soil carbon | g C $\times$ m$^{-2}$ ground area | | +| 1 | plantWoodInit | Initial wood carbon | g C * m^-2 ground area | above-ground + roots | +| 2 | laiInit | initial leaf area | m^2 leaves * m^-2 ground area | multiply by leafCSpWt to get initial plant leaf C | +| 3 | litterInit | Initial litter carbon | g C * m^-2 ground area | | +| 4 | soilInit | Initial soil carbon | g C * m^-2 ground area | | | 5 | litterWFracInit | | unitless | fraction of litterWHC | | 6 | soilWFracInit | | unitless | fraction of soilWHC | | 7 | snowInit | Initial snow water | cm water equiv. | | @@ -36,14 +36,14 @@ Model parameters that can change from one run to the next. These include initial | | Parameter Name | Definition | Units | notes | | :---- | :---- | :---- | :---- | :---- | -| 8 | aMax | max photosynthesis | nmol CO2 $\times$ g$^{-1}$ leaf $\times$ sec$^{-1}$ | assuming max. possible par, all intercepted, no temp, water or vpd stress | +| 8 | aMax | max photosynthesis | nmol CO2 * g^-1 leaf * sec^-1 | assuming max. possible par, all intercepted, no temp, water or vpd stress | | 9 | aMaxFrac | avg. daily aMax as fraction of instantaneous | | | | 10 | baseFolRespFrac | basal foliage resp. rate | | as % of max. net photosynth. rate | -| 11 | psnTMin | min temp at which net photosynthesis occurs | $\degree$C | | -| 12 | psnTOpt | optimal temp at which net photosynthesis occurs | $\degree$C | | -| 13 | dVpdSlope | used to calculate VPD effect on Psn | dimensionless | dVpd = 1 - dVpdSlope $\times$ vpd$^{\textrm{dVpdExp}}$ | -| 14 | dVpdExp | used to calculate VPD effect on Psn | dimensionless | dVpd = 1 - dVpdSlope $\times$ vpd$^{\textrm{dVpdExp}}$ | -| 15 | halfSatPar | par at which photosynthesis occurs at 1/2 theoretical maximum | Einsteins $\times$ m$^{-2}$ ground area $\times$ day$^{-1}$ | | +| 11 | psnTMin | min temp at which net photosynthesis occurs | °C | | +| 12 | psnTOpt | optimal temp at which net photosynthesis occurs | °C | | +| 13 | dVpdSlope | used to calculate VPD effect on Psn | dimensionless | dVpd = 1 - dVpdSlope * vpd^{\textrm{dVpdExp}} | +| 14 | dVpdExp | used to calculate VPD effect on Psn | dimensionless | dVpd = 1 - dVpdSlope * vpd^{\textrm{dVpdExp}} | +| 15 | halfSatPar | par at which photosynthesis occurs at 1/2 theoretical maximum | Einsteins * m^-2 ground area * day^-1 | | | 16 | attenuation | light attenuation coefficient | | | ### Phenology-related parameters @@ -54,7 +54,7 @@ Model parameters that can change from one run to the next. These include initial | 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 | leafOffDay | day when leaves disappear | | | -| 21 | leafGrowth | additional leaf growth at start of growing season | g C $\times$ m$^{-2}$ ground | | +| 21 | leafGrowth | additional leaf growth at start of growing season | g C * m^-2 ground | | | 22 | fracLeafFall | additional fraction of leaves that fall at end of growing season | | | | 23 | leafAllocation | fraction of NPP allocated to leaf growth | | | | 24 | leafTurnoverRate | average turnover rate of leaves | fraction per day | read in as per-year rate | @@ -64,24 +64,24 @@ Model parameters that can change from one run to the next. These include initial | | Parameter Name | Definition | Units | notes | | :---- | :---- | :---- | :---- | :---- | -| 25 | baseVegResp | vegetation maintenance respiration at 0 $\degree$C | g C respired $\times$ g$^{-1}$ plant C $\times$ 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) | +| 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) | | 26 | vegRespQ10 | scalar determining effect of temp on veg. resp. | | | | 27 | growthRespFrac | growth resp. as fraction of (GPP - woodResp - folResp) | | | | 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 | $\degree$C | | +| 29 | frozenSoilThreshold | soil temperature below which frozenSoilFolREff and frozenSoilEff kick in | °C | | ### Soil respiration parameters | | Parameter Name | Definition | Units | notes | | :---- | :---- | :---- | :---- | :---- | -| 30 | litterBreakdownRate | rate at which litter is converted to soil/respired at 0 $\degree$C and max soil moisture | g C broken down $\times$ g$^{-1}$ litter C $\times$ day$^{-1}$ | read in as per-year rate | +| 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 | | 31 | fracLitterRespired | of the litter broken down, fraction respired (the rest is transferred to soil pool) | | | -| 32 | baseSoilResp | soil respiration at 0 $\degree$C and max soil moisture | g C respired $\times$ g$^{-1}$ soil C $\times$ day$^{-1}$ | read in as per-year rate | -| 33 | baseSoilRespCold | soil respiration at 0 $\degree$C and max soil moisture when tsoil \< coldSoilThreshold | g C respired $\times$ g$^{-1}$ soil C $\times$ day$^{-1}$ | read in as per-year rate | +| 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 | +| 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 | soilRespQ10 | scalar determining effect of temp on soil resp. | | | | 35 | soilRespQ10Cold | scalar determining effect of temp on soil resp. when tsoil \< coldSoilThreshold | | | -| 36 | coldSoilThreshold | temp. at which use baseSoilRespCold and soilRespQ10Cold | $\degree$C | Not used if SEASONAL_R_SOIL is 0 | +| 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. | | | @@ -98,14 +98,14 @@ Model parameters that can change from one run to the next. These include initial | 44 | soilWHC | soil (transpiration layer) water holding capacity | cm | | | 45 | immedEvapFrac | fraction of rain that is immediately intercepted & evaporated | | | | 46 | fastFlowFrac | fraction of water entering soil that goes directly to drainage | | | -| 47 | snowMelt | rate at which snow melts | cm water equiv./$\degree$C/day | | +| 47 | snowMelt | rate at which snow melts | cm water equiv./°C/day | | | 48 | litWaterDrainRate | rate at which litter water drains into lower layer when litter layer fully moisture-saturated | c m water/day | | | 49 | rdConst | scalar determining amount of aerodynamic resistance | | | -| 50 | rSoilConst1 | | | soil resistance = e^(rSoilConst1 - rSoilConst2 $\times$ W1) , where W1 = (litterWater/litterWHC) | -| 51 | rSoilConst2 | | | soil resistance = e^(rSoilConst1 - rSoilConst2 $\times$ W1) , where W1 = (litterWater/litterWHC) | +| 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 | | | -| 53 | leafCSpWt | | g C $\times$ m$^{-2}$ leaf area | | -| 54 | cFracLeaf | | g leaf C $\times$ g$^{-1}$ leaf | | +| 53 | leafCSpWt | | g C * m^-2 leaf area | | +| 54 | cFracLeaf | | g leaf C * g^-1 leaf | | | 55 | woodTurnoverRate | average turnover rate of woody plant C | fraction per day | read in as per-year rate; leaf loss handled separately | ### Quality model parameters @@ -166,15 +166,15 @@ Model parameters that can change from one run to the next. These include initial | 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$\times$50 | assume that the most pts we can have is two per hour | +| MEAN_NPP_MAX_ENTRIES | MEAN_NPP_DAYS*50 | assume that the most pts we can have is two per hour | | MEAN_GPP_SOIL_DAYS 5 | 5 | over how many days do we keep the running mean | -| MEAN_GPP_SOIL_MAX_ENTRIES | MEAN_GPP_SOIL_DAYS$\times$50 | assume that the most pts we can have is one per hour | +| MEAN_GPP_SOIL_MAX_ENTRIES | MEAN_GPP_SOIL_DAYS*50 | assume that the most pts we can have is one per hour | | LAMBDA | 2501000 | latent heat of vaporization (J/kg) | | LAMBDA_S | 2835000 | latent heat of sublimation (J/kg) | -| RHO | 1.3 | air density (kg/m$^3$) | +| 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 $\degree$C (kPa) | +| E_STAR_SNOW | 0.6 | approximate saturation vapor pressure at 0°C (kPa) | ## 3. Climate driver inputs @@ -186,9 +186,9 @@ For each step of the model, for each location, the following inputs are needed. | 3 | day | day of start of this timestep | | 1 = Jan 1 | | 4 | time | time of start of this timestep | hour fraction | e.g. noon = 12.0, midnight = 0.0 | | 5 | length | length of this timestep | days | allow variable-length timesteps | -| 6 | tair | avg. air temp for this time step | $\degree$C | | -| 7 | tsoil | avg. soil temp for this time step | $\degree$C | | -| 8 | par | average par for this time step | Einsteins $\times$ m$^{-2}$ ground area $\times$ day$^{-1}$ | input is in Einsteins $\times$ m$^{-2}$ ground area, summed over entire time step | +| 6 | tair | avg. air temp for this time step | °C | | +| 7 | tsoil | avg. soil temp for this time step | °C | | +| 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 | | 9 | precip | total precip. for this time step | cm water equiv. - either rain or snow | input is in mm | | 10 | vpd | average vapor pressure deficit | kPa | input is in Pa | | 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 | @@ -208,13 +208,13 @@ For each step of the model, for each location, the following outputs are generat | 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$^2$ | +| 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 | | | 9 | coarseRootC | carbon in coarse roots | | | 10 | fineRootC | carbon in fine roots | | -| 11 | litter | carbon in litter | 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 | soilWetnessFrac | moisture in soil as fraction | |