removed latex formatting since it is not supported by github flavored…

… markdown, it was only being used for \times, \degree, and `^`
PecanProject · Aug 9, 2024 · 1c6e9e5 · 1c6e9e5
1 parent fe39e94
commit 1c6e9e5
Showing 1 changed file with 33 additions and 33 deletions.
diff --git 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 |   |