public void Calculate_Establishment(IEcoregionPnETVariables pnetvars, IEcoregionPnET ecoregion, float PAR, IHydrology hydrology)
{
foreach (ISpeciesPNET spc in PlugIn.SpeciesPnET.AllSpecies)
{
if (pnetvars.Tmin > spc.PsnTMin)
{
float frad = (float)Math.Pow(Cohort.ComputeFrad(PAR, spc.HalfSat), spc.EstRad);
float PressureHead = hydrology.GetPressureHead(ecoregion);
float fwater = (float)Math.Pow(Cohort.ComputeFWater(spc.H2, spc.H3, spc.H4, PressureHead), spc.EstMoist);
float pest = 1 - (float)Math.Pow(1.0 - (frad * fwater), Timestep);
if (!spc.PreventEstablishment)
{
if (pest > _pest[spc])
{
_pest[spc] = pest;
_fwater[spc] = fwater;
_frad[spc] = frad;
if (pest > (float)PlugIn.ContinuousUniformRandom())
{
if (HasEstablished(spc) == false)
{
_hasEstablished.Add(spc);
}
}
}
}
if (establishment_siteoutput != null)
{
establishment_siteoutput.Add(((int)pnetvars.Year).ToString() + "," + spc.Name + "," + pest + "," + fwater + "," + frad + "," + HasEstablished(spc));
// TODO: win time by reducing calls to write
establishment_siteoutput.Write();
}
}
}
}
public static SortedList <float, float> CalculateMonthlySoilTemps(SortedList <float, float> depthTempDict, IEcoregionPnET Ecoregion, int daysOfWinter, float snowPack, IHydrology hydrology, float lastTempBelowSnow)
{
//SortedList<float, float> depthTempDict = new SortedList<float, float>(); //for permafrost
//float lambAir = 0.023f;
//float lambIce = 2.29f;
//float omega = (float)(2 * Math.PI / 12.0);
float[] snowResults = CalculateSnowDepth(daysOfWinter, snowPack);
float sno_dep = snowResults[0];
float Psno_kg_m3 = snowResults[1];
if (Ecoregion.Variables.Tave >= 0)
{
float fracAbove0 = Ecoregion.Variables.Tmax / (Ecoregion.Variables.Tmax - Ecoregion.Variables.Tmin);
sno_dep = sno_dep * fracAbove0;
}
// from CLM model - https://escomp.github.io/ctsm-docs/doc/build/html/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.html#soil-and-snow-thermal-properties
// Eq. 85 - Jordan (1991)
//float lambda_Snow = (float)(lambAir + ((0.0000775 * Psno_kg_m3) + (0.000001105 * Math.Pow(Psno_kg_m3, 2))) * (lambIce - lambAir)) * 3.6F * 24F; //(kJ/m/d/K) includes unit conversion from W to kJ
//float damping = (float)Math.Sqrt(omega / (2.0F * lambda_Snow));
float damping = CalculateSnowDamping(Psno_kg_m3);
float DRz_snow = (float)Math.Exp(-1.0F * sno_dep * damping); // Damping ratio for snow - adapted from Kang et al. (2000) and Liang et al. (2014)
// Permafrost calculations - from "Soil thawing worksheet.xlsx"
//
//if (Ecoregion.Variables.Tave < minMonthlyAvgTemp)
// minMonthlyAvgTemp = Ecoregion.Variables.Tave;
float porosity = Ecoregion.Porosity / Ecoregion.RootingDepth; //m3/m3
float waterContent = hydrology.Water / Ecoregion.RootingDepth; //m3/m3
float ga = 0.035F + 0.298F * (waterContent / porosity);
float Fa = ((2.0F / 3.0F) / (1.0F + ga * ((Constants.lambda_a / Constants.lambda_w) - 1.0F))) + ((1.0F / 3.0F) / (1.0F + (1.0F - 2.0F * ga) * ((Constants.lambda_a / Constants.lambda_w) - 1.0F))); // ratio of air temp gradient
float Fs = PressureHeadSaxton_Rawls.GetFs(Ecoregion.SoilType);
float lambda_s = PressureHeadSaxton_Rawls.GetLambda_s(Ecoregion.SoilType);
float lambda_theta = (Fs * (1.0F - porosity) * lambda_s + Fa * (porosity - waterContent) * Constants.lambda_a + waterContent * Constants.lambda_w) / (Fs * (1.0F - porosity) + Fa * (porosity - waterContent) + waterContent); //soil thermal conductivity (kJ/m/d/K)
float D = lambda_theta / PressureHeadSaxton_Rawls.GetCTheta(Ecoregion.SoilType); //m2/day
float Dmonth = D * Ecoregion.Variables.DaySpan; // m2/month
float ks = Dmonth * 1000000F / (Ecoregion.Variables.DaySpan * (Constants.SecondsPerHour * 24)); // mm2/s
float d = (float)Math.Pow((Constants.omega / (2.0F * Dmonth)), (0.5));
float maxDepth = Ecoregion.RootingDepth + Ecoregion.LeakageFrostDepth;
float freezeDepth = maxDepth;
float testDepth = 0;
//if (lastTempBelowSnow == float.MaxValue)
//{
// //int mCount = Math.Min(12, data.Count());
// //float tSum = 0;
// //foreach (int z in Enumerable.Range(0, mCount))
// //{
// // tSum += data[z].Tave;
// //}
// //float annualTavg = tSum / mCount;
// float tempBelowSnow = Ecoregion.Variables.Tave;
// if (sno_dep > 0)
// {
// tempBelowSnow = annualTavg + (Ecoregion.Variables.Tave - annualTavg) * DRz_snow;
// }
// lastTempBelowSnow = tempBelowSnow;
// while (testDepth <= (maxDepth / 1000.0))
// {
// float DRz = (float)Math.Exp(-1.0F * testDepth * d); // adapted from Kang et al. (2000) and Liang et al. (2014)
// float zTemp = annualTavg + (tempBelowSnow - annualTavg) * DRz;
// depthTempDict[testDepth] = zTemp;
// if ((zTemp <= 0) && (testDepth < freezeDepth))
// freezeDepth = testDepth;
// testDepth += 0.25F;
// }
//}
//else
//{
float tempBelowSnow = Ecoregion.Variables.Tave;
if (sno_dep > 0)
{
tempBelowSnow = lastTempBelowSnow + (Ecoregion.Variables.Tave - lastTempBelowSnow) * DRz_snow;
}
lastTempBelowSnow = tempBelowSnow;
while (testDepth <= (maxDepth / 1000.0))
{
float DRz = (float)Math.Exp(-1.0F * testDepth * d); // adapted from Kang et al. (2000) and Liang et al. (2014)
float zTemp = depthTempDict[testDepth] + (tempBelowSnow - depthTempDict[testDepth]) * DRz;
depthTempDict[testDepth] = zTemp;
//if ((zTemp <= 0) && (testDepth < freezeDepth))
// freezeDepth = testDepth;
if (testDepth == 0f)
{
testDepth = 0.10f;
}
else if (testDepth == 0.10f)
{
testDepth = 0.25f;
}
else
{
testDepth += 0.25F;
}
}
//}
return(depthTempDict);
}
public bool CalculatePhotosynthesis(float PrecInByCanopyLayer, float LeakagePerCohort, IHydrology hydrology, ref float SubCanopyPar)
{
bool success = true;
// Leaf area index for the subcanopy layer by index. Function of specific leaf weight SLWMAX and the depth of the canopy
// Depth of the canopy is expressed by the mass of foliage above this subcanopy layer (i.e. slwdel * index/imax *fol)
LAI[index] = (1 / (float)PlugIn.IMAX) * fol / (species.SLWmax - species.SLWDel * index * (1 / (float)PlugIn.IMAX) * fol);
// Precipitation interception has a max in the upper canopy and decreases exponentially through the canopy
//Interception[index] = PrecInByCanopyLayer * (float)(1 - Math.Exp(-1 * ecoregion.PrecIntConst * LAI[index]));
//if (Interception[index] > PrecInByCanopyLayer) throw new System.Exception("Error adding water, PrecInByCanopyLayer = " + PrecInByCanopyLayer + " Interception[index] = " + Interception[index]);
// Incoming precipitation
//float waterIn = PrecInByCanopyLayer - Interception[index]; //mm
float waterIn = PrecInByCanopyLayer; //mm
// Add incoming precipitation to soil moisture
success = hydrology.AddWater(waterIn);
if (success == false) throw new System.Exception("Error adding water, waterIn = " + waterIn + " water = " + hydrology.Water);
// Instantaneous runoff (excess of porosity)
float runoff = Math.Max(hydrology.Water - ecoregion.Porosity, 0);
Hydrology.RunOff += runoff;
success = hydrology.AddWater(-1 * runoff);
if (success == false) throw new System.Exception("Error adding water, Hydrology.RunOff = " + Hydrology.RunOff + " water = " + hydrology.Water);
// Fast Leakage
float leakage = Math.Max(LeakagePerCohort * (hydrology.Water - ecoregion.FieldCap), 0);
Hydrology.Leakage += leakage;
// Remove fast leakage
success = hydrology.AddWater(-1 * leakage);
if (success == false) throw new System.Exception("Error adding water, Hydrology.Leakage = " + Hydrology.Leakage + " water = " + hydrology.Water);
// Maintenance respiration depends on biomass, non soluble carbon and temperature
MaintenanceRespiration[index] = (1 / (float)PlugIn.IMAX) * (float)Math.Min(NSC, ecoregion.Variables[Species.Name].MaintRespFTempResp * biomass);//gC //IMAXinverse
// Subtract mainenance respiration (gC/mo)
nsc -= MaintenanceRespiration[index];
// Woody decomposition: do once per year to reduce unnescessary computation time so with the last subcanopy layer
if (index == PlugIn.IMAX - 1)
{
// In the first month
if (ecoregion.Variables.Month == (int)Constants.Months.January)
{
float woodSenescence = Senescence();
addwoodydebris(woodSenescence, species.KWdLit);
lastWoodySenescence = woodSenescence;
// Release of nsc, will be added to biomass components next year
// Assumed that NSC will have a minimum concentration, excess is allocated to biomass
float Allocation = Math.Max(nsc - (species.DNSC * FActiveBiom * biomass), 0);
biomass += Allocation;
biomassmax = Math.Max(biomassmax, biomass);
nsc -= Allocation;
age++;
}
}
// When LeafOn becomes false for the first time in a year
if(ecoregion.Variables.Tmin < this.SpeciesPNET.PsnTMin)
{
if (leaf_on == true)
{
leaf_on = false;
float foliageSenescence = FoliageSenescence();
addlitter(foliageSenescence, SpeciesPNET);
lastFoliageSenescence = foliageSenescence;
}
}
else
{
leaf_on = true;
}
if (leaf_on)
{
// Foliage linearly increases with active biomass
float IdealFol = (species.FracFol * FActiveBiom * biomass);
// If the tree should have more filiage than it currently has
if (IdealFol > fol)
{
// Foliage allocation depends on availability of NSC (allows deficit at this time so no min nsc)
// carbon fraction of biomass to convert C to DW
float Folalloc = Math.Max(0, Math.Min(nsc, species.CFracBiomass * (IdealFol - fol))); // gC/mo
// Add foliage allocation to foliage
fol += Folalloc / species.CFracBiomass;// gDW
// Subtract from NSC
nsc -= Folalloc;
}
}
// Apply defoliation in month of june
if ((PlugIn.ModelCore.CurrentTime > 0) && (ecoregion.Variables.Month == (int)Constants.Months.June))
{
if (DefolProp > 0)
{
//Adjust defol prop for foliage longevity - defol only affects current foliage
float adjDefol = DefolProp * species.TOfol;
ReduceFoliage(adjDefol);
// Update LAI after defoliation
LAI[index] = (1 / (float)PlugIn.IMAX) * fol / (species.SLWmax - species.SLWDel * index * (1 / (float)PlugIn.IMAX) * fol);
}
}
// Reduction factor for radiation on photosynthesis
FRad[index] = ComputeFrad(SubCanopyPar, species.HalfSat);
// Below-canopy PAR if updated after each subcanopy layer
SubCanopyPar *= (float)Math.Exp(-species.K * LAI[index]);
// Get pressure head given ecoregion and soil water content (latter in hydrology)
float PressureHead = hydrology.GetPressureHead(ecoregion);
// Reduction water for sub or supra optimal soil water content
if(PlugIn.ModelCore.CurrentTime > 0)
FWater[index] = ComputeFWater(species.H2, species.H3, species.H4, PressureHead);
else // Ignore H2 parameter during spinup
FWater[index] = ComputeFWater(0, species.H3, species.H4, PressureHead);
// If trees are physiologically active
if (leaf_on)
{
// Compute net psn from stress factors and reference net psn
NetPsn[index] = (1 / (float)PlugIn.IMAX) * FWater[index] * FRad[index] * Fage * ecoregion.Variables[species.Name].FTempPSNRefNetPsn * fol;
// Net foliage respiration depends on reference psn (AMAX)
//float FTempRespDayRefResp = ecoregion.Variables[species.Name].FTempRespDay * ecoregion.Variables.DaySpan * ecoregion.Variables.Daylength * Constants.MC / Constants.billion * ecoregion.Variables[species.Name].Amax;
//Subistitute 24 hours in place of DayLength because foliar respiration does occur at night. FTempRespDay uses Tave temps reflecting both day and night temperatures.
float FTempRespDayRefResp = ecoregion.Variables[species.Name].FTempRespDay * ecoregion.Variables.DaySpan * (Constants.SecondsPerHour * 24) * Constants.MC / Constants.billion * ecoregion.Variables[species.Name].Amax;
// Actal foliage respiration (growth respiration)
FolResp[index] = FWater[index] * FTempRespDayRefResp * fol / (float)PlugIn.IMAX;
// Gross psn depends on net psn and foliage respiration
GrossPsn[index] = NetPsn[index] + FolResp[index];
// Transpiration depends on gross psn, water use efficiency (gCO2/mm water) and molecular weight (gC/gCO2)
Transpiration[index] = Math.Min(hydrology.Water, GrossPsn[index] / ecoregion.Variables[Species.Name].WUE / ecoregion.Variables[Species.Name].DelAmax * Constants.MCO2_MC);
// Subtract transpiration from hydrology
success = hydrology.AddWater(-1 * Transpiration[index]);
if (success == false) throw new System.Exception("Error adding water, Transpiration = " + Transpiration[index] + " water = " + hydrology.Water);
// Add net psn to non soluble carbons
nsc += NetPsn[index];
}
else
{
// Reset subcanopy layer values
NetPsn[index] = 0;
FolResp[index] = 0;
GrossPsn[index] = 0;
Transpiration[index] = 0;
}
if (index < PlugIn.IMAX - 1) index++;
return success;
}
public Dictionary<ISpeciesPNET, float> Calculate_Establishment_Month(IEcoregionPnETVariables pnetvars, IEcoregionPnET ecoregion, float PAR, IHydrology hydrology)
{
Dictionary<ISpeciesPNET, float> estabDict = new Dictionary<ISpeciesPNET, float>();
foreach (ISpeciesPNET spc in PlugIn.SpeciesPnET.AllSpecies)
{
if (pnetvars.Tmin > spc.PsnTMin)
{
float frad = (float)Math.Pow(Cohort.ComputeFrad(PAR, spc.HalfSat), spc.EstRad);
float PressureHead = hydrology.GetPressureHead(ecoregion);
float fwater = (float)Math.Pow(Cohort.ComputeFWater(spc.H2, spc.H3, spc.H4, PressureHead), spc.EstMoist);
float pest = 1 - (float)Math.Pow(1.0 - (frad * fwater), Timestep);
estabDict[spc] = pest;
if (fwater < _fwater[spc])
{
_fwater[spc] = fwater;
}
if (frad < _frad[spc])
{
_frad[spc] = frad;
}
/*if (establishment_siteoutput != null)
{
establishment_siteoutput.Add(((int)pnetvars.Year).ToString() + "," + spc.Name + "," + pest + "," + fwater + "," + frad + "," + HasEstablished(spc));
// TODO: win time by reducing calls to write
establishment_siteoutput.Write();
}
* */
}
}
return estabDict;
}
/*public static void Initialize(int timestep)
* {
* Timestep = timestep;
*
*
* }*/
public Dictionary <ISpeciesPNET, float> Calculate_Establishment_Month(IEcoregionPnETVariables pnetvars, IEcoregionPnET ecoregion, float PAR, IHydrology hydrology, float minHalfSat, float maxHalfSat, bool invertPest)
{
Dictionary <ISpeciesPNET, float> estabDict = new Dictionary <ISpeciesPNET, float>();
float halfSatRange = maxHalfSat - minHalfSat;
foreach (ISpeciesPNET spc in PlugIn.SpeciesPnET.AllSpecies)
{
if (pnetvars.Tmin > spc.PsnTMin && pnetvars.Tmax < spc.PsnTMax)
{
// Adjust HalfSat for CO2 effect
float halfSatIntercept = spc.HalfSat - 350 * spc.CO2HalfSatEff;
float adjHalfSat = spc.CO2HalfSatEff * pnetvars.CO2 + halfSatIntercept;
float frad = (float)(Math.Min(1.0, (Math.Pow(Cohort.ComputeFrad(PAR, adjHalfSat), 2) * (1 / (Math.Pow(spc.EstRad, 2))))));
float adjFrad = frad;
// Optional adjustment to invert Pest based on relative halfSat
if (invertPest && halfSatRange > 0)
{
float frad_adj_int = (spc.HalfSat - minHalfSat) / halfSatRange;
float frad_slope = (frad_adj_int * 2) - 1;
adjFrad = 1 - frad_adj_int + frad * frad_slope;
}
float PressureHead = hydrology.GetPressureHead(ecoregion);
float fwater = (float)(Math.Min(1.0, (Math.Pow(Cohort.ComputeFWater(spc.H1, spc.H2, spc.H3, spc.H4, PressureHead), 2) * (1 / (Math.Pow(spc.EstMoist, 2))))));
float pest = (float)Math.Min(1.0, adjFrad * fwater);
estabDict[spc] = pest;
_fwater[spc] = fwater;
_frad[spc] = adjFrad;
}
}
return(estabDict);
}
/*public void Calculate_Establishment(IEcoregionPnETVariables pnetvars, IEcoregionPnET ecoregion, float PAR, IHydrology hydrology)
* {
* foreach (ISpeciesPNET spc in PlugIn.SpeciesPnET.AllSpecies)
* {
*
*
* if (pnetvars.Tmin > spc.PsnTMin)
* {
* // Adjust HalfSat for CO2 effect
* float halfSatIntercept = spc.HalfSat - 350 * spc.CO2HalfSatEff;
* float adjHalfSat = spc.CO2HalfSatEff * pnetvars.CO2 + halfSatIntercept;
* float frad = (float)Math.Pow(Cohort.ComputeFrad(PAR, adjHalfSat), spc.EstRad);
*
*
* float PressureHead = hydrology.GetPressureHead(ecoregion);
*
* float fwater = (float)Math.Pow(Cohort.ComputeFWater(spc.H1,spc.H2, spc.H3, spc.H4, PressureHead), spc.EstMoist);
*
* float pest = 1 - (float)Math.Pow(1.0 - (frad * fwater), Timestep);
* if (!spc.PreventEstablishment)
* {
* if (pest > _pest[spc])
* {
* _pest[spc] = pest;
* _fwater[spc] = fwater;
* _frad[spc] = frad;
*
* if (pest > (float)PlugIn.ContinuousUniformRandom())
* {
* if (HasEstablished(spc) == false)
* {
* _hasEstablished.Add(spc);
* }
*
* }
*
* }
* }
* if (establishment_siteoutput != null)
* {
*
* establishment_siteoutput.Add(((int)pnetvars.Year).ToString() + "," + spc.Name + "," + pest + "," + fwater + "," + frad + "," + HasEstablished(spc));
*
* // TODO: win time by reducing calls to write
* establishment_siteoutput.Write();
* }
* }
* }
* }
*/
public Dictionary <ISpeciesPNET, float> Calculate_Establishment_Month(IEcoregionPnETVariables pnetvars, IEcoregionPnET ecoregion, float PAR, IHydrology hydrology, float minHalfSat, float maxHalfSat, bool invertPest)
{
Dictionary <ISpeciesPNET, float> estabDict = new Dictionary <ISpeciesPNET, float>();
//_fwater = new Dictionary<ISpeciesPNET, float>();
//_pest = new Dictionary<ISpeciesPNET, float>();
//_frad = new Dictionary<ISpeciesPNET, float>();
float halfSatRange = maxHalfSat - minHalfSat;
foreach (ISpeciesPNET spc in PlugIn.SpeciesPnET.AllSpecies)
{
if (pnetvars.Tmin > spc.PsnTMin && pnetvars.Tmax < spc.PsnTMax)
{
// Adjust HalfSat for CO2 effect
float halfSatIntercept = spc.HalfSat - 350 * spc.CO2HalfSatEff;
float adjHalfSat = spc.CO2HalfSatEff * pnetvars.CO2 + halfSatIntercept;
float frad = (float)(Math.Min(1.0, (Math.Pow(Cohort.ComputeFrad(PAR, adjHalfSat), 2) * (1 / (Math.Pow(spc.EstRad, 2))))));
float adjFrad = frad;
// Optional adjustment to invert Pest based on relative halfSat
if (invertPest && halfSatRange > 0)
{
float frad_adj_int = (spc.HalfSat - minHalfSat) / halfSatRange;
float frad_slope = (frad_adj_int * 2) - 1;
adjFrad = 1 - frad_adj_int + frad * frad_slope;
}
float PressureHead = hydrology.GetPressureHead(ecoregion);
float fwater = (float)(Math.Min(1.0, (Math.Pow(Cohort.ComputeFWater(spc.H1, spc.H2, spc.H3, spc.H4, PressureHead), 2) * (1 / (Math.Pow(spc.EstMoist, 2))))));
//float pest = 1 - (float)Math.Pow(1.0 - (frad * fwater * spc.MaxPest), Timestep);
float pest = (float)Math.Min(1.0, adjFrad * fwater);
estabDict[spc] = pest;
_pest[spc] = pest;
_fwater[spc] = fwater;
_frad[spc] = adjFrad;
/*if (fwater < _fwater[spc])
* {
* _fwater[spc] = fwater;
* }
* if (frad < _frad[spc])
* {
* _frad[spc] = frad;
* }
*/
/*if (establishment_siteoutput != null)
* {
*
* establishment_siteoutput.Add(((int)pnetvars.Year).ToString() + "," + spc.Name + "," + pest + "," + fwater + "," + frad + "," + HasEstablished(spc));
*
* // TODO: win time by reducing calls to write
* establishment_siteoutput.Write();
* }
* */
}
}
return(estabDict);
}
