public static void Initialize()
{
soiltype = (Landis.Library.Parameters.Ecoregions.AuxParm <string>)(Parameter <string>) PlugIn.GetParameter("SoilType");
climateFileName = (Landis.Library.Parameters.Ecoregions.AuxParm <string>)(Parameter <string>) PlugIn.GetParameter("ClimateFileName");
rootingdepth = (Landis.Library.Parameters.Ecoregions.AuxParm <float>)(Parameter <float>) PlugIn.GetParameter("RootingDepth", 0, 1000);
precintconst = (Landis.Library.Parameters.Ecoregions.AuxParm <float>)(Parameter <float>) PlugIn.GetParameter("PrecIntConst", 0, 1);
preclossfrac = (Landis.Library.Parameters.Ecoregions.AuxParm <float>)(Parameter <float>) PlugIn.GetParameter("PrecLossFrac", 0, 1);
snowsublimfrac = (Landis.Library.Parameters.Ecoregions.AuxParm <float>)(Parameter <float>) PlugIn.GetParameter("SnowSublimFrac", 0, 1);
latitude = (Landis.Library.Parameters.Ecoregions.AuxParm <float>)(Parameter <float>) PlugIn.GetParameter("Latitude", -90, 90);
leakageFrostDepth = (Landis.Library.Parameters.Ecoregions.AuxParm <float>)(Parameter <float>) PlugIn.GetParameter("LeakageFrostDepth", 0, 999999);
precipEvents = (Landis.Library.Parameters.Ecoregions.AuxParm <int>)(Parameter <int>) PlugIn.GetParameter("PrecipEvents", 1, 100);
winterSTD = (Landis.Library.Parameters.Ecoregions.AuxParm <float>)(Parameter <float>) PlugIn.GetParameter("WinterSTD", 0, 100);
mossDepth = (Landis.Library.Parameters.Ecoregions.AuxParm <float>)(Parameter <float>) PlugIn.GetParameter("MossDepth", 0, 1000);
wythers = ((Parameter <bool>)PlugIn.GetParameter("Wythers")).Value;
dtemp = ((Parameter <bool>)PlugIn.GetParameter("DTemp")).Value;
leakagefrac = (Landis.Library.Parameters.Ecoregions.AuxParm <float>)(Parameter <float>) PlugIn.GetParameter("LeakageFrac", 0, 1);
runoffcapture = (Landis.Library.Parameters.Ecoregions.AuxParm <float>)(Parameter <float>) PlugIn.GetParameter(Names.RunoffCapture, 0, 999999);
AllEcoregions = new Dictionary <IEcoregion, IEcoregionPnET>();
foreach (IEcoregion ecoregion in PlugIn.ModelCore.Ecoregions)
{
AllEcoregions.Add(ecoregion, new EcoregionPnET(ecoregion));
}
all_values = new Dictionary <IEcoregionPnET, Dictionary <DateTime, IEcoregionPnETVariables> >();
foreach (IEcoregionPnET ecoregion in EcoregionPnET.AllEcoregions.Values)
{
all_values[ecoregion] = new Dictionary <DateTime, IEcoregionPnETVariables>();
}
}
public SiteConditions(ActiveSite site, ICommunity initialCommunity)
{
cohorts = new SiteCohorts();
canopy = new Canopy();
if (PlugIn.HasSiteOutput[site] == true)
{
siteoutput = new SiteOutput(site);
estoutput = new EstablishmentOutput(site);
}
this.site = site;
foreach (ISpecies spc in PlugIn.modelCore.Species)
{
deadcohortages[spc] = new List <int>();
}
uint key = ComputeKey(initialCommunity.MapCode, PlugIn.ModelCore.Ecoregion[site].MapCode);
SiteConditions s = GetFromKey(key);
if (s != null)
{
return;
}
// If we don't have a sorted list of age cohorts for the initial
// community, make the list
List <Landis.Library.AgeOnlyCohorts.ICohort> sortedAgeCohorts;
if (!sortedCohorts.TryGetValue(initialCommunity.MapCode, out sortedAgeCohorts))
{
sortedAgeCohorts = PlugIn.RankCohortAgesOldToYoung(initialCommunity.Cohorts);
sortedCohorts[initialCommunity.MapCode] = sortedAgeCohorts;
}
hydrology = new Hydrology(PlugIn.modelCore.Ecoregion[site]);
forestfloor = new ForestFloor();
cohorts = new SiteCohorts();
establishment = new EstablishmentProbability(site);
if (sortedAgeCohorts.Count == 0)
{
return;
}
//PlugIn.ModelCore.UI.WriteLine("Making Biomass Cohorts "+ site);
BiomassSpinUp(sortedAgeCohorts, site);
initialSites[key] = this;
return;
}
//---------------------------------------------------------------------
/// <summary>
/// Computes the initial biomass at a site.
/// </summary>
/// <param name="site">
/// The selected site.
/// </param>
/// <param name="initialCommunity">
/// The initial community of age cohorts at the site.
/// </param>
public static InitialBiomass ComputeInitialBiomass(ActiveSite site,
ICommunity initialCommunity)
{
InitialBiomass initialBiomass;
IEcoregion ecoregion = PlugIn.ModelCore.Ecoregion[site];
uint key = ComputeKey(initialCommunity.MapCode, ecoregion.MapCode);
if (initialSites.TryGetValue(key, out initialBiomass) && HasSiteOutput[site] == false)
{
CanopyBiomass.CanopyLAImax[site] = initialBiomass.canopylaimax;
CanopyBiomass.CanopyLAI[site] = initialBiomass.canopylai;
Hydrology.Water[site] = initialBiomass.water;
Hydrology.AnnualTranspiration[site] = initialBiomass.annualtrans;
CanopyBiomass.SubCanopyPAR[site] = initialBiomass.subcanopypar;
return(initialBiomass);
}
// If we don't have a sorted list of age cohorts for the initial
// community, make the list
List <Landis.Library.AgeOnlyCohorts.ICohort> sortedAgeCohorts;
if (!sortedCohorts.TryGetValue(initialCommunity.MapCode, out sortedAgeCohorts))
{
sortedAgeCohorts = PlugIn.RankCohortAgesOldToYoung(initialCommunity.Cohorts);
sortedCohorts[initialCommunity.MapCode] = sortedAgeCohorts;
}
if (sortedAgeCohorts.Count == 0)
{
return(null);
}
ISiteCohorts cohorts = MakeBiomassCohorts(sortedAgeCohorts, site);
initialBiomass = new InitialBiomass(cohorts,
ForestFloor.WoodyDebris[site],
ForestFloor.Litter[site],
Hydrology.Water[site],
Hydrology.AnnualTranspiration[site],
CanopyBiomass.CanopyLAI[site],
CanopyBiomass.CanopyLAImax[site],
CanopyBiomass.SubCanopyPAR[site]);
initialSites[key] = initialBiomass;
return(initialBiomass);
}
public static void Allocate(object sitecohorts, Cohort cohort, ExtensionType disturbanceType, double fraction)
{
if (sitecohorts == null)
{
throw new System.Exception("sitecohorts should not be null");
}
//ReduceDeadPools(sitecohorts, disturbanceType); // moved to RemoveCohort and ReduceBiomass to avoid multiple calls
// By default, all material is allocated to the woody debris or the litter pool
float pwoodlost = 0;
float prootlost = 0;
float pfollost = 0;
Parameter <string> parameter;
if (disturbanceType != null && PlugIn.TryGetParameter(disturbanceType.Name, out parameter))
{
// If parameters are available, then set the loss fractions here.
if (parameter.ContainsKey("WoodReduction"))
{
pwoodlost = float.Parse(parameter["WoodReduction"]);
}
if (parameter.ContainsKey("RootReduction"))
{
prootlost = float.Parse(parameter["RootReduction"]);
}
if (parameter.ContainsKey("FolReduction"))
{
pfollost = float.Parse(parameter["FolReduction"]);
}
}
// Add new dead wood and litter
float woodAdded = (float)((1 - pwoodlost) * cohort.Wood * fraction);
float rootAdded = (float)((1 - prootlost) * cohort.Root * fraction);
float folAdded = (float)((1 - pfollost) * cohort.Fol * fraction);
((SiteCohorts)sitecohorts).AddWoodyDebris(woodAdded, cohort.SpeciesPNET.KWdLit);
((SiteCohorts)sitecohorts).AddWoodyDebris(rootAdded, cohort.SpeciesPNET.KWdLit);
((SiteCohorts)sitecohorts).AddLitter(folAdded, cohort.SpeciesPNET);
cohort.AccumulateWoodySenescence((int)(woodAdded + rootAdded));
cohort.AccumulateFoliageSenescence((int)(folAdded));
}
//---------------------------------------------------------------------
/// <summary>
/// Makes the set of biomass cohorts at a site based on the age cohorts
/// at the site, using a specified method for computing a cohort's
/// initial biomass.
/// </summary>
/// <param name="ageCohorts">
/// A sorted list of age cohorts, from oldest to youngest.
/// </param>
/// <param name="site">
/// Site where cohorts are located.
/// </param>
/// <param name="initialBiomassMethod">
/// The method for computing the initial biomass for a new cohort.
/// </param>
public static ISiteCohorts MakeBiomassCohorts(List <Landis.Library.AgeOnlyCohorts.ICohort> ageCohorts, ActiveSite site)
{
PlugIn.Cohorts[site] = new Library.BiomassCohortsPnET.SiteCohorts();
Hydrology.Initialize(site);
Hydrology.AnnualTranspiration[site] = 0;
CanopyBiomass.CanopyLAI[site] = 0;
if (ageCohorts.Count == 0)
{
return(PlugIn.Cohorts[site]);
}
System.DateTime SpinUpDate = PlugIn.StartDate.AddYears(-(ageCohorts[0].Age) + ((successionTimestep == 1) ? -1 : 0));
while (SpinUpDate.CompareTo(PlugIn.StartDate) < 0)
{
CanopyBiomass.SubCanopyPAR[site] = Static.PAR0[SpinUpDate];
// Add those cohorts that were born at the current year
foreach (Library.AgeOnlyCohorts.ICohort ageonlycohort in ageCohorts)
{
if (PlugIn.StartDate.Year - SpinUpDate.Year == ageonlycohort.Age)
{
Cohort cohort = new Cohort(ageonlycohort.Species, 1, ConstantParameters.InitialFol, 0, 0, 0, 0, SpinUpDate.Year, true);
PlugIn.Cohorts[site].AddNewCohort(cohort);
CohortOutput.WriteHeader(site, cohort);
SiteOutput.WriteHeader(site);
}
}
PlugIn.GrowCohorts(site, SpinUpDate, SpinUpDate.AddYears(1), false);
SpinUpDate = SpinUpDate.AddYears(1);
}
return(PlugIn.Cohorts[site]);
}
public static void Initialize()
{
Parameter <string> PressureHeadCalculationMethod = null;
if (PlugIn.TryGetParameter(Names.PressureHeadCalculationMethod, out PressureHeadCalculationMethod))
{
Parameter <string> p = PlugIn.GetParameter(Names.PressureHeadCalculationMethod);
pressureheadtable = new PressureHeadSaxton_Rawls();
}
else
{
string msg = "Missing presciption for calculating pressurehead, expected keyword " + Names.PressureHeadCalculationMethod + " in " + PlugIn.GetParameter(Names.PnETGenericParameters).Value + " or in " + PlugIn.GetParameter(Names.ExtensionName).Value;
throw new System.Exception(msg);
}
PlugIn.ModelCore.UI.WriteLine("Eco\tSoilt\tWiltPnt\tFieldCap(mm)\tFC-WP\tPorosity");
foreach (IEcoregionPnET eco in EcoregionPnET.Ecoregions)
{
if (eco.Active)
{
// Volumetric water content (mm/m) at field capacity
// −33 kPa (or −0.33 bar)
// Convert kPA to mH2o (/9.804139432) = 3.37
eco.FieldCap = (float)pressureheadtable.CalculateWaterContent(33, eco.SoilType);
// Volumetric water content (mm/m) at wilting point
// −1500 kPa (or −15 bar)
// Convert kPA to mH2o (/9.804139432) = 153.00
eco.WiltPnt = (float)pressureheadtable.CalculateWaterContent(1500, eco.SoilType);
// Volumetric water content (mm/m) at porosity
eco.Porosity = (float)pressureheadtable.Porosity(eco.SoilType);
float f = eco.FieldCap - eco.WiltPnt;
PlugIn.ModelCore.UI.WriteLine(eco.Name + "\t" + eco.SoilType + "\t" + eco.WiltPnt + "\t" + eco.FieldCap + "\t" + f + "\t" + eco.Porosity);
}
}
}
public void GrowCohorts(DateTime date,
DateTime ToTime,
bool issuccessionTimestep)
{
if (Cohorts == null)
{
return;
}
while (date.CompareTo(ToTime) < 0)
{
PlugIn.SetYear(date.Year);
if (date.Month == (int)Months.January || canopy == null)
{
canopylaimax = 0;
if (cohorts == null)
{
return;
}
}
if (date.Month == (int)Months.June)
{
Defoliate(site);
}
hydrology.UpdateSiteHydrology(date);
canopy.Grow(date, site, hydrology, forestfloor, cohorts, siteoutput);
canopylaimax = canopy.CanopyLAImax;
foreach (Cohort cohort in canopy.DeadCohorts)
{
DeadCohortAges[cohort.Species].Add(cohort.Age);
deadcohorts[cohort.Species]++;
Cohorts[cohort.Species].RemoveCohort(cohort, site, null);
canopy.ResetDeadCohorts();
}
if (issuccessionTimestep)
{
Establishment.ComputeEstablishment(date, this);
if (HasSiteOutput)
{
estoutput.UpdateEstData(date, this);
}
}
if (HasSiteOutput)
{
siteoutput.UpdateSiteData(date, this);
siteoutput.WriteSiteData();
}
if (date.Month == (int)Months.December)
{
Cohorts.IncrementCohortsAge();
forestfloor.Decompose();
forestfloor.Decompose();
}
date = date.AddMonths(1);
}
if (CohortBiomass.HasDeadCohorts)
{
CohortBiomass.HasDeadCohorts = false;
}
}
public static void Initialize(string fn, SortedDictionary <string, Parameter <string> > parameters)
{
Dictionary <string, Parameter <string> > DisturbanceReductionParameters = PlugIn.LoadTable(Names.DisturbanceReductions, Reductions, Disturbances);
foreach (KeyValuePair <string, Parameter <string> > parameter in DisturbanceReductionParameters)
{
if (parameters.ContainsKey(parameter.Key))
{
throw new System.Exception("Parameter " + parameter.Key + " was provided twice");
}
foreach (string value in parameter.Value.Values)
{
double v;
if (double.TryParse(value, out v) == false)
{
throw new System.Exception("Expecting digit value for " + parameter.Key);
}
if (v > 1 || v < 0)
{
throw new System.Exception("Expecting value for " + parameter.Key + " between 0.0 and 1.0. Found " + v);
}
}
}
DisturbanceReductionParameters.ToList().ForEach(x => parameters.Add("disturbance:" + x.Key, x.Value));
}
//---------------------------------------------------------------------
public PressureHeadSaxton_Rawls()
{
Landis.Library.Parameters.Ecoregions.AuxParm <string> SoilType = (Landis.Library.Parameters.Ecoregions.AuxParm <string>)PlugIn.GetParameter(Names.SoilType);
Landis.Library.Parameters.Ecoregions.AuxParm <float> RootingDepth = (Landis.Library.Parameters.Ecoregions.AuxParm <float>)(Parameter <float>) PlugIn.GetParameter(Names.RootingDepth, 0, float.MaxValue);
table = new Library.Parameters.Ecoregions.AuxParm <float[]>(PlugIn.ModelCore.Ecoregions);
Sand = PlugIn.GetParameter("sand");
Clay = PlugIn.GetParameter("clay");
PctOM = PlugIn.GetParameter("pctOM");
DensFactor = PlugIn.GetParameter("densFactor");
Gravel = PlugIn.GetParameter("gravel");
foreach (IEcoregion ecoregion in PlugIn.ModelCore.Ecoregions)
{
if (ecoregion.Active)
{
List <float> PressureHead = new List <float>();
if (tensionB.ContainsKey(SoilType[ecoregion]) == false)
{
double sand = double.Parse(Sand[SoilType[ecoregion]]);
double clay = double.Parse(Clay[SoilType[ecoregion]]);
double pctOM = double.Parse(PctOM[SoilType[ecoregion]]);
double densFactor = double.Parse(DensFactor[SoilType[ecoregion]]);
double gravel = double.Parse(Gravel[SoilType[ecoregion]]);
// Moisture at wilting point
double predMoist1500 = -0.024 * sand + 0.487 * clay + 0.006 * pctOM + 0.005 * sand * pctOM - 0.013 * clay * pctOM + 0.068 * sand * clay + 0.031;
double predMoist1500adj = predMoist1500 + 0.14 * predMoist1500 - 0.02;
// Moisture at field capacity
double predMoist33 = -0.251 * sand + 0.195 * clay + 0.011 * pctOM + 0.006 * sand * pctOM - 0.027 * clay * pctOM + 0.452 * sand * clay + 0.299;
double predMoist33Adj = predMoist33 + (1.283 * predMoist33 * predMoist33 - 0.374 * predMoist33 - 0.015);
double porosMoist33 = 0.278 * sand + 0.034 * clay + 0.022 * pctOM - 0.018 * sand * pctOM - 0.027 * clay * pctOM - 0.584 * sand * clay + 0.078;
double porosMoist33Adj = porosMoist33 + (0.636 * porosMoist33 - 0.107);
double satPor33 = porosMoist33Adj + predMoist33Adj;
double satSandAdj = -0.097 * sand + 0.043;
double sandAdjSat = satPor33 + satSandAdj;
double density_OM = (1.0 - sandAdjSat) * 2.65;
double density_comp = density_OM * (densFactor);
porosity_OM_comp.Add(SoilType[ecoregion], (float)(1.0 - (density_comp / 2.65)));
double porosity_change_comp = (1.0 - density_comp / 2.65) - (1.0 - density_OM / 2.65);
double moist33_comp = predMoist33Adj + 0.2 * porosity_change_comp;
double porosity_moist33_comp = porosity_OM_comp[SoilType[ecoregion]] - moist33_comp;
double lambda = (Math.Log(moist33_comp) - Math.Log(predMoist1500adj)) / (Math.Log(1500) - Math.Log(33));
double gravel_red_sat_cond = (1.0 - gravel) / (1.0 - gravel * (1.0 - 1.5 * (density_comp / 2.65)));
double satcond_mmhr = 1930 * Math.Pow((porosity_moist33_comp), (3.0 - lambda)) * gravel_red_sat_cond;
double gravels_vol = ((density_comp / 2.65) * gravel) / (1 - gravel * (1 - density_comp / 2.65));
double bulk_density = gravels_vol * 2.65 + (1 - gravels_vol) * density_comp; // g/cm3
tensionB.Add(SoilType[ecoregion], (float)((Math.Log(1500) - Math.Log(33.0)) / (Math.Log(moist33_comp) - Math.Log(predMoist1500adj))));
tensionA.Add(SoilType[ecoregion], (float)Math.Exp(Math.Log(33.0) + (tensionB[SoilType[ecoregion]] * Math.Log(moist33_comp))));
// For Permafrost
clayProp.Add(SoilType[ecoregion], (float)clay);
double cTheta_temp = Constants.cs * (1.0 - porosity_OM_comp[SoilType[ecoregion]]) + Constants.cw * porosity_OM_comp[SoilType[ecoregion]]; //specific heat of soil kJ/m3/K
cTheta.Add(SoilType[ecoregion], (float)cTheta_temp);
double lambda_s_temp = (1.0 - clay) * Constants.lambda_0 + clay * Constants.lambda_clay; //thermal conductivity soil kJ/m/d/K
lambda_s.Add(SoilType[ecoregion], (float)lambda_s_temp);
double Fs_temp = ((2.0 / 3.0) / (1.0 + Constants.gs * ((lambda_s_temp / Constants.lambda_w) - 1.0))) + ((1.0 / 3.0) / (1.0 + (1.0 - 2.0 * Constants.gs) * ((lambda_s_temp / Constants.lambda_w) - 1.0))); //ratio of solid temp gradient
Fs.Add(SoilType[ecoregion], (float)Fs_temp);
}
double watercontent = 0.0;
float pressureHead = float.MaxValue;
while (pressureHead > 0.01)
{
pressureHead = CalculateWaterPressure(watercontent, SoilType[ecoregion]);
PressureHead.Add(pressureHead);
watercontent += 0.01;
}
table[ecoregion] = PressureHead.ToArray();
}
}
}
