static Library.Biomass.Species.AuxParm <int> GetFirstActiveMonth(DateTime date, int timespan)
{
Library.Biomass.Species.AuxParm <int> FirstActiveMonth = new Library.Biomass.Species.AuxParm <int>(PlugIn.ModelCore.Species);
foreach (ISpecies spc in PlugIn.ModelCore.Species)
{
DateTime DateCounter = date.AddYears(-5);
bool FoundFirstActiveMonth = false;
int SumFirstActiveMonth = 0;
int c = 0;
while (DateCounter.CompareTo(date.AddYears(5)) < 1)
{
if (DateCounter.Month == 1)
{
FoundFirstActiveMonth = false;
}
if (DateCounter.Year >= FirstYearOnFile && DateCounter.Year < LastYearOnFile)
{
if (isactive[DateCounter][spc] && FoundFirstActiveMonth == false)
{
FoundFirstActiveMonth = true;
SumFirstActiveMonth += DateCounter.Month;
c++;
}
}
DateCounter = DateCounter.AddMonths(1);
}
FirstActiveMonth[spc] = (int)SumFirstActiveMonth / c;
}
return(FirstActiveMonth);
}
public VarEcoregionSpecies(string label)
{
values = new Library.Biomass.Ecoregions.AuxParm <Library.Biomass.Species.AuxParm <T> >(PlugIn.modelCore.Ecoregions);
//= new VarEcoregion<Library.Biomass.Species.AuxParm<T>>(label);
this.label = label;
foreach (IEcoregion eco in PlugIn.ModelCore.Ecoregions)
{
values[eco] = new Library.Biomass.Species.AuxParm <T>(PlugIn.modelCore.Species);
}
}
private static void SetEstablishmentMonths(IInputParameters Parameters, IEcoregion ecoregion)
{
DateTime date = DateRange[0];
int wettestmonth = -1;
Library.Biomass.Species.AuxParm <int> firstactivemonthspc = null;
Library.Biomass.Species.AuxParm <int> Firstpossibleestmonth = new Library.Biomass.Species.AuxParm <int>(PlugIn.modelCore.Species);
Library.Biomass.Species.AuxParm <int> Lastpossibleestmonth = new Library.Biomass.Species.AuxParm <int>(PlugIn.modelCore.Species);
while (date.CompareTo(DateRange[1]) < 0)
{
if (date.Month == 1 || wettestmonth < 0)
{
wettestmonth = GetWettestMonth(ecoregion, date.Year, 10);
}
if (date.Month == 1 || firstactivemonthspc == null)
{
firstactivemonthspc = new Library.Biomass.Species.AuxParm <int>(PlugIn.modelCore.Species);
foreach (ISpecies spc in PlugIn.ModelCore.Species)
{
firstactivemonthspc[spc] = GetFirstActiveMonth(spc, Parameters, date, ecoregion, 10);
Firstpossibleestmonth[spc] = Math.Min(wettestmonth - 1, firstactivemonthspc[spc]);
Lastpossibleestmonth[spc] = Math.Max(wettestmonth + 1, firstactivemonthspc[spc] + 3);
}
}
foreach (ISpecies spc in PlugIn.ModelCore.Species)
{
if (date.Month >= Firstpossibleestmonth[spc] && date.Month <= Lastpossibleestmonth[spc])
{
possibleestmonth[ecoregion, spc, date] = true;
}
}
date = date.AddMonths(1);
}
}
protected override IInsect Parse()
{
InputVar <string> landisData = new InputVar <string>("LandisData");
ReadVar(landisData);
if (landisData.Value.Actual != "InsectDefoliator")
{
throw new InputValueException(landisData.Value.String, "The value is not \"{0}\"", "InsectDefoliator");
}
Insect insect = new Insect(PlugIn.ModelCore.Species.Count);
InputVar <string> insectName = new InputVar <string>("InsectName");
ReadVar(insectName);
insect.Name = insectName.Value;
InputVar <double> mD = new InputVar <double>("MeanDuration");
ReadVar(mD);
insect.MeanDuration = mD.Value;
InputVar <int> mTBO = new InputVar <int>("MeanTimeBetweenOutbreaks");
ReadVar(mTBO);
insect.MeanTimeBetweenOutbreaks = mTBO.Value;
InputVar <int> sdTBO = new InputVar <int>("StdDevTimeBetweenOutbreaks");
ReadVar(sdTBO);
insect.StdDevTimeBetweenOutbreaks = sdTBO.Value;
InputVar <int> nhs = new InputVar <int>("NeighborhoodSize");
ReadVar(nhs);
insect.NeighborhoodDistance = nhs.Value;
InputVar <double> ipsc = new InputVar <double>("InitialPatchShapeCalibrator");
ReadVar(ipsc);
insect.InitialPatchShapeCalibrator = ipsc.Value;
InputVar <double> ipnc = new InputVar <double>("InitialPatchOutbreakSensitivity");
ReadVar(ipnc);
insect.InitialPatchOutbreakSensitivity = ipnc.Value;
InputVar <DistributionType> ipdt = new InputVar <DistributionType>("InitialPatchDistribution");
ReadVar(ipdt);
insect.InitialPatchDistr = ipdt.Value;
InputVar <double> ipv1 = new InputVar <double>("InitialPatchValue1");
ReadVar(ipv1);
insect.InitialPatchValue1 = ipv1.Value;
InputVar <double> ipv2 = new InputVar <double>("InitialPatchValue2");
ReadVar(ipv2);
insect.InitialPatchValue2 = ipv2.Value;
//--------- Read In Species Table ---------------------------------------
PlugIn.ModelCore.UI.WriteLine(" Begin parsing SPECIES table.");
ReadName("SpeciesParameters");
InputVar <string> annMort = new InputVar <string>("MortalityEstimate");
ReadVar(annMort);
insect.AnnMort = annMort.Value;
InputVar <string> sppName = new InputVar <string>("Species");
InputVar <int> susc = new InputVar <int>("Species Susceptibility");
InputVar <double> grs = new InputVar <double>("Growth Reduction Slope");
InputVar <double> gri = new InputVar <double>("Growth Reduction Intercept");
InputVar <double> msl = new InputVar <double>("Mortality Slope");
InputVar <double> min = new InputVar <double>("Mortality Intercept");
Dictionary <string, int> lineNumbers = new Dictionary <string, int>();
const string Susceptiblities = "Susceptibilities";
Landis.Library.Biomass.Species.AuxParm <bool> AccountedFor = new Library.Biomass.Species.AuxParm <bool>(PlugIn.ModelCore.Species);
while (!AtEndOfInput && CurrentName != Susceptiblities)
{
StringReader currentLine = new StringReader(CurrentLine);
ReadValue(sppName, currentLine);
ISpecies species = PlugIn.ModelCore.Species[sppName.Value.Actual];
if (species == null)
{
throw new InputValueException(sppName.Value.String,
"{0} is not a species name.",
sppName.Value.String);
}
int lineNumber;
if (lineNumbers.TryGetValue(species.Name, out lineNumber))
{
throw new InputValueException(sppName.Value.String,
"The species {0} was previously used on line {1} for insect " + insect.Name,
sppName.Value.String, lineNumber);
}
else
{
lineNumbers[species.Name] = LineNumber;
}
ReadValue(susc, currentLine);
insect.Susceptibility[species] = Landis.Library.Biomass.CheckParms.CheckBiomassParm(susc.Value, 1, 4);
ReadValue(grs, currentLine);
insect.GrowthReduceSlope[species] = Landis.Library.Biomass.CheckParms.CheckBiomassParm(grs.Value, double.MinValue, 0);
ReadValue(gri, currentLine);
insect.GrowthReduceIntercept[species] = Landis.Library.Biomass.CheckParms.CheckBiomassParm(gri.Value, 0, double.MaxValue);
ReadValue(msl, currentLine);
insect.MortalitySlope[species] = Landis.Library.Biomass.CheckParms.CheckBiomassParm(msl.Value, 0, double.MaxValue);
ReadValue(min, currentLine);
insect.MortalityIntercept[species] = Landis.Library.Biomass.CheckParms.CheckBiomassParm(min.Value, 0, double.MaxValue);
AccountedFor[species] = true;
CheckNoDataAfter("the " + min.Name + " column",
currentLine);
GetNextLine();
}
foreach (ISpecies species in PlugIn.ModelCore.Species)
{
if (AccountedFor[species] == false)
{
throw new System.Exception(species.Name + " is not parameterized for " + insect.Name);
}
}
// Read table of Susceptibilities.
// Susceptibilities are in decreasing order.
ReadName(Susceptiblities);
const string MapNames = "MapNames";
InputVar <byte> number = new InputVar <byte>("Susceptibility Number");
InputVar <DistributionType> dt = new InputVar <DistributionType>("Distribution");
InputVar <double> v1 = new InputVar <double>("Distribution Value 1");
InputVar <double> v2 = new InputVar <double>("Distribution Value 2");
byte previousNumber = 0;
while (!AtEndOfInput && CurrentName != MapNames)
{
StringReader currentLine = new StringReader(CurrentLine);
ISusceptible susceptible = new Susceptible();
insect.SusceptibleTable.Add(susceptible);
ReadValue(number, currentLine);
susceptible.Number = number.Value;
// Check that the current severity's number is 1 less than
// the previous number (numbers are must be in decreasing
// order).
if (number.Value.Actual != previousNumber + 1)
{
throw new InputValueException(number.Value.String,
"Expected the severity number {0}",
previousNumber + 1);
}
previousNumber = number.Value.Actual;
IDistribution distribution = new Distribution();
ReadValue(dt, currentLine);
distribution.Name = dt.Value;
ReadValue(v1, currentLine);
distribution.Value1 = v1.Value;
ReadValue(v2, currentLine);
distribution.Value2 = v2.Value;
susceptible.Distribution_80 = distribution; //.GetComplete();
distribution = new Distribution();
ReadValue(dt, currentLine);
distribution.Name = dt.Value;
ReadValue(v1, currentLine);
distribution.Value1 = v1.Value;
ReadValue(v2, currentLine);
distribution.Value2 = v2.Value;
susceptible.Distribution_60 = distribution; //.GetComplete();
distribution = new Distribution();
ReadValue(dt, currentLine);
distribution.Name = dt.Value;
ReadValue(v1, currentLine);
distribution.Value1 = v1.Value;
ReadValue(v2, currentLine);
distribution.Value2 = v2.Value;
susceptible.Distribution_40 = distribution; //.GetComplete();
distribution = new Distribution();
ReadValue(dt, currentLine);
distribution.Name = dt.Value;
ReadValue(v1, currentLine);
distribution.Value1 = v1.Value;
ReadValue(v2, currentLine);
distribution.Value2 = v2.Value;
susceptible.Distribution_20 = distribution; //.GetComplete();
distribution = new Distribution();
ReadValue(dt, currentLine);
distribution.Name = dt.Value;
ReadValue(v1, currentLine);
distribution.Value1 = v1.Value;
ReadValue(v2, currentLine);
distribution.Value2 = v2.Value;
susceptible.Distribution_0 = distribution; //.GetComplete();
CheckNoDataAfter("the " + v2.Name + " column",
currentLine);
GetNextLine();
}
if (insect.SusceptibleTable.Count == 0)
{
throw NewParseException("No susceptibilities defined.");
}
return(insect);//.GetComplete();
}
public static void Initialize(IInputParameters Parameters)
{
PlugIn.ModelCore.UI.WriteLine(" Reading climate date from " + Parameters.climateFileName);
climateFileName = Parameters.climateFileName;
SetDelimitor();
string[] Content = ReadContent();
SetFirstAndLastYearOnFile(Content);
firstpossibleestmonth = new DateVar <int>("firstpossibleestmonth", FirstYearOnFile, LastYearOnFile);
lastpossibleestmonth = new DateVar <int>("lastpossibleestmonth", FirstYearOnFile, LastYearOnFile);
possibleestmonth = new DateVar <bool>("PossibleEstmonth", FirstYearOnFile, LastYearOnFile);
tmax = new DateVar <float>("tmax", FirstYearOnFile, LastYearOnFile);
tmin = new DateVar <float>("tmin", FirstYearOnFile, LastYearOnFile);
co2 = new DateVar <float>("co2", FirstYearOnFile, LastYearOnFile);
tday = new DateVar <float>("tday", FirstYearOnFile, LastYearOnFile);
par0 = new DateVar <float>("par0", FirstYearOnFile, LastYearOnFile);
tave = new DateVar <float>("tave", FirstYearOnFile, LastYearOnFile);
prec = new DateVar <float>("prec", FirstYearOnFile, LastYearOnFile);
vpd = new DateVar <float>("vpd", FirstYearOnFile, LastYearOnFile);
dayspan = new DateVar <int>("dayspan", FirstYearOnFile, LastYearOnFile);
treesareactive = new DateVar <bool>("treesareactive", FirstYearOnFile, LastYearOnFile);
SetClimateFileHeaders(Content[0]);
FolNCon = Parameters.FolNCon;
BaseFolRespFrac = Parameters.BaseFolRespFrac;
DVPD1 = Parameters.DVPD1;
DVPD2 = Parameters.DVPD2;
AmaxA = Parameters.AmaxA;
AmaxB = Parameters.AmaxB;
WUEConst = Parameters.WUEConst;
RespQ10 = Parameters.RespQ10;
PsnTOpt = Parameters.PsnTOpt;
PsnTMin = Parameters.PsnTMin;
firstactivemonthspc = new DateVar <Landis.Library.Biomass.Species.AuxParm <int> >("wettestmonth", FirstYearOnFile, LastYearOnFile);
wettestmonth = new DateVar <int>("wettestmonth", FirstYearOnFile, LastYearOnFile);
dtemppsn = new DateVar <Library.Biomass.Species.AuxParm <float> >("dtemppsn", FirstYearOnFile, LastYearOnFile);
wue = new DateVar <Library.Biomass.Species.AuxParm <float> >("wue", FirstYearOnFile, LastYearOnFile);
delamax = new DateVar <Library.Biomass.Species.AuxParm <float> >("delamax", FirstYearOnFile, LastYearOnFile);
refnetpsn = new DateVar <Library.Biomass.Species.AuxParm <float> >("refnetpsn", FirstYearOnFile, LastYearOnFile);
refresp = new DateVar <Library.Biomass.Species.AuxParm <float> >("refresp", FirstYearOnFile, LastYearOnFile);
dTempResp = new DateVar <Library.Biomass.Species.AuxParm <float> >("dTempResp", FirstYearOnFile, LastYearOnFile);
dTempRespDay = new DateVar <Library.Biomass.Species.AuxParm <float> >("dTempRespDay", FirstYearOnFile, LastYearOnFile);
dTempRespNight = new DateVar <Library.Biomass.Species.AuxParm <float> >("dTempRespNight", FirstYearOnFile, LastYearOnFile);
wue_co2_corr = new DateVar <Library.Biomass.Species.AuxParm <float> >("wue_co2_corr", FirstYearOnFile, LastYearOnFile);
dvpd = new DateVar <Library.Biomass.Species.AuxParm <float> >("dvpd", FirstYearOnFile, LastYearOnFile);
resp_folbase = new DateVar <Library.Biomass.Species.AuxParm <float> >("resp_folbase", FirstYearOnFile, LastYearOnFile);
isactive = new DateVar <Library.Biomass.Species.AuxParm <bool> >("IsActive", FirstYearOnFile, LastYearOnFile);
gdd = new DateVar <Library.Biomass.Species.AuxParm <float> >("gdd", FirstYearOnFile, LastYearOnFile);
DateTime date = new DateTime(FirstYearOnFile, 1, 15);
while (date.CompareTo(new DateTime(LastYearOnFile, 12, 15)) <= 0)
{
// GetLine checks if year/month according to the loop is equal to the date read in
string[] terms = GetLine(date.Year, date.Month, Content).Split(delim);
if (terms.Count() != ColumnCount)
{
throw new System.Exception("Unexpected number of columns in " + Parameters.climateFileName + " date = " + date);
}
if (int.Parse(terms[0]) != date.Year || int.Parse(terms[1]) != date.Month)
{
throw new System.Exception("Missing month " + date + " in climate file");
}
try
{
tmax[date] = CheckInputValue(float.Parse(terms[TMaxCol]), -80, 80, "date = " + date);
tmin[date] = CheckInputValue(float.Parse(terms[TMinCol]), -80, tmax[date], "date = " + date);
co2[date] = CheckInputValue(float.Parse(terms[CO2Col]), 0, float.MaxValue, "date = " + date);
par0[date] = CheckInputValue(float.Parse(terms[PAR0col]), 0, float.MaxValue, "date = " + date);
prec[date] = CheckInputValue(float.Parse(terms[Preccol]), 0, float.MaxValue, "date = " + date);
if (prec[date] < 0)
{
throw new System.Exception("Precipitation = " + prec + "\t" + date);
}
float hr = Calculate_hr(date.DayOfYear, Parameters.Latitude);
float daylength = Calculate_DayLength(hr);
float nightlength = Calculate_NightLength(hr);
dayspan[date] = Calculate_DaySpan(date.Month);
tave[date] = (float)0.5 * (tmin[date] + tmax[date]);
tday[date] = (float)0.5 * (tmax[date] + tave[date]);
vpd[date] = Calculate_VPD(Tday[date], TMin[date]);
gdd[date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
isactive[date] = new Library.Biomass.Species.AuxParm <bool>(PlugIn.ModelCore.Species);
dtemppsn [date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
wue[date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
delamax[date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
refnetpsn[date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
refresp[date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
dTempResp [date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
dTempRespDay[date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
dTempRespNight[date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
wue_co2_corr[date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
resp_folbase[date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
gdd[date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
dvpd[date] = new Library.Biomass.Species.AuxParm <float>(PlugIn.ModelCore.Species);
foreach (ISpecies spc in PlugIn.ModelCore.Species)
{
float dGDD = Math.Max(0, (Tave[date] - PsnTMin[spc]) * DaySpan[date]);
if (date.Month == 1)
{
gdd[date][spc] = dGDD;
}
else
{
DateTime last_month = new DateTime(date.Year, date.Month - 1, 15);
gdd[date][spc] = gdd[last_month][spc] + dGDD;
}
if (tday[date] < PsnTMin[spc])
{
IsActive[date][spc] = false;
}
else
{
IsActive[date][spc] = true;
treesareactive[date] = true;
}
//dtemppsn[date][spc] = ParabolicPsnTempResponse(tday[date], PsnTOpt[spc], PsnTMin[spc]);
dtemppsn[date][spc] = LinearPsnTempResponse(tday[date], PsnTOpt[spc], PsnTMin[spc]);
dvpd[date][spc] = Math.Max(0, 1 - DVPD1[spc] * (float)Math.Pow(vpd[date], DVPD2[spc]));
float cicaRatio = (-0.075f * FolNCon[spc]) + 0.875f;
float ci350 = 350 * cicaRatio;
float Arel350 = 1.22f * ((ci350 - 68) / (ci350 + 136));
float ciElev = co2[date] * cicaRatio;
float ArelElev = 1.22f * ((ciElev - 68) / (ciElev + 136));
DelAmax[date][spc] = 1 + ((ArelElev - Arel350) / Arel350);
// CO2 effect on photosynthesis
// Calculate CO2 effect on conductance and set slope and intercept for A-gs relationship
float Delgs = DelAmax[date][spc] / ((co2[date] - co2[date] * cicaRatio) / (350.0f - ci350));
wue[date][spc] = (WUEConst[spc] / vpd[date]) * (1 + 1 - Delgs); //DWUE determined from CO2 effects on conductance
wue_co2_corr[date][spc] = wue[date][spc] / DelAmax[date][spc];
/*
* wue_co2_corr[spc] = WUEConst[spc];
* Delgs = DelAmax / ((site.CaMo[mo] - CiElev) / (350.0 - Ci350));
* DWUE = 1.0 + (1 - Delgs);
* gsSlope = (-1.1309 * DelAmax) + 1.9762; // used to determine ozone uptake
* gsInt = (0.4656 * DelAmax) - 0.9701;
*/
// NETPSN
float amax = DelAmax[date][spc] * (AmaxA[spc] + AmaxB[spc] * FolNCon[spc]);
//Reference net Psn (lab conditions)
RefNetPsn[date][spc] = Static.DaySpan[date] * (amax * dvpd[date][spc] * daylength * Constants.MC) / Constants.billion;
dTempRespDay[date][spc] = ((float)Math.Pow(RespQ10[spc], (Tday[date] - PsnTOpt[spc]) / 10));
dTempRespNight[date][spc] = ((float)Math.Pow(RespQ10[spc], (TMin[date] - PsnTOpt[spc]) / 10));
dTempResp[date][spc] = (float)Math.Min(1.0, (dTempRespDay[date][spc] * daylength + dTempRespNight[date][spc] * nightlength) / ((float)daylength + (float)nightlength));
// gC/day
RefResp[date][spc] = BaseFolRespFrac[spc] * Static.DaySpan[date] * (amax * daylength * Constants.MC) / Constants.billion;
}
date = date.AddMonths(1);
}
catch
{
throw new System.Exception("Cannot find climate date for (year,month) " + date.Year.ToString() + " " + date.Month.ToString());
}
}
while (date.CompareTo(new DateTime(LastYearOnFile, 12, 15)) < 0)
{
if (Parameters.EstMoistureSensitivity != null)
{
wettestmonth[date] = GetWettestMonth(date, 10);
}
if (Parameters.EstRadSensitivity != null)
{
firstactivemonthspc[date] = GetFirstActiveMonth(date, 10);
}
foreach (ISpecies spc in PlugIn.ModelCore.Species)
{
int Firstpossibleestmonth = Math.Min(wettestmonth[date] - 1, firstactivemonthspc[date][spc]);
int Lastpossibleestmonth = Math.Max(wettestmonth[date] + 1, firstactivemonthspc[date][spc] + 3);
if (date.Month >= Firstpossibleestmonth && date.Month <= Lastpossibleestmonth)
{
possibleestmonth[date] = true;
}
}
date = date.AddMonths(1);
}
}
