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Finalized details for v6.6
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@rmscheller
rmscheller committed Feb 9, 2021
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Binary file modified deploy/installer/LANDIS-II-V7 NECN Succession 6.6-setup.exe
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Binary file modified docs/LANDIS-II Net Ecosystem CN Succession v6.6 User Guide.docx
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Binary file modified docs/LANDIS-II Net Ecosystem CN Succession v6.6 User Guide.pdf
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8 changes: 4 additions & 4 deletions docs/index.md
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@@ -1,6 +1,6 @@
# What is the NECN Succession Extension?

The Net Ecosystem Carbon & Nitrogen (NECN) Succession extension implements succession with full accounting of above and below ground carbon and nitrogen. Aboveground biomass is represented with cohorts that have biomass (g m-2). In addition, below ground processing of Carbon and Nitrogen is simulated following the core logic of the Century nutrient cycling model (v4.0).
The NECN Succession extension was designed to provide total ecosystem accounting of Carbon and Nitrogen and to allow species to respond dynamically to a changing climate via establishment and growth. NECN calculates how cohorts grow, reproduce, age, and die. Dead biomass is tracked over time, divided into four pools: surface wood, soil wood (dead coarse roots), surface litter (dead leaves), and soil litter (dead fine roots). In addition, three principle soil pools: fast (soil organic matter (SOM) 1), slow (SOM2), and passive (SOM3) are simulated, following the Century soil model.

# Features

Expand All @@ -12,9 +12,9 @@ The Net Ecosystem Carbon & Nitrogen (NECN) Succession extension implements succe

# Release Notes

- Latest official release: Version 6.4.1 — May 2020
- Latest official release: Version 6.6 — February 2021
- This extension was formerly named Century Succession.
- [NECN User Guide](https://github.com/LANDIS-II-Foundation/Extension-NECN-Succession/blob/master/docs/LANDIS-II%20Net%20Ecosystem%20CN%20Succession%20v6.4%20User%20Guide.pdf).
- [NECN User Guide](https://github.com/LANDIS-II-Foundation/Extension-NECN-Succession/blob/master/docs/LANDIS-II%20Net%20Ecosystem%20CN%20Succession%20v6.6%20User%20Guide.pdf).
- [User Guide for Climate Library](https://github.com/LANDIS-II-Foundation/Library-Climate/blob/master/docs/LANDIS-II%20Climate%20Library%20v4.1%20User%20Guide.pdf)
- Full release details found in the NECN User Guide and on GitHub.

Expand All @@ -27,7 +27,7 @@ To use NECN, you need:

# Download

Version 6.4.1 can be downloaded [here](https://github.com/LANDIS-II-Foundation/Extension-NECN-Succession/blob/master/deploy/past-releases/LANDIS-II-V7%20NECN%20Succession%206.4.1-setup.exe). To install it on your computer, just launch the installer.
Version 6.6 can be downloaded [here](https://github.com/LANDIS-II-Foundation/Extension-NECN-Succession/blob/master/deploy/installer/LANDIS-II-V7%20NECN%20Succession%206.6-setup.exe). To install it on your computer, just launch the installer.

# Citation

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2 changes: 1 addition & 1 deletion src/AvailableN.cs
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Expand Up @@ -333,7 +333,7 @@ public static void AdjustAvailableN(ICohort cohort, ActiveSite site, double[] ac
CalibrateLog.resorbedNused = resorbedNused;
CalibrateLog.mineralNused = Nuptake;
CalibrateLog.demand_N = totalNdemand;
Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},{2:0.00},", resorbedNused, Nuptake, totalNdemand);
//Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},{2:0.00},", resorbedNused, Nuptake, totalNdemand);
}

}
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29 changes: 14 additions & 15 deletions src/CohortBiomass.cs
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Expand Up @@ -55,7 +55,7 @@ public float[] ComputeChange(ICohort cohort, ActiveSite site)
CalibrateLog.cohortAge = cohort.Age;
CalibrateLog.cohortWoodB = cohort.WoodBiomass;
CalibrateLog.cohortLeafB = cohort.LeafBiomass;
Outputs.CalibrateLog.Write("{0},{1},{2},{3},{4},{5:0.0},{6:0.0},", PlugIn.ModelCore.CurrentTime, Main.Month + 1, ecoregion.Index, cohort.Species.Name, cohort.Age, cohort.WoodBiomass, cohort.LeafBiomass);
//Outputs.CalibrateLog.Write("{0},{1},{2},{3},{4},{5:0.0},{6:0.0},", PlugIn.ModelCore.CurrentTime, Main.Month + 1, ecoregion.Index, cohort.Species.Name, cohort.Age, cohort.WoodBiomass, cohort.LeafBiomass);
}


Expand Down Expand Up @@ -155,8 +155,10 @@ public float[] ComputeChange(ICohort cohort, ActiveSite site)

if (OtherData.CalibrateMode && PlugIn.ModelCore.CurrentTime > 0)
{
CalibrateLog.deltaLeaf = deltaLeaf;
CalibrateLog.deltaWood = deltaWood;
CalibrateLog.WriteLogFile();
Outputs.CalibrateLog.WriteLine("{0:0.00},{1:0.00},{2:0.00},{3:0.00},", deltaWood, deltaLeaf, totalMortality[0], totalMortality[1]);
//Outputs.CalibrateLog.WriteLine("{0:0.00},{1:0.00},{2:0.00},{3:0.00},", deltaWood, deltaLeaf, totalMortality[0], totalMortality[1]);
}

return deltas;
Expand Down Expand Up @@ -185,7 +187,7 @@ private double[] ComputeActualANPP(ICohort cohort,
// RMS 03/2016: Testing alternative more similar to how Biomass Succession operates: REMOVE FOR NEXT RELEASE
//double limitCapacity = 1.0 - Math.Min(1.0, Math.Exp(siteBiomass / maxBiomass * 5.0) / Math.Exp(5.0));

double competition_limit = calculateCompetition_Limit(cohort, site);
double competition_limit = calculate_LAI_Competition(cohort, site);

double potentialNPP = maxNPP * limitLAI * limitH20 * limitT * competition_limit;

Expand Down Expand Up @@ -243,9 +245,9 @@ private double[] ComputeActualANPP(ICohort cohort,
CalibrateLog.actualWoodNPP = woodNPP;
CalibrateLog.actualLeafNPP = leafNPP;

Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},{2:0.00},{3:0.00},", limitLAI, limitH20, limitT, limitN);
Outputs.CalibrateLog.Write("{0},{1},{2},{3:0.0},{4:0.0},", maxNPP, maxBiomass, (int)siteBiomass, (cohort.WoodBiomass + cohort.LeafBiomass), SiteVars.SoilTemperature[site]);
Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},", woodNPP, leafNPP);
//Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},{2:0.00},{3:0.00},", limitLAI, limitH20, limitT, limitN);
//Outputs.CalibrateLog.Write("{0},{1},{2},{3:0.0},{4:0.0},", maxNPP, maxBiomass, (int)siteBiomass, (cohort.WoodBiomass + cohort.LeafBiomass), SiteVars.SoilTemperature[site]);
//Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},", woodNPP, leafNPP);
}

return new double[2]{woodNPP, leafNPP};
Expand Down Expand Up @@ -295,7 +297,7 @@ private double[] ComputeAgeMortality(ICohort cohort, ActiveSite site)
{
CalibrateLog.mortalityAGEleaf = M_AGE_leaf;
CalibrateLog.mortalityAGEwood = M_AGE_wood;
Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},", M_AGE_wood, M_AGE_leaf);
//Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},", M_AGE_wood, M_AGE_leaf);
}

return M_AGE;
Expand Down Expand Up @@ -359,7 +361,7 @@ private double[] ComputeGrowthMortality(ICohort cohort, ActiveSite site, double
{
CalibrateLog.mortalityBIOwood = M_wood;
CalibrateLog.mortalityBIOleaf = M_leaf;
Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},", M_wood, M_leaf);
//Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},", M_wood, M_leaf);
}

SiteVars.WoodMortality[site] += (M_wood);
Expand Down Expand Up @@ -512,7 +514,7 @@ private double calculateN_Limit(ActiveSite site, ICohort cohort, double NPP, dou
{
CalibrateLog.mineralNalloc = mineralNallocation;
CalibrateLog.resorbedNalloc = resorbedNallocation;
Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},", mineralNallocation, resorbedNallocation);
//Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},", mineralNallocation, resorbedNallocation);
}

return Math.Max(limitN, 0.0);
Expand Down Expand Up @@ -617,18 +619,15 @@ private static double calculateLAI_Limit(ICohort cohort, ActiveSite site)
CalibrateLog.actual_LAI = lai;
CalibrateLog.base_lai = base_lai;
CalibrateLog.seasonal_adjustment = seasonal_adjustment;
Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},{2:0.00},", lai, base_lai, seasonal_adjustment);
//Outputs.CalibrateLog.Write("{0:0.00},{1:0.00},{2:0.00},", lai, base_lai, seasonal_adjustment);
}

//PlugIn.ModelCore.UI.WriteLine("Yr={0},Mo={1}. Spp={2}, leafC={3:0.0}, woodC={4:0.00}.", PlugIn.ModelCore.CurrentTime, month + 1, species.Name, leafC, largeWoodC);
//PlugIn.ModelCore.UI.WriteLine("Yr={0},Mo={1}. Spp={2}, lai={3:0.0}, woodC={4:0.00}.", PlugIn.ModelCore.CurrentTime, month + 1, species.Name, lai, largeWoodC);
//PlugIn.ModelCore.UI.WriteLine("Yr={0},Mo={1}. LAI Limits: lai={2:0.0}, woodLAI={3:0.0}, leafLAI={4:0.0}, LAIlimit={5:0.00}.", PlugIn.ModelCore.CurrentTime, month + 1, lai, woodLAI, leafLAI, LAI_limit);

return LAI_Growth_limit;

}

private static double calculateCompetition_Limit(ICohort cohort, ActiveSite site)
private static double calculate_LAI_Competition(ICohort cohort, ActiveSite site)
{
double k = -0.14; // This is the value given for all temperature ecosystems. I started with 0.1
double monthly_cumulative_LAI = SiteVars.MonthlyLAI[site][Main.Month];
Expand Down Expand Up @@ -709,7 +708,7 @@ private static double calculateWater_Limit(ActiveSite site, IEcoregion ecoregion
if (PlugIn.ModelCore.CurrentTime > 0 && OtherData.CalibrateMode)
{
CalibrateLog.availableWater = SiteVars.AvailableWater[site];
Outputs.CalibrateLog.Write("{0:0.00},", SiteVars.AvailableWater[site]);
//Outputs.CalibrateLog.Write("{0:0.00},", SiteVars.AvailableWater[site]);
}

return WaterLimit;
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72 changes: 36 additions & 36 deletions src/Outputs.cs
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Expand Up @@ -17,7 +17,7 @@ namespace Landis.Extension.Succession.NECN
{
public class Outputs
{
public static StreamWriter CalibrateLog;
//public static StreamWriter CalibrateLog;
public static MetadataTable<MonthlyLog> monthlyLog;
public static MetadataTable<PrimaryLog> primaryLog;
public static MetadataTable<PrimaryLogShort> primaryLogShort;
Expand Down Expand Up @@ -467,44 +467,44 @@ public static void WriteMonthlyLogFile(int month)
}

//Write log file for growth and limits
public static void CreateCalibrateLogFile()
{
string logFileName = "NECN-calibrate-OLD-log.csv";
PlugIn.ModelCore.UI.WriteLine("******************WARNING************************", logFileName);
PlugIn.ModelCore.UI.WriteLine("******YOU ARE CURRENTLY IN CALIBRATE MODE********", logFileName);
PlugIn.ModelCore.UI.WriteLine("*************************************************", logFileName);
PlugIn.ModelCore.UI.WriteLine(" Opening NECN calibrate log file \"{0}\" ...", logFileName);
try
{
CalibrateLog = new StreamWriter(logFileName);
}
catch (Exception err)
{
string mesg = string.Format("{0}", err.Message);
throw new System.ApplicationException(mesg);
}

CalibrateLog.AutoFlush = true;

CalibrateLog.Write("Year, Month, ClimateRegionIndex, SpeciesName, CohortAge, CohortWoodB, CohortLeafB, "); // from ComputeChange
CalibrateLog.Write("MortalityAGEwood, MortalityAGEleaf, "); // from ComputeAgeMortality
CalibrateLog.Write("availableWater,"); //from Water_limit
CalibrateLog.Write("LAI, tlai, rlai,"); // from ComputeChange
CalibrateLog.Write("mineralNalloc, resorbedNalloc, "); // from calculateN_Limit

// These three together:
CalibrateLog.Write("limitLAI, limitH20, limitT, limitN, "); //from ComputeActualANPP
CalibrateLog.Write("maxNPP, Bmax, Bsite, Bcohort, soilTemp, "); //from ComputeActualANPP
CalibrateLog.Write("actualWoodNPP, actualLeafNPP, "); //from ComputeActualANPP

CalibrateLog.Write("MortalityBIOwood, MortalityBIOleaf, "); // from ComputeGrowthMortality
CalibrateLog.Write("NPPwood_C, NPPleaf_C, "); //from ComputeNPPcarbon
CalibrateLog.Write("resorbedNused, mineralNused, Ndemand,"); // from AdjustAvailableN
CalibrateLog.WriteLine("deltaWood, deltaLeaf, totalMortalityWood, totalMortalityLeaf"); // from ComputeChange
//public static void CreateCalibrateLogFile()
//{
// string logFileName = "NECN-calibrate-OLD-log.csv";
// PlugIn.ModelCore.UI.WriteLine("******************WARNING************************", logFileName);
// PlugIn.ModelCore.UI.WriteLine("******YOU ARE CURRENTLY IN CALIBRATE MODE********", logFileName);
// PlugIn.ModelCore.UI.WriteLine("*************************************************", logFileName);
// PlugIn.ModelCore.UI.WriteLine(" Opening NECN calibrate log file \"{0}\" ...", logFileName);
// try
// {
// CalibrateLog = new StreamWriter(logFileName);
// }
// catch (Exception err)
// {
// string mesg = string.Format("{0}", err.Message);
// throw new System.ApplicationException(mesg);
// }

// CalibrateLog.AutoFlush = true;

// CalibrateLog.Write("Year, Month, ClimateRegionIndex, SpeciesName, CohortAge, CohortWoodB, CohortLeafB, "); // from ComputeChange
// CalibrateLog.Write("MortalityAGEwood, MortalityAGEleaf, "); // from ComputeAgeMortality
// CalibrateLog.Write("availableWater,"); //from Water_limit
// CalibrateLog.Write("LAI, tlai, rlai,"); // from ComputeChange
// CalibrateLog.Write("mineralNalloc, resorbedNalloc, "); // from calculateN_Limit

// // These three together:
// CalibrateLog.Write("limitLAI, limitH20, limitT, limitN, "); //from ComputeActualANPP
// CalibrateLog.Write("maxNPP, Bmax, Bsite, Bcohort, soilTemp, "); //from ComputeActualANPP
// CalibrateLog.Write("actualWoodNPP, actualLeafNPP, "); //from ComputeActualANPP

// CalibrateLog.Write("MortalityBIOwood, MortalityBIOleaf, "); // from ComputeGrowthMortality
// CalibrateLog.Write("NPPwood_C, NPPleaf_C, "); //from ComputeNPPcarbon
// CalibrateLog.Write("resorbedNused, mineralNused, Ndemand,"); // from AdjustAvailableN
// CalibrateLog.WriteLine("deltaWood, deltaLeaf, totalMortalityWood, totalMortalityLeaf"); // from ComputeChange



}
//}

public static void WriteMaps()
{
Expand Down
5 changes: 2 additions & 3 deletions src/PlugIn.cs
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Expand Up @@ -139,9 +139,8 @@ public override void Initialize()

InitializeSites(Parameters.InitialCommunities, Parameters.InitialCommunitiesMap, modelCore);

if (Parameters.CalibrateMode)
Outputs.CreateCalibrateLogFile();
//Establishment.InitializeLogFile();
//if (Parameters.CalibrateMode)
// Outputs.CreateCalibrateLogFile();

B_MAX = 0;
foreach (ISpecies species in ModelCore.Species)
Expand Down
9 changes: 9 additions & 0 deletions src/metadata/CalibrateLog.cs
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Expand Up @@ -19,6 +19,7 @@ public class CalibrateLog
public static double limitLAI, limitH20, limitT, limitN;
public static double maxNPP, maxB, siteB, cohortB, soilTemp;
public static double actualWoodNPP, actualLeafNPP;
public static double deltaWood, deltaLeaf;
public static double mortalityBIOwood, mortalityBIOleaf;
// CalibrateLog.Write("NPPwood_C, NPPleaf_C, "); //from ComputeNPPcarbon
public static double resorbedNused, mineralNused, demand_N;
Expand Down Expand Up @@ -58,6 +59,8 @@ public static void WriteLogFile()
clog.SoilTemperature = soilTemp;
clog.ActualWoodANPP = actualWoodNPP;
clog.ActualLeafANPP = actualLeafNPP;
clog.DeltaWood = deltaWood;
clog.DeltaLeaf = deltaLeaf;
clog.TotalNDemand = demand_N;


Expand Down Expand Up @@ -134,6 +137,12 @@ public static void WriteLogFile()
[DataFieldAttribute(Unit = "g_B_m2_month1", Desc = "Actual Leaf ANPP", Format = "0.0000")]
public double ActualLeafANPP { set; get; }
// ********************************************************************
[DataFieldAttribute(Unit = "g_B_m2_month1", Desc = "Change in Wood Biomass", Format = "0.000")]
public double DeltaWood { set; get; }
// ********************************************************************
[DataFieldAttribute(Unit = "g_B_m2_month1", Desc = "Change in Leaf Biomass", Format = "0.0000")]
public double DeltaLeaf { set; get; }
// ********************************************************************
[DataFieldAttribute(Unit = FieldUnits.g_B_m2, Desc = "Cohort Maximum Biomass")]
public double CohortMaximumBiomass { set; get; }
// ********************************************************************
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