private void DoUnderstoryWaterBalance()
{
UnderstoryCoverGreen = UnderstoryCoverMax * (1 - cover_green);
UnderstoryPEP = eo * UnderstoryCoverGreen * (1 - cover_green);
MyPaddock.Get("Soil Water.sw_dep", out sw_dep); //need to get latest copy of swdep because OP will have taken water up.
for (int j = 0; j < ll15_dep.Length; j++)
{
UnderstoryPotSWUptake[j] = Math.Max(0.0, RootProportion(j, UnderstoryRootDepth) * UnderstoryKLmax * UnderstoryCoverGreen * (sw_dep[j] - ll15_dep[j]));
}
double TotUnderstoryPotSWUptake = MathUtility.Sum(UnderstoryPotSWUptake);
UnderstoryEP = 0.0;
for (int j = 0; j < ll15_dep.Length; j++)
{
UnderstorySWUptake[j] = UnderstoryPotSWUptake[j] * Math.Min(1.0, UnderstoryPEP / TotUnderstoryPotSWUptake);
UnderstoryEP += UnderstorySWUptake[j];
sw_dep[j] = sw_dep[j] - UnderstorySWUptake[j];
}
if (!MyPaddock.Set("Soil Water.sw_dep", sw_dep))
{
throw new Exception("Unable to set sw_dep");
}
if (UnderstoryPEP > 0.0)
{
UnderstoryFW = UnderstoryEP / UnderstoryPEP;
}
else
{
UnderstoryFW = 1.0;
}
}
private void DoGrowth()
{
double OPCover = 0;
if (!MyPaddock.Get("OilPalm.cover_green", out OPCover))
{
OPCover = 0.0;
}
double RUE = 1.3;
DltDM = RUE * Radn * cover_green * (1 - OPCover) * FW;
}
private bool empty = true; // tracks if the header has been printed for the interval value data
[EventHandler] public void Ondodcaps()
{
int DOY = 0;
double latitude = 0;
double maxT = 0;
double minT = 0;
double radn = 0;
double RootShootRatio = 0;
double SLN = 0;
double SWAvailable = 0;
double lai = 0;
MyPaddock.Get("DOY", out DOY);
MyPaddock.Get("latitude", out latitude);
MyPaddock.Get("maxT", out maxT);
MyPaddock.Get("minT", out minT);
MyPaddock.Get("radn", out radn);
MyPaddock.Get("RootShootRatio", out RootShootRatio);
MyPaddock.Get("SLN", out SLN);
MyPaddock.Get("SWAvailable", out SWAvailable);
MyPaddock.Get("lai", out lai);
// Model the photosynthesis
DCAPSTModel DM = Classic.SetUpModel(CP, PP, DOY, latitude, maxT, minT, radn);
// Optional values
DM.PrintIntervalValues = false; // Switch to print extra data (default = false)
DM.Biolimit = 0; // Biological transpiration limit of the crop (0 disables mechanism)
DM.Reduction = 0; // Excess water reduction fraction for bio-limited transpiration (0 disables mechanism)
// Run the simulation
DM.DailyRun(lai, SLN, SWAvailable, RootShootRatio);
if (DM.PrintIntervalValues)
{
if (empty)
{
writer.WriteLine(DM.PrintResultHeader());
empty = false;
}
writer.WriteLine(DM.IntervalResults);
}
// Outputs
RootShoot = RootShootRatio;
BIOshootDAY = dcaps[0] = DM.ActualBiomass;
BIOtotalDAY = BIOshootDAY * (1 + RootShoot);
EcanDemand = dcaps[1] = DM.WaterDemanded;
EcanSupply = dcaps[2] = DM.WaterSupplied;
RadIntDcapst = dcaps[3] = DM.InterceptedRadiation;
RUE = (RadIntDcapst == 0 ? 0 : BIOshootDAY / RadIntDcapst);
TE = (EcanSupply == 0 ? 0 : BIOshootDAY / EcanSupply);
BIOshootDAYPot = dcaps[4] = DM.PotentialBiomass;
}
public override void DoWaterUptake(double Amount)
{
Uptake = Amount;
if (TalkDirectlyToRoot)
{
MyPaddock.Set(OurName + "Root.SWUptake", Amount);
}
else
{
List <string> ModelNames = new List <string>();
List <double> Supply = new List <double>();
foreach (Paddock SubPaddock in MyPaddock.ChildPaddocks)
{
double[] SWSupply;
string ModelName = SubPaddock.FullName + "." + Plant.Name + "Root";
MyPaddock.Get(ModelName + ".SWSupply", out SWSupply);
Supply.Add(MathUtility.Sum(SWSupply));
ModelNames.Add(ModelName);
}
double fraction = Amount / MathUtility.Sum(Supply);
if (fraction > 1)
{
throw new Exception("Requested SW uptake > Available supplies.");
}
int i = 0;
foreach (string ModelName in ModelNames)
{
MyPaddock.Set(ModelName + ".SWUptake", Supply[i] * fraction);
i++;
}
}
}
public override void DoSWUptake(double SWDemand)
{
// Firstly grow roots.
// the layer with root front
int layer = FindLayerNo(RootDepth);
dltRootDepth = RootDepthRate.Value * RootAdvanceFactorTemp.Value *
Math.Min(RootAdvanceFactorWaterStress.Value, SWFactorRootDepth.Value) *
xf[layer];
// prevent roots partially entering layers where xf == 0
int deepest_layer;
for (deepest_layer = xf.Length - 1;
deepest_layer >= 0 &&
(xf[deepest_layer] <= 0.0 || getModifiedKL(deepest_layer) <= 0.0);
deepest_layer--)
{
; /* nothing */
}
int RootLayerMax = deepest_layer + 1;
double RootDepthMax = MathUtility.Sum(dlayer, 0, deepest_layer + 1, 0.0);
dltRootDepth = MathUtility.Constrain(dltRootDepth, double.MinValue, RootDepthMax - RootDepth);
if (dltRootDepth < 0.0)
{
throw new Exception("negative root growth??");
}
Util.Debug("Root.dltRootDepth=%f", dltRootDepth);
Util.Debug("Root.root_layer_max=%i", RootLayerMax);
Util.Debug("Root.root_depth_max=%f", RootDepthMax);
// potential extractable sw
DoPotentialExtractableSW();
// actual extractable sw (sw-ll)
DoSWAvailable();
DoSWSupply();
if (SwimIsPresent)
{
MyPaddock.Get("uptake_water_" + Plant.CropType, out dlt_sw_dep);
dlt_sw_dep = MathUtility.Multiply_Value(dlt_sw_dep, -1); // make them negative numbers.
}
else
{
DoWaterUptakeInternal(SWDemand);
}
Util.Debug("Root.dlt_sw_dep=%f", MathUtility.Sum(dlt_sw_dep));
}
public void OnInitialised()
{
/* IMPORTANT - Do NOT change the order of these values */
CP = Classic.SetUpCanopy(
CanopyType.C3, // Canopy type
370, // CO2 partial pressure
0.7, // Empirical curvature factor
0.047, // Diffusivity-solubility ratio
210000, // O2 partial pressure
0.78, // PAR diffuse extinction coefficient
0.8, // NIR diffuse extinction coefficient
0.036, // PAR diffuse reflection coefficient
0.389, // NIR diffuse reflection coefficient
60, // Leaf angle
0.15, // PAR leaf scattering coefficient
0.8, // NIR leaf scattering coefficient
0.05, // Leaf width
1.3, // SLN ratio at canopy top
14, // Minimum structural nitrogen
1.5, // Wind speed
1.5); // Wind speed profile distribution coefficient
PP = Classic.SetUpPathway(
0, // Electron transport minimum temperature
30.0, // Electron transport optimum temperature
45.0, // Electron transport maximum temperature
0.911017958600129, // Electron transport scaling constant
1, // Electron transport Beta value
6048.95289, //mesophyll conductance factor
273.422964228666, // Kc25 - Michaelis Menten constant of Rubisco carboxylation at 25 degrees C
93720, // KcFactor
165824.064155384, // Ko25 - Michaelis Menten constant of Rubisco oxygenation at 25 degrees C
33600, // KoFactor
4.59217066521612, // VcVo25 - Rubisco carboxylation to oxygenation at 25 degrees C
35713.19871277176, // VcVoFactor
0.0, // Kp25 - Michaelis Menten constant of PEPc activity at 25 degrees C (Unused in C3)
0.0, // KpFactor (Unused in C3)
65330, // VcFactor
46390, // RdFactor
57043.2677590512, // VpFactor
0.0, // PEPc regeneration (Unused in C3)
0.15, // Spectral correction factor
0.1, // Photosystem II activity fraction
0.003, // Bundle sheath CO2 conductance
1.1 * PsiFactor, // Max Rubisco activity to SLN ratio
1.85 * PsiFactor, // Max electron transport to SLN ratio
0.0 * PsiFactor, // Respiration to SLN ratio
1.0 * PsiFactor, // Max PEPc activity to SLN ratio
0.00412 * PsiFactor, // Mesophyll CO2 conductance to SLN ratio
0.75, // Extra ATP cost
0.7); // Intercellular CO2 to air CO2 ratio
//Set the LAI trigger
MyPaddock.Set("DCaPSTTriggerLAI", LAITrigger);
MyPaddock.Get("PsModelName1", out PsModelName1);
}
public void Ondodcaps()
{
int DOY = 0;
double latitude = 0;
double maxT = 0;
double minT = 0;
double radn = 0;
double RootShootRatio = 0;
double SLN = 0;
double SWAvailable = 0;
double lai = 0;
MyPaddock.Get("DOY", out DOY);
MyPaddock.Get("latitude", out latitude);
MyPaddock.Get("maxT", out maxT);
MyPaddock.Get("minT", out minT);
MyPaddock.Get("radn", out radn);
MyPaddock.Get("RootShootRatio", out RootShootRatio);
MyPaddock.Get("SLN", out SLN);
MyPaddock.Get("SWAvailable", out SWAvailable);
MyPaddock.Get("lai", out lai);
// Model the photosynthesis
double rpar = 0.5;
DCAPSTModel DM = Classic.SetUpModel(CP, PP, DOY, latitude, maxT, minT, radn, rpar);
// Optional values
DM.PrintIntervalValues = false; // Switch to print extra data (default = false)
DM.Biolimit = 0; // Biological transpiration limit of the crop (0 disables mechanism)
DM.Reduction = 0; // Excess water reduction fraction for bio-limited transpiration (0 disables mechanism)
// Run the simulation
DM.DailyRun(lai, SLN, SWAvailable, RootShootRatio);
// Daily Outputs
RootShoot = RootShootRatio;
BIOshootDAY = dcaps[0] = DM.ActualBiomass;
BIOtotalDAY = BIOshootDAY * (1 + RootShoot);
EcanDemand = dcaps[1] = DM.WaterDemanded;
EcanSupply = dcaps[2] = DM.WaterSupplied;
RadIntDcapst = dcaps[3] = DM.InterceptedRadiation;
RUE = (RadIntDcapst == 0 ? 0 : BIOshootDAY / RadIntDcapst);
TE = (EcanSupply == 0 ? 0 : BIOshootDAY / EcanSupply);
BIOshootDAYPot = dcaps[4] = DM.PotentialBiomass;
SoilWater = SWAvailable;
// Interval outputs
foreach (var interval in DM.Intervals)
{
Hour = interval.Time;
SunlitTemperature = interval.Sunlit.Temperature;
ShadedTemperature = interval.Shaded.Temperature;
SunlitAc1 = interval.Sunlit.Ac1.Assimilation;
SunlitAc2 = interval.Sunlit.Ac2.Assimilation;
SunlitAj = interval.Sunlit.Aj.Assimilation;
ShadedAc1 = interval.Shaded.Ac1.Assimilation;
ShadedAc2 = interval.Shaded.Ac2.Assimilation;
ShadedAj = interval.Shaded.Aj.Assimilation;
if (IntervalStep != null)
{
IntervalStep.Invoke();
}
}
}
// The following event handler will be called once at the beginning of the simulation
[EventHandler] public void OnInitialised()
{
string path = "IntervalValues.csv";
stream = new FileStream(path, FileMode.Create);
writer = new StreamWriter(stream);
/* Do NOT change the order of these values */
CP = Classic.SetUpCanopy(
CanopyType.CCM, // Canopy type
370, // CO2 partial pressure
0.7, // Empirical curvature factor
0.047, // Diffusivity-solubility ratio (Used in CCM)
210000, // O2 partial pressure
0.78, // PAR diffuse extinction coefficient
0.8, // NIR diffuse extinction coefficient
0.036, // PAR diffuse reflection coefficient
0.389, // NIR diffuse reflection coefficient
60, // Leaf angle
0.15, // PAR leaf scattering coefficient
0.8, // NIR leaf scattering coefficient
0.05, // Leaf width
1.3, // SLN ratio at canopy top
14, // Minimum structural nitrogen
1.5, // Wind speed
1.5); // Wind speed profile distribution coefficient
PP = Classic.SetUpPathway(
0, // Electron transport minimum temperature
30.0, // Electron transport optimum temperature
45.0, // Electron transport maximum temperature
0.911017958600129, // Electron transport scaling constant
1, // Electron transport Beta value
0, // Mesophyll conductance minimum temperature
29.2338417788683, // Mesophyll conductance optimum temperature
45, // Mesophyll conductance maximum temperature
0.875790608584141, // Mesophyll conductance scaling constant
1, // Mesophyll conductance Beta value
17.52 * 273.422964228666, // Kc25 - Michaelis Menten constant of Rubisco carboxylation at 25 degrees C (Changed in CCM)*********************
93720, // KcFactor
1.34 * 165824.064155384, // Ko25 - Michaelis Menten constant of Rubisco oxygenation at 25 degrees C (Changed in CCM)*********************
33600, // KoFactor
13.07 * 4.59217066521612, // VcVo25 - Rubisco carboxylation to oxygenation at 25 degrees C (Changed in CCM)*********************
35713.19871277176, // VcVoFactor
75, // Kp25 - Michaelis Menten constant of PEPc activity at 25 degrees C (Used in CCM)
36300, // KpFactor (Used in CCM)
65330, // VcFactor
46390, // RdFactor
57043.2677590512, // VpFactor (Used in CCM)
400.0, // PEPc regeneration (Used in CCM)
0.15, // Spectral correction factor
0.1, // Photosystem II activity fraction (used in CCM)
0.003, // Bundle sheath CO2 conductance (Used in CCM)********************
1.1 * PsiFactor, // Max Rubisco activity to SLN ratio
1.9484 * PsiFactor, // Max electron transport to SLN ratio (Changed in CCM)********************
0.0 * PsiFactor, // Respiration to SLN ratio
1 * PsiFactor, // Max PEPc activity to SLN ratio (Changed in CCM)*********************0.373684157583268
0.00412 * PsiFactor, // Mesophyll CO2 conductance to SLN ratio
0.75, // Extra ATP cost (Changed in CCM)*********************
0.7); // Intercellular CO2 to air CO2 ratio
//Set the LAI trigger
MyPaddock.Set("DCaPSTTriggerLAI", LAITrigger);
MyPaddock.Get("PsModelName1", out PsModelName1);
}
//Called each daily timestep
[EventHandler] void OnProcess()
{
//Delta arrays for each variable
rainAmt += rain;
double[] dlt_ks = new double[oc.Length];
double[] dlt_dul = new double[oc.Length];
double[] dlt_ll = new double[oc.Length];
double[] dlt_bd = new double[oc.Length];
double[] dlt_swcon = new double[oc.Length];
double[] dlt_sat = new double[oc.Length];
double[] dlt_hum = new double[oc.Length];
double[] dlt_biom = new double[oc.Length];
double[] dlt_ph = new double[oc.Length];
double[] dlt_n_avail = new double[oc.Length];
double[] dlt_biochar_c = new double[oc.Length];
double[] bc_nh4_dlt = new double[oc.Length];
double[] dlt_kl = new double[oc.Length];
for (int i = 0; i < oc.Length; i++)//Since kl's effect is multiplicative, its default needs to be 1
{
dlt_kl[i] = 1.0;
}
//computeDULandBD(out saxon_dul, out saxon_bd, 0);
//saxon_ll = computeLL(0);
//saxon_sat = giveSAT(0);
if (Today < date)
{
for (int i = 0; i < dlayer.Length; i++)
{
saxon_bd[i] = bd[i];
}
}
if (Today == date)
{
//Step 1
applyBiochar();
}
if (Today > date)
{
for (int i = 0; i < oc.Length; i++) //try looping through all layers
{
MyPaddock.Get(soil_name + " Nitrogen.tf", out tf); //This si why soil name needs to be an input parameter
MassComparison[i] = (BiocharC[i] / frac_c_biochar) / (LayerMass[i]);
double n_demand, dlt_n_min_tot_bc;
//double rd_hum_fac = 0.0, rd_biom_fac = 0.0, rd_carb_fac = 0.0, rd_cell_fac = 0.0, rd_lign_fac = 0.0, rd_ef_fac = 0.0, rd_fr_fac = 0.0;
double nh4_change;
double new_ph;
//Local variables for this specific soil layer
double new_layer_ll, new_layer_bd, new_layer_dul, new_layer_ks, new_layer_sat, new_layer_swcon = 0.0;
//step 2
//When biochar functionality is expanded, every instance of a '0' method argument or array index will be changed to a layer index, and layers that biochar
//alters will be iterated over in a for loop, but for now biochar only changes the first layer
dlt_c_min_biochar[i] = computeDailyBCCarbDecomp(i);
//step 3
computeDLTs(out dlt_c_biochar_biom[i], out dlt_c_biochar_hum[i], out dlt_c_biochar_co2[i], dlt_c_min_biochar[i]);
//step 4 -inactive
n_demand = getNDemand(dlt_c_biochar_biom[i], dlt_c_biochar_hum[i]);
dlt_n_min_tot_bc = computeNFromDecomp(dlt_c_min_biochar[i]);
n_demand_bc[i] = n_demand;
n_avail_bc[i] = dlt_n_min_tot_bc;
dlt_n_min_biochar[i] = dlt_n_min_tot_bc - n_demand; //This will get added to dlt_n_min_tot I think
//Step 5 happens in model
//Step 6
get_rd_factors(out rd_hum_fac, out rd_biom_fac, out rd_carb_fac, out rd_cell_fac, out rd_lign_fac,
out rd_ef_fac, out rd_fr_fac, out rd_ef_fom_fac, out rd_fr_fom_fac, i);
//Step 7
nh4_change = get_NH4_changes(i);
//Step 8
soil_cec[i] = get_new_cec(i);
new_ph = get_new_ph(i);
//For computing delta locally.
getCurrentSoilWatValues();
//Step 9
new_layer_ll = computeLL(i);
computeDULandBD(out new_layer_dul, out new_layer_bd, i);
//new_layer_sat = giveSAT(i); //Active but not being used
/**
* new_layer_swcon = computeSWCON(0, new_layer_sat, new_layer_bd);
* new_layer_ks = computeKS(0, new_layer_sat, new_layer_dul, new_layer_ll);
**/
//End of steps
/**
* The biochar decomposed event requires that changes be in terms of delta.
* However, our equations give the total value, not the change, so we must compute
* the change within this script.
**/
//dlt_ks[0] = new_layer_ks - ks[0];
dlt_dul[i] = new_layer_dul; // -dul[i];
dlt_ll[i] = new_layer_ll; // -ll15[i];
//not actually a delta, model stops working if it is. Instead, is the next wanted value of bd
if (BiocharC[i] != 0.0)
{
dlt_bd[i] = new_layer_bd + saxon_bd[i];
}
else
{
dlt_bd[i] = initialBD[i];
}
dlt_hum[i] = dlt_c_biochar_hum[i];
dlt_biom[i] = dlt_c_biochar_biom[i];
dlt_biochar_c[i] = dlt_c_min_biochar[i];
dlt_ph[i] = new_ph - ph[i];
dlt_n_avail[i] = dlt_n_min_biochar[i];
bc_nh4_dlt[i] = nh4_change;
if (kl_switch.Equals("on")) //So that kl does not go to 0
{
dlt_kl[i] = 1; //what became of step 10
}
}
//End of loop
//The data structure for our decomposition event
BiocharDecomposedType BiocharDecomp = new BiocharDecomposedType();
getCurrentSoilWatValues();
//region for andales saxon mergeing - to later integrate with
double[] andales_bd = AndalesBD();
double[] bd_new = biggest_bd_dlt(dlt_bd, andales_bd);
double[] sat_dlt_new = sat_in_terms_of_dlt(bd_new);
for (int i = 0; i < oc.Length; i++)
{
double temp;
saxon_sat[i] = (-(dlt_bd[i] - saxon_bd[i]) / 2.65) * 0.9 + sat[i];
saxon_bd[i] = dlt_bd[i];
till_bd[i] = andales_bd[i];
till_sat[i] = (-(andales_bd[i] - biochar_bd[i]) / 2.65) * 0.9 + sat[i];
temp = 100 / (bd_new[i] * init_soil_fac[i]);
dlt_dlayer[i] = temp - dlayer[i];
}
biochar_bd = bd_new;
//Script control area
if (dul_switch.Equals("on"))
{
BiocharDecomp.dlt_dul = dlt_dul;
}
if (ll_switch.Equals("on"))
{
BiocharDecomp.dlt_ll = dlt_ll;
}
if (sat_switch.Equals("on"))
{
BiocharDecomp.dlt_sat = sat_dlt_new;
}
//Since errors occur if bd is in terms of delta, we need to ensure that if bd is off, we still get what we want
if (bd_switch.Equals("on"))
{
BiocharDecomp.dlt_bd = bd;
//BiocharDecomp.dlt_bd = bd_new;
//MyPaddock.Set("dlt_dlayer", dlt_dlayer);
}
else
{
BiocharDecomp.dlt_bd = bd;
}
if (swcon_switch.Equals("on"))
{
BiocharDecomp.dlt_swcon = dlt_swcon;
}
if (ks_switch.Equals("on"))
{
BiocharDecomp.dlt_ks = dlt_ks;
}
if (biochar_c_switch.Equals("on"))
{
BiocharDecomp.hum_c = dlt_hum;
BiocharDecomp.biom_c = dlt_biom;
BiocharDecomp.dlt_biochar_c = dlt_biochar_c;
}
if (nitrification_switch.Equals("on"))
{
BiocharDecomp.bc_nh4_change = bc_nh4_dlt;
}
if (decomp_switch.Equals("on"))
{
BiocharDecomp.dlt_rd_hum = rd_hum_fac;
BiocharDecomp.dlt_rd_biom = rd_biom_fac;
BiocharDecomp.dlt_rd_carb = rd_carb_fac;
BiocharDecomp.dlt_rd_cell = rd_cell_fac;
BiocharDecomp.dlt_rd_lign = rd_lign_fac;
BiocharDecomp.dlt_rd_ef = rd_ef_fac;
BiocharDecomp.dlt_rd_fr = rd_fr_fac;
BiocharDecomp.dlt_rd_ef_fom = rd_ef_fom_fac;
BiocharDecomp.dlt_rd_fr_fom = rd_fr_fom_fac;
}
BiocharDecomp.dlt_n_biochar = dlt_n_avail;
if (ph_switch.Equals("on"))
{
BiocharDecomp.dlt_ph = dlt_ph;
}
BiocharDecomp.bc_wfps_factor = 1.0 - this.bc_wfps_factor;
BiocharDecomp.dlt_kl = dlt_kl; //Since KL is a multiplicative effect, if we do not always assign this KL will go to 0
//If uninitialized, it is 0 by default
BiocharDecomposed.Invoke(BiocharDecomp);
Console.WriteLine("Biochar bd: " + biochar_bd[0]);
}
for (int i = 0; i < oc.Length; i++)
{
yesterday_oc[i] = oc[i]; //Make a deep copy
}
}