public void Process()
{
// + Purpose
// This routine performs the soil C and N balance, daily.
// - Assesses potential decomposition of surface residues (adjust decompostion if needed, accounts for mineralisation/immobilisation of N)
// - Calculates hydrolysis of urea, denitrification, transformations on soil organic matter (including N mineralisation/immobilition) and nitrification.
int nLayers = g.dlayer.Length; // number of layers in the soil
double[,] dlt_fom_n = new double[3, nLayers]; // fom N mineralised in each fraction (kg/ha)
if (g.is_pond_active)
{
// dsg 190508, If there is a pond, the POND module will decompose residues - not SoilNitrogen
// dsg 110708 Get the biom & hum C decomposed in the pond and add to soil - on advice of MEP
// increment the hum and biom C pools in top soil layer
hum_c[0] += g.pond_hum_C; // humic material from breakdown of residues in pond
biom_c[0] += g.pond_biom_C; // biom material from breakdown of residues in pond
// reset the N amounts of N in hum and biom pools
hum_n[0] = MathUtilities.Divide(hum_c[0], g.hum_cn, 0.0);
biom_n[0] = MathUtilities.Divide(biom_c[0], g.biom_cn, 0.0);
}
else
{
// Decompose residues
// assess the potential decomposition of surface residues and calculate actual mineralisation/immobilisation
DecomposeResidues();
// update C content in hum and biom pools
for (int layer = 0; layer < nLayers; layer++)
{
hum_c[layer] += SumDoubleArray(dlt_c_res_2_hum[layer]);
biom_c[layer] += SumDoubleArray(dlt_c_res_2_biom[layer]);
}
// update N content in hum and biom pools as well as the mineral N
for (int layer = 0; layer < nLayers; layer++)
{
hum_n[layer] = MathUtilities.Divide(hum_c[layer], g.hum_cn, 0.0);
biom_n[layer] = MathUtilities.Divide(biom_c[layer], g.biom_cn, 0.0);
// update soil mineral N
_nh4[layer] += dlt_nh4_decomp[layer];
_no3[layer] += dlt_no3_decomp[layer];
}
}
// now take each layer in turn and compute N processes
for (int layer = 0; layer < nLayers; layer++)
{
// urea hydrolysis
dlt_urea_hydrolised[layer] = UreaHydrolysis(layer);
_nh4[layer] += dlt_urea_hydrolised[layer];
_urea[layer] -= dlt_urea_hydrolised[layer];
// nitrate-N denitrification
switch (g.n2o_approach)
{
case 1:
dlt_no3_dnit[layer] = Denitrification_NEMIS(layer);
//n2o_atm[layer] is calculated in Nitrification_NEMIS
break;
case 2:
dlt_no3_dnit[layer] = Denitrification_WNMM(layer);
//n2o_atm[layer] is calculated in Nitrification_WNMM
break;
case 3:
dlt_no3_dnit[layer] = Denitrification_CENT(layer);
//n2o_atm[layer] is calculated in Nitrification_CENT
break;
case 0:
default:
dlt_no3_dnit[layer] = Denitrification(layer);
break;
}
_no3[layer] -= dlt_no3_dnit[layer];
// N2O loss to atmosphere - due to denitrification
n2o_atm[layer] = 0.0;
double N2N2O = Denitrification_Nratio(layer);
n2o_atm[layer] = dlt_no3_dnit[layer] / (N2N2O + 1.0);
// Calculate transformations of soil organic matter (C and N)
// humic pool mineralisation
MineraliseHumus(layer);
// microbial biomass pool mineralisation
MineraliseBiomass(layer);
// mineralisation of fresh organic matter pools
// need to be revisited - create FOM pools as array
//for (int fract = 0; fract < 3; fract++)
//{
// MinFom(layer, fract);
// dlt_c_fom_2_biom[fract][layer] = dlt_fc_biom[fract];
// dlt_c_fom_2_hum[fract][layer] = dlt_fc_hum[fract];
// dlt_c_fom_2_atm[fract][layer] = dlt_fc_atm[fract];
// dlt_fom_n[fract, layer] = dlt_f_n[fract];
//}
double[] dlt_f_n;
double[] dlt_fc_biom;
double[] dlt_fc_hum;
double[] dlt_fc_atm;
FOMdecompData MineralisedFOM = new FOMdecompData();
if (g.useNewProcesses)
{
MineralisedFOM = MineraliseFOM1(layer);
for (int fract = 0; fract < 3; fract++)
{
dlt_c_fom_2_hum[fract][layer] = MineralisedFOM.dlt_c_hum[fract];
dlt_c_fom_2_biom[fract][layer] = MineralisedFOM.dlt_c_biom[fract];
dlt_c_fom_2_atm[fract][layer] = MineralisedFOM.dlt_c_atm[fract];
dlt_fom_n[fract, layer] = MineralisedFOM.dlt_fom_n[fract];
}
dlt_n_fom_2_min[layer] = MineralisedFOM.dlt_n_min;
}
else
{
MineraliseFOM(layer, out dlt_fc_biom, out dlt_fc_hum, out dlt_fc_atm, out dlt_f_n, out dlt_n_fom_2_min[layer]);
for (int fract = 0; fract < 3; fract++)
{
dlt_c_fom_2_biom[fract][layer] = dlt_fc_biom[fract];
dlt_c_fom_2_hum[fract][layer] = dlt_fc_hum[fract];
dlt_c_fom_2_atm[fract][layer] = dlt_fc_atm[fract];
dlt_fom_n[fract, layer] = dlt_f_n[fract];
}
}
// update pools C an N contents
hum_c[layer] += dlt_c_biom_2_hum[layer] - dlt_c_hum_2_biom[layer] - dlt_c_hum_2_atm[layer] +
dlt_c_fom_2_hum[0][layer] + dlt_c_fom_2_hum[1][layer] + dlt_c_fom_2_hum[2][layer];
hum_n[layer] = MathUtilities.Divide(hum_c[layer], g.hum_cn, 0.0);
biom_c[layer] += dlt_c_hum_2_biom[layer] - dlt_c_biom_2_hum[layer] - dlt_c_biom_2_atm[layer] +
dlt_c_fom_2_biom[0][layer] + dlt_c_fom_2_biom[1][layer] + dlt_c_fom_2_biom[2][layer];
biom_n[layer] = MathUtilities.Divide(biom_c[layer], g.biom_cn, 0.0);
fom_c_pool1[layer] -= (dlt_c_fom_2_hum[0][layer] + dlt_c_fom_2_biom[0][layer] + dlt_c_fom_2_atm[0][layer]);
fom_c_pool2[layer] -= (dlt_c_fom_2_hum[1][layer] + dlt_c_fom_2_biom[1][layer] + dlt_c_fom_2_atm[1][layer]);
fom_c_pool3[layer] -= (dlt_c_fom_2_hum[2][layer] + dlt_c_fom_2_biom[2][layer] + dlt_c_fom_2_atm[2][layer]);
fom_n_pool1[layer] -= dlt_fom_n[0, layer];
fom_n_pool2[layer] -= dlt_fom_n[1, layer];
fom_n_pool3[layer] -= dlt_fom_n[2, layer];
// dsg these 3 dlts are calculated for the benefit of soilp which needs to 'get' them
dlt_fom_c_pool1[layer] = dlt_c_fom_2_hum[0][layer] + dlt_c_fom_2_biom[0][layer] + dlt_c_fom_2_atm[0][layer];
dlt_fom_c_pool2[layer] = dlt_c_fom_2_hum[1][layer] + dlt_c_fom_2_biom[1][layer] + dlt_c_fom_2_atm[1][layer];
dlt_fom_c_pool3[layer] = dlt_c_fom_2_hum[2][layer] + dlt_c_fom_2_biom[2][layer] + dlt_c_fom_2_atm[2][layer];
// add up fom in each layer in each of the pools
//double fom_c = fom_c_pool1[layer] + fom_c_pool2[layer] + fom_c_pool3[layer];
//fom_n[layer] = fom_n_pool1[layer] + fom_n_pool2[layer] + fom_n_pool3[layer];
// update soil mineral N after mineralisation/immobilisation
// starts with nh4
_nh4[layer] += dlt_n_hum_2_min[layer] + dlt_n_biom_2_min[layer] + dlt_n_fom_2_min[layer];
// check whether there is enough NH4 to be immobilised
nh4_deficit_immob = new double[g.dlayer.Length];
if (_nh4[layer] < g.nh4_min[layer])
{
nh4_deficit_immob[layer] = g.nh4_min[layer] - _nh4[layer];
_nh4[layer] = g.nh4_min[layer];
}
// now change no3
_no3[layer] -= nh4_deficit_immob[layer];
if (_no3[layer] < g.no3_min[layer] - g.EPSILON)
{
// note: tests for adequate mineral N for immobilisation have been made so this no3 should not go below no3_min
throw new Exception("N immobilisation resulted in mineral N in layer(" + (layer + 1).ToString() + ") to go below minimum");
}
// NITRIFICATION
switch (g.n2o_approach)
{
case 1:
dlt_nitrification[layer] = Nitrification(layer); //using default APSIM process for NEMIS
dlt_nh4_dnit[layer] = N2OLostInNitrification_ApsimSoilNitrogen(layer);
break;
case 2:
dlt_nitrification[layer] = Nitrification_WNMM(layer);
// dlt_nh4_dnit[layer] & n2o_atm[layer] are calculated in Nitrification_WNMM
break;
case 3:
dlt_nitrification[layer] = Nitrification_CENT(layer);
// dlt_nh4_dnit[layer] & n2o_atm[layer] are calculated in Nitrification_CENT
break;
case 0:
default:
// nitrification of ammonium-N (total)
dlt_nitrification[layer] = Nitrification(layer);
// denitrification loss during nitrification (- n2o_atm )
dlt_nh4_dnit[layer] = N2OLostInNitrification_ApsimSoilNitrogen(layer);
// N2O loss to atmosphere from nitrification
n2o_atm[layer] += dlt_nh4_dnit[layer];
break;
}
// effective or net nitrification
effective_nitrification[layer] = dlt_nitrification[layer] - dlt_nh4_dnit[layer];
// update soil mineral N
_no3[layer] += effective_nitrification[layer];
_nh4[layer] -= dlt_nitrification[layer];
// check some of the values
if (Math.Abs(_urea[layer]) < g.EPSILON)
_urea[layer] = 0.0;
if (Math.Abs(_nh4[layer]) < g.EPSILON)
_nh4[layer] = 0.0;
if (Math.Abs(_no3[layer]) < g.EPSILON)
_no3[layer] = 0.0;
if (_urea[layer] < g.urea_min[layer] || _urea[layer] > 9000.0)
throw new Exception("Value for urea(layer) is out of range");
if (_nh4[layer] < g.nh4_min[layer] || _nh4[layer] > 9000.0)
throw new Exception("Value for NH4(layer) is out of range");
if (_no3[layer] < g.no3_min[layer] || _no3[layer] > 9000.0)
throw new Exception("Value for NO3(layer) is out of range");
// net N tansformations
nh4_transform_net[layer] = dlt_nh4_decomp[layer] + dlt_n_fom_2_min[layer] + dlt_n_biom_2_min[layer] + dlt_n_hum_2_min[layer] - dlt_nitrification[layer] + dlt_urea_hydrolised[layer] + nh4_deficit_immob[layer];
no3_transform_net[layer] = dlt_no3_decomp[layer] - dlt_no3_dnit[layer] + effective_nitrification[layer] - nh4_deficit_immob[layer];
// net deltas
dlt_nh4_net[layer] = _nh4[layer] - nh4_yesterday[layer];
dlt_no3_net[layer] = _no3[layer] - no3_yesterday[layer];
// store these values so they may be used tomorrow
nh4_yesterday[layer] = _nh4[layer];
no3_yesterday[layer] = _no3[layer];
}
}
private FOMdecompData MineraliseFOM1(int layer)
{
// + Purpose
// Calculate the daily transformation of the soil fresh organic matter pools, mineralisation (+ve) or immobilisation (-ve)
double[] dlt_c_hum = new double[3]; // dlt_c from fom to humus
double[] dlt_c_biom = new double[3]; // dlt_c from fom to biomass
double[] dlt_c_atm = new double[3]; // dlt_c from fom to atmosphere
double[] dlt_fom_n = new double[3]; // dlt_n from fom pools to OM
double dlt_n_min = 0.0; // dlt_n from fom to mineral
// dsg 200508 use different values for some constants when anaerobic conditions dominate
// index = 1 for aerobic conditions, 2 for anaerobic conditions
int index = (!g.is_pond_active) ? 1 : 2;
// get total available mineral N (kg/ha)
double nitTot = Math.Max(0.0, (_no3[layer] - g.no3_min[layer]) + (_nh4[layer] - g.nh4_min[layer]));
// fresh organic carbon (kg/ha)
double fomC = fom_c_pool1[layer] + fom_c_pool2[layer] + fom_c_pool3[layer];
// fresh organic nitrogen (kg/ha)
double fomN = fom_n_pool1[layer] + fom_n_pool2[layer] + fom_n_pool3[layer];
// ratio of C in fresh OM to N available for decay
double cnr = MathUtilities.Divide(fomC, fomN + nitTot, 0.0);
// calculate the C:N ratio factor - Bound to [0, 1]
double cnrf = Math.Max(0.0, Math.Min(1.0, Math.Exp(-g.cnrf_coeff * (cnr - g.cnrf_optcn) / g.cnrf_optcn)));
if (g.useNewProcesses)
cnrf = CNratioFactor(layer, index, g.CNFactorMinerFOM_OptCN, g.CNFactorMinerFOM_RateCN);
// get the soil temperature factor
double tf = (g.SoilCNParameterSet == "rothc") ? RothcTF(layer, index) : TF(layer, index);
if (g.useNewSTFFunction)
if (g.useSingleMinerFactors)
{
tf = SoilTempFactor(layer, index, g.TempFactorData_MinerSOM);
}
else
{
if (g.useFactorsByFOMpool)
{
}
else
{
tf = SoilTempFactor(layer, index, g.TempFactorData_MinerFOM);
}
}
// get the soil water factor
double wf = WF(layer, index);
if (g.useNewSWFFunction)
if (g.useSingleMinerFactors)
{
wf = SoilMoistFactor(layer, index, g.MoistFactorData_MinerSOM);
}
else
{
if (g.useFactorsByFOMpool)
{
}
else
{
wf = SoilMoistFactor(layer, index, g.MoistFactorData_MinerFOM);
}
}
// calculate gross amount of C & N released due to mineralisation of the fresh organic matter.
if (fomC >= g.fom_min)
{
double dlt_n_min_fom = 0.0; // amount of fresh organic N mineralised across fpools (kg/ha)
double dlt_c_min_fom = 0.0; // total C mineralised (kg/ha) summed across fpools
double[] dlt_n_min_tot = new double[3]; // amount of fresh organic N mineralised in each pool (kg/ha)
double[] dlt_c_min_tot = new double[3]; // amount of C mineralised (kg/ha) from each pool
// C:N ratio of fom
double fom_cn = MathUtilities.Divide(fomC, fomN, 0.0);
// get the decomposition of carbohydrate-like, cellulose-like and lignin-like fractions (fpools) in turn.
for (int fractn = 0; fractn < 3; fractn++)
{
// get the max decomposition rate for each fpool
double decomp_rate = FractRDFom(fractn)[index - 1] * cnrf * tf * wf;
// calculate the gross amount of fresh organic carbon mineralised (kg/ha)
double gross_c_decomp = decomp_rate * FractFomC(fractn)[layer];
// calculate the gross amount of N released from fresh organic matter (kg/ha)
double gross_n_decomp = decomp_rate * FractFomN(fractn)[layer];
dlt_n_min_fom += gross_n_decomp;
dlt_c_min_tot[fractn] = gross_c_decomp;
dlt_n_min_tot[fractn] = gross_n_decomp;
dlt_c_min_fom += gross_c_decomp;
}
// calculate potential transfers of C mineralised to biomass
double dlt_c_biom_tot = dlt_c_min_fom * g.ef_fom * g.fr_fom_biom;
// calculate potential transfers of C mineralised to humus
double dlt_c_hum_tot = dlt_c_min_fom * g.ef_fom * (1.0 - g.fr_fom_biom);
// test whether there is adequate N available to meet immobilisation demand
double n_demand = MathUtilities.Divide(dlt_c_biom_tot, g.biom_cn, 0.0) + MathUtilities.Divide(dlt_c_hum_tot, g.hum_cn, 0.0);
double n_avail = nitTot + dlt_n_min_fom;
// factor to reduce mineralisation rates if insufficient N to meet immobilisation demand
double Navail_factor = 1.0;
if (n_demand > n_avail)
Navail_factor = Math.Max(0.0, Math.Min(1.0, MathUtilities.Divide(nitTot, n_demand - dlt_n_min_fom, 0.0)));
// now adjust carbon transformations etc. and similarly for npools
for (int fractn = 0; fractn < 3; fractn++)
{
dlt_c_hum[fractn] = dlt_c_min_tot[fractn] * g.ef_fom * (1.0 - g.fr_fom_biom) * Navail_factor;
dlt_c_biom[fractn] = dlt_c_min_tot[fractn] * g.ef_fom * g.fr_fom_biom * Navail_factor;
dlt_c_atm[fractn] = dlt_c_min_tot[fractn] * (1.0 - g.ef_fom) * Navail_factor;
dlt_fom_n[fractn] = dlt_n_min_tot[fractn] * Navail_factor;
dlt_c_hum[fractn] = MathUtilities.RoundToZero(dlt_c_hum[fractn]);
dlt_c_biom[fractn] = MathUtilities.RoundToZero(dlt_c_biom[fractn]);
dlt_c_atm[fractn] = MathUtilities.RoundToZero(dlt_c_atm[fractn]);
dlt_fom_n[fractn] = MathUtilities.RoundToZero(dlt_fom_n[fractn]);
}
dlt_n_min = (dlt_n_min_fom - n_demand) * Navail_factor;
}
FOMdecompData Result = new FOMdecompData();
Result.dlt_c_hum = dlt_c_hum;
Result.dlt_c_biom = dlt_c_biom;
Result.dlt_c_atm = dlt_c_atm;
Result.dlt_fom_n = dlt_fom_n;
Result.dlt_n_min = dlt_n_min;
return Result;
}
