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468 | werner | 2 | #include "snag.h" |
3 | #include "tree.h" |
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4 | #include "species.h" |
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5 | #include "globalsettings.h" |
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6 | #include "expression.h" |
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490 | werner | 7 | // for calculation of climate decomposition |
8 | #include "resourceunit.h" |
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9 | #include "watercycle.h" |
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10 | #include "climate.h" |
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541 | werner | 11 | #include "model.h" |
468 | werner | 12 | |
13 | /** @class Snag |
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14 | Snag deals with carbon / nitrogen fluxes from the forest until the reach soil pools. |
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490 | werner | 15 | Snag lives on the level of the ResourceUnit; carbon fluxes from trees enter Snag, and parts of the biomass of snags |
468 | werner | 16 | is subsequently forwarded to the soil sub model. |
522 | werner | 17 | Carbon is stored in three classes (depending on the size) |
528 | werner | 18 | The Snag dynamics class uses the following species parameter: |
19 | cnFoliage, cnFineroot, cnWood, snagHalflife, snagKSW |
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468 | werner | 20 | |
21 | */ |
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22 | // static variables |
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528 | werner | 23 | double Snag::mDBHLower = -1.; |
522 | werner | 24 | double Snag::mDBHHigher = 0.; |
25 | double Snag::mCarbonThreshold[] = {0., 0., 0.}; |
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26 | |||
534 | werner | 27 | double CNPair::biomassCFraction = biomassCFraction; // get global from globalsettings.h |
468 | werner | 28 | |
534 | werner | 29 | /// add biomass and weigh the parameter_value with the current C-content of the pool |
30 | void CNPool::addBiomass(const double biomass, const double CNratio, const double parameter_value) |
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31 | { |
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32 | if (biomass==0.) |
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33 | return; |
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34 | double new_c = biomass*biomassCFraction; |
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35 | double p_old = C / (new_c + C); |
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36 | mParameter = mParameter*p_old + parameter_value*(1.-p_old); |
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37 | CNPair::addBiomass(biomass, CNratio); |
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38 | } |
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39 | |||
40 | // increase pool (and weigh the value) |
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41 | void CNPool::operator+=(const CNPool &s) |
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42 | { |
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43 | if (s.C==0.) |
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44 | return; |
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45 | mParameter = parameter(s); // calculate weighted parameter |
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46 | C+=s.C; |
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47 | N+=s.N; |
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48 | } |
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49 | |||
50 | double CNPool::parameter(const CNPool &s) const |
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51 | { |
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52 | if (s.C==0.) |
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53 | return parameter(); |
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54 | double p_old = C / (s.C + C); |
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55 | double result = mParameter*p_old + s.parameter()*(1.-p_old); |
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56 | return result; |
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57 | } |
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58 | |||
59 | |||
522 | werner | 60 | void Snag::setupThresholds(const double lower, const double upper) |
61 | { |
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62 | if (mDBHLower == lower) |
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63 | return; |
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64 | mDBHLower = lower; |
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65 | mDBHHigher = upper; |
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66 | mCarbonThreshold[0] = lower / 2.; |
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67 | mCarbonThreshold[1] = lower + (upper - lower)/2.; |
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68 | mCarbonThreshold[2] = upper + (upper - lower)/2.; |
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69 | //# threshold levels for emptying out the dbh-snag-classes |
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70 | //# derived from Psme woody allometry, converted to C, with a threshold level set to 10% |
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71 | //# values in kg! |
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72 | for (int i=0;i<3;i++) |
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73 | mCarbonThreshold[i] = 0.10568*pow(mCarbonThreshold[i],2.4247)*0.5*0.1; |
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74 | } |
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75 | |||
76 | |||
468 | werner | 77 | Snag::Snag() |
78 | { |
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490 | werner | 79 | mRU = 0; |
534 | werner | 80 | CNPair::setCFraction(biomassCFraction); |
468 | werner | 81 | } |
82 | |||
490 | werner | 83 | void Snag::setup( const ResourceUnit *ru) |
468 | werner | 84 | { |
490 | werner | 85 | mRU = ru; |
86 | mClimateFactor = 0.; |
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468 | werner | 87 | // branches |
88 | mBranchCounter=0; |
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89 | for (int i=0;i<3;i++) { |
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90 | mTimeSinceDeath[i] = 0.; |
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91 | mNumberOfSnags[i] = 0.; |
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522 | werner | 92 | mAvgDbh[i] = 0.; |
93 | mAvgHeight[i] = 0.; |
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94 | mAvgVolume[i] = 0.; |
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95 | mKSW[i] = 0.; |
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96 | mCurrentKSW[i] = 0.; |
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468 | werner | 97 | } |
475 | werner | 98 | mTotalSnagCarbon = 0.; |
528 | werner | 99 | if (mDBHLower<=0) |
100 | throw IException("Snag::setupThresholds() not called or called with invalid parameters."); |
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468 | werner | 101 | } |
102 | |||
475 | werner | 103 | // debug outputs |
104 | QList<QVariant> Snag::debugList() |
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105 | { |
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106 | // list columns |
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107 | // for three pools |
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108 | QList<QVariant> list; |
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109 | |||
523 | werner | 110 | // totals |
111 | list << mTotalSnagCarbon << mTotalIn.C << mTotalToAtm.C << mSWDtoSoil.C << mSWDtoSoil.N; |
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477 | werner | 112 | // fluxes to labile soil pool and to refractory soil pool |
524 | werner | 113 | list << mLabileFlux.C << mLabileFlux.N << mRefractoryFlux.C << mRefractoryFlux.N; |
475 | werner | 114 | |
115 | for (int i=0;i<3;i++) { |
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116 | // pools "swdx_c", "swdx_n", "swdx_count", "swdx_tsd", "toswdx_c", "toswdx_n" |
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117 | list << mSWD[i].C << mSWD[i].N << mNumberOfSnags[i] << mTimeSinceDeath[i] << mToSWD[i].C << mToSWD[i].N; |
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524 | werner | 118 | list << mAvgDbh[i] << mAvgHeight[i] << mAvgVolume[i]; |
475 | werner | 119 | } |
120 | |||
540 | werner | 121 | // branch/coarse wood pools (5 yrs) |
122 | for (int i=0;i<5;i++) { |
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123 | list << mOtherWood[i].C << mOtherWood[i].N; |
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124 | } |
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125 | // list << mOtherWood[mBranchCounter].C << mOtherWood[mBranchCounter].N |
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126 | // << mOtherWood[(mBranchCounter+1)%5].C << mOtherWood[(mBranchCounter+1)%5].N |
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127 | // << mOtherWood[(mBranchCounter+2)%5].C << mOtherWood[(mBranchCounter+2)%5].N |
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128 | // << mOtherWood[(mBranchCounter+3)%5].C << mOtherWood[(mBranchCounter+3)%5].N |
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129 | // << mOtherWood[(mBranchCounter+4)%5].C << mOtherWood[(mBranchCounter+4)%5].N; |
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475 | werner | 130 | return list; |
131 | } |
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132 | |||
468 | werner | 133 | void Snag::newYear() |
134 | { |
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135 | for (int i=0;i<3;i++) { |
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136 | mToSWD[i].clear(); // clear transfer pools to standing-woody-debris |
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522 | werner | 137 | mCurrentKSW[i] = 0.; |
468 | werner | 138 | } |
139 | mLabileFlux.clear(); |
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140 | mRefractoryFlux.clear(); |
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476 | werner | 141 | mTotalToAtm.clear(); |
142 | mTotalToExtern.clear(); |
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143 | mTotalIn.clear(); |
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477 | werner | 144 | mSWDtoSoil.clear(); |
468 | werner | 145 | } |
146 | |||
490 | werner | 147 | /// calculate the dynamic climate modifier for decomposition 're' |
522 | werner | 148 | /// calculation is done on the level of ResourceUnit because the water content per day is needed. |
490 | werner | 149 | double Snag::calculateClimateFactors() |
150 | { |
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546 | werner | 151 | double deficit; |
490 | werner | 152 | double ft, fw; |
547 | werner | 153 | const double top_layer_content = mRU->waterCycle()->topLayerWaterContent(); |
490 | werner | 154 | double f_sum = 0.; |
155 | for (const ClimateDay *day=mRU->climate()->begin(); day!=mRU->climate()->end(); ++day) |
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156 | { |
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546 | werner | 157 | deficit = mRU->waterCycle()->waterDeficit_mm(day->day); |
540 | werner | 158 | |
490 | werner | 159 | ft = exp(308.56*(1./56.02-1./((273.+day->temperature)-227.13))); // empirical variable Q10 model of Lloyd and Taylor (1994), see also Adair et al. (2008) |
546 | werner | 160 | fw = 1. - limit(deficit / top_layer_content, 0., 1.); |
161 | // the water effect: depends on the water deficit; if the deficit is higher than the parameterized |
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162 | // content of the top layer (where most microbial activity is located), than then fw gets 0. |
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540 | werner | 163 | |
490 | werner | 164 | f_sum += ft*fw; |
165 | } |
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166 | // the climate factor is defined as the arithmentic annual mean value |
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167 | mClimateFactor = f_sum / double(mRU->climate()->daysOfYear()); |
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168 | return mClimateFactor; |
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169 | } |
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170 | |||
522 | werner | 171 | /// do the yearly calculation |
172 | /// see http://iland.boku.ac.at/snag+dynamics |
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526 | werner | 173 | void Snag::calculateYear() |
468 | werner | 174 | { |
522 | werner | 175 | mSWDtoSoil.clear(); |
532 | werner | 176 | const double climate_factor_re = calculateClimateFactors(); // calculate anyway, because also the soil module needs it (and currently one can have Snag and Soil only as a couple) |
477 | werner | 177 | if (isEmpty()) // nothing to do |
475 | werner | 178 | return; |
179 | |||
468 | werner | 180 | // process branches: every year one of the five baskets is emptied and transfered to the refractory soil pool |
540 | werner | 181 | mRefractoryFlux+=mOtherWood[mBranchCounter]; |
182 | |||
183 | mOtherWood[mBranchCounter].clear(); |
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468 | werner | 184 | mBranchCounter= (mBranchCounter+1) % 5; // increase index, roll over to 0. |
540 | werner | 185 | // decay of branches/coarse roots |
186 | for (int i=0;i<5;i++) { |
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187 | if (mOtherWood[i].C>0.) { |
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188 | double survive_rate = exp(- climate_factor_re * mOtherWood[i].parameter() ); // parameter: the "kyr" value... |
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189 | mOtherWood[i].C *= survive_rate; |
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190 | } |
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191 | } |
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468 | werner | 192 | |
193 | // process standing snags. |
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194 | // the input of the current year is in the mToSWD-Pools |
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195 | for (int i=0;i<3;i++) { |
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196 | |||
522 | werner | 197 | // update the swd-pool with this years' input |
198 | if (!mToSWD[i].isEmpty()) { |
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199 | // update decay rate (apply average yearly input to the state parameters) |
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200 | mKSW[i] = mKSW[i]*(mSWD[i].C/(mSWD[i].C+mToSWD[i].C)) + mCurrentKSW[i]*(mToSWD[i].C/(mSWD[i].C+mToSWD[i].C)); |
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201 | //move content to the SWD pool |
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202 | mSWD[i] += mToSWD[i]; |
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203 | } |
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475 | werner | 204 | |
522 | werner | 205 | if (mSWD[i].C > 0) { |
206 | // reduce the Carbon (note: the N stays, thus the CN ratio changes) |
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207 | // use the decay rate that is derived as a weighted average of all standing woody debris |
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523 | werner | 208 | double survive_rate = exp(-mKSW[i] *climate_factor_re * 1. ); // 1: timestep |
209 | mTotalToAtm.C += mSWD[i].C * (1. - survive_rate); |
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210 | mSWD[i].C *= survive_rate; |
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468 | werner | 211 | |
522 | werner | 212 | // transition to downed woody debris |
213 | // update: use negative exponential decay, species parameter: half-life |
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214 | // modified for the climatic effect on decomposition, i.e. if decomp is slower, snags stand longer and vice versa |
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215 | // this is loosely oriented on Standcarb2 (http://andrewsforest.oregonstate.edu/pubs/webdocs/models/standcarb2.htm), |
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216 | // where lag times for cohort transitions are linearly modified with re although here individual good or bad years have |
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217 | // an immediate effect, the average climatic influence should come through (and it is inherently transient) |
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218 | // note that swd.hl is species-specific, and thus a weighted average over the species in the input (=mortality) |
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219 | // needs to be calculated, followed by a weighted update of the previous swd.hl. |
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220 | // As weights here we use stem number, as the processes here pertain individual snags |
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221 | // calculate the transition probability of SWD to downed dead wood |
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468 | werner | 222 | |
522 | werner | 223 | double half_life = mHalfLife[i] / climate_factor_re; |
224 | double rate = -M_LN2 / half_life; // M_LN2: math. constant |
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225 | |||
226 | // higher decay rate for the class with smallest diameters |
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227 | if (i==0) |
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228 | rate*=2.; |
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229 | |||
523 | werner | 230 | double transfer = 1. - exp(rate); |
522 | werner | 231 | |
468 | werner | 232 | // calculate flow to soil pool... |
522 | werner | 233 | mSWDtoSoil += mSWD[i] * transfer; |
234 | mRefractoryFlux += mSWD[i] * transfer; |
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235 | mSWD[i] *= (1.-transfer); // reduce pool |
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468 | werner | 236 | // calculate the stem number of remaining snags |
522 | werner | 237 | mNumberOfSnags[i] = mNumberOfSnags[i] * (1. - transfer); |
523 | werner | 238 | |
239 | mTimeSinceDeath[i] += 1.; |
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522 | werner | 240 | // if stems<0.5, empty the whole cohort into DWD, i.e. release the last bit of C and N and clear the stats |
241 | // also, if the Carbon of an average snag is less than 10% of the original average tree |
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242 | // (derived from allometries for the three diameter classes), the whole cohort is emptied out to DWD |
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243 | if (mNumberOfSnags[i] < 0.5 || mSWD[i].C / mNumberOfSnags[i] < mCarbonThreshold[i]) { |
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244 | // clear the pool: add the rest to the soil, clear statistics of the pool |
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468 | werner | 245 | mRefractoryFlux += mSWD[i]; |
522 | werner | 246 | mSWDtoSoil += mSWD[i]; |
468 | werner | 247 | mSWD[i].clear(); |
522 | werner | 248 | mAvgDbh[i] = 0.; |
249 | mAvgHeight[i] = 0.; |
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250 | mAvgVolume[i] = 0.; |
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251 | mKSW[i] = 0.; |
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252 | mCurrentKSW[i] = 0.; |
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253 | mHalfLife[i] = 0.; |
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254 | mTimeSinceDeath[i] = 0.; |
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468 | werner | 255 | } |
522 | werner | 256 | |
468 | werner | 257 | } |
522 | werner | 258 | |
468 | werner | 259 | } |
522 | werner | 260 | // total carbon in the snag-container on the RU *after* processing is the content of the |
475 | werner | 261 | // standing woody debris pools + the branches |
262 | mTotalSnagCarbon = mSWD[0].C + mSWD[1].C + mSWD[2].C + |
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540 | werner | 263 | mOtherWood[0].C + mOtherWood[1].C + mOtherWood[2].C + mOtherWood[3].C + mOtherWood[4].C; |
468 | werner | 264 | } |
265 | |||
266 | /// foliage and fineroot litter is transferred during tree growth. |
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267 | void Snag::addTurnoverLitter(const Tree *tree, const double litter_foliage, const double litter_fineroot) |
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268 | { |
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534 | werner | 269 | mLabileFlux.addBiomass(litter_foliage, tree->species()->cnFoliage(), tree->species()->snagKyl()); |
270 | mLabileFlux.addBiomass(litter_fineroot, tree->species()->cnFineroot(), tree->species()->snagKyl()); |
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468 | werner | 271 | } |
272 | |||
273 | /// after the death of the tree the five biomass compartments are processed. |
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274 | void Snag::addMortality(const Tree *tree) |
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275 | { |
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528 | werner | 276 | const Species *species = tree->species(); |
468 | werner | 277 | |
278 | // immediate flows: 100% of foliage, 100% of fine roots: they go to the labile pool |
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534 | werner | 279 | mLabileFlux.addBiomass(tree->biomassFoliage(), species->cnFoliage(), tree->species()->snagKyl()); |
280 | mLabileFlux.addBiomass(tree->biomassFineRoot(), species->cnFineroot(), tree->species()->snagKyl()); |
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468 | werner | 281 | |
540 | werner | 282 | // branches and coarse roots are equally distributed over five years: |
283 | double biomass_rest = (tree->biomassBranch()+tree->biomassCoarseRoot()) * 0.2; |
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468 | werner | 284 | for (int i=0;i<5; i++) |
540 | werner | 285 | mOtherWood[i].addBiomass(biomass_rest, species->cnWood(), tree->species()->snagKyr()); |
468 | werner | 286 | |
540 | werner | 287 | // just for book-keeping: keep track of all inputs into branches / roots / swd |
288 | mTotalIn.addBiomass(tree->biomassBranch() + tree->biomassCoarseRoot() + tree->biomassStem(), species->cnWood()); |
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468 | werner | 289 | // stem biomass is transferred to the standing woody debris pool (SWD), increase stem number of pool |
522 | werner | 290 | int pi = poolIndex(tree->dbh()); // get right transfer pool |
291 | |||
292 | // update statistics - stemnumber-weighted averages |
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293 | // note: here the calculations are repeated for every died trees (i.e. consecutive weighting ... but delivers the same results) |
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294 | double p_old = mNumberOfSnags[pi] / (mNumberOfSnags[pi] + 1); // weighting factor for state vars (based on stem numbers) |
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295 | double p_new = 1. / (mNumberOfSnags[pi] + 1); // weighting factor for added tree (p_old + p_new = 1). |
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296 | mAvgDbh[pi] = mAvgDbh[pi]*p_old + tree->dbh()*p_new; |
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297 | mAvgHeight[pi] = mAvgHeight[pi]*p_old + tree->height()*p_new; |
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298 | mAvgVolume[pi] = mAvgVolume[pi]*p_old + tree->volume()*p_new; |
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299 | mTimeSinceDeath[pi] = mTimeSinceDeath[pi]*p_old + 1.*p_new; |
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528 | werner | 300 | mHalfLife[pi] = mHalfLife[pi]*p_old + species->snagHalflife()* p_new; |
522 | werner | 301 | |
302 | // average the decay rate (ksw); this is done based on the carbon content |
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303 | // aggregate all trees that die in the current year (and save weighted decay rates to CurrentKSW) |
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304 | if (tree->biomassStem()==0) |
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305 | throw IException("Snag::addMortality: tree without stem biomass!!"); |
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306 | p_old = mToSWD[pi].C / (mToSWD[pi].C + tree->biomassStem()* biomassCFraction); |
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307 | p_new =tree->biomassStem()* biomassCFraction / (mToSWD[pi].C + tree->biomassStem()* biomassCFraction); |
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534 | werner | 308 | mCurrentKSW[pi] = mCurrentKSW[pi]*p_old + species->snagKsw() * p_new; |
522 | werner | 309 | mNumberOfSnags[pi]++; |
523 | werner | 310 | |
311 | // finally add the biomass |
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534 | werner | 312 | CNPool &to_swd = mToSWD[pi]; |
313 | to_swd.addBiomass(tree->biomassStem(), species->cnWood(), tree->species()->snagKyr()); |
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468 | werner | 314 | } |
315 | |||
316 | /// add residual biomass of 'tree' after harvesting. |
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522 | werner | 317 | /// remove_{stem, branch, foliage}_fraction: percentage of biomass compartment that is *removed* by the harvest operation (i.e.: not to stay in the system) |
528 | werner | 318 | /// records on harvested biomass is collected (mTotalToExtern-pool). |
468 | werner | 319 | void Snag::addHarvest(const Tree* tree, const double remove_stem_fraction, const double remove_branch_fraction, const double remove_foliage_fraction ) |
320 | { |
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528 | werner | 321 | const Species *species = tree->species(); |
468 | werner | 322 | |
323 | // immediate flows: 100% of residual foliage, 100% of fine roots: they go to the labile pool |
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534 | werner | 324 | mLabileFlux.addBiomass(tree->biomassFoliage() * (1. - remove_foliage_fraction), species->cnFoliage(), tree->species()->snagKyl()); |
325 | mLabileFlux.addBiomass(tree->biomassFineRoot(), species->cnFineroot(), tree->species()->snagKyl()); |
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540 | werner | 326 | |
528 | werner | 327 | // for branches, add all biomass that remains in the forest to the soil |
534 | werner | 328 | mRefractoryFlux.addBiomass(tree->biomassBranch()*(1.-remove_branch_fraction), species->cnWood(), tree->species()->snagKyr()); |
528 | werner | 329 | // the same treatment for stem residuals |
534 | werner | 330 | mRefractoryFlux.addBiomass(tree->biomassStem() * remove_stem_fraction, species->cnWood(), tree->species()->snagKyr()); |
468 | werner | 331 | |
540 | werner | 332 | // split the corase wood biomass into parts (slower decay) |
333 | double biomass_rest = (tree->biomassCoarseRoot()) * 0.2; |
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334 | for (int i=0;i<5; i++) |
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335 | mOtherWood[i].addBiomass(biomass_rest, species->cnWood(), tree->species()->snagKyr()); |
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336 | |||
337 | |||
528 | werner | 338 | // for book-keeping... |
339 | mTotalToExtern.addBiomass(tree->biomassFoliage()*remove_foliage_fraction + |
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340 | tree->biomassBranch()*remove_branch_fraction + |
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341 | tree->biomassStem()*remove_stem_fraction, species->cnWood()); |
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468 | werner | 342 | } |
343 | |||
534 | werner | 344 | |
345 | |||
346 |