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1 | |||
91 | Werner | 2 | #include <QtCore> |
3 | #include <QtSql> |
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4 | #include "global.h" |
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393 | werner | 5 | #include "globalsettings.h" |
102 | Werner | 6 | #include "xmlhelper.h" |
90 | Werner | 7 | #include "speciesset.h" |
91 | Werner | 8 | #include "species.h" |
387 | werner | 9 | #include "model.h" |
10 | #include "seeddispersal.h" |
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393 | werner | 11 | #include "modelsettings.h" |
90 | Werner | 12 | |
13 | SpeciesSet::SpeciesSet() |
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14 | { |
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91 | Werner | 15 | mSetupQuery = 0; |
90 | Werner | 16 | } |
91 | Werner | 17 | |
18 | SpeciesSet::~SpeciesSet() |
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19 | { |
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20 | clear(); |
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21 | } |
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22 | |||
23 | void SpeciesSet::clear() |
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24 | { |
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25 | qDeleteAll(mSpecies.values()); |
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387 | werner | 26 | qDeleteAll(mSeedDispersal); |
91 | Werner | 27 | mSpecies.clear(); |
179 | werner | 28 | mActiveSpecies.clear(); |
91 | Werner | 29 | } |
30 | |||
111 | Werner | 31 | const Species *SpeciesSet::species(const int &index) |
32 | { |
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33 | foreach(Species *s, mSpecies) |
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34 | if (s->index() == index) |
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35 | return s; |
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36 | return NULL; |
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37 | } |
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91 | Werner | 38 | |
39 | /** loads active species from a database table and creates/setups the species. |
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40 | The function uses the global database-connection. |
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41 | */ |
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102 | Werner | 42 | int SpeciesSet::setup() |
91 | Werner | 43 | { |
102 | Werner | 44 | const XmlHelper &xml = GlobalSettings::instance()->settings(); |
191 | werner | 45 | QString tableName = xml.value("model.species.source", "species"); |
318 | werner | 46 | mName = tableName; |
191 | werner | 47 | QString readerFile = xml.value("model.species.reader", "reader.bin"); |
102 | Werner | 48 | readerFile = GlobalSettings::instance()->path(readerFile, "lip"); |
49 | mReaderStamp.load(readerFile); |
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50 | |||
91 | Werner | 51 | QSqlQuery query(GlobalSettings::instance()->dbin()); |
52 | mSetupQuery = &query; |
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53 | QString sql = QString("select * from %1").arg(tableName); |
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54 | query.exec(sql); |
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270 | werner | 55 | if (query.lastError().isValid()){ |
56 | throw IException(QString("Error loading species set: %1 \n %2").arg(sql, query.lastError().text()) ); |
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57 | } |
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58 | |||
91 | Werner | 59 | clear(); |
60 | qDebug() << "attempting to load a species set from" << tableName; |
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61 | while (query.next()) { |
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62 | if (var("active").toInt()==0) |
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63 | continue; |
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64 | |||
65 | Species *s = new Species(this); // create |
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99 | Werner | 66 | // call setup routine (which calls SpeciesSet::var() to retrieve values |
91 | Werner | 67 | s->setup(); |
68 | |||
69 | mSpecies.insert(s->id(), s); // store |
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179 | werner | 70 | if (s->active()) |
71 | mActiveSpecies.append(s); |
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577 | werner | 72 | |
73 | Expression::addConstant(s->id(), s->index()); |
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91 | Werner | 74 | } // while query.next() |
75 | qDebug() << "loaded" << mSpecies.count() << "active species:"; |
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575 | werner | 76 | qDebug() << "index, id, name"; |
77 | foreach(const Species *s, mActiveSpecies) |
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78 | qDebug() << s->index() << s->id() << s->name(); |
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91 | Werner | 79 | |
80 | mSetupQuery = 0; |
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209 | werner | 81 | |
82 | // setup nitrogen response |
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83 | XmlHelper resp(xml.node("model.species.nitrogenResponseClasses")); |
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84 | if (!resp.isValid()) |
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85 | throw IException("model.species.nitrogenResponseClasses not present!"); |
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86 | mNitrogen_1a = resp.valueDouble("class_1_a"); |
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87 | mNitrogen_1b = resp.valueDouble("class_1_b"); |
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88 | mNitrogen_2a = resp.valueDouble("class_2_a"); |
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89 | mNitrogen_2b = resp.valueDouble("class_2_b"); |
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90 | mNitrogen_3a = resp.valueDouble("class_3_a"); |
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91 | mNitrogen_3b = resp.valueDouble("class_3_b"); |
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92 | if (mNitrogen_1a*mNitrogen_1b*mNitrogen_2a*mNitrogen_2b*mNitrogen_3a*mNitrogen_3b == 0) |
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93 | throw IException("at least one parameter of model.species.nitrogenResponseClasses is not valid (value=0)!"); |
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94 | |||
95 | // setup CO2 response |
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96 | XmlHelper co2(xml.node("model.species.CO2Response")); |
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97 | mCO2base = co2.valueDouble("baseConcentration"); |
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98 | mCO2comp = co2.valueDouble("compensationPoint"); |
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99 | mCO2beta0 = co2.valueDouble("beta0"); |
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100 | mCO2p0 = co2.valueDouble("p0"); |
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101 | if (mCO2base*mCO2comp*(mCO2base-mCO2comp)*mCO2beta0*mCO2p0==0) |
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102 | throw IException("at least one parameter of model.species.CO2Response is not valid!"); |
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103 | |||
274 | werner | 104 | // setup Light responses |
105 | XmlHelper light(xml.node("model.species.lightResponse")); |
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106 | mLightResponseTolerant.setAndParse(light.value("shadeTolerant")); |
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107 | mLightResponseIntolerant.setAndParse(light.value("shadeIntolerant")); |
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428 | werner | 108 | mLightResponseTolerant.linearize(0., 1.); |
109 | mLightResponseIntolerant.linearize(0., 1.); |
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274 | werner | 110 | if (mLightResponseTolerant.expression().isEmpty() || mLightResponseIntolerant.expression().isEmpty()) |
111 | throw IException("at least one parameter of model.species.lightResponse is empty!"); |
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425 | werner | 112 | // lri-correction |
113 | mLRICorrection.setAndParse(light.value("LRImodifier","1")); |
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428 | werner | 114 | // x: LRI, y: relative heigth |
115 | mLRICorrection.linearize2d(0., 1., 0., 1.); |
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391 | werner | 116 | return mSpecies.count(); |
387 | werner | 117 | |
391 | werner | 118 | } |
119 | |||
120 | void SpeciesSet::setupRegeneration() |
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121 | { |
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122 | foreach(Species *s, mActiveSpecies) { |
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123 | SeedDispersal *sd = new SeedDispersal(s); |
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124 | sd->setup(); // setup memory for the seed map (grid) |
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125 | s->setSeedDispersal(sd); // establish the link between species and the map |
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387 | werner | 126 | } |
391 | werner | 127 | qDebug() << "Setup of seed dispersal maps finished."; |
128 | } |
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91 | Werner | 129 | |
475 | werner | 130 | Species *nc_seed_distribution(Species *species) |
131 | { |
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132 | species->setRandomGenerator(); |
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479 | werner | 133 | species->seedDispersal()->execute(); |
475 | werner | 134 | return species; |
135 | } |
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391 | werner | 136 | void SpeciesSet::regeneration() |
137 | { |
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393 | werner | 138 | if (!GlobalSettings::instance()->model()->settings().regenerationEnabled) |
139 | return; |
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615 | werner | 140 | |
141 | |||
475 | werner | 142 | ThreadRunner runner(mActiveSpecies); // initialize a thread runner object with all active species |
143 | runner.run(nc_seed_distribution); |
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391 | werner | 144 | |
475 | werner | 145 | if (logLevelDebug()) |
146 | qDebug() << "seed dispersal finished."; |
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91 | Werner | 147 | } |
211 | werner | 148 | |
391 | werner | 149 | /** newYear is called by Model::runYear at the beginning of a year before any growth occurs. |
150 | This is used for various initializations, e.g. to clear seed dispersal maps |
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151 | */ |
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152 | void SpeciesSet::newYear() |
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153 | { |
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393 | werner | 154 | if (!GlobalSettings::instance()->model()->settings().regenerationEnabled) |
155 | return; |
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391 | werner | 156 | foreach(Species *s, mActiveSpecies) { |
415 | werner | 157 | s->newYear(); |
391 | werner | 158 | } |
159 | } |
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211 | werner | 160 | |
91 | Werner | 161 | /** retrieves variables from the datasource available during the setup of species. |
162 | */ |
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163 | QVariant SpeciesSet::var(const QString& varName) |
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164 | { |
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94 | Werner | 165 | Q_ASSERT(mSetupQuery!=0); |
91 | Werner | 166 | |
167 | int idx = mSetupQuery->record().indexOf(varName); |
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168 | if (idx>=0) |
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169 | return mSetupQuery->value(idx); |
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125 | Werner | 170 | throw IException(QString("SpeciesSet: variable not set: %1").arg(varName)); |
120 | Werner | 171 | //throw IException(QString("load species parameter: field %1 not found!").arg(varName)); |
91 | Werner | 172 | // lookup in defaults |
119 | Werner | 173 | //qDebug() << "variable" << varName << "not found - using default."; |
174 | //return GlobalSettings::instance()->settingDefaultValue(varName); |
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91 | Werner | 175 | } |
209 | werner | 176 | |
177 | inline double SpeciesSet::nitrogenResponse(const double &availableNitrogen, const double &NA, const double &NB) const |
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178 | { |
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179 | if (availableNitrogen<=NB) |
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180 | return 0; |
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181 | double x = 1. - exp(NA * (availableNitrogen-NB)); |
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182 | return x; |
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183 | } |
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184 | |||
185 | /// calculate nitrogen response for a given amount of available nitrogen and a respone class |
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186 | /// for fractional values, the response value is interpolated between the fixedly defined classes (1,2,3) |
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187 | double SpeciesSet::nitrogenResponse(const double availableNitrogen, const double &responseClass) const |
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188 | { |
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189 | double value1, value2, value3; |
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190 | if (responseClass>2.) { |
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191 | if (responseClass==3.) |
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192 | return nitrogenResponse(availableNitrogen, mNitrogen_3a, mNitrogen_3b); |
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193 | else { |
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194 | // interpolate between 2 and 3 |
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195 | value2 = nitrogenResponse(availableNitrogen, mNitrogen_2a, mNitrogen_2b); |
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196 | value3 = nitrogenResponse(availableNitrogen, mNitrogen_3a, mNitrogen_3b); |
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197 | return value2 + (responseClass-2)*(value3-value2); |
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198 | } |
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199 | } |
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200 | if (responseClass==2) |
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201 | return nitrogenResponse(availableNitrogen, mNitrogen_2a, mNitrogen_2b); |
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202 | if (responseClass==1) |
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203 | return nitrogenResponse(availableNitrogen, mNitrogen_1a, mNitrogen_1b); |
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204 | // last ressort: interpolate between 1 and 2 |
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205 | value1 = nitrogenResponse(availableNitrogen, mNitrogen_1a, mNitrogen_1b); |
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206 | value2 = nitrogenResponse(availableNitrogen, mNitrogen_2a, mNitrogen_2b); |
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207 | return value1 + (responseClass-1)*(value2-value1); |
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208 | } |
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209 | |||
210 | /** calculation for the CO2 response for the ambientCO2 for the water- and nitrogen responses given. |
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211 | The calculation follows Friedlingsstein 1995 (see also links to equations in code) |
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534 | werner | 212 | see also: http://iland.boku.ac.at/CO2+response |
213 | @param ambientCO2 current CO2 concentration (ppm) |
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214 | @param nitrogenResponse (yearly) nitrogen response of the species |
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215 | @param soilWaterReponse soil water response (mean value for a month) |
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209 | werner | 216 | */ |
217 | double SpeciesSet::co2Response(const double ambientCO2, const double nitrogenResponse, const double soilWaterResponse) const |
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218 | { |
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210 | werner | 219 | if (nitrogenResponse==0) |
220 | return 0.; |
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221 | |||
209 | werner | 222 | double co2_water = 2. - soilWaterResponse; |
223 | double beta = mCO2beta0 * co2_water * nitrogenResponse; |
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224 | |||
225 | double r =1. + M_LN2 * beta; // NPP increase for a doubling of atmospheric CO2 (Eq. 17) |
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226 | |||
227 | // fertilization function (cf. Farquhar, 1980) based on Michaelis-Menten expressions |
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228 | double deltaC = mCO2base - mCO2comp; |
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229 | double K2 = ((2*mCO2base - mCO2comp) - r*deltaC ) / ((r-1.)*deltaC*(2*mCO2base - mCO2comp)); // Eq. 16 |
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230 | double K1 = (1. + K2*deltaC) / deltaC; |
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231 | |||
232 | double response = mCO2p0 * K1*(ambientCO2 - mCO2comp) / (1 + K2*(ambientCO2-mCO2comp)); // Eq. 16 |
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233 | return response; |
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234 | |||
235 | } |
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211 | werner | 236 | |
274 | werner | 237 | /** calculates the lightResponse based on a value for LRI and the species lightResponseClass. |
238 | LightResponse is classified from 1 (very shade inolerant) and 5 (very shade tolerant) and interpolated for values between 1 and 5. |
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298 | werner | 239 | Returns a value between 0..1 |
240 | @sa http://iland.boku.ac.at/allocation#reserve_and_allocation_to_stem_growth */ |
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470 | werner | 241 | double SpeciesSet::lightResponse(const double lightResourceIndex, const double lightResponseClass) const |
274 | werner | 242 | { |
243 | double low = mLightResponseIntolerant.calculate(lightResourceIndex); |
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244 | double high = mLightResponseTolerant.calculate(lightResourceIndex); |
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245 | double result = low + 0.25*(lightResponseClass-1.)*(high-low); |
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246 | return limit(result, 0., 1.); |
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214 | werner | 247 | |
274 | werner | 248 | } |
249 | |||
250 | |||
251 |