Rev 318 | Rev 391 | Go to most recent revision | Details | Compare with Previous | Last modification | View Log | RSS feed
Rev | Author | Line No. | Line |
---|---|---|---|
1 | |||
91 | Werner | 2 | #include <QtCore> |
3 | #include <QtSql> |
||
4 | #include "global.h" |
||
102 | Werner | 5 | #include "xmlhelper.h" |
90 | Werner | 6 | #include "speciesset.h" |
91 | Werner | 7 | #include "species.h" |
387 | werner | 8 | #include "model.h" |
9 | #include "seeddispersal.h" |
||
90 | Werner | 10 | |
11 | SpeciesSet::SpeciesSet() |
||
12 | { |
||
91 | Werner | 13 | mSetupQuery = 0; |
90 | Werner | 14 | } |
91 | Werner | 15 | |
16 | SpeciesSet::~SpeciesSet() |
||
17 | { |
||
18 | clear(); |
||
19 | } |
||
20 | |||
21 | void SpeciesSet::clear() |
||
22 | { |
||
23 | qDeleteAll(mSpecies.values()); |
||
387 | werner | 24 | qDeleteAll(mSeedDispersal); |
91 | Werner | 25 | mSpecies.clear(); |
179 | werner | 26 | mActiveSpecies.clear(); |
91 | Werner | 27 | } |
28 | |||
111 | Werner | 29 | const Species *SpeciesSet::species(const int &index) |
30 | { |
||
31 | foreach(Species *s, mSpecies) |
||
32 | if (s->index() == index) |
||
33 | return s; |
||
34 | return NULL; |
||
35 | } |
||
91 | Werner | 36 | |
37 | /** loads active species from a database table and creates/setups the species. |
||
38 | The function uses the global database-connection. |
||
39 | */ |
||
102 | Werner | 40 | int SpeciesSet::setup() |
91 | Werner | 41 | { |
102 | Werner | 42 | const XmlHelper &xml = GlobalSettings::instance()->settings(); |
191 | werner | 43 | QString tableName = xml.value("model.species.source", "species"); |
318 | werner | 44 | mName = tableName; |
191 | werner | 45 | QString readerFile = xml.value("model.species.reader", "reader.bin"); |
102 | Werner | 46 | readerFile = GlobalSettings::instance()->path(readerFile, "lip"); |
47 | mReaderStamp.load(readerFile); |
||
48 | |||
91 | Werner | 49 | QSqlQuery query(GlobalSettings::instance()->dbin()); |
50 | mSetupQuery = &query; |
||
51 | QString sql = QString("select * from %1").arg(tableName); |
||
52 | query.exec(sql); |
||
270 | werner | 53 | if (query.lastError().isValid()){ |
54 | throw IException(QString("Error loading species set: %1 \n %2").arg(sql, query.lastError().text()) ); |
||
55 | } |
||
56 | |||
91 | Werner | 57 | clear(); |
58 | qDebug() << "attempting to load a species set from" << tableName; |
||
59 | while (query.next()) { |
||
60 | if (var("active").toInt()==0) |
||
61 | continue; |
||
62 | |||
63 | Species *s = new Species(this); // create |
||
99 | Werner | 64 | // call setup routine (which calls SpeciesSet::var() to retrieve values |
91 | Werner | 65 | s->setup(); |
66 | |||
67 | mSpecies.insert(s->id(), s); // store |
||
179 | werner | 68 | if (s->active()) |
69 | mActiveSpecies.append(s); |
||
91 | Werner | 70 | } // while query.next() |
71 | qDebug() << "loaded" << mSpecies.count() << "active species:"; |
||
72 | qDebug() << mSpecies.keys(); |
||
73 | |||
74 | mSetupQuery = 0; |
||
209 | werner | 75 | |
76 | // setup nitrogen response |
||
77 | XmlHelper resp(xml.node("model.species.nitrogenResponseClasses")); |
||
78 | if (!resp.isValid()) |
||
79 | throw IException("model.species.nitrogenResponseClasses not present!"); |
||
80 | mNitrogen_1a = resp.valueDouble("class_1_a"); |
||
81 | mNitrogen_1b = resp.valueDouble("class_1_b"); |
||
82 | mNitrogen_2a = resp.valueDouble("class_2_a"); |
||
83 | mNitrogen_2b = resp.valueDouble("class_2_b"); |
||
84 | mNitrogen_3a = resp.valueDouble("class_3_a"); |
||
85 | mNitrogen_3b = resp.valueDouble("class_3_b"); |
||
86 | if (mNitrogen_1a*mNitrogen_1b*mNitrogen_2a*mNitrogen_2b*mNitrogen_3a*mNitrogen_3b == 0) |
||
87 | throw IException("at least one parameter of model.species.nitrogenResponseClasses is not valid (value=0)!"); |
||
88 | |||
89 | // setup CO2 response |
||
90 | XmlHelper co2(xml.node("model.species.CO2Response")); |
||
91 | mCO2base = co2.valueDouble("baseConcentration"); |
||
92 | mCO2comp = co2.valueDouble("compensationPoint"); |
||
93 | mCO2beta0 = co2.valueDouble("beta0"); |
||
94 | mCO2p0 = co2.valueDouble("p0"); |
||
95 | if (mCO2base*mCO2comp*(mCO2base-mCO2comp)*mCO2beta0*mCO2p0==0) |
||
96 | throw IException("at least one parameter of model.species.CO2Response is not valid!"); |
||
97 | |||
274 | werner | 98 | // setup Light responses |
99 | XmlHelper light(xml.node("model.species.lightResponse")); |
||
100 | mLightResponseTolerant.setAndParse(light.value("shadeTolerant")); |
||
101 | mLightResponseIntolerant.setAndParse(light.value("shadeIntolerant")); |
||
102 | if (mLightResponseTolerant.expression().isEmpty() || mLightResponseIntolerant.expression().isEmpty()) |
||
103 | throw IException("at least one parameter of model.species.lightResponse is empty!"); |
||
104 | |||
387 | werner | 105 | // setup of regeneration related stuff like seed dispersal maps |
106 | if (xml.valueBool("model.settings.regenerationEnabled", false)) { |
||
107 | foreach(Species *s, mActiveSpecies) { |
||
108 | SeedDispersal *sd = new SeedDispersal(s); |
||
109 | sd->setup(); // setup memory for the seed map (grid) |
||
110 | s->setSeedDispersal(sd); // establish the link between species and the map |
||
111 | |||
112 | } |
||
113 | } |
||
91 | Werner | 114 | return mSpecies.count(); |
115 | |||
116 | } |
||
211 | werner | 117 | |
118 | |||
91 | Werner | 119 | /** retrieves variables from the datasource available during the setup of species. |
120 | */ |
||
121 | QVariant SpeciesSet::var(const QString& varName) |
||
122 | { |
||
94 | Werner | 123 | Q_ASSERT(mSetupQuery!=0); |
91 | Werner | 124 | |
125 | int idx = mSetupQuery->record().indexOf(varName); |
||
126 | if (idx>=0) |
||
127 | return mSetupQuery->value(idx); |
||
125 | Werner | 128 | throw IException(QString("SpeciesSet: variable not set: %1").arg(varName)); |
120 | Werner | 129 | //throw IException(QString("load species parameter: field %1 not found!").arg(varName)); |
91 | Werner | 130 | // lookup in defaults |
119 | Werner | 131 | //qDebug() << "variable" << varName << "not found - using default."; |
132 | //return GlobalSettings::instance()->settingDefaultValue(varName); |
||
91 | Werner | 133 | } |
209 | werner | 134 | |
135 | inline double SpeciesSet::nitrogenResponse(const double &availableNitrogen, const double &NA, const double &NB) const |
||
136 | { |
||
137 | if (availableNitrogen<=NB) |
||
138 | return 0; |
||
139 | double x = 1. - exp(NA * (availableNitrogen-NB)); |
||
140 | return x; |
||
141 | } |
||
142 | |||
143 | /// calculate nitrogen response for a given amount of available nitrogen and a respone class |
||
144 | /// for fractional values, the response value is interpolated between the fixedly defined classes (1,2,3) |
||
145 | double SpeciesSet::nitrogenResponse(const double availableNitrogen, const double &responseClass) const |
||
146 | { |
||
147 | double value1, value2, value3; |
||
148 | if (responseClass>2.) { |
||
149 | if (responseClass==3.) |
||
150 | return nitrogenResponse(availableNitrogen, mNitrogen_3a, mNitrogen_3b); |
||
151 | else { |
||
152 | // interpolate between 2 and 3 |
||
153 | value2 = nitrogenResponse(availableNitrogen, mNitrogen_2a, mNitrogen_2b); |
||
154 | value3 = nitrogenResponse(availableNitrogen, mNitrogen_3a, mNitrogen_3b); |
||
155 | return value2 + (responseClass-2)*(value3-value2); |
||
156 | } |
||
157 | } |
||
158 | if (responseClass==2) |
||
159 | return nitrogenResponse(availableNitrogen, mNitrogen_2a, mNitrogen_2b); |
||
160 | if (responseClass==1) |
||
161 | return nitrogenResponse(availableNitrogen, mNitrogen_1a, mNitrogen_1b); |
||
162 | // last ressort: interpolate between 1 and 2 |
||
163 | value1 = nitrogenResponse(availableNitrogen, mNitrogen_1a, mNitrogen_1b); |
||
164 | value2 = nitrogenResponse(availableNitrogen, mNitrogen_2a, mNitrogen_2b); |
||
165 | return value1 + (responseClass-1)*(value2-value1); |
||
166 | } |
||
167 | |||
168 | /** calculation for the CO2 response for the ambientCO2 for the water- and nitrogen responses given. |
||
169 | The calculation follows Friedlingsstein 1995 (see also links to equations in code) |
||
170 | */ |
||
171 | double SpeciesSet::co2Response(const double ambientCO2, const double nitrogenResponse, const double soilWaterResponse) const |
||
172 | { |
||
210 | werner | 173 | if (nitrogenResponse==0) |
174 | return 0.; |
||
175 | |||
209 | werner | 176 | double co2_water = 2. - soilWaterResponse; |
177 | double beta = mCO2beta0 * co2_water * nitrogenResponse; |
||
178 | |||
179 | double r =1. + M_LN2 * beta; // NPP increase for a doubling of atmospheric CO2 (Eq. 17) |
||
180 | |||
181 | // fertilization function (cf. Farquhar, 1980) based on Michaelis-Menten expressions |
||
182 | double deltaC = mCO2base - mCO2comp; |
||
183 | double K2 = ((2*mCO2base - mCO2comp) - r*deltaC ) / ((r-1.)*deltaC*(2*mCO2base - mCO2comp)); // Eq. 16 |
||
184 | double K1 = (1. + K2*deltaC) / deltaC; |
||
185 | |||
186 | double response = mCO2p0 * K1*(ambientCO2 - mCO2comp) / (1 + K2*(ambientCO2-mCO2comp)); // Eq. 16 |
||
187 | return response; |
||
188 | |||
189 | } |
||
211 | werner | 190 | |
274 | werner | 191 | /** calculates the lightResponse based on a value for LRI and the species lightResponseClass. |
192 | LightResponse is classified from 1 (very shade inolerant) and 5 (very shade tolerant) and interpolated for values between 1 and 5. |
||
298 | werner | 193 | Returns a value between 0..1 |
194 | @sa http://iland.boku.ac.at/allocation#reserve_and_allocation_to_stem_growth */ |
||
274 | werner | 195 | double SpeciesSet::lightResponse(const double lightResourceIndex, const double lightResponseClass) |
196 | { |
||
197 | QMutexLocker l(&mMutex); // serialize access to calculations |
||
198 | double low = mLightResponseIntolerant.calculate(lightResourceIndex); |
||
199 | double high = mLightResponseTolerant.calculate(lightResourceIndex); |
||
200 | double result = low + 0.25*(lightResponseClass-1.)*(high-low); |
||
201 | return limit(result, 0., 1.); |
||
214 | werner | 202 | |
274 | werner | 203 | } |
204 | |||
205 | |||
206 |