Subversion Repositories public iLand

/********************************************************************************************

**    iLand - an individual based forest landscape and disturbance model

**    http://iland.boku.ac.at

**    Copyright (C) 2009-  Werner Rammer, Rupert Seidl

**

**    This program is free software: you can redistribute it and/or modify

**    it under the terms of the GNU General Public License as published by

**    the Free Software Foundation, either version 3 of the License, or

**    (at your option) any later version.

**

**    This program is distributed in the hope that it will be useful,

**    but WITHOUT ANY WARRANTY; without even the implied warranty of

**    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

**    GNU General Public License for more details.

**

**    You should have received a copy of the GNU General Public License

**    along with this program.  If not, see <http://www.gnu.org/licenses/>.

********************************************************************************************/

#include <QtCore>

#include <QtSql>

#include <QVector>

#include "global.h"

#include "globalsettings.h"

#include "xmlhelper.h"

#include "speciesset.h"

#include "species.h"

#include "model.h"

#include "seeddispersal.h"

#include "modelsettings.h"

#include "debugtimer.h"

/** @class SpeciesSet

    A SpeciesSet acts as a container for individual Species objects. In iLand, theoretically,

    multiple species sets can be used in parallel.

  */

SpeciesSet::SpeciesSet()

{

    mSetupQuery = 0;

}

SpeciesSet::~SpeciesSet()

{

   clear();

}

void SpeciesSet::clear()

{

    qDeleteAll(mSpecies.values());

    qDeleteAll(mSeedDispersal);

    mSpecies.clear();

    mActiveSpecies.clear();

}

const Species *SpeciesSet::species(const int &index)

{

    foreach(Species *s, mSpecies)

        if (s->index() == index)

            return s;

    return NULL;

}

/** loads active species from a database table and creates/setups the species.

    The function uses the global database-connection.

  */

int SpeciesSet::setup()

{

    const XmlHelper &xml = GlobalSettings::instance()->settings();

    QString tableName = xml.value("model.species.source", "species");

    mName = tableName;

    QString readerFile = xml.value("model.species.reader", "reader.bin");

    readerFile = GlobalSettings::instance()->path(readerFile, "lip");

    mReaderStamp.load(readerFile);

    if (GlobalSettings::instance()->settings().paramValueBool("debugDumpStamps", false) )

        qDebug() << mReaderStamp.dump();

    QSqlQuery query(GlobalSettings::instance()->dbin());

    mSetupQuery = &query;

    QString sql = QString("select * from %1").arg(tableName);

    query.exec(sql);

    if (query.lastError().isValid()){

        throw IException(QString("Error loading species set: %1 \n %2").arg(sql, query.lastError().text()) );

    }

    clear();

    qDebug() << "attempting to load a species set from" << tableName;

    while (query.next()) {

        if (var("active").toInt()==0)

            continue;

        Species *s = new Species(this); // create

        // call setup routine (which calls SpeciesSet::var() to retrieve values

        s->setup();

        mSpecies.insert(s->id(), s); // store

        if (s->active())

            mActiveSpecies.append(s);

        Expression::addConstant(s->id(), s->index());

    } // while query.next()

    qDebug() << "loaded" << mSpecies.count() << "active species:";

    qDebug() << "index, id, name";

    foreach(const Species *s, mActiveSpecies)

        qDebug() << s->index() << s->id() << s->name();

    mSetupQuery = 0;

    // setup nitrogen response

    XmlHelper resp(xml.node("model.species.nitrogenResponseClasses"));

    if (!resp.isValid())

        throw IException("model.species.nitrogenResponseClasses not present!");

    mNitrogen_1a = resp.valueDouble("class_1_a");

    mNitrogen_1b = resp.valueDouble("class_1_b");

    mNitrogen_2a = resp.valueDouble("class_2_a");

    mNitrogen_2b = resp.valueDouble("class_2_b");

    mNitrogen_3a = resp.valueDouble("class_3_a");

    mNitrogen_3b = resp.valueDouble("class_3_b");

    if (mNitrogen_1a*mNitrogen_1b*mNitrogen_2a*mNitrogen_2b*mNitrogen_3a*mNitrogen_3b == 0)

        throw IException("at least one parameter of model.species.nitrogenResponseClasses is not valid (value=0)!");

    // setup CO2 response

    XmlHelper co2(xml.node("model.species.CO2Response"));

    mCO2base = co2.valueDouble("baseConcentration");

    mCO2comp = co2.valueDouble("compensationPoint");

    mCO2beta0 = co2.valueDouble("beta0");

    mCO2p0 = co2.valueDouble("p0");

    if (mCO2base*mCO2comp*(mCO2base-mCO2comp)*mCO2beta0*mCO2p0==0)

        throw IException("at least one parameter of model.species.CO2Response is not valid!");

    // setup Light responses

    XmlHelper light(xml.node("model.species.lightResponse"));

    mLightResponseTolerant.setAndParse(light.value("shadeTolerant"));

    mLightResponseIntolerant.setAndParse(light.value("shadeIntolerant"));

    mLightResponseTolerant.linearize(0., 1.);

    mLightResponseIntolerant.linearize(0., 1.);

    if (mLightResponseTolerant.expression().isEmpty() || mLightResponseIntolerant.expression().isEmpty())

        throw IException("at least one parameter of model.species.lightResponse is empty!");

    // lri-correction

    mLRICorrection.setAndParse(light.value("LRImodifier","1"));

    // x: LRI, y: relative heigth

    mLRICorrection.linearize2d(0., 1., 0., 1.);

    createRandomSpeciesOrder();

    return mSpecies.count();

}

void SpeciesSet::setupRegeneration()

{

    SeedDispersal::setupExternalSeeds();

    foreach(Species *s, mActiveSpecies) {

        SeedDispersal *sd = new SeedDispersal(s);

        sd->setup(); // setup memory for the seed map (grid)

        s->setSeedDispersal(sd); // establish the link between species and the map

    }

    SeedDispersal::finalizeExternalSeeds();

    qDebug() << "Setup of seed dispersal maps finished.";

}

void nc_seed_distribution(Species *species)

{

    species->seedDispersal()->execute();

}

void SpeciesSet::regeneration()

{

    if (!GlobalSettings::instance()->model()->settings().regenerationEnabled)

        return;

    DebugTimer t("seed dispersal (all species)");

    ThreadRunner runner(mActiveSpecies); // initialize a thread runner object with all active species

    runner.run(nc_seed_distribution);

    if (logLevelDebug())

        qDebug() << "seed dispersal finished.";

}

/** newYear is called by Model::runYear at the beginning of a year before any growth occurs.

  This is used for various initializations, e.g. to clear seed dispersal maps

  */

void SpeciesSet::newYear()

{

    if (!GlobalSettings::instance()->model()->settings().regenerationEnabled)

        return;

    foreach(Species *s, mActiveSpecies) {

        s->newYear();

    }

}

/** retrieves variables from the datasource available during the setup of species.

  */

QVariant SpeciesSet::var(const QString& varName)

{

    Q_ASSERT(mSetupQuery!=0);

    int idx = mSetupQuery->record().indexOf(varName);

    if (idx>=0)

        return mSetupQuery->value(idx);

    throw IException(QString("SpeciesSet: variable not set: %1").arg(varName));

    //throw IException(QString("load species parameter: field %1 not found!").arg(varName));

    // lookup in defaults

    //qDebug() << "variable" << varName << "not found - using default.";

    //return GlobalSettings::instance()->settingDefaultValue(varName);

}

void SpeciesSet::randomSpeciesOrder(QVector<int>::const_iterator &rBegin, QVector<int>::const_iterator &rEnd)

{

    int iset = irandom(0,mNRandomSets);

    rBegin=mRandomSpeciesOrder.begin() + iset * mActiveSpecies.size();

    rEnd=rBegin+mActiveSpecies.size();

}

//

void SpeciesSet::createRandomSpeciesOrder()

{

    mRandomSpeciesOrder.clear();

    mRandomSpeciesOrder.reserve(mActiveSpecies.size() * mNRandomSets);

    for (int i=0;i<mNRandomSets;++i) {

        QList<int> samples;

        // fill list

        foreach (const Species* s, mActiveSpecies)

            samples.push_back(s->index());

        // sample and reduce list

        while (!samples.isEmpty()) {

            mRandomSpeciesOrder.push_back( samples.takeAt(irandom(0, samples.size()))  );

        }

    }

}

inline double SpeciesSet::nitrogenResponse(const double &availableNitrogen, const double &NA, const double &NB) const

{

    if (availableNitrogen<=NB)

        return 0;

    double x = 1. - exp(NA * (availableNitrogen-NB));

    return x;

}

/// calculate nitrogen response for a given amount of available nitrogen and a respone class

/// for fractional values, the response value is interpolated between the fixedly defined classes (1,2,3)

double SpeciesSet::nitrogenResponse(const double availableNitrogen, const double &responseClass) const

{

    double value1, value2, value3;

    if (responseClass>2.) {

        if (responseClass==3.)

            return nitrogenResponse(availableNitrogen, mNitrogen_3a, mNitrogen_3b);

        else {

            // interpolate between 2 and 3

            value2 = nitrogenResponse(availableNitrogen, mNitrogen_2a, mNitrogen_2b);

            value3 = nitrogenResponse(availableNitrogen, mNitrogen_3a, mNitrogen_3b);

            return value2 + (responseClass-2)*(value3-value2);

        }

    }

    if (responseClass==2.)

        return nitrogenResponse(availableNitrogen, mNitrogen_2a, mNitrogen_2b);

    if (responseClass==1.)

        return nitrogenResponse(availableNitrogen, mNitrogen_1a, mNitrogen_1b);

    // last ressort: interpolate between 1 and 2

    value1 = nitrogenResponse(availableNitrogen, mNitrogen_1a, mNitrogen_1b);

    value2 = nitrogenResponse(availableNitrogen, mNitrogen_2a, mNitrogen_2b);

    return value1 + (responseClass-1)*(value2-value1);

}

/** calculation for the CO2 response for the ambientCO2 for the water- and nitrogen responses given.

    The calculation follows Friedlingsstein 1995 (see also links to equations in code)

    see also: http://iland.boku.ac.at/CO2+response

    @param ambientCO2 current CO2 concentration (ppm)

    @param nitrogenResponse (yearly) nitrogen response of the species

    @param soilWaterReponse soil water response (mean value for a month)

*/

double SpeciesSet::co2Response(const double ambientCO2, const double nitrogenResponse, const double soilWaterResponse) const

{

    if (nitrogenResponse==0.)

        return 0.;

    double co2_water = 2. - soilWaterResponse;

    double beta = mCO2beta0 * co2_water * nitrogenResponse;

    double r =1. +  M_LN2 * beta; // NPP increase for a doubling of atmospheric CO2 (Eq. 17)

    // fertilization function (cf. Farquhar, 1980) based on Michaelis-Menten expressions

    double deltaC = mCO2base - mCO2comp;

    double K2 = ((2*mCO2base - mCO2comp) - r*deltaC ) / ((r-1.)*deltaC*(2*mCO2base - mCO2comp)); // Eq. 16

    double K1 = (1. + K2*deltaC) / deltaC;

    double response = mCO2p0 * K1*(ambientCO2 - mCO2comp) / (1 + K2*(ambientCO2-mCO2comp)); // Eq. 16

    return response;

}

/** calculates the lightResponse based on a value for LRI and the species lightResponseClass.

    LightResponse is classified from 1 (very shade inolerant) and 5 (very shade tolerant) and interpolated for values between 1 and 5.

    Returns a value between 0..1

    @sa http://iland.boku.ac.at/allocation#reserve_and_allocation_to_stem_growth */

double SpeciesSet::lightResponse(const double lightResourceIndex, const double lightResponseClass) const

{

    double low = mLightResponseIntolerant.calculate(lightResourceIndex);

    double high = mLightResponseTolerant.calculate(lightResourceIndex);

    double result = low + 0.25*(lightResponseClass-1.)*(high-low);

    return limit(result, 0., 1.);

}