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agomez |
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#include "prey.h" |
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#include "errorhandler.h" |
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#include "readword.h" |
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#include "readaggregation.h" |
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#include "keeper.h" |
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#include "mathfunc.h" |
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#include "gadget.h" |
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#include "global.h" |
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Prey::Prey(CommentStream& infile, const IntVector& Areas,
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const char* givenname, const TimeClass* const TimeInfo, Keeper* const keeper)
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: HasName(givenname), LivesOnAreas(Areas), CI(0) {
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char text[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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int i;
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//read the prey length group data
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DoubleVector preylengths;
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CharPtrVector preylenindex;
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char aggfilename[MaxStrLength];
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strncpy(aggfilename, "", MaxStrLength);
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ifstream datafile;
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CommentStream subdata(datafile);
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readWordAndValue(infile, "preylengths", aggfilename);
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datafile.open(aggfilename, ios::in);
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handle.checkIfFailure(datafile, aggfilename);
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handle.Open(aggfilename);
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i = readLengthAggregation(subdata, preylengths, preylenindex);
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handle.Close();
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datafile.close();
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datafile.clear();
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LgrpDiv = new LengthGroupDivision(preylengths);
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if (LgrpDiv->Error())
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handle.logMessage(LOGFAIL, "Error in prey - failed to create length group");
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//read the energy content of this prey
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infile >> ws;
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char c = infile.peek();
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if ((c == 'e') || (c == 'E'))
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readWordAndModelVariable(infile, "energycontent", energy, TimeInfo, keeper);
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else
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energy.setValue(1.0);
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//read from file - initialise things
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int numlen = LgrpDiv->numLengthGroups();
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int numarea = areas.Size();
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PopInfo nullpop;
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preynumber.AddRows(numarea, numlen, nullpop);
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biomass.AddRows(numarea, numlen, 0.0);
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cons.AddRows(numarea, numlen, 0.0);
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consumption.AddRows(numarea, numlen, 0.0);
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isoverconsumption.resize(numarea, 0);
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total.resize(numarea, 0.0);
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ratio.AddRows(numarea, numlen, 0.0);
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useratio.AddRows(numarea, numlen, 0.0);
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consratio.AddRows(numarea, numlen, 0.0);
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overconsumption.AddRows(numarea, numlen, 0.0);
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//preylenindex is not required - free up memory
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for (i = 0; i < preylenindex.Size(); i++)
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delete[] preylenindex[i];
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}
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Prey::Prey(CommentStream& infile, const char* givenname,
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const IntVector& Areas, const TimeClass* const TimeInfo, Keeper* const keeper)
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: HasName(givenname), LivesOnAreas(Areas) {
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char text[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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//read the length information
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DoubleVector lengths(2, 0.0);
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infile >> text >> ws;
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if (strcasecmp(text, "lengths") != 0)
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handle.logFileUnexpected(LOGFAIL, "lengths", text);
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infile >> lengths[0] >> lengths[1] >> ws;
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LgrpDiv = new LengthGroupDivision(lengths);
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if (LgrpDiv->Error())
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handle.logMessage(LOGFAIL, "Error in prey - failed to create length group");
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CI = new ConversionIndex(LgrpDiv, LgrpDiv);
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if (CI->Error())
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handle.logMessage(LOGFAIL, "Error in prey - error when checking length structure");
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//read the energy content of this prey
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infile >> ws;
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char c = infile.peek();
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if ((c == 'e') || (c == 'E'))
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readWordAndModelVariable(infile, "energycontent", energy, TimeInfo, keeper);
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else
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energy.setValue(1.0);
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int numlen = LgrpDiv->numLengthGroups();
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int numarea = areas.Size();
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PopInfo nullpop;
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preynumber.AddRows(numarea, numlen, nullpop);
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biomass.AddRows(numarea, numlen, 0.0);
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cons.AddRows(numarea, numlen, 0.0);
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consumption.AddRows(numarea, numlen, 0.0);
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isoverconsumption.resize(numarea, 0);
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total.resize(numarea, 0.0);
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ratio.AddRows(numarea, numlen, 0.0);
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useratio.AddRows(numarea, numlen, 0.0);
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consratio.AddRows(numarea, numlen, 0.0);
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overconsumption.AddRows(numarea, numlen, 0.0);
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}
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Prey::~Prey() {
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delete CI;
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delete LgrpDiv;
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}
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void Prey::setCI(const LengthGroupDivision* const GivenLDiv) {
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if (!checkLengthGroupStructure(GivenLDiv, LgrpDiv))
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handle.logMessage(LOGFAIL, "Error in prey - invalid length group structure for consumption of", this->getName());
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if (GivenLDiv->minLength() < LgrpDiv->minLength())
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handle.logMessage(LOGFAIL, "Error in prey - invalid minimum length group for consumption of", this->getName());
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if (!isSmall(LgrpDiv->minLength() - GivenLDiv->minLength()))
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handle.logMessage(LOGWARN, "Warning in prey - minimum lengths don't match for consumption of", this->getName());
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if (GivenLDiv->maxLength() > LgrpDiv->maxLength())
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handle.logMessage(LOGFAIL, "Error in prey - invalid maximum length group for consumption of", this->getName());
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if (!isSmall(LgrpDiv->maxLength() - GivenLDiv->maxLength()))
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handle.logMessage(LOGWARN, "Warning in prey - maximum lengths don't match for consumption of", this->getName());
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CI = new ConversionIndex(GivenLDiv, LgrpDiv);
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if (CI->Error())
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handle.logMessage(LOGFAIL, "Error in prey - error when checking length structure for", this->getName());
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}
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void Prey::Print(ofstream& outfile) const {
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int i, area;
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outfile << "\nPrey\n\tName " << this->getName() << "\n\tEnergy content " << energy << "\n\t";
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LgrpDiv->Print(outfile);
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for (area = 0; area < areas.Size(); area++) {
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outfile << "\tNumber of prey on internal area " << areas[area] << ":\n\t";
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for (i = 0; i < LgrpDiv->numLengthGroups(); i++)
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outfile << setw(smallwidth) << setprecision(smallprecision) << preynumber[area][i].N << sep;
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outfile << "\n\tWeight of prey on internal area " << areas[area] << ":\n\t";
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for (i = 0; i < LgrpDiv->numLengthGroups(); i++)
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outfile << setw(smallwidth) << setprecision(smallprecision) << preynumber[area][i].W << sep;
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outfile << "\n\tConsumption of prey on internal area " << areas[area] << ":\n\t";
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for (i = 0; i < LgrpDiv->numLengthGroups(); i++)
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outfile << setw(smallwidth) << setprecision(smallprecision) << consumption[area][i] << sep;
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outfile << "\n\tOverconsumption of prey on internal area " << areas[area] << ":\n\t";
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for (i = 0; i < LgrpDiv->numLengthGroups(); i++)
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outfile << setw(smallwidth) << setprecision(smallprecision) << overconsumption[area][i] << sep;
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outfile << endl;
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}
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}
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//reduce the population of the stock by the consumption
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void Prey::Subtract(AgeBandMatrix& Alkeys, int area) {
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Alkeys.Subtract(consratio[this->areaNum(area)], *CI);
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}
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//adds the consumption by biomass
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void Prey::addBiomassConsumption(int area, const DoubleVector& predcons) {
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int i, inarea = this->areaNum(area);
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if (predcons.Size() != cons[inarea].Size())
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handle.logMessage(LOGFAIL, "Error in consumption - cannot add different size vectors");
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for (i = 0; i < predcons.Size(); i++)
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cons[inarea][i] += predcons[i];
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}
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//adds the consumption by numbers
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void Prey::addNumbersConsumption(int area, const DoubleVector& predcons) {
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int i, inarea = this->areaNum(area);
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if (predcons.Size() != cons[inarea].Size())
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handle.logMessage(LOGFAIL, "Error in consumption - cannot add different size vectors");
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for (i = 0; i < predcons.Size(); i++)
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cons[inarea][i] += (predcons[i] * preynumber[inarea][i].W);
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}
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//check if more is consumed of prey than was available. If this is
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//the case a flag is set. Changed 22 - May 1997 so that only 95% of a prey
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//in an area can be eaten in one timestep. This is to avoid problems
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//with survey indices etc.
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void Prey::checkConsumption(int area, const TimeClass* const TimeInfo) {
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int i, over = 0;
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int inarea = this->areaNum(area);
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double timeratio = 1.0;
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double maxRatio = TimeInfo->getMaxRatioConsumed();
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if (TimeInfo->numSubSteps() != 1) {
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timeratio = 1.0 / TimeInfo->getSubStep();
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for (i = 0; i < LgrpDiv->numLengthGroups(); i++)
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useratio[inarea][i] *= (1.0 - timeratio);
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}
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for (i = 0; i < LgrpDiv->numLengthGroups(); i++) {
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if (isZero(biomass[inarea][i])) {
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//no prey biomass available to consume
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ratio[inarea][i] = 0.0;
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consratio[inarea][i] = 0.0;
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if (!(isZero(cons[inarea][i]))) {
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//consumption required but no prey exists
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over = 1;
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overconsumption[inarea][i] += cons[inarea][i];
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}
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} else {
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//prey available to consume so only need to check overconsumption
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ratio[inarea][i] = cons[inarea][i] / biomass[inarea][i];
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if (ratio[inarea][i] > maxRatio) {
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over = 1;
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overconsumption[inarea][i] += (ratio[inarea][i] - maxRatio) * biomass[inarea][i];
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consratio[inarea][i] = 1.0 - maxRatio;
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useratio[inarea][i] += (timeratio * maxRatio);
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cons[inarea][i] = biomass[inarea][i] * maxRatio;
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} else {
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consratio[inarea][i] = 1.0 - ratio[inarea][i];
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useratio[inarea][i] += (timeratio * ratio[inarea][i]);
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}
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//finally add the consumption
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consumption[inarea][i] += cons[inarea][i];
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}
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}
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//JMB changed to deal with substeps a little better
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if (over)
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isoverconsumption[inarea] = over;
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}
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void Prey::Reset(const TimeClass* const TimeInfo) {
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consumption.setToZero();
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overconsumption.setToZero();
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useratio.setToZero();
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isoverconsumption.setToZero();
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energy.Update(TimeInfo);
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if (isZero(energy))
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handle.logMessage(LOGWARN, "Warning in prey - energy content should be non-zero");
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if (handle.getLogLevel() >= LOGMESSAGE)
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handle.logMessage(LOGMESSAGE, "Reset consumption data for prey", this->getName());
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}
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int Prey::isPreyArea(int area) {
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if (this->isInArea(area) == 0)
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return 0;
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if (total[this->areaNum(area)] < 0.0)
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| 247 : |
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handle.logMessage(LOGWARN, "Warning in prey - negative amount consumed for", this->getName());
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if (isZero(total[this->areaNum(area)]))
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return 0;
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return 1;
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}
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int Prey::isOverConsumption(int area) {
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| 254 : |
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if (this->isInArea(area) == 0)
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return 0;
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return isoverconsumption[this->areaNum(area)];
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| 257 : |
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}
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double Prey::getTotalOverConsumption(int area) const {
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| 260 : |
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int inarea = this->areaNum(area);
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if (inarea == -1)
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return 0.0;
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int i;
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| 265 : |
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double total = 0.0;
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| 266 : |
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for (i = 0; i < LgrpDiv->numLengthGroups(); i++)
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| 267 : |
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total += overconsumption[inarea][i];
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return total;
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}
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