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agomez |
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#include "migration.h" |
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#include "readfunc.h" |
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#include "readword.h" |
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#include "errorhandler.h" |
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#include "mathfunc.h" |
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#include "migrationarea.h" |
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#include "gadget.h" |
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#include "global.h" |
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// ********************************************************
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// Functions for base Migration
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// ********************************************************
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Migration::Migration(const IntVector& Areas, const char* givenname)
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: HasName(givenname), LivesOnAreas(Areas) {
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if (areas.Size() == 1)
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handle.logMessage(LOGWARN, "Warning in migration - only one area defined");
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}
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// ********************************************************
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// Functions for MigrationNumbers
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// ********************************************************
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MigrationNumbers::MigrationNumbers(CommentStream& infile, const IntVector& Areas,
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const AreaClass* const Area, const TimeClass* const TimeInfo,
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const char* givenname, Keeper* const keeper)
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: Migration(Areas, givenname) {
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int i, j;
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ifstream subfile;
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CommentStream subcomment(subfile);
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char text[MaxStrLength];
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char filename[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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strncpy(filename, "", MaxStrLength);
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keeper->addString("migrationmatrix");
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// Open and read year and step information
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readWordAndValue(infile, "yearstepfile", filename);
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subfile.open(filename, ios::in);
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handle.checkIfFailure(subfile, filename);
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handle.Open(filename);
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this->readTimeStepData(subcomment, TimeInfo);
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handle.Close();
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subfile.close();
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subfile.clear();
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// Open and read information about how the matrices are defined
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infile >> text >> filename >> ws;
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subfile.open(filename, ios::in);
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handle.checkIfFailure(subfile, filename);
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handle.Open(filename);
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if (strcasecmp(text, "definematrices") == 0) {
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this->readGivenMatrices(subcomment, keeper);
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} else if (strcasecmp(text, "defineratios") == 0) {
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this->readGivenRatios(subcomment, keeper, Area);
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} else
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handle.logFileUnexpected(LOGFAIL, "definematrices or defineratios", text);
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handle.Close();
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subfile.close();
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subfile.clear();
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this->checkMatrixIndex();
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handle.logMessage(LOGMESSAGE, "Read migration numbers file - number of migration matrices", readMigration.Size());
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keeper->clearLast();
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}
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MigrationNumbers::~MigrationNumbers() {
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int i;
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for (i = 0; i < timeindex.Size(); i++)
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if (timeindex[i] != -1)
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delete[] allmatrixnames[i];
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for (i = 0; i < usedmatrixnames.Size(); i++) {
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delete[] usedmatrixnames[i];
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delete readMigration[i];
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delete calcMigration[i];
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}
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}
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void MigrationNumbers::readTimeStepData(CommentStream& infile, const TimeClass* const TimeInfo) {
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int year, step, timeid, count;
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char text[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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// check the number of columns in the inputfile
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infile >> ws;
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if (countColumns(infile) != 3)
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handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 3");
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year = step = count = 0;
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allmatrixnames.resizeBlank(TimeInfo->numTotalSteps() + 1);
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timeindex.resize(TimeInfo->numTotalSteps() + 1, -1);
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while (!infile.eof()) {
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infile >> year >> step >> text >> ws;
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if (TimeInfo->isWithinPeriod(year, step)) {
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timeid = TimeInfo->calcSteps(year, step);
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timeindex[timeid] = 0;
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allmatrixnames[timeid] = new char[strlen(text) + 1];
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strcpy(allmatrixnames[timeid], text);
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count++;
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}
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}
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if (count == 0)
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handle.logMessage(LOGWARN, "Warning in migration - found no migration data");
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if (count != TimeInfo->numTotalSteps())
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handle.logMessage(LOGWARN, "Warning in migration - migration data doesnt span time range");
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handle.logMessage(LOGMESSAGE, "Read migration time data - number of entries", count);
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}
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void MigrationNumbers::readGivenRatios(CommentStream& infile, Keeper* const keeper, const AreaClass* const Area) {
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int innerrow, innercol, fromArea, toArea;
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int i, j, k, count;
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int numAreas = areas.Size();
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char text[MaxStrLength];
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char name[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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strncpy(name, "", MaxStrLength);
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/* File format:
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[migrationmatrix]
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name matrixname
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fromarea toarea ratio
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[migrationmatrix]
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...
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*/
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toArea = fromArea = 0;
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// Read ratio information from file
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while (!infile.eof() && !infile.fail()) {
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infile >> text >> ws;
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if (strcasecmp(text, "[migrationmatrix]") != 0)
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handle.logFileUnexpected(LOGFAIL, "[migrationmatrix]", text);
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readWordAndValue(infile, "name", name);
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if (this->useMatrix(name)) {
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this->setMatrixName(name);
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count = readMigration.Size();
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checkvalues.AddRows(1, numAreas, 0);
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readMigration.resize(new FormulaMatrix(numAreas, numAreas, 0.0));
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infile >> ws;
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while (!infile.eof() && !infile.fail() && (infile.peek() != '[')) {
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if (!(isdigit(infile.peek()))) {
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infile >> text >> ws;
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handle.logFileUnexpected(LOGFAIL, "[migrationmatrix] or area number", text);
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}
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infile >> fromArea >> toArea >> ws;
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innerrow = Area->getInnerArea(toArea);
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innercol = Area->getInnerArea(fromArea);
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if (!this->isInArea(innerrow) || !this->isInArea(innercol))
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handle.logMessage(LOGFAIL, "Error in migration - invalid area for matrix", name);
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toArea = this->areaNum(innerrow);
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fromArea = this->areaNum(innercol);
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infile >> (*readMigration[count])[toArea][fromArea] >> ws;
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checkvalues[count][fromArea]++;
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}
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} else {
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handle.logMessage(LOGWARN, "Warning in migration - matrix not used in the simulation", name);
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infile >> ws;
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while (!infile.eof() && !infile.fail() && infile.peek() != '[')
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infile >> text >> ws;
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}
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}
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// Finished reading from file, now check the values
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Formula missing;
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missing.setValue(1.0);
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for (i = 0; i < readMigration.Size(); i++) {
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for (j = 0; j < readMigration[i]->Nrow(); j++) {
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if (checkvalues[i][j] == 0) {
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// no data read for migration from this area
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(*readMigration[i])[j][j].setValue(1.0);
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} else if (checkvalues[i][j] == numAreas) {
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// nothing to do - data read for migration from this area to every other area
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} else if (isZero((*readMigration[i])[j][j])) {
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// read data for migration from this area to other areas
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// so simply subtract the migration from 1 to find those that are left
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count = 0;
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vector<Formula*> checklist;
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for (k = 0; k < readMigration[i]->Ncol(); k++) {
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if (!(isZero((*readMigration[i])[k][j]))) {
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checklist.push_back(&(*readMigration[i])[k][j]);
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count++;
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}
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}
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if (count == 0)
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handle.logFileMessage(LOGFAIL, "missing data for migration matrix", usedmatrixnames[i]);
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checklist.insert(checklist.begin(), &missing);
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Formula* missingValue = new Formula(MINUS, checklist);
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(*readMigration[i])[j][j] = *missingValue;
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delete missingValue;
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} else if (checkvalues[i][j] == (numAreas - 1)) {
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// read migration data from this area to all other areas but 1
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count = -1;
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vector<Formula*> checklist;
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for (k = 0; k < readMigration[i]->Ncol(); k++) {
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if (isZero((*readMigration[i])[k][j]))
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count = k;
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else
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checklist.push_back(&(*readMigration[i])[k][j]);
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}
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if (count == -1)
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handle.logFileMessage(LOGFAIL, "missing data for migration matrix", usedmatrixnames[i]);
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checklist.insert(checklist.begin(), &missing);
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Formula* missingValue = new Formula(MINUS, checklist);
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(*readMigration[i])[count][j] = *missingValue;
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delete missingValue;
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} else {
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// havent read enough information to reliably construct matrix
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handle.logFileMessage(LOGFAIL, "missing data for migration matrix", usedmatrixnames[i]);
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}
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}
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}
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| 228 : |
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| 229 : |
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// Inform keeper of the values and resize
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for (i = 0; i < readMigration.Size(); i++) {
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(*readMigration[i]).Inform(keeper);
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calcMigration.resize(new DoubleMatrix(numAreas, numAreas, 0.0));
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}
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}
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void MigrationNumbers::readGivenMatrices(CommentStream& infile, Keeper* const keeper) {
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| 237 : |
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int i, j, count;
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int numAreas = areas.Size();
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char text[MaxStrLength];
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char name[MaxStrLength];
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| 242 : |
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strncpy(text, "", MaxStrLength);
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strncpy(name, "", MaxStrLength);
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| 244 : |
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/* File format:
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| 246 : |
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[migrationmatrix]
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| 247 : |
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name matrixname
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| 248 : |
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x11 ... x1n
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| 249 : |
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...
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xn1 ... xnn
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| 251 : |
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[migrationmatrix]
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...
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*/
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// Read matrix information from file
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while (!infile.eof() && !infile.fail()) {
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| 257 : |
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infile >> text >> ws;
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| 258 : |
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if (strcasecmp(text, "[migrationmatrix]") != 0)
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| 259 : |
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handle.logFileUnexpected(LOGFAIL, "[migrationmatrix]", text);
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| 260 : |
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| 261 : |
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readWordAndValue(infile, "name", name);
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| 262 : |
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if (this->useMatrix(name)) {
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| 263 : |
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this->setMatrixName(name);
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| 264 : |
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count = readMigration.Size();
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| 265 : |
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readMigration.resize(new FormulaMatrix(numAreas, numAreas, 0.0));
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| 266 : |
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| 267 : |
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infile >> ws;
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| 268 : |
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if (infile.peek() == '[' || infile.eof()) {
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| 269 : |
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for (i = 0; i < numAreas; i++)
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| 270 : |
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(*readMigration[count])[i][i].setValue(1.0);
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| 271 : |
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| 272 : |
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} else if (isdigit(infile.peek()) || infile.peek() == '#' || infile.peek() == '(') {
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| 273 : |
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// look for a number or a formula as the next entry to be read
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| 274 : |
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for (i = 0; i < numAreas; i++)
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| 275 : |
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for (j = 0; j < numAreas; j++)
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| 276 : |
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if (!(infile >> (*readMigration[count])[i][j]))
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| 277 : |
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handle.logMessage(LOGFAIL, "Error in migration - failed to read matrix", name);
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| 278 : |
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infile >> ws; //JMB strip whitespace
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| 279 : |
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| 280 : |
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} else {
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| 281 : |
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infile >> text;
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| 282 : |
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handle.logFileUnexpected(LOGFAIL, "[migrationmatrix] or matrix value", text);
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| 283 : |
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}
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| 284 : |
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| 285 : |
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} else {
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| 286 : |
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handle.logMessage(LOGWARN, "Warning in migration - matrix not used in the simulation", name);
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| 287 : |
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infile >> ws;
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| 288 : |
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while (!infile.eof() && !infile.fail() && infile.peek() != '[')
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| 289 : |
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infile >> text >> ws;
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| 290 : |
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}
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| 291 : |
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}
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| 292 : |
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| 293 : |
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// Inform keeper of the values and resize
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| 294 : |
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for (i = 0; i < readMigration.Size(); i++) {
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| 295 : |
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(*readMigration[i]).Inform(keeper);
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| 296 : |
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calcMigration.resize(new DoubleMatrix(numAreas, numAreas, 0.0));
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| 297 : |
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}
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| 298 : |
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}
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| 299 : |
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| 300 : |
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void MigrationNumbers::checkMatrixIndex() {
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| 301 : |
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int i, j, check;
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| 302 : |
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| 303 : |
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for (i = 0; i < timeindex.Size(); i++) {
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| 304 : |
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if (timeindex[i] == 0) {
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| 305 : |
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check = -1;
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| 306 : |
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for (j = 0; j < usedmatrixnames.Size(); j++)
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| 307 : |
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if (strcasecmp(allmatrixnames[i], usedmatrixnames[j]) == 0)
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| 308 : |
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check = j;
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| 309 : |
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| 310 : |
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if (check == -1)
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| 311 : |
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handle.logMessage(LOGFAIL, "Error in migration - failed to read matrix", allmatrixnames[i]);
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| 312 : |
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timeindex[i] = check;
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| 313 : |
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| 314 : |
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} else if (timeindex[i] != -1) {
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| 315 : |
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handle.logMessage(LOGFAIL, "Error in migration - repeated migration matrix", i);
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| 316 : |
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}
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| 317 : |
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}
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| 318 : |
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}
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| 319 : |
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| 320 : |
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void MigrationNumbers::Print(ofstream& outfile) {
|
| 321 : |
|
|
int i, j, k;
|
| 322 : |
|
|
outfile << "\nMigration\n\tNames of migration matrices:\n\t";
|
| 323 : |
|
|
for (i = 0; i < timeindex.Size(); i++)
|
| 324 : |
|
|
if (timeindex[i] != -1)
|
| 325 : |
|
|
outfile << allmatrixnames[i] << sep;
|
| 326 : |
|
|
outfile << "\n\n\tMigration matrices";
|
| 327 : |
|
|
for (i = 0; i < calcMigration.Size(); i++) {
|
| 328 : |
|
|
outfile << "\n\tMatrix name: " << usedmatrixnames[i] << "\n\t";
|
| 329 : |
|
|
for (j = 0; j < calcMigration[i]->Nrow(); j++) {
|
| 330 : |
|
|
for (k = 0; k < calcMigration[i]->Ncol(j); k++)
|
| 331 : |
|
|
outfile << setw(smallwidth) << (*calcMigration[i])[j][k] << sep;
|
| 332 : |
|
|
outfile << "\n\t";
|
| 333 : |
|
|
}
|
| 334 : |
|
|
}
|
| 335 : |
|
|
outfile.flush();
|
| 336 : |
|
|
}
|
| 337 : |
|
|
|
| 338 : |
|
|
const DoubleMatrix& MigrationNumbers::getMigrationMatrix(const TimeClass* const TimeInfo) {
|
| 339 : |
|
|
return (*calcMigration[timeindex[TimeInfo->getTime()]]);
|
| 340 : |
|
|
}
|
| 341 : |
|
|
|
| 342 : |
|
|
void MigrationNumbers::setMatrixName(char* name) {
|
| 343 : |
|
|
int i;
|
| 344 : |
|
|
// check to ensure that this matrix name is unique
|
| 345 : |
|
|
for (i = 0; i < usedmatrixnames.Size(); i++)
|
| 346 : |
|
|
if (strcasecmp(usedmatrixnames[i], name) == 0)
|
| 347 : |
|
|
handle.logMessage(LOGFAIL, "Error in migration - repeated matrix", name);
|
| 348 : |
|
|
|
| 349 : |
|
|
// store the new matrix name
|
| 350 : |
|
|
char* tempname = new char[strlen(name) + 1];
|
| 351 : |
|
|
strcpy(tempname, name);
|
| 352 : |
|
|
usedmatrixnames.resize(tempname);
|
| 353 : |
|
|
}
|
| 354 : |
|
|
|
| 355 : |
|
|
void MigrationNumbers::Reset() {
|
| 356 : |
|
|
//JMB need to reset the penalty vector first
|
| 357 : |
|
|
penalty.Reset();
|
| 358 : |
|
|
|
| 359 : |
|
|
int i, j, k;
|
| 360 : |
|
|
double colsum;
|
| 361 : |
|
|
for (i = 0; i < readMigration.Size(); i++) {
|
| 362 : |
|
|
for (k = 0; k < readMigration[i]->Ncol(); k++) {
|
| 363 : |
|
|
colsum = 0.0;
|
| 364 : |
|
|
for (j = 0; j < readMigration[i]->Nrow(); j++) {
|
| 365 : |
|
|
if (isZero((*readMigration[i])[j][k])) {
|
| 366 : |
|
|
(*calcMigration[i])[j][k] = 0.0;
|
| 367 : |
|
|
} else if ((*readMigration[i])[j][k] < 0.0) {
|
| 368 : |
|
|
penalty.resize(1, (*readMigration[i])[j][k]);
|
| 369 : |
|
|
(*calcMigration[i])[j][k] = 0.0;
|
| 370 : |
|
|
handle.logMessage(LOGWARN, "Warning in migration - value outside bounds", (*readMigration[i])[j][k]);
|
| 371 : |
|
|
} else if ((*readMigration[i])[j][k] > 1.0) {
|
| 372 : |
|
|
penalty.resize(1, (*readMigration[i])[j][k]);
|
| 373 : |
|
|
(*calcMigration[i])[j][k] = 1.0;
|
| 374 : |
|
|
handle.logMessage(LOGWARN, "Warning in migration - value outside bounds", (*readMigration[i])[j][k]);
|
| 375 : |
|
|
} else
|
| 376 : |
|
|
(*calcMigration[i])[j][k] = (*readMigration[i])[j][k];
|
| 377 : |
|
|
|
| 378 : |
|
|
colsum += (*calcMigration[i])[j][k];
|
| 379 : |
|
|
}
|
| 380 : |
|
|
|
| 381 : |
|
|
if (isZero(colsum)) {
|
| 382 : |
|
|
handle.logMessage(LOGWARN, "Warning in migration - column sum is zero");
|
| 383 : |
|
|
// just putting anything here ... AJ 23.06.05, Needs to be changed!!!!!
|
| 384 : |
|
|
penalty.resize(1, 1.0);
|
| 385 : |
|
|
for (j = 0; j < readMigration[i]->Nrow(); j++) {
|
| 386 : |
|
|
if (k == j)
|
| 387 : |
|
|
(*calcMigration[i])[j][k] = 1.0;
|
| 388 : |
|
|
else
|
| 389 : |
|
|
(*calcMigration[i])[j][k] = 0.0;
|
| 390 : |
|
|
}
|
| 391 : |
|
|
|
| 392 : |
|
|
} else if (isEqual(colsum, 1.0)) {
|
| 393 : |
|
|
// everything is OK ...
|
| 394 : |
|
|
|
| 395 : |
|
|
} else {
|
| 396 : |
|
|
penalty.resize(1, colsum);
|
| 397 : |
|
|
colsum = 1.0 / colsum;
|
| 398 : |
|
|
for (j = 0; j < readMigration[i]->Nrow(); j++)
|
| 399 : |
|
|
(*calcMigration[i])[j][k] *= colsum;
|
| 400 : |
|
|
}
|
| 401 : |
|
|
}
|
| 402 : |
|
|
}
|
| 403 : |
|
|
|
| 404 : |
|
|
if (handle.getLogLevel() >= LOGMESSAGE)
|
| 405 : |
|
|
handle.logMessage(LOGMESSAGE, "Reset migration data for stock", this->getName());
|
| 406 : |
|
|
}
|
| 407 : |
|
|
|
| 408 : |
|
|
int MigrationNumbers::useMatrix(char* name) {
|
| 409 : |
|
|
int i;
|
| 410 : |
|
|
for (i = 0; i < timeindex.Size(); i++)
|
| 411 : |
|
|
if ((timeindex[i] != -1) && (strcasecmp(allmatrixnames[i], name) == 0))
|
| 412 : |
|
|
return 1;
|
| 413 : |
|
|
return 0;
|
| 414 : |
|
|
}
|
| 415 : |
|
|
|
| 416 : |
|
|
int MigrationNumbers::isMigrationStep(const TimeClass* const TimeInfo) {
|
| 417 : |
|
|
if (timeindex[TimeInfo->getTime()] == -1)
|
| 418 : |
|
|
return 0;
|
| 419 : |
|
|
return 1;
|
| 420 : |
|
|
}
|
| 421 : |
|
|
|
| 422 : |
|
|
// ********************************************************
|
| 423 : |
|
|
// Functions for MigrationFunction
|
| 424 : |
|
|
// ********************************************************
|
| 425 : |
|
|
MigrationFunction::MigrationFunction(CommentStream& infile, const IntVector& Areas,
|
| 426 : |
|
|
const AreaClass* const Area, const TimeClass* const TimeInfo,
|
| 427 : |
|
|
const char* givenname, Keeper* const keeper)
|
| 428 : |
|
|
: Migration(Areas, givenname) {
|
| 429 : |
|
|
|
| 430 : |
|
|
int i;
|
| 431 : |
|
|
ifstream subfile;
|
| 432 : |
|
|
CommentStream subcomment(subfile);
|
| 433 : |
|
|
char text[MaxStrLength];
|
| 434 : |
|
|
char filename[MaxStrLength];
|
| 435 : |
|
|
strncpy(text, "", MaxStrLength);
|
| 436 : |
|
|
strncpy(filename, "", MaxStrLength);
|
| 437 : |
|
|
keeper->addString("migrationfunction");
|
| 438 : |
|
|
|
| 439 : |
|
|
readWordAndModelVariable(infile, "diffusion", diffusion, TimeInfo, keeper);
|
| 440 : |
|
|
readWordAndModelVariable(infile, "driftx", driftx, TimeInfo, keeper);
|
| 441 : |
|
|
readWordAndModelVariable(infile, "drifty", drifty, TimeInfo, keeper);
|
| 442 : |
|
|
readWordAndVariable(infile, "lambda", lambda);
|
| 443 : |
|
|
delta = TimeInfo->getTimeStepLength() / TimeInfo->numSubSteps();
|
| 444 : |
|
|
|
| 445 : |
|
|
// Open and read given year and step information
|
| 446 : |
|
|
readWordAndValue(infile, "areadefinition", filename);
|
| 447 : |
|
|
subfile.open(filename, ios::in);
|
| 448 : |
|
|
handle.checkIfFailure(subfile, filename);
|
| 449 : |
|
|
handle.Open(filename);
|
| 450 : |
|
|
this->readAreaData(subcomment, Area, TimeInfo, keeper);
|
| 451 : |
|
|
handle.Close();
|
| 452 : |
|
|
subfile.close();
|
| 453 : |
|
|
subfile.clear();
|
| 454 : |
|
|
|
| 455 : |
|
|
calcMigration.AddRows(oceanareas.Size(), oceanareas.Size(), 0.0);
|
| 456 : |
|
|
if (oceanareas.Size() != areas.Size())
|
| 457 : |
|
|
handle.logMessage(LOGWARN, "Warning in migration - migration data doesnt cover all areas");
|
| 458 : |
|
|
|
| 459 : |
|
|
handle.logMessage(LOGMESSAGE, "Read migration function file - number of migration areas", oceanareas.Size());
|
| 460 : |
|
|
keeper->clearLast();
|
| 461 : |
|
|
}
|
| 462 : |
|
|
|
| 463 : |
|
|
void MigrationFunction::readAreaData(CommentStream& infile, const AreaClass* const Area,
|
| 464 : |
|
|
const TimeClass* const TimeInfo, Keeper* const keeper) {
|
| 465 : |
|
|
|
| 466 : |
|
|
int area, inarea;
|
| 467 : |
|
|
ifstream subfile;
|
| 468 : |
|
|
CommentStream subcomment(subfile);
|
| 469 : |
|
|
char text[MaxStrLength];
|
| 470 : |
|
|
char filename[MaxStrLength];
|
| 471 : |
|
|
char areaname[MaxStrLength];
|
| 472 : |
|
|
strncpy(text, "", MaxStrLength);
|
| 473 : |
|
|
strncpy(filename, "", MaxStrLength);
|
| 474 : |
|
|
strncpy(areaname, "", MaxStrLength);
|
| 475 : |
|
|
|
| 476 : |
|
|
/* File format:
|
| 477 : |
|
|
[area]
|
| 478 : |
|
|
name areaname
|
| 479 : |
|
|
number areanumber
|
| 480 : |
|
|
rectangles filename containing the rectangle information
|
| 481 : |
|
|
[area]
|
| 482 : |
|
|
...
|
| 483 : |
|
|
*/
|
| 484 : |
|
|
|
| 485 : |
|
|
// Read area information from file
|
| 486 : |
|
|
infile >> ws;
|
| 487 : |
|
|
while (!infile.eof() && !infile.fail()) {
|
| 488 : |
|
|
infile >> text >> ws;
|
| 489 : |
|
|
if (strcasecmp(text, "[area]") != 0)
|
| 490 : |
|
|
handle.logFileUnexpected(LOGFAIL, "[area]", text);
|
| 491 : |
|
|
|
| 492 : |
|
|
readWordAndValue(infile, "name", areaname);
|
| 493 : |
|
|
readWordAndVariable(infile, "number", area);
|
| 494 : |
|
|
readWordAndValue(infile, "rectangles", filename);
|
| 495 : |
|
|
|
| 496 : |
|
|
inarea = Area->getInnerArea(area);
|
| 497 : |
|
|
if (!this->isInArea(inarea))
|
| 498 : |
|
|
handle.logMessage(LOGFAIL, "Error in migration - invalid area", area);
|
| 499 : |
|
|
|
| 500 : |
|
|
subfile.open(filename, ios::in);
|
| 501 : |
|
|
handle.checkIfFailure(subfile, filename);
|
| 502 : |
|
|
handle.Open(filename);
|
| 503 : |
|
|
oceanareas.resize(new MigrationArea(subcomment, areaname, inarea));
|
| 504 : |
|
|
handle.Close();
|
| 505 : |
|
|
subfile.close();
|
| 506 : |
|
|
subfile.clear();
|
| 507 : |
|
|
}
|
| 508 : |
|
|
}
|
| 509 : |
|
|
|
| 510 : |
|
|
MigrationFunction::~MigrationFunction() {
|
| 511 : |
|
|
int i;
|
| 512 : |
|
|
for (i = 0; i < oceanareas.Size(); i++)
|
| 513 : |
|
|
delete oceanareas[i];
|
| 514 : |
|
|
}
|
| 515 : |
|
|
|
| 516 : |
|
|
void MigrationFunction::Print(ofstream& outfile) {
|
| 517 : |
|
|
int i, j;
|
| 518 : |
|
|
outfile << "\nMigration\n\n\tMigration matrix\n\t";
|
| 519 : |
|
|
for (i = 0; i < calcMigration.Nrow(); i++) {
|
| 520 : |
|
|
for (j = 0; j < calcMigration.Ncol(i); j++)
|
| 521 : |
|
|
outfile << setw(smallwidth) << calcMigration[i][j] << sep;
|
| 522 : |
|
|
outfile << "\n\t";
|
| 523 : |
|
|
}
|
| 524 : |
|
|
outfile.flush();
|
| 525 : |
|
|
}
|
| 526 : |
|
|
|
| 527 : |
|
|
const DoubleMatrix& MigrationFunction::getMigrationMatrix(const TimeClass* const TimeInfo) {
|
| 528 : |
|
|
if (this->updateVariables(TimeInfo))
|
| 529 : |
|
|
this->recalcMatrix();
|
| 530 : |
|
|
return calcMigration;
|
| 531 : |
|
|
}
|
| 532 : |
|
|
|
| 533 : |
|
|
void MigrationFunction::recalcMatrix() {
|
| 534 : |
|
|
int from, to, idfrom, idto, i, j;
|
| 535 : |
|
|
double mig, sa;
|
| 536 : |
|
|
double colsum, sum;
|
| 537 : |
|
|
|
| 538 : |
|
|
for (from = 0; from < oceanareas.Size(); from++) {
|
| 539 : |
|
|
idfrom = this->areaNum(oceanareas[from]->getAreaID());
|
| 540 : |
|
|
colsum = 0.0;
|
| 541 : |
|
|
for (to = 0; to < oceanareas.Size(); to++) {
|
| 542 : |
|
|
idto = this->areaNum(oceanareas[to]->getAreaID());
|
| 543 : |
|
|
sum = 0.0;
|
| 544 : |
|
|
for (i = 0; i < oceanareas[from]->getNumRectangles(); i++) {
|
| 545 : |
|
|
sa = (oceanareas[from]->getRectangles()[i])->getArea();
|
| 546 : |
|
|
if (!(isZero(sa))) {
|
| 547 : |
|
|
for (j = 0; j < oceanareas[to]->getNumRectangles(); j++) {
|
| 548 : |
|
|
mig = this->getMigrationFunction(oceanareas[from]->getRectangles()[i], oceanareas[to]->getRectangles()[j]);
|
| 549 : |
|
|
sum += (mig * sa);
|
| 550 : |
|
|
}
|
| 551 : |
|
|
}
|
| 552 : |
|
|
}
|
| 553 : |
|
|
|
| 554 : |
|
|
calcMigration[idto][idfrom] = sum / oceanareas[from]->getArea();
|
| 555 : |
|
|
colsum += calcMigration[idto][idfrom];
|
| 556 : |
|
|
}
|
| 557 : |
|
|
|
| 558 : |
|
|
if (isZero(colsum)) {
|
| 559 : |
|
|
handle.logMessage(LOGWARN, "Warning in migration - column sum is zero");
|
| 560 : |
|
|
penalty.resize(1, 1.0);
|
| 561 : |
|
|
calcMigration[idfrom][idfrom] = 1.0;
|
| 562 : |
|
|
|
| 563 : |
|
|
} else if (isEqual(colsum, 1.0)) {
|
| 564 : |
|
|
// everything is OK ...
|
| 565 : |
|
|
|
| 566 : |
|
|
} else {
|
| 567 : |
|
|
handle.logMessage(LOGWARN, "Warning in migration - column sum", colsum);
|
| 568 : |
|
|
penalty.resize(1, colsum);
|
| 569 : |
|
|
colsum = 1.0 / colsum;
|
| 570 : |
|
|
for (i = 0; i < calcMigration.Ncol(); i++)
|
| 571 : |
|
|
calcMigration[i][idfrom] *= colsum;
|
| 572 : |
|
|
}
|
| 573 : |
|
|
}
|
| 574 : |
|
|
}
|
| 575 : |
|
|
|
| 576 : |
|
|
void MigrationFunction::Reset() {
|
| 577 : |
|
|
//JMB need to reset the penalty vector
|
| 578 : |
|
|
penalty.Reset();
|
| 579 : |
|
|
if (handle.getLogLevel() >= LOGMESSAGE)
|
| 580 : |
|
|
handle.logMessage(LOGMESSAGE, "Reset migration data for stock", this->getName());
|
| 581 : |
|
|
}
|
| 582 : |
|
|
|
| 583 : |
|
|
int MigrationFunction::isMigrationStep(const TimeClass* const TimeInfo) {
|
| 584 : |
|
|
return 1;
|
| 585 : |
|
|
}
|
| 586 : |
|
|
|
| 587 : |
|
|
int MigrationFunction::updateVariables(const TimeClass* const TimeInfo) {
|
| 588 : |
|
|
//update the values of the variables that can change
|
| 589 : |
|
|
delta = TimeInfo->getTimeStepLength() / TimeInfo->numSubSteps();
|
| 590 : |
|
|
diffusion.Update(TimeInfo);
|
| 591 : |
|
|
driftx.Update(TimeInfo);
|
| 592 : |
|
|
drifty.Update(TimeInfo);
|
| 593 : |
|
|
|
| 594 : |
|
|
if ((TimeInfo->didStepSizeChange()) || (diffusion.didChange(TimeInfo))
|
| 595 : |
|
|
|| (driftx.didChange(TimeInfo)) || (drifty.didChange(TimeInfo)))
|
| 596 : |
|
|
return 1;
|
| 597 : |
|
|
return 0;
|
| 598 : |
|
|
}
|
| 599 : |
|
|
|
| 600 : |
|
|
double MigrationFunction::getMigrationFunction(Rectangle* fromRec, Rectangle* toRec) {
|
| 601 : |
|
|
double fx, fy;
|
| 602 : |
|
|
double dx, dy;
|
| 603 : |
|
|
double xiL, yiL, xiU, yiU;
|
| 604 : |
|
|
double xfL, yfL, xfU, yfU;
|
| 605 : |
|
|
|
| 606 : |
|
|
if (isZero(diffusion) || isZero(lambda)) // prevent divide by zero errors ...
|
| 607 : |
|
|
return 0.0;
|
| 608 : |
|
|
|
| 609 : |
|
|
xiL = fromRec->getLowerX();
|
| 610 : |
|
|
yiL = fromRec->getLowerY();
|
| 611 : |
|
|
xiU = fromRec->getUpperX();
|
| 612 : |
|
|
yiU = fromRec->getUpperY();
|
| 613 : |
|
|
xfL = toRec->getLowerX();
|
| 614 : |
|
|
yfL = toRec->getLowerY();
|
| 615 : |
|
|
xfU = toRec->getUpperX();
|
| 616 : |
|
|
yfU = toRec->getUpperY();
|
| 617 : |
|
|
|
| 618 : |
|
|
dx = delta * diffusion;
|
| 619 : |
|
|
dy = dx * lambda;
|
| 620 : |
|
|
|
| 621 : |
|
|
// functions from Violeta ...
|
| 622 : |
|
|
fx = -f1x(xfU,xiU,dx,driftx) + f1x(xfU,xiL,dx,driftx) + f1x(xfL,xiU,dx,driftx) - f1x(xfL,xiL,dx,driftx) - f2x(xfU,xiU,dx,driftx) + f2x(xfU,xiL,dx,driftx) + f2x(xfL,xiU,dx,driftx) - f2x(xfL,xiL,dx,driftx);
|
| 623 : |
|
|
|
| 624 : |
|
|
if (fx < verysmall)
|
| 625 : |
|
|
return 0.0;
|
| 626 : |
|
|
|
| 627 : |
|
|
fy = -f1x(yfU,yiU,dy,drifty) + f1x(yfU,yiL,dy,drifty) + f1x(yfL,yiU,dy,drifty) - f1x(yfL,yiL,dy,drifty) - f2x(yfU,yiU,dy,drifty) + f2x(yfU,yiL,dy,drifty) + f2x(yfL,yiU,dy,drifty) - f2x(yfL,yiL,dy,drifty);
|
| 628 : |
|
|
|
| 629 : |
|
|
if (fy < verysmall)
|
| 630 : |
|
|
return 0.0;
|
| 631 : |
|
|
|
| 632 : |
|
|
return (0.5 * fx * fy);
|
| 633 : |
|
|
}
|
| 634 : |
|
|
|
| 635 : |
|
|
double MigrationFunction::f1x(double w, double u, double D, double beta) {
|
| 636 : |
|
|
return ((2/sqrt(pivalue))*sqrt(D)*exp(-(w-(beta*delta)-u)*(w-(beta*delta)-u)/(4*D)));
|
| 637 : |
|
|
}
|
| 638 : |
|
|
|
| 639 : |
|
|
double MigrationFunction::f2x(double w, double u, double D, double beta) {
|
| 640 : |
|
|
return ((w-(beta*delta)-u)*erf((w-(beta*delta)-u)/(2*sqrt(D))));
|
| 641 : |
|
|
}
|
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