| 1 : |
agomez |
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#include "initialcond.h" |
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#include "errorhandler.h" |
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#include "readfunc.h" |
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#include "readword.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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void InitialCond::readNormalConditionData(CommentStream& infile, Keeper* const keeper,
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int numage, int minage, const AreaClass* const Area) {
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int noareas = areas.Size();
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int i, age, area, ageid, areaid, tmparea, keepdata, count, reject;
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char c;
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//Resize the matrices to hold the data
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areaFactor.AddRows(noareas, numage, 0.0);
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ageFactor.AddRows(noareas, numage, 0.0);
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meanLength.AddRows(noareas, numage, 0.0);
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sdevLength.AddRows(noareas, numage, 0.0);
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relCond.AddRows(noareas, numage, 0.0);
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//Find the start of the data in the following format
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//age - area - agedist - areadist - meanlen - standdev - relcond
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infile >> ws;
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if (countColumns(infile) != 7)
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handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 7");
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area = age = ageid = count = reject = 0;
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keeper->addString("meandata");
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| 31 : |
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while (!infile.eof()) {
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| 32 : |
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//crude check to see if something has gone wrong and avoid infinite loops
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if (!(isdigit(infile.peek())))
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handle.logFileMessage(LOGFAIL, "failed to read data from file");
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keepdata = 1;
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infile >> age >> area >> ws;
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//crude age data check - perhaps there should be a better check?
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if ((age < minage) || (age >= (numage + minage)))
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keepdata = 0;
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else
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ageid = age - minage;
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//crude area data check
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areaid = -1;
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tmparea = Area->getInnerArea(area);
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for (i = 0; i < noareas; i++)
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if (areas[i] == tmparea)
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areaid = i;
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if (areaid == -1)
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keepdata = 0;
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if (keepdata == 1) {
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//initial data is required, so store it
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count++;
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infile >> ageFactor[areaid][ageid] >> ws;
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infile >> areaFactor[areaid][ageid] >> ws;
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infile >> meanLength[areaid][ageid] >> ws;
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infile >> sdevLength[areaid][ageid] >> ws;
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infile >> relCond[areaid][ageid] >> ws;
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} else { //initial data not required - skip rest of line
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reject++;
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infile.get(c);
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while (c != '\n' && !infile.eof())
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infile.get(c);
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infile >> ws;
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}
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}
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if (count == 0)
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handle.logMessage(LOGWARN, "Warning in initial conditions - found no data in the data file");
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else if (count < (noareas * numage))
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handle.logMessage(LOGWARN, "Warning in initial conditions - missing entries from data file");
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else if (count > (noareas * numage))
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handle.logMessage(LOGWARN, "Warning in initial conditions - repeated entries in data file");
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if (reject != 0)
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handle.logMessage(LOGMESSAGE, "Discarded invalid initial conditions data - number of invalid entries", reject);
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handle.logMessage(LOGMESSAGE, "Read initial conditions data file - number of entries", count);
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areaFactor.Inform(keeper);
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ageFactor.Inform(keeper);
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meanLength.Inform(keeper);
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sdevLength.Inform(keeper);
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relCond.Inform(keeper);
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| 89 : |
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keeper->clearLast();
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| 90 : |
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}
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| 91 : |
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| 92 : |
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void InitialCond::readNormalParameterData(CommentStream& infile, Keeper* const keeper,
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| 93 : |
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int numage, int minage, const AreaClass* const Area) {
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| 94 : |
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| 95 : |
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int noareas = areas.Size();
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| 96 : |
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int i, age, area, ageid, areaid, tmparea, keepdata, count, reject;
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| 97 : |
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char c;
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| 98 : |
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| 99 : |
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//Resize the matrices to hold the data
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| 100 : |
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areaFactor.AddRows(noareas, numage, 0.0);
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ageFactor.AddRows(noareas, numage, 0.0);
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| 102 : |
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meanLength.AddRows(noareas, numage, 0.0);
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| 103 : |
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sdevLength.AddRows(noareas, numage, 0.0);
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| 104 : |
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alpha.AddRows(noareas, numage, 0.0);
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| 105 : |
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beta.AddRows(noareas, numage, 0.0);
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| 106 : |
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| 107 : |
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//Find the start of the data in the following format
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| 108 : |
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//age - area - agedist - areadist - meanlen - standdev - alpha - beta
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| 109 : |
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infile >> ws;
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| 110 : |
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if (countColumns(infile) != 8)
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| 111 : |
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handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 8");
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| 112 : |
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| 113 : |
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area = age = ageid = count = reject = 0;
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keeper->addString("meandata");
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| 115 : |
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while (!infile.eof()) {
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| 116 : |
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//crude check to see if something has gone wrong and avoid infinite loops
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| 117 : |
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if (!(isdigit(infile.peek())))
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| 118 : |
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handle.logFileMessage(LOGFAIL, "failed to read data from file");
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keepdata = 1;
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| 121 : |
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infile >> age >> area >> ws;
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| 122 : |
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| 123 : |
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//crude age data check - perhaps there should be a better check?
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| 124 : |
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if ((age < minage) || (age >= (numage + minage)))
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| 125 : |
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keepdata = 0;
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| 126 : |
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else
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| 127 : |
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ageid = age - minage;
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| 128 : |
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| 129 : |
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//crude area data check
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areaid = -1;
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| 131 : |
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tmparea = Area->getInnerArea(area);
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| 132 : |
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for (i = 0; i < noareas; i++)
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| 133 : |
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if (areas[i] == tmparea)
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areaid = i;
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| 135 : |
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| 136 : |
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if (areaid == -1)
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| 137 : |
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keepdata = 0;
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| 138 : |
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| 139 : |
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if (keepdata == 1) {
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| 140 : |
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//initial data is required, so store it
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| 141 : |
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count++;
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| 142 : |
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infile >> ageFactor[areaid][ageid] >> ws;
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| 143 : |
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infile >> areaFactor[areaid][ageid] >> ws;
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| 144 : |
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infile >> meanLength[areaid][ageid] >> ws;
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| 145 : |
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infile >> sdevLength[areaid][ageid] >> ws;
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| 146 : |
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infile >> alpha[areaid][ageid] >> ws;
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| 147 : |
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infile >> beta[areaid][ageid] >> ws;
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| 148 : |
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} else { //initial data not required - skip rest of line
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| 150 : |
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reject++;
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infile.get(c);
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while (c != '\n' && !infile.eof())
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| 153 : |
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infile.get(c);
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infile >> ws;
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}
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}
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| 157 : |
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| 158 : |
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if (count == 0)
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| 159 : |
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handle.logMessage(LOGWARN, "Warning in initial conditions - found no data in the data file");
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| 160 : |
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else if (count < (noareas * numage))
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| 161 : |
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handle.logMessage(LOGWARN, "Warning in initial conditions - missing entries from data file");
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| 162 : |
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else if (count > (noareas * numage))
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| 163 : |
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handle.logMessage(LOGWARN, "Warning in initial conditions - repeated entries in data file");
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| 164 : |
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| 165 : |
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if (reject != 0)
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handle.logMessage(LOGMESSAGE, "Discarded invalid initial conditions data - number of invalid entries", reject);
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| 167 : |
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| 168 : |
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handle.logMessage(LOGMESSAGE, "Read initial conditions data file - number of entries", count);
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| 169 : |
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areaFactor.Inform(keeper);
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| 170 : |
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ageFactor.Inform(keeper);
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| 171 : |
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meanLength.Inform(keeper);
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| 172 : |
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sdevLength.Inform(keeper);
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alpha.Inform(keeper);
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beta.Inform(keeper);
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keeper->clearLast();
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}
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| 177 : |
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| 178 : |
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void InitialCond::readNumberData(CommentStream& infile, Keeper* const keeper,
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| 179 : |
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int numage, int minage, const AreaClass* const Area) {
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| 180 : |
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| 181 : |
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int i, age, area, tmparea, count, reject;
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| 182 : |
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int keepdata, areaid, lengthid;
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double length;
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| 184 : |
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char c;
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int noareas = areas.Size();
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| 186 : |
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int numlen = LgrpDiv->numLengthGroups();
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| 187 : |
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//initialise things
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for (areaid = 0; areaid < noareas; areaid++) {
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| 190 : |
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initialNumber.resize(new FormulaMatrix(numage, numlen, 0.0));
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initialPop[areaid].setToZero();
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}
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| 193 : |
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| 194 : |
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//Find the start of the data in the following format
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| 195 : |
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//area - age - meanlength - number - weight
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| 196 : |
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infile >> ws;
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| 197 : |
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if (countColumns(infile) != 5)
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| 198 : |
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handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 5");
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| 199 : |
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| 200 : |
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area = age = count = reject = 0;
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keeper->addString("numberdata");
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| 202 : |
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while (!infile.eof()) {
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| 203 : |
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//crude check to see if something has gone wrong and avoid infinite loops
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| 204 : |
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if (!(isdigit(infile.peek())))
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| 205 : |
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handle.logFileMessage(LOGFAIL, "failed to read data from file");
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| 206 : |
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| 207 : |
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keepdata = 1;
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| 208 : |
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infile >> area >> age >> length >> ws;
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| 209 : |
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| 210 : |
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//crude area data check
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| 211 : |
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areaid = -1;
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| 212 : |
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tmparea = Area->getInnerArea(area);
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| 213 : |
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for (i = 0; i < noareas; i++)
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| 214 : |
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if (areas[i] == tmparea)
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| 215 : |
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areaid = i;
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| 216 : |
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| 217 : |
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if (areaid == -1)
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| 218 : |
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keepdata = 0;
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| 219 : |
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| 220 : |
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//crude age data check - perhaps there should be a better check?
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| 221 : |
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if ((age < minage) || (age >= (numage + minage)))
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| 222 : |
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keepdata = 0;
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| 223 : |
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| 224 : |
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//crude length data check
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| 225 : |
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lengthid = -1;
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| 226 : |
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for (i = 0; i < numlen; i++)
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| 227 : |
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if (isEqual(length, LgrpDiv->minLength(i)))
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| 228 : |
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lengthid = i;
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| 229 : |
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| 230 : |
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//OK the length doesnt match a minimum length so find the length group it is in
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| 231 : |
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if ((lengthid == -1) && (length > LgrpDiv->minLength()) && (length < LgrpDiv->maxLength())) {
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| 232 : |
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for (i = 1; i < numlen; i++) {
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| 233 : |
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if (length < LgrpDiv->minLength(i)) {
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| 234 : |
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lengthid = i - 1;
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| 235 : |
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break;
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| 236 : |
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}
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| 237 : |
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}
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| 238 : |
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if (lengthid == -1)
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| 239 : |
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lengthid = numlen - 1; //then this must be the last length group
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| 240 : |
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}
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| 241 : |
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| 242 : |
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if (lengthid == -1)
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| 243 : |
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keepdata = 0;
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| 244 : |
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| 245 : |
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if (keepdata == 1) {
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| 246 : |
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//initial data is required, so store it
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| 247 : |
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infile >> (*initialNumber[areaid])[age - minage][lengthid] >> ws;
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| 248 : |
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infile >> initialPop[areaid][age][lengthid].W >> ws;
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| 249 : |
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count++;
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| 250 : |
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| 251 : |
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} else { //initial data not required - skip rest of line
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| 252 : |
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reject++;
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| 253 : |
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infile.get(c);
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| 254 : |
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while (c != '\n' && !infile.eof())
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| 255 : |
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infile.get(c);
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| 256 : |
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infile >> ws;
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| 257 : |
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}
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| 258 : |
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}
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| 259 : |
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| 260 : |
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for (i = 0; i < initialNumber.Size(); i++)
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| 261 : |
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(*initialNumber[i]).Inform(keeper);
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| 262 : |
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| 263 : |
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if (count == 0)
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| 264 : |
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handle.logMessage(LOGWARN, "Warning in initial conditions - found no data in the data file");
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| 265 : |
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else if (count < (noareas * numage * numlen))
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| 266 : |
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handle.logMessage(LOGWARN, "Warning in initial conditions - missing entries from data file");
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| 267 : |
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else if (count > (noareas * numage * numlen))
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| 268 : |
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handle.logMessage(LOGWARN, "Warning in initial conditions - repeated entries in data file");
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| 269 : |
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| 270 : |
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if (reject != 0)
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| 271 : |
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handle.logMessage(LOGMESSAGE, "Discarded invalid initial conditions data - number of invalid entries", reject);
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| 272 : |
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| 273 : |
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handle.logMessage(LOGMESSAGE, "Read initial conditions data file - number of entries", count);
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| 274 : |
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keeper->clearLast();
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| 275 : |
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}
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| 276 : |
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| 277 : |
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InitialCond::InitialCond(CommentStream& infile, const IntVector& Areas,
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| 278 : |
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Keeper* const keeper, const char* refWeightFile,
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| 279 : |
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const char* givenname, const AreaClass* const Area, double DL)
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| 280 : |
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: HasName(givenname), LivesOnAreas(Areas), LgrpDiv(0), CI(0) {
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| 281 : |
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| 282 : |
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ifstream subfile;
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| 283 : |
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CommentStream subcomment(subfile);
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| 284 : |
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char text[MaxStrLength];
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| 285 : |
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strncpy(text, "", MaxStrLength);
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| 286 : |
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| 287 : |
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int i, j, k;
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| 288 : |
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int minage, maxage;
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| 289 : |
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char c;
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| 290 : |
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double minlength, maxlength, dl;
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| 291 : |
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| 292 : |
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keeper->addString("initialcond");
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| 293 : |
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| 294 : |
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infile >> ws;
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| 295 : |
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c = infile.peek();
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| 296 : |
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if ((c == 'n') || (c == 'N'))
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| 297 : |
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infile >> text >> ws; //read in the word 'numbers' if it exists
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| 298 : |
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| 299 : |
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readWordAndVariable(infile, "minage", minage);
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| 300 : |
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readWordAndVariable(infile, "maxage", maxage);
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| 301 : |
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readWordAndVariable(infile, "minlength", minlength);
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| 302 : |
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readWordAndVariable(infile, "maxlength", maxlength);
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| 303 : |
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int numage = maxage - minage + 1;
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| 304 : |
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| 305 : |
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//JMB - changed to make the reading of dl optional
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| 306 : |
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//if it isnt specifed here, it will default to the dl value of the stock
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| 307 : |
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infile >> ws;
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| 308 : |
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c = infile.peek();
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| 309 : |
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if ((c == 'd') || (c == 'D'))
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| 310 : |
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readWordAndVariable(infile, "dl", dl);
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| 311 : |
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else
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| 312 : |
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dl = DL;
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| 313 : |
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| 314 : |
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LgrpDiv = new LengthGroupDivision(minlength, maxlength, dl);
|
| 315 : |
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if (LgrpDiv->Error())
|
| 316 : |
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handle.logMessage(LOGFAIL, "Error in initial conditions - failed to create length group");
|
| 317 : |
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| 318 : |
|
|
//read the standard deviation multiplier - default to 1.0
|
| 319 : |
|
|
keeper->addString("sdevmultiplier");
|
| 320 : |
|
|
infile >> ws;
|
| 321 : |
|
|
c = infile.peek();
|
| 322 : |
|
|
if ((c == 's') || (c == 'S'))
|
| 323 : |
|
|
readWordAndVariable(infile, "sdev", sdevMult);
|
| 324 : |
|
|
else
|
| 325 : |
|
|
sdevMult.setValue(1.0);
|
| 326 : |
|
|
sdevMult.Inform(keeper);
|
| 327 : |
|
|
keeper->clearLast();
|
| 328 : |
|
|
|
| 329 : |
|
|
//create the initialPop object of the correct size
|
| 330 : |
|
|
PopInfo tmppop;
|
| 331 : |
|
|
tmppop.N = 1.0;
|
| 332 : |
|
|
PopInfoMatrix popmatrix(numage, LgrpDiv->numLengthGroups(), tmppop);
|
| 333 : |
|
|
initialPop.resize(areas.Size(), minage, 0, popmatrix);
|
| 334 : |
|
|
|
| 335 : |
|
|
infile >> text >> ws;
|
| 336 : |
|
|
if ((strcasecmp(text, "initstockfile") == 0) || (strcasecmp(text, "normalcondfile") == 0)) {
|
| 337 : |
|
|
//read initial data in mean length format, using the reference weight file
|
| 338 : |
|
|
readoption = 0;
|
| 339 : |
|
|
infile >> text >> ws;
|
| 340 : |
|
|
subfile.open(text, ios::in);
|
| 341 : |
|
|
handle.checkIfFailure(subfile, text);
|
| 342 : |
|
|
handle.Open(text);
|
| 343 : |
|
|
this->readNormalConditionData(subcomment, keeper, numage, minage, Area);
|
| 344 : |
|
|
handle.Close();
|
| 345 : |
|
|
subfile.close();
|
| 346 : |
|
|
subfile.clear();
|
| 347 : |
|
|
|
| 348 : |
|
|
//read information on reference weights.
|
| 349 : |
|
|
DoubleMatrix tmpRefW;
|
| 350 : |
|
|
keeper->addString("referenceweights");
|
| 351 : |
|
|
subfile.open(refWeightFile, ios::in);
|
| 352 : |
|
|
handle.checkIfFailure(subfile, refWeightFile);
|
| 353 : |
|
|
handle.Open(refWeightFile);
|
| 354 : |
|
|
readRefWeights(subcomment, tmpRefW);
|
| 355 : |
|
|
handle.Close();
|
| 356 : |
|
|
subfile.close();
|
| 357 : |
|
|
subfile.clear();
|
| 358 : |
|
|
|
| 359 : |
|
|
//Interpolate the reference weights. First there are some error checks.
|
| 360 : |
|
|
if (LgrpDiv->meanLength(0) < tmpRefW[0][0] ||
|
| 361 : |
|
|
LgrpDiv->meanLength(LgrpDiv->numLengthGroups() - 1) > tmpRefW[tmpRefW.Nrow() - 1][0])
|
| 362 : |
|
|
handle.logFileMessage(LOGFAIL, "lengths for reference weights must span the range of initial condition lengths");
|
| 363 : |
|
|
|
| 364 : |
|
|
//Aggregate the reference weight data to be the same format
|
| 365 : |
|
|
double ratio, tmplen;
|
| 366 : |
|
|
refWeight.resize(LgrpDiv->numLengthGroups(), 0.0);
|
| 367 : |
|
|
int pos = 0;
|
| 368 : |
|
|
for (j = 0; j < LgrpDiv->numLengthGroups(); j++) {
|
| 369 : |
|
|
tmplen = LgrpDiv->meanLength(j);
|
| 370 : |
|
|
for (i = pos; i < tmpRefW.Nrow() - 1; i++) {
|
| 371 : |
|
|
if (((tmplen > tmpRefW[i][0]) || (isEqual(tmplen, tmpRefW[i][0]))) &&
|
| 372 : |
|
|
((tmplen < tmpRefW[i + 1][0]) || (isEqual(tmplen, tmpRefW[i + 1][0])))) {
|
| 373 : |
|
|
|
| 374 : |
|
|
ratio = (tmplen - tmpRefW[i][0]) / (tmpRefW[i + 1][0] - tmpRefW[i][0]);
|
| 375 : |
|
|
refWeight[j] = tmpRefW[i][1] + ratio * (tmpRefW[i + 1][1] - tmpRefW[i][1]);
|
| 376 : |
|
|
pos = i;
|
| 377 : |
|
|
}
|
| 378 : |
|
|
}
|
| 379 : |
|
|
}
|
| 380 : |
|
|
keeper->clearLast();
|
| 381 : |
|
|
|
| 382 : |
|
|
} else if ((strcasecmp(text, "normalparamfile") == 0)) {
|
| 383 : |
|
|
//read initial data in mean length format, using a length weight relationship
|
| 384 : |
|
|
readoption = 1;
|
| 385 : |
|
|
infile >> text >> ws;
|
| 386 : |
|
|
subfile.open(text, ios::in);
|
| 387 : |
|
|
handle.checkIfFailure(subfile, text);
|
| 388 : |
|
|
handle.Open(text);
|
| 389 : |
|
|
this->readNormalParameterData(subcomment, keeper, numage, minage, Area);
|
| 390 : |
|
|
handle.Close();
|
| 391 : |
|
|
subfile.close();
|
| 392 : |
|
|
subfile.clear();
|
| 393 : |
|
|
|
| 394 : |
|
|
} else if ((strcasecmp(text, "numberfile") == 0)) {
|
| 395 : |
|
|
//read initial data in number format
|
| 396 : |
|
|
readoption = 2;
|
| 397 : |
|
|
infile >> text >> ws;
|
| 398 : |
|
|
subfile.open(text, ios::in);
|
| 399 : |
|
|
handle.checkIfFailure(subfile, text);
|
| 400 : |
|
|
handle.Open(text);
|
| 401 : |
|
|
this->readNumberData(subcomment, keeper, numage, minage, Area);
|
| 402 : |
|
|
handle.Close();
|
| 403 : |
|
|
subfile.close();
|
| 404 : |
|
|
subfile.clear();
|
| 405 : |
|
|
|
| 406 : |
|
|
} else
|
| 407 : |
|
|
handle.logFileMessage(LOGFAIL, "unrecognised initial conditions format", text);
|
| 408 : |
|
|
|
| 409 : |
|
|
keeper->clearLast();
|
| 410 : |
|
|
}
|
| 411 : |
|
|
|
| 412 : |
|
|
InitialCond::~InitialCond() {
|
| 413 : |
|
|
int i;
|
| 414 : |
|
|
delete LgrpDiv;
|
| 415 : |
|
|
delete CI;
|
| 416 : |
|
|
for (i = 0; i < initialNumber.Size(); i++)
|
| 417 : |
|
|
delete initialNumber[i];
|
| 418 : |
|
|
}
|
| 419 : |
|
|
|
| 420 : |
|
|
void InitialCond::setCI(const LengthGroupDivision* const GivenLDiv) {
|
| 421 : |
|
|
if (!checkLengthGroupStructure(GivenLDiv, LgrpDiv))
|
| 422 : |
|
|
handle.logMessage(LOGFAIL, "Error in initial conditions - invalid length group structure for stock", this->getName());
|
| 423 : |
|
|
//check minimum and maximum lengths
|
| 424 : |
|
|
if (LgrpDiv->minLength() < GivenLDiv->minLength())
|
| 425 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - minimum length less than stock length for stock", this->getName());
|
| 426 : |
|
|
if (LgrpDiv->maxLength() > GivenLDiv->maxLength())
|
| 427 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - maximum length greater than stock length for stock"), this->getName();
|
| 428 : |
|
|
CI = new ConversionIndex(LgrpDiv, GivenLDiv);
|
| 429 : |
|
|
if (CI->Error())
|
| 430 : |
|
|
handle.logMessage(LOGFAIL, "Error in initial conditions - error when checking length structure for stock", this->getName());
|
| 431 : |
|
|
}
|
| 432 : |
|
|
|
| 433 : |
|
|
void InitialCond::Print(ofstream& outfile) const {
|
| 434 : |
|
|
int i, j;
|
| 435 : |
|
|
|
| 436 : |
|
|
outfile << "\nInitial conditions\n";
|
| 437 : |
|
|
for (i = 0; i < areas.Size(); i++) {
|
| 438 : |
|
|
outfile << "\tInternal area " << areas[i] << endl;
|
| 439 : |
|
|
initialPop[i].printNumbers(outfile);
|
| 440 : |
|
|
}
|
| 441 : |
|
|
|
| 442 : |
|
|
if ((readoption == 0) || (readoption == 1)) {
|
| 443 : |
|
|
//JMB print the multipliers that are used to scale the population
|
| 444 : |
|
|
outfile << "\tArea multipliers used to scale the population\n";
|
| 445 : |
|
|
for (i = 0; i < areaFactor.Nrow(); i++) {
|
| 446 : |
|
|
for (j = 0; j < areaFactor.Ncol(i); j++)
|
| 447 : |
|
|
outfile << TAB << areaFactor[i][j];
|
| 448 : |
|
|
outfile << endl;
|
| 449 : |
|
|
}
|
| 450 : |
|
|
outfile << "\tAge multipliers used to scale the population\n";
|
| 451 : |
|
|
for (i = 0; i < ageFactor.Nrow(); i++) {
|
| 452 : |
|
|
for (j = 0; j < ageFactor.Ncol(i); j++)
|
| 453 : |
|
|
outfile << TAB << ageFactor[i][j];
|
| 454 : |
|
|
outfile << endl;
|
| 455 : |
|
|
}
|
| 456 : |
|
|
}
|
| 457 : |
|
|
|
| 458 : |
|
|
outfile << endl;
|
| 459 : |
|
|
outfile.flush();
|
| 460 : |
|
|
}
|
| 461 : |
|
|
|
| 462 : |
|
|
void InitialCond::Initialise(AgeBandMatrixPtrVector& Alkeys) {
|
| 463 : |
|
|
|
| 464 : |
|
|
int area, age, l;
|
| 465 : |
|
|
int minage, maxage;
|
| 466 : |
|
|
double mult, scaler, dnorm;
|
| 467 : |
|
|
|
| 468 : |
|
|
if (readoption == 0) {
|
| 469 : |
|
|
if (isZero(sdevMult)) //JMB this should never happen ...
|
| 470 : |
|
|
handle.logMessage(LOGFAIL, "Error in initial conditions - multiplier for standard deviation is zero");
|
| 471 : |
|
|
|
| 472 : |
|
|
for (area = 0; area < areas.Size(); area++) {
|
| 473 : |
|
|
minage = initialPop[area].minAge();
|
| 474 : |
|
|
maxage = initialPop[area].maxAge();
|
| 475 : |
|
|
for (age = minage; age <= maxage; age++) {
|
| 476 : |
|
|
|
| 477 : |
|
|
//JMB check that the length data is valid
|
| 478 : |
|
|
if (isZero(meanLength[area][age - minage]) || sdevLength[area][age - minage] < 0.04) {
|
| 479 : |
|
|
//JMB the limit has been set at 0.04 to keep the exponential calculation sane
|
| 480 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - invalid length data for stock", this->getName());
|
| 481 : |
|
|
|
| 482 : |
|
|
//JMB set the population to zero
|
| 483 : |
|
|
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++)
|
| 484 : |
|
|
initialPop[area][age][l].setToZero();
|
| 485 : |
|
|
|
| 486 : |
|
|
} else {
|
| 487 : |
|
|
//JMB check that the mean length is within the length group range
|
| 488 : |
|
|
if (meanLength[area][age - minage] < LgrpDiv->minLength())
|
| 489 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - mean length is less than minimum length for stock", this->getName());
|
| 490 : |
|
|
if (meanLength[area][age - minage] > LgrpDiv->maxLength())
|
| 491 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - mean length is greater than maximum length for stock", this->getName());
|
| 492 : |
|
|
|
| 493 : |
|
|
scaler = 0.0;
|
| 494 : |
|
|
mult = 1.0 / (sdevLength[area][age - minage] * sdevMult);
|
| 495 : |
|
|
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++) {
|
| 496 : |
|
|
dnorm = (LgrpDiv->meanLength(l) - meanLength[area][age - minage]) * mult;
|
| 497 : |
|
|
initialPop[area][age][l].N = exp(-(dnorm * dnorm) * 0.5);
|
| 498 : |
|
|
scaler += initialPop[area][age][l].N;
|
| 499 : |
|
|
}
|
| 500 : |
|
|
|
| 501 : |
|
|
if (isZero(scaler)) {
|
| 502 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial population - calculated zero population");
|
| 503 : |
|
|
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++)
|
| 504 : |
|
|
initialPop[area][age][l].setToZero();
|
| 505 : |
|
|
|
| 506 : |
|
|
} else {
|
| 507 : |
|
|
scaler = 10000.0 / scaler;
|
| 508 : |
|
|
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++) {
|
| 509 : |
|
|
initialPop[area][age][l].N *= scaler;
|
| 510 : |
|
|
initialPop[area][age][l].W = refWeight[l] * relCond[area][age - minage];
|
| 511 : |
|
|
if ((handle.getLogLevel() >= LOGWARN) && (isZero(initialPop[area][age][l].W)) && (initialPop[area][age][l].N > 0.0))
|
| 512 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - zero mean weight for stock", this->getName());
|
| 513 : |
|
|
}
|
| 514 : |
|
|
}
|
| 515 : |
|
|
}
|
| 516 : |
|
|
}
|
| 517 : |
|
|
}
|
| 518 : |
|
|
|
| 519 : |
|
|
} else if (readoption == 1) {
|
| 520 : |
|
|
if (isZero(sdevMult)) //JMB this should never happen ...
|
| 521 : |
|
|
handle.logMessage(LOGFAIL, "Error in initial conditions - multiplier for standard deviation is zero for stock", this->getName());
|
| 522 : |
|
|
|
| 523 : |
|
|
for (area = 0; area < areas.Size(); area++) {
|
| 524 : |
|
|
minage = initialPop[area].minAge();
|
| 525 : |
|
|
maxage = initialPop[area].maxAge();
|
| 526 : |
|
|
for (age = minage; age <= maxage; age++) {
|
| 527 : |
|
|
|
| 528 : |
|
|
//JMB check that the length data is valid
|
| 529 : |
|
|
if (isZero(meanLength[area][age - minage]) || sdevLength[area][age - minage] < 0.04) {
|
| 530 : |
|
|
//JMB the limit has been set at 0.04 to keep the exponential calculation sane
|
| 531 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - invalid length data");
|
| 532 : |
|
|
|
| 533 : |
|
|
//JMB set the population to zero
|
| 534 : |
|
|
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++)
|
| 535 : |
|
|
initialPop[area][age][l].setToZero();
|
| 536 : |
|
|
|
| 537 : |
|
|
} else {
|
| 538 : |
|
|
//JMB check that the mean length is within the length group range
|
| 539 : |
|
|
if (meanLength[area][age - minage] < LgrpDiv->minLength())
|
| 540 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - mean length is less than minimum length for stock", this->getName());
|
| 541 : |
|
|
if (meanLength[area][age - minage] > LgrpDiv->maxLength())
|
| 542 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - mean length is greater than maximum length for stock", this->getName());
|
| 543 : |
|
|
|
| 544 : |
|
|
scaler = 0.0;
|
| 545 : |
|
|
mult = 1.0 / (sdevLength[area][age - minage] * sdevMult);
|
| 546 : |
|
|
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++) {
|
| 547 : |
|
|
dnorm = (LgrpDiv->meanLength(l) - meanLength[area][age - minage]) * mult;
|
| 548 : |
|
|
initialPop[area][age][l].N = exp(-(dnorm * dnorm) * 0.5);
|
| 549 : |
|
|
scaler += initialPop[area][age][l].N;
|
| 550 : |
|
|
}
|
| 551 : |
|
|
|
| 552 : |
|
|
if (isZero(scaler)) {
|
| 553 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial population - calculated zero population for stock", this->getName());
|
| 554 : |
|
|
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++)
|
| 555 : |
|
|
initialPop[area][age][l].setToZero();
|
| 556 : |
|
|
|
| 557 : |
|
|
} else {
|
| 558 : |
|
|
scaler = 10000.0 / scaler;
|
| 559 : |
|
|
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++) {
|
| 560 : |
|
|
initialPop[area][age][l].N *= scaler;
|
| 561 : |
|
|
initialPop[area][age][l].W = alpha[area][age - minage] * pow(LgrpDiv->meanLength(l), beta[area][age - minage]);
|
| 562 : |
|
|
if ((handle.getLogLevel() >= LOGWARN) && (isZero(initialPop[area][age][l].W)) && (initialPop[area][age][l].N > 0.0))
|
| 563 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - zero mean weight for stock", this->getName());
|
| 564 : |
|
|
}
|
| 565 : |
|
|
}
|
| 566 : |
|
|
}
|
| 567 : |
|
|
}
|
| 568 : |
|
|
}
|
| 569 : |
|
|
|
| 570 : |
|
|
} else if (readoption == 2) {
|
| 571 : |
|
|
for (area = 0; area < areas.Size(); area++) {
|
| 572 : |
|
|
minage = initialPop[area].minAge();
|
| 573 : |
|
|
maxage = initialPop[area].maxAge();
|
| 574 : |
|
|
for (age = minage; age <= maxage; age++) {
|
| 575 : |
|
|
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++) {
|
| 576 : |
|
|
initialPop[area][age][l].N = (*initialNumber[area])[age - minage][l];
|
| 577 : |
|
|
if (handle.getLogLevel() >= LOGWARN) {
|
| 578 : |
|
|
if (initialPop[area][age][l].N < 0.0)
|
| 579 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - negative initial population for stock", this->getName());
|
| 580 : |
|
|
if ((isZero(initialPop[area][age][l].W)) && (initialPop[area][age][l].N > 0.0))
|
| 581 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - zero mean weight for stock", this->getName());
|
| 582 : |
|
|
}
|
| 583 : |
|
|
}
|
| 584 : |
|
|
}
|
| 585 : |
|
|
}
|
| 586 : |
|
|
|
| 587 : |
|
|
} else
|
| 588 : |
|
|
handle.logMessage(LOGFAIL, "Error in initial conditions - unrecognised data format");
|
| 589 : |
|
|
|
| 590 : |
|
|
mult = 1.0;
|
| 591 : |
|
|
for (area = 0; area < areas.Size(); area++) {
|
| 592 : |
|
|
Alkeys[area].setToZero();
|
| 593 : |
|
|
//check minimum and maximum ages
|
| 594 : |
|
|
if (handle.getLogLevel() >= LOGWARN) {
|
| 595 : |
|
|
if (initialPop[area].minAge() < Alkeys[area].minAge())
|
| 596 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - minimum age less than stock age for stock", this->getName());
|
| 597 : |
|
|
if (initialPop[area].maxAge() > Alkeys[area].maxAge())
|
| 598 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - maximum age greater than stock age for stock", this->getName());
|
| 599 : |
|
|
}
|
| 600 : |
|
|
|
| 601 : |
|
|
minage = max(Alkeys[area].minAge(), initialPop[area].minAge());
|
| 602 : |
|
|
maxage = min(Alkeys[area].maxAge(), initialPop[area].maxAge());
|
| 603 : |
|
|
if (maxage < minage)
|
| 604 : |
|
|
handle.logMessage(LOGFAIL, "Error in initial conditions - maximum age less than minimum age for stock", this->getName());
|
| 605 : |
|
|
|
| 606 : |
|
|
for (age = minage; age <= maxage; age++) {
|
| 607 : |
|
|
if ((readoption == 0) || (readoption == 1))
|
| 608 : |
|
|
mult = areaFactor[area][age - minage] * ageFactor[area][age - minage];
|
| 609 : |
|
|
|
| 610 : |
|
|
if (mult < 0.0) {
|
| 611 : |
|
|
handle.logMessage(LOGWARN, "Warning in initial conditions - negative stock multiplier", mult);
|
| 612 : |
|
|
mult = -mult;
|
| 613 : |
|
|
}
|
| 614 : |
|
|
|
| 615 : |
|
|
Alkeys[area][age].Add(initialPop[area][age], *CI, mult);
|
| 616 : |
|
|
}
|
| 617 : |
|
|
}
|
| 618 : |
|
|
|
| 619 : |
|
|
if (handle.getLogLevel() >= LOGMESSAGE)
|
| 620 : |
|
|
handle.logMessage(LOGMESSAGE, "Calculated initial condition data for stock", this->getName());
|
| 621 : |
|
|
}
|
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