Annotation of /trunk/gadget/naturalm.cc

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1 :	agomez	1	#include "naturalm.h"
2 :			#include "readfunc.h"
3 :			#include "areatime.h"
4 :			#include "readword.h"
5 :			#include "keeper.h"
6 :			#include "errorhandler.h"
7 :			#include "gadget.h"
8 :			#include "global.h"
9 :
10 :			NaturalMortality::NaturalMortality(CommentStream& infile, int minage, int numage,
11 :			const char* givenname, const IntVector& Areas, const TimeClass* const TimeInfo,
12 :			Keeper* const keeper) : HasName(givenname), LivesOnAreas(Areas) {
13 :
14 :			minStockAge = minage;
15 :			readoption = 0;
16 :			proportion.AddRows(areas.Size(), numage, 0.0);
17 :			keeper->addString("naturalmortality");
18 :
19 :			infile >> ws;
20 :			char c = infile.peek();
21 :			if ((c == 'm') || (c == 'M')) {
22 :			//JMB experimental mortality function
23 :			readoption = 1;
24 :			char text[MaxStrLength];
25 :			strncpy(text, "", MaxStrLength);
26 :			readWordAndValue(infile, "mortalityfunction", text);
27 :			if (strcasecmp(text, "constant") == 0)
28 :			fnMortality = new ConstSelectFunc();
29 :			else if (strcasecmp(text, "straightline") == 0)
30 :			fnMortality = new StraightSelectFunc();
31 :			else if (strcasecmp(text, "exponential") == 0)
32 :			fnMortality = new ExpSelectFunc();
33 :			else
34 :			handle.logFileMessage(LOGFAIL, "unrecognised mortality function", text);
35 :			fnMortality->readConstants(infile, TimeInfo, keeper);
36 :
37 :			} else {
38 :			mortality.setsize(numage);
39 :			mortality.read(infile, TimeInfo, keeper);
40 :			}
41 :
42 :			keeper->clearLast();
43 :			}
44 :
45 :			NaturalMortality::~NaturalMortality() {
46 :			if (readoption == 1)
47 :			delete fnMortality;
48 :			}
49 :
50 :			void NaturalMortality::Reset(const TimeClass* const TimeInfo) {
51 :			if (readoption == 0) {
52 :			mortality.Update(TimeInfo);
53 :			if (mortality.didChange(TimeInfo) || TimeInfo->didStepSizeChange()) {
54 :			int i, j;
55 :			for (i = 0; i < proportion.Nrow(); i++) {
56 :			for (j = 0; j < proportion.Ncol(i); j++) {
57 :			if (mortality[j] > verysmall)
58 :			proportion[i][j] = exp(-mortality[j] * TimeInfo->getTimeStepSize());
59 :			else
60 :			proportion[i][j] = 1.0; //use mortality rate 0
61 :			}
62 :			}
63 :
64 :			if (handle.getLogLevel() >= LOGMESSAGE)
65 :			handle.logMessage(LOGMESSAGE, "Reset natural mortality data for stock", this->getName());
66 :			}
67 :
68 :			} else if (readoption == 1) {
69 :			//JMB experimental mortality function
70 :			fnMortality->updateConstants(TimeInfo);
71 :			if (fnMortality->didChange(TimeInfo) || TimeInfo->didStepSizeChange()) {
72 :			int i, j;
73 :			double m;
74 :			for (i = 0; i < proportion.Nrow(); i++) {
75 :			for (j = 0; j < proportion.Ncol(i); j++) {
76 :			m = fnMortality->calculate(double(minStockAge + j));
77 :			if (m > verysmall)
78 :			proportion[i][j] = exp(-m * TimeInfo->getTimeStepSize());
79 :			else
80 :			proportion[i][j] = 1.0; //use mortality rate 0
81 :			}
82 :			}
83 :
84 :			if (handle.getLogLevel() >= LOGMESSAGE)
85 :			handle.logMessage(LOGMESSAGE, "Reset natural mortality data for stock", this->getName());
86 :			}
87 :
88 :			} else
89 :			handle.logMessage(LOGFAIL, "Error in natural mortality - unrecognised mortality function", readoption);
90 :			}
91 :
92 :			void NaturalMortality::Print(ofstream& outfile) {
93 :			int i;
94 :			outfile << "Natural mortality\n\t";
95 :			if (readoption == 0) {
96 :			for (i = 0; i < mortality.Size(); i++)
97 :			outfile << mortality[i] << sep;
98 :			outfile << endl;
99 :
100 :			} else if (readoption == 1) {
101 :			double m;
102 :			for (i = 0; i < proportion.Ncol(); i++) {
103 :			m = fnMortality->calculate(double(minStockAge + i));
104 :			outfile << m << sep;
105 :			}
106 :			outfile << endl;
107 :
108 :			} else
109 :			handle.logMessage(LOGFAIL, "Error in natural mortality - unrecognised mortality function", readoption);
110 :			}

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