Annotation of /trunk/gadget/initialcond.h

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1 :	agomez	1	#ifndef initialcond_h
2 :			#define initialcond_h
3 :
4 :			#include "formulamatrixptrvector.h"
5 :			#include "areatime.h"
6 :			#include "conversionindex.h"
7 :			#include "commentstream.h"
8 :			#include "agebandmatrixptrvector.h"
9 :			#include "livesonareas.h"
10 :			#include "keeper.h"
11 :
12 :			/**
13 :			* \class InitialCond
14 :			* \brief This is the class used to calculate the initial population of a stock
15 :			*
16 :			* This class calculates the initial population for a model run. There are 2 ways to do this - either by specifying a normal distribution or by specifying the actual population to be used.
17 :			*
18 :			* For the normal distribution, Gadget will calculate a length distribution for a population of 10,000 fish for each age group, which will then be multiplied by age and area factors to give the initial population.
19 :			*
20 :			* For the numbers, Gadget will read a list of the population in each age-length cell for each area.
21 :			*
22 :			* The initial weight for each age-length cell will be set to the reference weight, multiplied by a conditioning factor.
23 :			*/
24 :			class InitialCond : public HasName, protected LivesOnAreas {
25 :			public:
26 :			/**
27 :			* \brief This is the InitialCond constructor
28 :			* \param infile is the CommentStream to read the initial conditions data from
29 :			* \param areas is the IntVector of areas that the initial population will be calculated on
30 :			* \param keeper is the Keeper for the current model
31 :			* \param refWeightFile is the name of the reference weight file
32 :			* \param givenname is the name of the stock for this InitialCond class
33 :			* \param Area is the AreaClass for the current model
34 :			* \param DL is the step length of the length groups of the stock
35 :			*/
36 :			InitialCond(CommentStream& infile, const IntVector& areas, Keeper* const keeper,
37 :			const char* refWeightFile, const char* givenname, const AreaClass* const Area, double DL);
38 :			/**
39 :			* \brief This is the default InitialCond destructor
40 :			*/
41 :			~InitialCond();
42 :			/**
43 :			* \brief This function will set the initial population of the stock to that specified in the initial conditions file
44 :			* \param Alkeys is the AgeBandMatrixPtrVector that will contain the initial population of the stock
45 :			*/
46 :			void Initialise(AgeBandMatrixPtrVector& Alkeys);
47 :			/**
48 :			* \brief This will set the ConversionIndex required for to calculate the initial conditions
49 :			* \param GivenLDiv is the LengthGroupDivision for the stock
50 :			*/
51 :			void setCI(const LengthGroupDivision* const GivenLDiv);
52 :			/**
53 :			* \brief This function will print the initial population
54 :			* \param outfile is the ofstream that all the model information gets sent to
55 :			*/
56 :			void Print(ofstream& outfile) const;
57 :			protected:
58 :			/**
59 :			* \brief This is the function used to read the normal distribution and condition factor for the initial condtion data
60 :			* \param infile is the CommentStream to read the initial conditions data from
61 :			* \param keeper is the Keeper for the current model
62 :			* \param numage is the number of age groups for the initial population
63 :			* \param minage is the minimum age for the initial population
64 :			* \param Area is the AreaClass for the current model
65 :			*/
66 :			void readNormalConditionData(CommentStream& infile, Keeper* const keeper,
67 :			int numage, int minage, const AreaClass* const Area);
68 :			/**
69 :			* \brief This is the function used to read the normal distribution for the initial condtion data
70 :			* \param infile is the CommentStream to read the initial conditions data from
71 :			* \param keeper is the Keeper for the current model
72 :			* \param numage is the number of age groups for the initial population
73 :			* \param minage is the minimum age for the initial population
74 :			* \param Area is the AreaClass for the current model
75 :			*/
76 :			void readNormalParameterData(CommentStream& infile, Keeper* const keeper,
77 :			int numage, int minage, const AreaClass* const Area);
78 :			/**
79 :			* \brief This is the function used to read the numbers of the initial population
80 :			* \param infile is the CommentStream to read the initial conditions data from
81 :			* \param keeper is the Keeper for the current model
82 :			* \param numage is the number of age groups for the initial population
83 :			* \param minage is the minimum age for the initial population
84 :			* \param Area is the AreaClass for the current model
85 :			*/
86 :			void readNumberData(CommentStream& infile, Keeper* const keeper,
87 :			int numage, int minage, const AreaClass* const Area);
88 :			/**
89 :			* \brief This is the LengthGroupDivision of the initial population of the stock
90 :			*/
91 :			LengthGroupDivision* LgrpDiv;
92 :			/**
93 :			* \brief This is the ConversionIndex used to convert from the initial population LengthGroupDivision to the stock LengthGroupDivision
94 :			*/
95 :			ConversionIndex* CI;
96 :			/**
97 :			* \brief This is the AgeBandMatrixPtrVector used to store the initial population
98 :			*/
99 :			AgeBandMatrixPtrVector initialPop;
100 :			/**
101 :			* \brief This is the FormulaMatrixPtrVector that contains the number (from the input file) of the initial population
102 :			*/
103 :			FormulaMatrixPtrVector initialNumber;
104 :			/**
105 :			* \brief This is the FormulaMatrix of the area factor used to calculate the initial population
106 :			*/
107 :			FormulaMatrix areaFactor;
108 :			/**
109 :			* \brief This is the FormulaMatrix of the age factor used to calculate the initial population
110 :			*/
111 :			FormulaMatrix ageFactor;
112 :			/**
113 :			* \brief This is the FormulaMatrix of the condition factor used to calculate the weight of the initial population
114 :			*/
115 :			FormulaMatrix relCond;
116 :			/**
117 :			* \brief This is the FormulaMatrix of the mean length at age used to calculate the initial population
118 :			*/
119 :			FormulaMatrix meanLength;
120 :			/**
121 :			* \brief This is the FormulaMatrix of the standard deviation of the length at age used to calculate the initial population
122 :			*/
123 :			FormulaMatrix sdevLength;
124 :			/**
125 :			* \brief This is the FormulaMatrix of the alpha parameter used when calculating the length weight relationship
126 :			*/
127 :			FormulaMatrix alpha;
128 :			/**
129 :			* \brief This is the FormulaMatrix of the beta parameter used when calculating the length weight relationship
130 :			*/
131 :			FormulaMatrix beta;
132 :			/**
133 :			* \brief This is the optional factor used when calculating the standard deviation of the length
134 :			*/
135 :			Formula sdevMult;
136 :			/**
137 :			* \brief This is the DoubleVector of the reference weight values
138 :			*/
139 :			DoubleVector refWeight;
140 :			/**
141 :			* \brief This is the identifier of the function to be used to read the initial population data from file
142 :			*/
143 :			int readoption;
144 :			};
145 :
146 :			#endif

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