--- trunk/gadget/growthcalc.h	2014/02/10 17:09:07	1
+++ trunk/gadget/growthcalc.h	2015/04/30 17:32:47	4
@@ -9,6 +9,7 @@
 #include "livesonareas.h"
 #include "modelvariablevector.h"
 #include "keeper.h"
+#include "matrix.h"
 
 /**
  * \class GrowthCalcBase
@@ -26,6 +27,7 @@
    * \brief This is the default GrowthCalcBase destructor
    */
   ~GrowthCalcBase() {};
+  //FIXME doc
   /**
    * \brief This is the function that calculates the growth
    * \param area is the area that the growth is being calculated on
@@ -39,10 +41,15 @@
    * \param LgrpDiv is the LengthGroupDivision of the stock
    * \note This will be overridden by the derived classes that actually calculate the growth
    */
-  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
-    const PopInfoVector& numGrow, const AreaClass* const Area,
-    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
-    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv) = 0;
+//  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
+//    const PopInfoVector& numGrow, const AreaClass* const Area,
+//    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+//    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv) = 0;
+
+  virtual void calcGrowth(int area, double* Lgrowth, double* Wgrowth,
+      const PopInfoVector& numGrow, const AreaClass* const Area,
+      const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+      const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv, int size) = 0;
   /**
    * \brief This will return the power term of the length - weight relationship
    * \return 0 (will be overridden in derived classes)
@@ -86,10 +93,15 @@
    * \param MaxCon is the DoubleVector of the maximum consumption of the stock
    * \param LgrpDiv is the LengthGroupDivision of the stock
    */
-  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
-    const PopInfoVector& numGrow, const AreaClass* const Area,
-    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
-    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+//  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
+//    const PopInfoVector& numGrow, const AreaClass* const Area,
+//    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+//    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+
+  virtual void calcGrowth(int area, double* Lgrowth, double* Wgrowth,
+          const PopInfoVector& numGrow, const AreaClass* const Area,
+          const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+          const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv, int size);
 protected:
   /**
    * \brief This is the number of growth parameters (set to 9)
@@ -134,10 +146,15 @@
    * \param MaxCon is the DoubleVector of the maximum consumption of the stock
    * \param LgrpDiv is the LengthGroupDivision of the stock
    */
-  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
-    const PopInfoVector& numGrow, const AreaClass* const Area,
-    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
-    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+//  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
+//    const PopInfoVector& numGrow, const AreaClass* const Area,
+//    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+//    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+
+  virtual void calcGrowth(int area, double* Lgrowth, double* Wgrowth,
+          const PopInfoVector& numGrow, const AreaClass* const Area,
+          const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+          const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv, int size);
 protected:
   /**
    * \brief This is the FormulaMatrixPtrVector of increase in length for each length group
@@ -182,10 +199,15 @@
    * \param MaxCon is the DoubleVector of the maximum consumption of the stock
    * \param LgrpDiv is the LengthGroupDivision of the stock
    */
-  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
-    const PopInfoVector& numGrow, const AreaClass* const Area,
-    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
-    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+//  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
+//    const PopInfoVector& numGrow, const AreaClass* const Area,
+//    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+//    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+
+  virtual void calcGrowth(int area, double* Lgrowth, double* Wgrowth,
+          const PopInfoVector& numGrow, const AreaClass* const Area,
+          const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+          const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv, int size);
   /**
    * \brief This will return the power term of the length - weight relationship
    * \return lgrowthPar[7]
@@ -252,10 +274,15 @@
    * \param MaxCon is the DoubleVector of the maximum consumption of the stock
    * \param LgrpDiv is the LengthGroupDivision of the stock
    */
-  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
-    const PopInfoVector& numGrow, const AreaClass* const Area,
-    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
-    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+//  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
+//    const PopInfoVector& numGrow, const AreaClass* const Area,
+//    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+//    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+
+  virtual void calcGrowth(int area, double* Lgrowth, double* Wgrowth,
+          const PopInfoVector& numGrow, const AreaClass* const Area,
+          const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+          const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv, int size);
   /**
    * \brief This will return the power term of the length - weight relationship
    * \return lgrowthPar[7]
@@ -322,10 +349,15 @@
    * \param MaxCon is the DoubleVector of the maximum consumption of the stock
    * \param LgrpDiv is the LengthGroupDivision of the stock
    */
-  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
-    const PopInfoVector& numGrow, const AreaClass* const Area,
-    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
-    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+//  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
+//    const PopInfoVector& numGrow, const AreaClass* const Area,
+//    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+//    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+
+  virtual void calcGrowth(int area, double* Lgrowth, double* Wgrowth,
+          const PopInfoVector& numGrow, const AreaClass* const Area,
+          const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+          const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv, int size);
   /**
    * \brief This will return the power term of the length - weight relationship
    * \return lgrowthPar[7]
@@ -404,10 +436,15 @@
    * \param MaxCon is the DoubleVector of the maximum consumption of the stock
    * \param LgrpDiv is the LengthGroupDivision of the stock
    */
-  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
-    const PopInfoVector& numGrow, const AreaClass* const Area,
-    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
-    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+//  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
+//    const PopInfoVector& numGrow, const AreaClass* const Area,
+//    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+//    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+
+  virtual void calcGrowth(int area, double* Lgrowth, double* Wgrowth,
+          const PopInfoVector& numGrow, const AreaClass* const Area,
+          const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+          const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv, int size);
 protected:
   /**
    * \brief This is the number of growth parameters (set to 2)
@@ -456,10 +493,15 @@
    * \param MaxCon is the DoubleVector of the maximum consumption of the stock
    * \param LgrpDiv is the LengthGroupDivision of the stock
    */
-  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
-    const PopInfoVector& numGrow, const AreaClass* const Area,
-    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
-    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+//  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
+//    const PopInfoVector& numGrow, const AreaClass* const Area,
+//    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+//    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+
+  virtual void calcGrowth(int area, double* Lgrowth, double* Wgrowth,
+          const PopInfoVector& numGrow, const AreaClass* const Area,
+          const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+          const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv, int size);
 protected:
   /**
    * \brief This is the number of growth parameters (set to 2)
@@ -506,10 +548,17 @@
    * \param MaxCon is the DoubleVector of the maximum consumption of the stock
    * \param LgrpDiv is the LengthGroupDivision of the stock
    */
-  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
-    const PopInfoVector& numGrow, const AreaClass* const Area,
-    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
-    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+//  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
+//    const PopInfoVector& numGrow, const AreaClass* const Area,
+//    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+//    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+
+
+  virtual void calcGrowth(int area, double* Lgrowth, double* Wgrowth,
+      const PopInfoVector& numGrow, const AreaClass* const Area,
+      const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+      const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv, int size);
+
   /**
    * \brief This will return the power term of the length - weight relationship
    * \return growthPar[3]
@@ -562,10 +611,15 @@
    * \param MaxCon is the DoubleVector of the maximum consumption of the stock
    * \param LgrpDiv is the LengthGroupDivision of the stock
    */
-  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
-    const PopInfoVector& numGrow, const AreaClass* const Area,
-    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
-    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+//  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
+//    const PopInfoVector& numGrow, const AreaClass* const Area,
+//    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+//    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+
+  virtual void calcGrowth(int area, double* Lgrowth, double* Wgrowth,
+        const PopInfoVector& numGrow, const AreaClass* const Area,
+        const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+        const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv, int size);
   /**
    * \brief This will return the power term of the length - weight relationship
    * \return growthPar[4]
@@ -618,10 +672,16 @@
    * \param MaxCon is the DoubleVector of the maximum consumption of the stock
    * \param LgrpDiv is the LengthGroupDivision of the stock
    */
-  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
-    const PopInfoVector& numGrow, const AreaClass* const Area,
-    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
-    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+//  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
+//    const PopInfoVector& numGrow, const AreaClass* const Area,
+//    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+//    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+
+
+  virtual void calcGrowth(int area, double* Lgrowth, double* Wgrowth,
+          const PopInfoVector& numGrow, const AreaClass* const Area,
+          const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+          const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv, int size);
   /**
    * \brief This will return the power term of the length - weight relationship
    * \return growthPar[4]
@@ -674,10 +734,15 @@
    * \param MaxCon is the DoubleVector of the maximum consumption of the stock
    * \param LgrpDiv is the LengthGroupDivision of the stock
    */
-  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
-    const PopInfoVector& numGrow, const AreaClass* const Area,
-    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
-    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+//  virtual void calcGrowth(int area, DoubleVector& Lgrowth, DoubleVector& Wgrowth,
+//    const PopInfoVector& numGrow, const AreaClass* const Area,
+//    const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+//    const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv);
+
+  virtual void calcGrowth(int area, double* Lgrowth, double* Wgrowth,
+          const PopInfoVector& numGrow, const AreaClass* const Area,
+          const TimeClass* const TimeInfo, const DoubleVector& Fphi,
+          const DoubleVector& MaxCon, const LengthGroupDivision* const LgrpDiv, int size);
   /**
    * \brief This will return the power term of the length - weight relationship
    * \return growthPar[4]