fix problem with growth after lin_grow transition

Rick-Methot-NOAA · Rick-Methot-NOAA · commit c19da3cfe332 · 2026-03-24T15:06:52.000-07:00
diff --git a/SS_biofxn.tpl b/SS_biofxn.tpl
@@ -462,7 +462,7 @@ FUNCTION void get_growth2(const int y)
 					{
             switch (Grow_type)
             {
-              case 1:
+              case 1:  // standard von Bertallanfy in styr
               {
                 for (a = 0; a <= nages; a++)
                 {
@@ -591,7 +591,7 @@ FUNCTION void get_growth2(const int y)
             if (do_once == 1) echoinput<<"ready to update growth by season " << y << " VBK_w " << VBK_work << " seas " << VBK_seas(s) << " byseas " << VBK_by_seas << endl << " lingrow " <<lin_grow << endl;
             switch (Grow_type)
             {
-              case 1:  // standard von Bertallanfy
+              case 1:  // standard von Bertallanfy - seasonal growth
               {
                 //  SS_Label_Info_16.2.4.2.1  #standard von Bert growth, loop ages to get size at age at beginning of next season (t+1) which is subseas=1
                 Ave_Size(t + 1, 1, g, 0) = Ave_Size(t, 1, g, 0); // carryforward, but may be overwritten in some circumstances
@@ -626,7 +626,7 @@ FUNCTION void get_growth2(const int y)
                   }
                   else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX;  lin_grow will stay at -1 for all remaining subseas of this season
                   {
-                    Ave_Size(t + 1, 1, g, k2) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK_work * VBK_seas(s) * (real_age(g, ALK_idx2, k2) - AFIX)) - 1.0) * Cohort_Growth(y, a);
+                    Ave_Size(t + 1, 1, g, k2) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK_work * VBK_seas(s) * seasdur(s) * (real_age(g, ALK_idx2, k2) - AFIX)) - 1.0) * Cohort_Growth(y, a);
                     echoinput<<" age: "<<k2<<" Lmin "<<Cohort_Lmin(gp, y, a)<<" time:  "<<real_age(g, ALK_idx2, k2) - AFIX << " " <<Ave_Size(t + 1, 1, g, k2) <<endl;
                   }
                   else // in linear phase
@@ -660,7 +660,7 @@ FUNCTION void get_growth2(const int y)
                   }
                   else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX;  lin_grow will stay at -1 for all remaining subseas of this season
                   {
-                    temp = LminR + (LminR - LinfR) * (mfexp(VBK_work * VBK_seas(s) * (real_age(g, ALK_idx2, k2) - AFIX)) - 1.0) * Cohort_Growth(y, a);
+                    temp = LminR + (LminR - LinfR) * (mfexp(VBK_work * VBK_seas(s) * seasdur(s) * (real_age(g, ALK_idx2, k2) - AFIX)) - 1.0) * Cohort_Growth(y, a);
                     Ave_Size(t + 1, 1, g, k2) = pow(temp, inv_Richards);
                   }
                   else // in linear phase for subseas
@@ -726,7 +726,7 @@ FUNCTION void get_growth2(const int y)
                   }
                   else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX;  lin_grow will stay at -1 for all remaining subseas of this season
                   {
-                    Ave_Size(t + 1, 1, g, k2) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, a) * VBK_seas(s) * (real_age(g, ALK_idx2, k2) - AFIX)) - 1.0) * Cohort_Growth(y, a);
+                    Ave_Size(t + 1, 1, g, k2) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, a) * VBK_seas(s) * seasdur(s) * (real_age(g, ALK_idx2, k2) - AFIX)) - 1.0) * Cohort_Growth(y, a);
                   }
                   else // in linear phase
                   {
@@ -817,7 +817,7 @@ FUNCTION void get_growth3(const int y, const int t, const int s, const int subse
       gp = GP(g);
       switch (Grow_type)
       {
-        case 1: // regular von B
+        case 1:   // standard von Bertallanfy  inseason growth
         {
           for (a = 0; a <= nages; a++)
           {
@@ -842,7 +842,7 @@ FUNCTION void get_growth3(const int y, const int t, const int s, const int subse
             // NOTE:  there is no seasonal interpolation, age-specific K uses calendar age, not real age.  Maybe someday....
             else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX;  lin_grow will stay at -1 for all remaining subseas of this season
             {
-              Ave_Size(t, subseas, g, a) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, 0) * VBK_seas(s) * (real_age(g, ALK_idx, a) - AFIX)) - 1.0) * Cohort_Growth(y, a);
+              Ave_Size(t, subseas, g, a) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, 0) * VBK_seas(s) * seasdur(s) * (real_age(g, ALK_idx, a) - AFIX)) - 1.0) * Cohort_Growth(y, a);
             }
           }
           break;
@@ -873,7 +873,7 @@ FUNCTION void get_growth3(const int y, const int t, const int s, const int subse
             else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX;  lin_grow will stay at -1 for all remaining subseas of this season
             {
               //              temp=Cohort_Lmin(gp,y,a) + (Cohort_Lmin(gp,y,a)-LinfR)*
-              temp = LminR + (LminR - LinfR) * (mfexp(VBK(gp, 0) * VBK_seas(s) * (real_age(g, ALK_idx, a) - AFIX)) - 1.0) * Cohort_Growth(y, a);
+              temp = LminR + (LminR - LinfR) * (mfexp(VBK(gp, 0) * VBK_seas(s) * seasdur(s) * (real_age(g, ALK_idx, a) - AFIX)) - 1.0) * Cohort_Growth(y, a);
               Ave_Size(t, subseas, g, a) = pow(temp, inv_Richards);
             }
           } // done ageloop
@@ -923,7 +923,7 @@ FUNCTION void get_growth3(const int y, const int t, const int s, const int subse
             // NOTE:  there is no seasonal interpolation, age-specific K uses calendar age, not real age.  Maybe someday....
             else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX;  lin_grow will stay at -1 for all remaining subseas of this season
             {
-              Ave_Size(t, subseas, g, a) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, a) * VBK_seas(s) * (real_age(g, ALK_idx, a) - AFIX) ) - 1.0) * Cohort_Growth(y, a);
+              Ave_Size(t, subseas, g, a) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, a) * VBK_seas(s) * seasdur(s) * (real_age(g, ALK_idx, a) - AFIX) ) - 1.0) * Cohort_Growth(y, a);
             }
           }
           break;
diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
@@ -487,11 +487,13 @@
         {
           ALK_idx = (s - 1) * N_subseas + subseas;
           settle_time = settle_g(g);
-          //   real_age is real age since settlement and is used in growth calculations
-          //   calen_age is real age since the beginning of the year in which spawning occurred
+          //  real_age is real age since settlement and is used in growth calculations
+          //  calen_age is real age since the beginning of the year in which spawning occurred
+          //  except with seas-as-years, sumseas is < 1.0 so calen_age needs to be in terms of season count, not age
+          //  so, divide by sumseas
           for (a = 0; a <= nages; a++)
           {
-            calen_age(g, ALK_idx, a) = r_ages(a) + azero_seas(s) + double(subseas - 1) / double(N_subseas) * seasdur(s);
+            calen_age(g, ALK_idx, a) = r_ages(a) + azero_seas(s) + double(subseas - 1) / double(N_subseas) * seasdur(s) / (sumseas / 12.);
             if (a < Settle_age(settle_time))
             {
               real_age(g, ALK_idx, a) = 0.;
@@ -979,10 +981,11 @@
   N_M_Grow_parms = N_natMparms + N_growparms;
   lin_grow.initialize();
   
-  echoinput << "g a seas subseas ALK_idx real_age calen_age lin_grow first_grow_age" << endl;
+  echoinput << "g a seas subseas ALK_idx real_age calen_age lin_grow first_grow_age setfirstgrow" << endl;
   for (g = 1; g <= gmorph; g++)
     if (use_morph(g) > 0)
     {
+      int setfirstgrowage = -1;
       for (a = 0; a <= nages; a++)
       {
         for (s = 1; s <= nseas; s++)
@@ -999,11 +1002,12 @@
             {
               lin_grow(g, ALK_idx, a) = 1.0; //  at the transition from linear to VBK growth
             }
-            else if (first_grow_age(g) == 0)
+            else if (setfirstgrowage == -1)
             {
               lin_grow(g, ALK_idx, a) = -1.0; //  flag for first age on growth curve beyond AFIX
               if (subseas == N_subseas) {
                 first_grow_age(g) = a;
+                setfirstgrowage = a;
               } //  so that lingrow will be -1 for rest of this season
             }
             else
@@ -1012,7 +1016,7 @@
             } //  flag for being in growth curve
   
             if (a < 4) echoinput << g << " " << a << " " << s << " " << subseas << " " << ALK_idx << " " << real_age(g, ALK_idx, a)
-                                 << " " << calen_age(g, ALK_idx, a) << " " << lin_grow(g, ALK_idx, a) << " " << first_grow_age(g) << endl;
+                                 << " " << calen_age(g, ALK_idx, a) << " " << lin_grow(g, ALK_idx, a) << " " << first_grow_age(g) << " " << setfirstgrowage << endl;
           }
       }
     }
diff --git a/SS_readdata_330.tpl b/SS_readdata_330.tpl
@@ -146,6 +146,7 @@
   echoinput << subseasdur_delta << " processed subseason duration (frac. of year) " << endl;
   echoinput << " processed subseason cumulative annual time within season " << endl
             << subseasdur << endl;
+  echoinput << sumseas << " sum of season durations; used in seas-as-years" << endl;
   if (seas_as_year == 1)
   {
     warnstream << "Season durations sum to <11.9, so SS3 assumes you are doing years as pseudo-seasons." << endl

Original file line number	Diff line number	Diff line change
`@@ -462,7 +462,7 @@ FUNCTION void get_growth2(const int y)`
`462`	`462`	`{`
`463`	`463`	`switch (Grow_type)`
`464`	`464`	`{`
`465`		`- case 1:`
	`465`	`+ case 1: // standard von Bertallanfy in styr`
`466`	`466`	`{`
`467`	`467`	`for (a = 0; a <= nages; a++)`
`468`	`468`	`{`
`@@ -591,7 +591,7 @@ FUNCTION void get_growth2(const int y)`
`591`	`591`	`if (do_once == 1) echoinput<<"ready to update growth by season " << y << " VBK_w " << VBK_work << " seas " << VBK_seas(s) << " byseas " << VBK_by_seas << endl << " lingrow " <<lin_grow << endl;`
`592`	`592`	`switch (Grow_type)`
`593`	`593`	`{`
`594`		`- case 1: // standard von Bertallanfy`
	`594`	`+ case 1: // standard von Bertallanfy - seasonal growth`
`595`	`595`	`{`
`596`	`596`	`// SS_Label_Info_16.2.4.2.1 #standard von Bert growth, loop ages to get size at age at beginning of next season (t+1) which is subseas=1`
`597`	`597`	`Ave_Size(t + 1, 1, g, 0) = Ave_Size(t, 1, g, 0); // carryforward, but may be overwritten in some circumstances`
`@@ -626,7 +626,7 @@ FUNCTION void get_growth2(const int y)`
`626`	`626`	`}`
`627`	`627`	`else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season`
`628`	`628`	`{`
`629`		`- Ave_Size(t + 1, 1, g, k2) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK_work * VBK_seas(s) * (real_age(g, ALK_idx2, k2) - AFIX)) - 1.0) * Cohort_Growth(y, a);`
	`629`	`+ Ave_Size(t + 1, 1, g, k2) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK_work * VBK_seas(s) * seasdur(s) * (real_age(g, ALK_idx2, k2) - AFIX)) - 1.0) * Cohort_Growth(y, a);`
`630`	`630`	`echoinput<<" age: "<<k2<<" Lmin "<<Cohort_Lmin(gp, y, a)<<" time: "<<real_age(g, ALK_idx2, k2) - AFIX << " " <<Ave_Size(t + 1, 1, g, k2) <<endl;`
`631`	`631`	`}`
`632`	`632`	`else // in linear phase`
`@@ -660,7 +660,7 @@ FUNCTION void get_growth2(const int y)`
`660`	`660`	`}`
`661`	`661`	`else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season`
`662`	`662`	`{`
`663`		`- temp = LminR + (LminR - LinfR) * (mfexp(VBK_work * VBK_seas(s) * (real_age(g, ALK_idx2, k2) - AFIX)) - 1.0) * Cohort_Growth(y, a);`
	`663`	`+ temp = LminR + (LminR - LinfR) * (mfexp(VBK_work * VBK_seas(s) * seasdur(s) * (real_age(g, ALK_idx2, k2) - AFIX)) - 1.0) * Cohort_Growth(y, a);`
`664`	`664`	`Ave_Size(t + 1, 1, g, k2) = pow(temp, inv_Richards);`
`665`	`665`	`}`
`666`	`666`	`else // in linear phase for subseas`
`@@ -726,7 +726,7 @@ FUNCTION void get_growth2(const int y)`
`726`	`726`	`}`
`727`	`727`	`else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season`
`728`	`728`	`{`
`729`		`- Ave_Size(t + 1, 1, g, k2) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, a) * VBK_seas(s) * (real_age(g, ALK_idx2, k2) - AFIX)) - 1.0) * Cohort_Growth(y, a);`
	`729`	`+ Ave_Size(t + 1, 1, g, k2) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, a) * VBK_seas(s) * seasdur(s) * (real_age(g, ALK_idx2, k2) - AFIX)) - 1.0) * Cohort_Growth(y, a);`
`730`	`730`	`}`
`731`	`731`	`else // in linear phase`
`732`	`732`	`{`
`@@ -817,7 +817,7 @@ FUNCTION void get_growth3(const int y, const int t, const int s, const int subse`
`817`	`817`	`gp = GP(g);`
`818`	`818`	`switch (Grow_type)`
`819`	`819`	`{`
`820`		`- case 1: // regular von B`
	`820`	`+ case 1: // standard von Bertallanfy inseason growth`
`821`	`821`	`{`
`822`	`822`	`for (a = 0; a <= nages; a++)`
`823`	`823`	`{`
`@@ -842,7 +842,7 @@ FUNCTION void get_growth3(const int y, const int t, const int s, const int subse`
`842`	`842`	`// NOTE: there is no seasonal interpolation, age-specific K uses calendar age, not real age. Maybe someday....`
`843`	`843`	`else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season`
`844`	`844`	`{`
`845`		`- Ave_Size(t, subseas, g, a) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, 0) * VBK_seas(s) * (real_age(g, ALK_idx, a) - AFIX)) - 1.0) * Cohort_Growth(y, a);`
	`845`	`+ Ave_Size(t, subseas, g, a) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, 0) * VBK_seas(s) * seasdur(s) * (real_age(g, ALK_idx, a) - AFIX)) - 1.0) * Cohort_Growth(y, a);`
`846`	`846`	`}`
`847`	`847`	`}`
`848`	`848`	`break;`
`@@ -873,7 +873,7 @@ FUNCTION void get_growth3(const int y, const int t, const int s, const int subse`
`873`	`873`	`else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season`
`874`	`874`	`{`
`875`	`875`	`// temp=Cohort_Lmin(gp,y,a) + (Cohort_Lmin(gp,y,a)-LinfR)*`
`876`		`- temp = LminR + (LminR - LinfR) * (mfexp(VBK(gp, 0) * VBK_seas(s) * (real_age(g, ALK_idx, a) - AFIX)) - 1.0) * Cohort_Growth(y, a);`
	`876`	`+ temp = LminR + (LminR - LinfR) * (mfexp(VBK(gp, 0) * VBK_seas(s) * seasdur(s) * (real_age(g, ALK_idx, a) - AFIX)) - 1.0) * Cohort_Growth(y, a);`
`877`	`877`	`Ave_Size(t, subseas, g, a) = pow(temp, inv_Richards);`
`878`	`878`	`}`
`879`	`879`	`} // done ageloop`
`@@ -923,7 +923,7 @@ FUNCTION void get_growth3(const int y, const int t, const int s, const int subse`
`923`	`923`	`// NOTE: there is no seasonal interpolation, age-specific K uses calendar age, not real age. Maybe someday....`
`924`	`924`	`else if (lin_grow(g, ALK_idx, a) == -1.0) // first time point beyond AFIX; lin_grow will stay at -1 for all remaining subseas of this season`
`925`	`925`	`{`
`926`		`- Ave_Size(t, subseas, g, a) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, a) * VBK_seas(s) * (real_age(g, ALK_idx, a) - AFIX) ) - 1.0) * Cohort_Growth(y, a);`
	`926`	`+ Ave_Size(t, subseas, g, a) = Cohort_Lmin(gp, y, a) + (Cohort_Lmin(gp, y, a) - L_inf(gp)) * (mfexp(VBK(gp, a) * VBK_seas(s) * seasdur(s) * (real_age(g, ALK_idx, a) - AFIX) ) - 1.0) * Cohort_Growth(y, a);`
`927`	`927`	`}`
`928`	`928`	`}`
`929`	`929`	`break;`
Original file line number	Diff line number	Diff line change
`@@ -487,11 +487,13 @@`
`487`	`487`	`{`
`488`	`488`	`ALK_idx = (s - 1) * N_subseas + subseas;`
`489`	`489`	`settle_time = settle_g(g);`
`490`		`- // real_age is real age since settlement and is used in growth calculations`
`491`		`- // calen_age is real age since the beginning of the year in which spawning occurred`
	`490`	`+ // real_age is real age since settlement and is used in growth calculations`
	`491`	`+ // calen_age is real age since the beginning of the year in which spawning occurred`
	`492`	`+ // except with seas-as-years, sumseas is < 1.0 so calen_age needs to be in terms of season count, not age`
	`493`	`+ // so, divide by sumseas`
`492`	`494`	`for (a = 0; a <= nages; a++)`
`493`	`495`	`{`
`494`		`- calen_age(g, ALK_idx, a) = r_ages(a) + azero_seas(s) + double(subseas - 1) / double(N_subseas) * seasdur(s);`
	`496`	`+ calen_age(g, ALK_idx, a) = r_ages(a) + azero_seas(s) + double(subseas - 1) / double(N_subseas) * seasdur(s) / (sumseas / 12.);`
`495`	`497`	`if (a < Settle_age(settle_time))`
`496`	`498`	`{`
`497`	`499`	`real_age(g, ALK_idx, a) = 0.;`
`@@ -979,10 +981,11 @@`
`979`	`981`	`N_M_Grow_parms = N_natMparms + N_growparms;`
`980`	`982`	`lin_grow.initialize();`
`981`	`983`
`982`		`- echoinput << "g a seas subseas ALK_idx real_age calen_age lin_grow first_grow_age" << endl;`
	`984`	`+ echoinput << "g a seas subseas ALK_idx real_age calen_age lin_grow first_grow_age setfirstgrow" << endl;`
`983`	`985`	`for (g = 1; g <= gmorph; g++)`
`984`	`986`	`if (use_morph(g) > 0)`
`985`	`987`	`{`
	`988`	`+ int setfirstgrowage = -1;`
`986`	`989`	`for (a = 0; a <= nages; a++)`
`987`	`990`	`{`
`988`	`991`	`for (s = 1; s <= nseas; s++)`
`@@ -999,11 +1002,12 @@`
`999`	`1002`	`{`
`1000`	`1003`	`lin_grow(g, ALK_idx, a) = 1.0; // at the transition from linear to VBK growth`
`1001`	`1004`	`}`
`1002`		`- else if (first_grow_age(g) == 0)`
	`1005`	`+ else if (setfirstgrowage == -1)`
`1003`	`1006`	`{`
`1004`	`1007`	`lin_grow(g, ALK_idx, a) = -1.0; // flag for first age on growth curve beyond AFIX`
`1005`	`1008`	`if (subseas == N_subseas) {`
`1006`	`1009`	`first_grow_age(g) = a;`
	`1010`	`+ setfirstgrowage = a;`
`1007`	`1011`	`} // so that lingrow will be -1 for rest of this season`
`1008`	`1012`	`}`
`1009`	`1013`	`else`
`@@ -1012,7 +1016,7 @@`
`1012`	`1016`	`} // flag for being in growth curve`
`1013`	`1017`
`1014`	`1018`	`if (a < 4) echoinput << g << " " << a << " " << s << " " << subseas << " " << ALK_idx << " " << real_age(g, ALK_idx, a)`
`1015`		`- << " " << calen_age(g, ALK_idx, a) << " " << lin_grow(g, ALK_idx, a) << " " << first_grow_age(g) << endl;`
	`1019`	`+ << " " << calen_age(g, ALK_idx, a) << " " << lin_grow(g, ALK_idx, a) << " " << first_grow_age(g) << " " << setfirstgrowage << endl;`
`1016`	`1020`	`}`
`1017`	`1021`	`}`
`1018`	`1022`	`}`
Original file line number	Diff line number	Diff line change
`@@ -146,6 +146,7 @@`
`146`	`146`	`echoinput << subseasdur_delta << " processed subseason duration (frac. of year) " << endl;`
`147`	`147`	`echoinput << " processed subseason cumulative annual time within season " << endl`
`148`	`148`	`<< subseasdur << endl;`
	`149`	`+ echoinput << sumseas << " sum of season durations; used in seas-as-years" << endl;`
`149`	`150`	`if (seas_as_year == 1)`
`150`	`151`	`{`
`151`	`152`	`warnstream << "Season durations sum to <11.9, so SS3 assumes you are doing years as pseudo-seasons." << endl`