From bbe7f8e4c0a86ef6fdd3bd13318bb9b2dd002d03 Mon Sep 17 00:00:00 2001
From: iantaylor-NOAA <ian.taylor@noaa.gov>
Date: Tue, 26 Aug 2025 09:47:13 -0700
Subject: [PATCH 1/8] turn off extra switches when Do_More_Std == 1

---
 SS_readcontrol_330.tpl | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 52e3eaa2..57b0ddbe 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -5636,6 +5636,14 @@
     Do_Dyn_Bzero = More_Std_Input(12);
     Do_se_smrybio = More_Std_Input(13);
   }
+  else 
+  {
+    // if Do_More_Std == 1, these options should be turned off
+    Do_NatM_Std = 0;
+    NatM_Std_Cnt = 0;
+    Do_Dyn_Bzero = 0;
+    Do_se_smrybio = 0;
+  }
   // clang-format off
  END_CALCS
 

From 3980415ce50c9b3491d9aff7d2675d48be7a0dec Mon Sep 17 00:00:00 2001
From: iantaylor-NOAA <ian.taylor@noaa.gov>
Date: Tue, 26 Aug 2025 12:18:05 -0700
Subject: [PATCH 2/8] revise switches for extra std inputs

- suggestion from https://github.com/nmfs-ost/ss3-source-code/pull/713#pullrequestreview-3156740744
---
 SS_readcontrol_330.tpl | 41 +++++++++++++++--------------------------
 1 file changed, 15 insertions(+), 26 deletions(-)

diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 57b0ddbe..4d8493e3 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -5585,24 +5585,21 @@
   // clang-format on
   Extra_Std_N = 0;
   
-  // don't read any extra std inputs
-  if (Do_More_Std == 0)
-  {
-    Do_Selex_Std = 0;
-    Selex_Std_AL = 1;
-    Selex_Std_Year = endyr;
-    Selex_Std_Cnt = 0;
-    Do_Growth_Std = 0;
-    Growth_Std_Cnt = 0;
-    Do_NatAge_Std = 0;
-    NatAge_Std_Cnt = 0;
-    NatAge_Std_Year = endyr;
-    Do_NatM_Std = 0;
-    NatM_Std_Cnt = 0;
-    Do_Dyn_Bzero = 0;
-    Do_se_smrybio = 0;
-    Do_se_LnSSB = 0;
-  }
+  // Itialize all switches for extra std inputs
+  Do_Selex_Std = 0;
+  Selex_Std_AL = 1;
+  Selex_Std_Year = endyr;
+  Selex_Std_Cnt = 0;
+  Do_Growth_Std = 0;
+  Growth_Std_Cnt = 0;
+  Do_NatAge_Std = 0;
+  NatAge_Std_Cnt = 0;
+  NatAge_Std_Year = endyr;
+  Do_NatM_Std = 0;
+  NatM_Std_Cnt = 0;
+  Do_Dyn_Bzero = 0;
+  Do_se_smrybio = 0;
+  Do_se_LnSSB = 0;
   
   // read standard extra std inputs (only option prior to 3.30.15)
   if (Do_More_Std > 0)
@@ -5636,14 +5633,6 @@
     Do_Dyn_Bzero = More_Std_Input(12);
     Do_se_smrybio = More_Std_Input(13);
   }
-  else 
-  {
-    // if Do_More_Std == 1, these options should be turned off
-    Do_NatM_Std = 0;
-    NatM_Std_Cnt = 0;
-    Do_Dyn_Bzero = 0;
-    Do_se_smrybio = 0;
-  }
   // clang-format off
  END_CALCS
 

From 3c2e2c42272d27b4b177bcce5ea2e1561c95fca8 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Tue, 26 Aug 2025 15:44:34 -0700
Subject: [PATCH 3/8] more robust retro_yr usage

---
 SS_readcontrol_330.tpl | 20 +++++++++-----------
 SS_write_report.tpl    |  1 -
 2 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 4d8493e3..df5009ea 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -5620,19 +5620,17 @@
     if (Do_NatAge_Std == 0) NatAge_Std_Cnt = 0;
     Do_NatM_Std = 0; // value replaced below if Do_More_Std==2
     NatM_Std_Cnt = 0; // value replaced below if Do_More_Std==2
-  }
-  
-  // read additional extra std inputs for NatM (added in 3.30.15)
-  if (Do_More_Std == 2)
-  {
-    Do_NatM_Std = More_Std_Input(10);
-    NatM_Std_Cnt = More_Std_Input(11);
-    if (Do_NatM_Std <= 0) {
-      NatM_Std_Cnt = 0;
+    // read additional extra std inputs for NatM (added in 3.30.15)
+    if (Do_More_Std == 2)
+    {
+      Do_NatM_Std = More_Std_Input(10);
+      NatM_Std_Cnt = More_Std_Input(11);
+      if (Do_NatM_Std <= 0) NatM_Std_Cnt = 0;
+      Do_Dyn_Bzero = More_Std_Input(12);
+      Do_se_smrybio = More_Std_Input(13);
     }
-    Do_Dyn_Bzero = More_Std_Input(12);
-    Do_se_smrybio = More_Std_Input(13);
   }
+  
   // clang-format off
  END_CALCS
 
diff --git a/SS_write_report.tpl b/SS_write_report.tpl
index 2ccfc224..d706a7dc 100644
--- a/SS_write_report.tpl
+++ b/SS_write_report.tpl
@@ -1741,7 +1741,6 @@ FUNCTION void write_bigoutput()
     double cross = 0.0;
     double Durbin = 0.0;
     double var = 0.0;
-     warning << recdev_first << " "<<recdev_start << " " << styr << endl;
     for (y = recdev_first; y <= recdev_end; y++)
     {
       temp1 = recdev(y);

From 24c2cbd5f7cf61f49a274b20874ad47ab2a0961d Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Wed, 27 Aug 2025 10:25:08 -0700
Subject: [PATCH 4/8] add more echoinput checks

---
 SS_readcontrol_330.tpl | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index df5009ea..9addfd44 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1608,6 +1608,7 @@
   //  labels for the types are found in:  MGtype_Lbl
  LOCAL_CALCS
       // clang-format on
+      echoinput<<"start assigning MGparm_type"<<endl;
       gp = 0;
   for (gg = 1; gg <= gender; gg++)
     for (GPat = 1; GPat <= N_GP; GPat++)
@@ -1618,6 +1619,8 @@
       Ip += N_natMparms;
       mgp_type(Ip, Ip + N_growparms - 1) = 2; // growth parms
 
+      echoinput<<"new check on Lmin: "<<Ip<<endl;
+      echoinput<<MGparm_1(Ip)(1,3)<<endl;
       // check on out of bound Lmin values.  Only check females because males can be offset from females
       if ( gp == 1 && WTage_rd == 0 && MGparm_1(Ip,1) < len_bins(1))
       {
@@ -1629,6 +1632,7 @@
         warnstream << "parm init value for Lmin: " << MGparm_1(Ip,3) << " cannot be less than population min length bin " << len_bins(1);
         write_message (FATAL, 0); // EXIT!
       }
+      echoinput<<"check on CV parms"<<endl;
   
       //  check on estimation of variance parameters for CV_young and CV_old
       for (int kk = Ip + N_growparms - 2; kk <= Ip + N_growparms - 1; kk++)
@@ -1655,12 +1659,15 @@
     mgp_type(MGparm_Hermaphro, MGparm_Hermaphro + 2) = 3;
   } //   herma parameters done with wtlen and fecundity
   if (recr_dist_method < 4) mgp_type(Ip, MGP_CGD - 1) = 4; // recruit apportionments
+  echoinput<<"recrdist: "<<Ip<<" "<<MGP_CGD-1<<endl;
   mgp_type(MGP_CGD) = 2; // cohort growth dev
+  echoinput<<"CGD: "<<Ip<<" "<<MGP_CGD<<endl;
   if (do_migration > 0) mgp_type(MGP_CGD + 1, N_MGparm) = 5; // note that it fills until end of MGparm list, but some get overwritten
   if (N_platoon > 1 && sd_ratio_rd < 0) mgp_type(sd_ratio_param_ptr) = 2;
   if (Use_AgeKeyZero > 0) mgp_type(AgeKeyParm, N_MGparm) = 6;
   if (catch_mult_pointer > 0) mgp_type(catch_mult_pointer, N_MGparm) = 7;
   for (f = frac_female_pointer; f <= frac_female_pointer + N_GP - 1; f++) mgp_type(f) = 4;
+  echoinput<<"fracfemale: "<<frac_female_pointer<<" "<<frac_female_pointer + N_GP - 1<<endl;
   if (N_pred > 0) mgp_type(predparm_pointer(1), predparm_pointer(1) + N_predparms - 1) = 1;
   echoinput << "mgparm_type for each parm:"<<endl;
   for (f = 1; f<= N_MGparm; f++) echoinput << f << " " << MGtype_Lbl(mgp_type(f)) << endl;

From 7e5eb73dc7b3e9ceb03719ece27bc10ef355cd3d Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Wed, 27 Aug 2025 10:56:48 -0700
Subject: [PATCH 5/8] think I fixed it

---
 SS_readcontrol_330.tpl | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 9addfd44..ac337ab2 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1619,18 +1619,21 @@
       Ip += N_natMparms;
       mgp_type(Ip, Ip + N_growparms - 1) = 2; // growth parms
 
-      echoinput<<"new check on Lmin: "<<Ip<<endl;
-      echoinput<<MGparm_1(Ip)(1,3)<<endl;
       // check on out of bound Lmin values.  Only check females because males can be offset from females
-      if ( gp == 1 && WTage_rd == 0 && MGparm_1(Ip,1) < len_bins(1))
+      if ( gp == 1 && WTage_rd == 0)
       {
-        warnstream << "parm min for Lmin: " << MGparm_1(Ip,1) << " cannot be less than population min length bin " << len_bins(1);
-        write_message (FATAL, 0); // EXIT!
-      }
-      if ( gp == 1 && WTage_rd == 0 &&  MGparm_1(Ip,3) < len_bins(1))
-      {
-        warnstream << "parm init value for Lmin: " << MGparm_1(Ip,3) << " cannot be less than population min length bin " << len_bins(1);
-        write_message (FATAL, 0); // EXIT!
+      echoinput<<"new check on Lmin: "<<Ip<<endl;
+      echoinput<<MGparm_1(Ip)(1,3)<<endl;
+        if (MGparm_1(Ip,1) < len_bins(1))
+        {
+          warnstream << "parm min for Lmin: " << MGparm_1(Ip,1) << " cannot be less than population min length bin " << len_bins(1);
+          write_message (FATAL, 0); // EXIT!
+        }
+        if (MGparm_1(Ip,3) < len_bins(1))
+        {
+          warnstream << "parm init value for Lmin: " << MGparm_1(Ip,3) << " cannot be less than population min length bin " << len_bins(1);
+          write_message (FATAL, 0); // EXIT!
+        }
       }
       echoinput<<"check on CV parms"<<endl;
   

From e62a5d780c9c93058ee146730b7d66cd3bf5e29b Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Wed, 27 Aug 2025 13:13:34 -0700
Subject: [PATCH 6/8] remove Lmin check

---
 SS_readcontrol_330.tpl | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index ac337ab2..b687e4e0 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1620,7 +1620,8 @@
       mgp_type(Ip, Ip + N_growparms - 1) = 2; // growth parms
 
       // check on out of bound Lmin values.  Only check females because males can be offset from females
-      if ( gp == 1 && WTage_rd == 0)
+  /*
+     if ( gp == 1 && WTage_rd == 0)
       {
       echoinput<<"new check on Lmin: "<<Ip<<endl;
       echoinput<<MGparm_1(Ip)(1,3)<<endl;
@@ -1635,7 +1636,8 @@
           write_message (FATAL, 0); // EXIT!
         }
       }
-      echoinput<<"check on CV parms"<<endl;
+  */
+       echoinput<<"check on CV parms"<<endl;
   
       //  check on estimation of variance parameters for CV_young and CV_old
       for (int kk = Ip + N_growparms - 2; kk <= Ip + N_growparms - 1; kk++)

From 9358921152661d49c8079bde10094881ad32d8c8 Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 28 Aug 2025 12:03:18 -0700
Subject: [PATCH 7/8] restore Lmin check

---
 SS_readcontrol_330.tpl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index b687e4e0..945ba2b2 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1620,7 +1620,7 @@
       mgp_type(Ip, Ip + N_growparms - 1) = 2; // growth parms
 
       // check on out of bound Lmin values.  Only check females because males can be offset from females
-  /*
+
      if ( gp == 1 && WTage_rd == 0)
       {
       echoinput<<"new check on Lmin: "<<Ip<<endl;
@@ -1636,7 +1636,7 @@
           write_message (FATAL, 0); // EXIT!
         }
       }
-  */
+
        echoinput<<"check on CV parms"<<endl;
   
       //  check on estimation of variance parameters for CV_young and CV_old

From f8d2b5fcb64bda7a5c13d87dc22fd25866167b9c Mon Sep 17 00:00:00 2001
From: Richard Methot <richard.methot@noaa.gov>
Date: Thu, 28 Aug 2025 12:51:11 -0700
Subject: [PATCH 8/8] remove debug output

---
 SS_readcontrol_330.tpl | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/SS_readcontrol_330.tpl b/SS_readcontrol_330.tpl
index 945ba2b2..3e76b021 100644
--- a/SS_readcontrol_330.tpl
+++ b/SS_readcontrol_330.tpl
@@ -1623,8 +1623,6 @@
 
      if ( gp == 1 && WTage_rd == 0)
       {
-      echoinput<<"new check on Lmin: "<<Ip<<endl;
-      echoinput<<MGparm_1(Ip)(1,3)<<endl;
         if (MGparm_1(Ip,1) < len_bins(1))
         {
           warnstream << "parm min for Lmin: " << MGparm_1(Ip,1) << " cannot be less than population min length bin " << len_bins(1);
@@ -1636,9 +1634,6 @@
           write_message (FATAL, 0); // EXIT!
         }
       }
-
-       echoinput<<"check on CV parms"<<endl;
-  
       //  check on estimation of variance parameters for CV_young and CV_old
       for (int kk = Ip + N_growparms - 2; kk <= Ip + N_growparms - 1; kk++)
       {
@@ -1664,15 +1659,12 @@
     mgp_type(MGparm_Hermaphro, MGparm_Hermaphro + 2) = 3;
   } //   herma parameters done with wtlen and fecundity
   if (recr_dist_method < 4) mgp_type(Ip, MGP_CGD - 1) = 4; // recruit apportionments
-  echoinput<<"recrdist: "<<Ip<<" "<<MGP_CGD-1<<endl;
   mgp_type(MGP_CGD) = 2; // cohort growth dev
-  echoinput<<"CGD: "<<Ip<<" "<<MGP_CGD<<endl;
   if (do_migration > 0) mgp_type(MGP_CGD + 1, N_MGparm) = 5; // note that it fills until end of MGparm list, but some get overwritten
   if (N_platoon > 1 && sd_ratio_rd < 0) mgp_type(sd_ratio_param_ptr) = 2;
   if (Use_AgeKeyZero > 0) mgp_type(AgeKeyParm, N_MGparm) = 6;
   if (catch_mult_pointer > 0) mgp_type(catch_mult_pointer, N_MGparm) = 7;
   for (f = frac_female_pointer; f <= frac_female_pointer + N_GP - 1; f++) mgp_type(f) = 4;
-  echoinput<<"fracfemale: "<<frac_female_pointer<<" "<<frac_female_pointer + N_GP - 1<<endl;
   if (N_pred > 0) mgp_type(predparm_pointer(1), predparm_pointer(1) + N_predparms - 1) = 1;
   echoinput << "mgparm_type for each parm:"<<endl;
   for (f = 1; f<= N_MGparm; f++) echoinput << f << " " << MGtype_Lbl(mgp_type(f)) << endl;