new_filename_and_folder_for_outputs

SS_benchfore.tpl

@@ -1483,12 +1483,20 @@ FUNCTION void Get_Forecast()
       for(subseas=1;subseas<=N_subseas;subseas++)  //  do all subseasons in first year
       {
         get_growth3(y,t,s, subseas);  //  in case needed for Lorenzen M
-        Make_AgeLength_Key(s, subseas);
+        Make_AgeLength_Key(s, subseas);  //  which also updates Wt_Age_beg, etc.
+      }
+      if(s==spawn_seas) 
+      {
+        if(WTage_rd==1)
+        {
+          Wt_Age_beg(s)=Wt_Age_t(t,0);  //  used for smrybio
+          Wt_Age_mid(s)=Wt_Age_t(t,-1);
+          if(s==spawn_seas) fec=Wt_Age_t(t,-2);
+        }
+        else
+        {get_mat_fec();}
       }
-//      if(s==spawn_seas) Make_Fecundity();
-      if(s==spawn_seas) get_mat_fec();
     }
-//      get_mat_fec();
   }
 
     for (y=endyr+1;y<=YrMax;y++)

SS_global.tpl

@@ -62,25 +62,20 @@ GLOBALS_SECTION
   #include <fvar.hpp>
   #include <vector>
   #include <iostream>
+  #include <sys/types.h>
+  #include <sys/stat.h>
   time_t start,finish;
   long hour,minute,second;
   double elapsed_time;
 
-//  SS_Label_Info_10.1 #Open output files using ofstream
-  ofstream warning("warning.sso");
-  ofstream echoinput("echoinput.sso");
-  ofstream ParmTrace("ParmTrace.sso");
-  ofstream report5("Forecast-report.sso");
-  ofstream report2("CumReport.sso",ios::app);
-  ofstream bodywtout("wtatage.ss_new");
-  ofstream SS2out;   // this is just a create
-
 //  SS_Label_Info_10.2 #Define some adstring variables
   adstring_array ParmLabel;  // extendable array to hold the parameter labels
   adstring_array Parm_info;  // extendable array to hold the parameter labels
   adstring_array SzFreq_units_label;
   adstring_array SzFreq_scale_label;
   adstring_array fleetname;
+  adstring ssnew_pathname;
+  adstring sso_pathname;
   adstring fleetnameread;
   adstring depletion_basis_label;
   adstring F_report_label;
@@ -89,6 +84,8 @@ GLOBALS_SECTION
   adstring onenum2(4);
   adstring anystring;
   adstring anystring2;
+  adstring report_sso_filename;
+
   adstring_array version_info;
   adstring_array version_info2;
   adstring_array Starter_Comments;
@@ -103,6 +100,25 @@ GLOBALS_SECTION
   adstring_array pick_report_name;  //  name of report
   adstring_array pick_report_use;  //  X if used; 0 if not
 
+//  SS_Label_Info_10.1 #Open output files using ofstream
+  ofstream warning;
+  ofstream echoinput;
+  ofstream ParmTrace;
+  ofstream report5;  //  forecast-report
+  ofstream report2;  //  control.ss_new
+  ofstream bodywtout;
+  ofstream SS2out;   // this is just a create
+  ofstream SS_compout;   // this is just a create
+  ofstream report1;  //  for data.ss_new
+  ofstream covarout;
+  ofstream rebuilder;
+  ofstream rebuild_dat;
+  ofstream posts;
+  ofstream der_posts;
+  ofstream post_vecs;
+  ofstream post_obj_func;
+  ofstream SS_smry;
+  ofstream SIS_table;
 //  declare some entities that need global access
   int ParCount; int timevary_parm_cnt; int N_warn;
   int styr; int endyr; int YrMax; int nseas; int Ncycle; int seas_as_year;
@@ -668,7 +684,7 @@ FINAL_SECTION
 
   if(No_Report==1)
   {
-    cout<<"MCMC finished; note: .sso and .ss_new files not produced after MCMC "<<endl;
+    cout<<"MCMC finished; *.ss_new files not written after MCMC or MCEVAL"<<endl;
   }
 
   else
@@ -679,7 +695,8 @@ FINAL_SECTION
     {N_warn++;  warning<<N_warn<<" "<<"Final gradient: "<<objective_function_value::pobjfun->gmax <<" is larger than final_conv: "<<final_conv<<endl;}
 
 //  SS_Label_Info_12.2 #Output the covariance matrix to covar.sso
-    ofstream covarout("covar.sso");
+    anystring=sso_pathname+"covar.sso";
+    covarout.open(anystring);
     covarout<<version_info<<endl;
     covarout<<"start_time: "<<ctime(&start)<<endl;
     covarout<<active_parms<<" "<<CoVar_Count<<endl;
@@ -706,6 +723,34 @@ FINAL_SECTION
 
 //  SS_Label_Info_12.3 #Go thru time series calculations again to get extra output quantities
 //  SS_Label_Info_12.3.2 #Set save_for_report=1 then call initial_conditions and time_series to get other output quantities
+    if(Do_Dyn_Bzero>0) //  do dynamic Bzero
+    {
+      save_gparm=0;
+      fishery_on_off=0;
+      setup_recdevs();
+      y=styr;
+      get_initial_conditions();
+      get_time_series();
+      if(Do_Forecast>0)
+      {
+        show_MSY=0;
+        Get_Forecast();
+      }
+      k=Do_Dyn_Bzero;
+      for(j=styr-2; j<=YrMax;j++)
+      {
+        Extra_Std(k)=SSB_yr(j); k++;
+      }
+      if(More_Std_Input(12)==2)
+    	{
+        for(j=styr-2; j<=YrMax;j++)
+        {
+          Extra_Std(k)=exp_rec(j,4); k++;
+        }
+      }
+    }  //  end dynamic Bzero
+
+    fishery_on_off=1;
     save_for_report=1;
     bigsaver=1;
     save_gparm=0;
@@ -785,7 +830,7 @@ FINAL_SECTION
 //  SS_Label_Info_12.4.6 #Call fxn write_Bzero_output()  appended to report.sso
     if (pick_report_use(59)=="Y")
     {
-        cout<<"dynamic Bzero: ";
+        cout<<"dynamic Bzero in FINAL_SECTION: ";
         write_Bzero_output();
         cout<<" finished "<<endl;
     }
@@ -914,6 +959,6 @@ REPORT_SECTION
     cout<<"Wrote bigoutput and bodywt for last_phase in REPORT_SECTION and before hessian, no benchmark or forecast "<<endl;
     save_for_report=0;
     write_bodywt=0;
-    SS2out.close();
+//    SS2out.close();
     }
   }  //  end standard report section

SS_objfunc.tpl

@@ -1355,27 +1355,28 @@ FUNCTION void get_posteriors()
     // but will play through just fine
     // NOTE:  "del" works on Windows only; use "rm" on other operating systems
     //  solution here is to open file to the first record
-    ofstream rebuilder("rebuild.sso",ios::out);
-    ofstream posts("posteriors.sso",ios::out);
-    ofstream der_posts("derived_posteriors.sso",ios::out);
-    ofstream post_vecs("posterior_vectors.sso",ios::out);
-	ofstream post_obj_func("posterior_obj_func.sso",ios::out);
-    if(rundetail>0) cout<<" did system commands "<<endl;
-  };
+    rebuilder.open(sso_pathname+"rebuild.sso",ios::out);
+    posts.open(sso_pathname+"posteriors.sso",ios::out);
+    der_posts.open(sso_pathname+"derived_posteriors.sso",ios::out);
+    post_vecs.open(sso_pathname+"posterior_vectors.sso",ios::out);
+    post_obj_func.open(sso_pathname+"posterior_obj_func.sso",ios::out);
+  }
+  else 
+  {
   // define the mcmc output files;
-  ofstream rebuilder("rebuild.sso",ios::app);
-  ofstream posts("posteriors.sso",ios::app);
-  ofstream der_posts("derived_posteriors.sso",ios::app);
-  ofstream post_vecs("posterior_vectors.sso",ios::app);
-  ofstream post_obj_func("posterior_obj_func.sso",ios::app);
+  rebuilder.open(sso_pathname+"rebuild.sso",ios::app);
+  posts.open(sso_pathname+"posteriors.sso",ios::app);
+  der_posts.open(sso_pathname+"derived_posteriors.sso",ios::app);
+  post_vecs.open(sso_pathname+"posterior_vectors.sso",ios::app);
+  post_obj_func.open(sso_pathname+"posterior_obj_func.sso",ios::app);
+  }
 
   if(mceval_header==0)    // first pass through the mceval phase
   {
     mceval_header=1;
     // produce the appropriate headers for the posteriors.rep
     // and derived_posteriors.rep files
     // parameters.rep matches "PARAMETERS" section in Report.SSO file
-    if(rundetail>0) cout<<" write mcmc headers "<<endl;
     posts<<"Iter Objective_function ";
     for (i=1;i<=active_count;i++) {posts<<" "<<ParmLabel(active_parm(i));}
     posts << endl;
@@ -1525,10 +1526,8 @@ FUNCTION void get_posteriors()
     }
   };  //  end writing headers for mceval_counter==1
 
-
   // produce standard output of all estimated parameters
   posts<<mceval_counter<<" "<<obj_fun<<" ";
-
   for (j=1;j<=N_MGparm2;j++)
   {
     if(active(MGparm(j))) posts<<MGparm(j)<<" ";
@@ -1688,5 +1687,8 @@ FUNCTION void get_posteriors()
 
       post_obj_func<<endl;
   }
-
+  posts.close();
+  der_posts.close();
+  post_vecs.close();
+  post_obj_func.close();
   }  //  end get_posteriors

SS_proced.tpl

@@ -17,6 +17,7 @@ PROCEDURE_SECTION
   CrashPen.initialize();
   niter++;
   if(mceval_phase() ) mceval_counter ++;   // increment the counter
+
   if(initial_params::mc_phase==1) //  in MCMC phase
   {
 
@@ -82,20 +83,14 @@ PROCEDURE_SECTION
 //  SS_Label_Info_7.6 #If sdphase or mcevalphase, do benchmarks and forecast and derived quantities
     if( (sd_phase() || mceval_phase()) && (initial_params::mc_phase==0))
     {
-
     if(Do_Dyn_Bzero>0) //  do dynamic Bzero
-    	{
+    {
       save_gparm=0;
       fishery_on_off=0;
       setup_recdevs();
       y=styr;
       get_initial_conditions();
       get_time_series();
-      setup_Benchmark();
-      if(Do_Benchmark>0)
-      {
-        Get_Benchmarks(show_MSY); // should not be needed, but something critical is getting setup
-      }
       if(Do_Forecast>0)
       {
         show_MSY=0;
@@ -112,9 +107,8 @@ PROCEDURE_SECTION
         {
           Extra_Std(k)=exp_rec(j,4); k++;
         }
-    	}
-//  end dynamic Bzero
-    	}
+      }
+    }  //  end dynamic Bzero calculations, will write after big report
 
       save_gparm=0;
       fishery_on_off=1;
@@ -126,6 +120,7 @@ PROCEDURE_SECTION
       setup_Benchmark();
 //  SS_Label_Info_7.6.1 #Call fxn Get_Benchmarks()
       if(mceval_phase()==0) {show_MSY=1;}  //  so only show details if not in mceval
+      if(mceval_phase()>0) save_for_report=1;
       if(show_MSY==1) cout<<"do benchmark and forecast if requested in sdphase"<<endl;
       if(Do_Benchmark>0)
       {
@@ -304,11 +299,35 @@ PROCEDURE_SECTION
       if(obj_fun<=last_objfun) last_objfun=obj_fun;
      docheckup=0;  // turn off reporting to checkup.sso
 //  SS_Label_Info_7.11 #Call fxn get_posteriors if in mceval_phase
-     if(mceval_phase()) get_posteriors();
+     if(mceval_phase()) 
+      {
+        get_posteriors();
+
+//SS_Label_Info_7.12 #write report_mce_XXXX.sso and compreport_mce_XXXX.sso for each MCEVAL
+        if(mcmc_output_detail>=2)
+        {
+        write_bodywt=0;
+        pick_report_use(54)=0;
+        pick_report_use(55)=0;
+//  is the following call to the functions necessary??
+        save_for_report=1;
+        save_gparm=0;
+        y=styr;
+        setup_recdevs();
+        get_initial_conditions();
+        get_time_series();
+        evaluate_the_objective_function();
+//  end call to the functions
+        write_bigoutput();
+        if(Do_Dyn_Bzero>0) write_Bzero_output();
+        save_for_report=0;
+        write_bodywt=0;
+        }
+      }
   }  //  end doing of the calculations
   if(mceval_phase() || initial_params::mc_phase==1)
   {
     No_Report=1;  //  flag to skip output reports after MCMC and McEVAL
   }
   }
-//  SS_Label_Info_7.12 #End of PROCEDURE_SECTION
+//  SS_Label_Info_7.13 #End of PROCEDURE_SECTION

SS_readstarter.tpl

@@ -270,6 +270,36 @@
   init_int reportdetail
   int rd_background
 
+ LOCAL_CALCS
+   struct stat pathinfo;
+    if( stat( "./ssnew", &pathinfo ) != 0 )
+    {
+      ssnew_pathname="";
+    }
+    else
+      {
+        ssnew_pathname="./ssnew/";
+      }
+
+    if( stat( "./sso", &pathinfo ) != 0 )
+    {
+      sso_pathname="";
+    }
+    else
+      {
+        sso_pathname="./sso/";
+      }
+
+  warning.open(sso_pathname+"warning.sso");
+  echoinput.open(sso_pathname+"echoinput.sso");
+  ParmTrace.open(sso_pathname+"ParmTrace.sso");
+  report5.open(sso_pathname+"Forecast-report.sso");
+  report2.open(sso_pathname+"CumReport.sso",ios::app);
+  bodywtout.open(ssnew_pathname+"wtatage.ss_new");
+
+ END_CALCS
+
+
  LOCAL_CALCS
   if (reportdetail < 0 || reportdetail > 3) reportdetail = 0;
   echoinput<<reportdetail<<"  reportdetail 0=minimal for data-limited, 1=all, 2=no growth, 3=custom"<<endl;
@@ -558,8 +588,8 @@
      echoinput<<"read MCMC_output_detail.MCMC_bump as a single real number;  separate values will be parsed from integer and fraction"<<endl;
      mcmc_output_detail = int(tempin);
      MCMC_bump=tempin-mcmc_output_detail;
-     if (mcmc_output_detail < 0 || mcmc_output_detail > 3) mcmc_output_detail = 0;
-     echoinput<<"MCMC output detail:  "<<mcmc_output_detail<<endl;
+     if (mcmc_output_detail < 0 || mcmc_output_detail > 2) mcmc_output_detail = 0;
+     echoinput<<"MCMC output detail(1=more_detail_to_posts; 2=write_report_for_each_mceval):  "<<mcmc_output_detail<<endl;
      echoinput<<"MCMC bump to R0:  "<<MCMC_bump<<endl;
 
      echoinput<<"Now get ALK tolerance (0.0 is OK for no compression; 0.1 is too big;  suggest 0.0001)"<<endl;