Defined Global_numTask and Global_myRank

stephaneguindon · Jul 14, 2020 · 2ae8fb0 · 2ae8fb0
1 parent ac88949
commit 2ae8fb0
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Showing 7 changed files with 191 additions and 63 deletions.
diff --git a/src/mcmc.c b/src/mcmc.c
diff --git a/src/mpi_boot.c b/src/mpi_boot.c
@@ -12,6 +12,10 @@ the GNU public licence. See http://www.opensource.org for details.
 
 #include "mpi_boot.h"
 
+int Global_numTask;
+int Global_myRank;
+
+
 /* #ifdef MPI */
 
 /*********************************************************/

diff --git a/src/mpi_boot.h b/src/mpi_boot.h
@@ -28,8 +28,8 @@ the GNU public licence. See http://www.opensource.org for details.
 #define BootTreeTag 0
 #define BootStatTag 1
 
-extern int Global_numTask, Global_myRank;
-
+extern int Global_numTask;
+extern int Global_myRank;
 
 void Bootstrap_MPI(t_tree *tree);
 void Print_Fp_Out_Lines_MPI(t_tree *tree, option *io, int n_data_set, char *bootStr);

diff --git a/src/phyrex.c b/src/phyrex.c
@@ -359,14 +359,14 @@ void PHYREX_XML(char *xml_filename)
 
 
   /* Initialize parameters of migrep model */
-  mixt_tree->mmod->lbda = 1.;
-  mixt_tree->mmod->mu   = 0.8;
+  mixt_tree->mmod->lbda = 10.0;
+  mixt_tree->mmod->mu   = 1.0;
 
   if(mixt_tree->mmod->id == SLFV_GAUSSIAN || mixt_tree->mmod->id == SLFV_UNIFORM)
     mixt_tree->mmod->rad  = 0.05*((mixt_tree->mmod->lim_up->lonlat[0]-mixt_tree->mmod->lim_do->lonlat[0])+
                                   (mixt_tree->mmod->lim_up->lonlat[1]-mixt_tree->mmod->lim_do->lonlat[1]));
   else if(mixt_tree->mmod->id == RW || mixt_tree->mmod->id == RRW)
-    mixt_tree->mmod->rad  = 2.0*((mixt_tree->mmod->lim_up->lonlat[0]-mixt_tree->mmod->lim_do->lonlat[0])+
+    mixt_tree->mmod->rad  = 1.0*((mixt_tree->mmod->lim_up->lonlat[0]-mixt_tree->mmod->lim_do->lonlat[0])+
                                  (mixt_tree->mmod->lim_up->lonlat[1]-mixt_tree->mmod->lim_do->lonlat[1]));
   else assert(FALSE);
 
@@ -378,7 +378,7 @@ void PHYREX_XML(char *xml_filename)
     {
     case 0 : case 1 :
       {
-        PHYREX_Simulate_Backward_Core(mixt_tree->young_disk,YES,mixt_tree);
+        PHYREX_Simulate_Backward_Core(mixt_tree->young_disk,NO,mixt_tree);
         PHYREX_Ldsk_To_Tree(mixt_tree);
         break;
       }
@@ -391,6 +391,9 @@ void PHYREX_XML(char *xml_filename)
 
   Update_Ancestors(mixt_tree->n_root,mixt_tree->n_root->v[2],mixt_tree);
   Update_Ancestors(mixt_tree->n_root,mixt_tree->n_root->v[1],mixt_tree);  
+
+  mixt_tree->mmod->rad = 0.1;
+
 
   MIXT_Set_Ignore_Root(YES,mixt_tree);
   MIXT_Set_Bl_From_Rt(YES,mixt_tree);
@@ -749,6 +752,7 @@ phydbl *PHYREX_MCMC(t_tree *tree)
       PhyML_Fprintf(fp_stats,"%s\t","lnP");
       PhyML_Fprintf(fp_stats,"%s\t","alnL");
       PhyML_Fprintf(fp_stats,"%s\t","glnL");
+      PhyML_Fprintf(fp_stats,"%s\t","coalescent");
       PhyML_Fprintf(fp_stats,"%s\t","clock");
       PhyML_Fprintf(fp_stats,"%s\t","evolrate");
       PhyML_Fprintf(fp_stats,"%s\t","lbda");
@@ -881,6 +885,7 @@ phydbl *PHYREX_MCMC(t_tree *tree)
           PhyML_Fprintf(fp_stats,"%g\t",tree->c_lnL+tree->mmod->c_lnL+tree->rates->c_lnL_rates);
           PhyML_Fprintf(fp_stats,"%g\t",tree->c_lnL);
           PhyML_Fprintf(fp_stats,"%g\t",tree->mmod->c_lnL);
+          PhyML_Fprintf(fp_stats,"%g\t",tree->times->c_lnL_times);
           PhyML_Fprintf(fp_stats,"%g\t",tree->rates->clock_r);
           PhyML_Fprintf(fp_stats,"%g\t",RATES_Realized_Substitution_Rate(tree));
           PhyML_Fprintf(fp_stats,"%g\t",tree->mmod->lbda);
@@ -975,6 +980,7 @@ phydbl *PHYREX_MCMC(t_tree *tree)
           tree->mcmc->sample_num++;
         }
 
+
       if(!strcmp(tree->mcmc->move_name[move],"phyrex_lbda"))
         MCMC_PHYREX_Lbda(tree);
 

diff --git a/src/rrw.c b/src/rrw.c
@@ -20,12 +20,10 @@ phydbl RRW_Lk(t_tree *tree)
   phydbl d_fwd,d_ic,d_coal,d_sigsq_scale;
   phydbl t_dum;
   int idx_dum;
-
+      
   assert(tree->mmod->id == RRW);
 
   #ifdef PHYREX
-  /* PHYREX_Update_Lindisk_List(tree); */
-  /* PHYREX_Ldsk_To_Tree(tree); */
   if(PHYREX_Total_Number_Of_Intervals(tree) > tree->mmod->max_num_of_intervals) return UNLIKELY;
   #endif
 
@@ -41,7 +39,6 @@ phydbl RRW_Lk(t_tree *tree)
   // Make sure node times are set back to their original values
   assert(fabs(t_dum - tree->times->nd_t[idx_dum]) < 1.E-4);
 
-  tree->times->c_lnL_times = d_coal;
   /* tree->mmod->c_lnL = d_fwd - d_ic + d_coal + d_sigsq_scale; */
   tree->mmod->c_lnL = d_fwd + d_coal + d_sigsq_scale;
 

diff --git a/src/times.c b/src/times.c
@@ -864,7 +864,6 @@ phydbl TIMES_Wrap_Lk_Coalescent(t_edge *b, t_tree *tree, supert_tree *stree)
 /*////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////*/
 
-
 phydbl TIMES_Lk_Coalescent(t_tree *tree)
 {
   t_node *n;

diff --git a/src/utilities.h b/src/utilities.h
@@ -17,6 +17,7 @@ the GNU public licence. See http://www.opensource.org for details.
 
 #define _POSIX_C_SOURCE 200112L
 
+
 #include <stdio.h>
 #include <stdarg.h>
 #include <stdlib.h>