(milestone) ready for monte carlo iterations

analysis/etc/detectors_jitters.yaml

 MC config:
-  UUID: '000000'
-  style: center
-  when: '2024-01-27 15:35:54.582813'
-U3O8: 0.0
-UF4: 0.0
-bleu: 0.0
-gris: 0.0
-pm_U3O8: 1.0
-pm_UF4: 1.0
+  UUID: b6c84d
+  style: mc
+  when: '2024-02-02 07:24:26.599547'
+U3O8: -0.07206028767999986
+UF4: -0.026505841150632217
+bleu: -4.237939034819274
+gris: 8.591494689546018
+pm_U3O8: 0.1
+pm_UF4: 0.1
 pm_bleu: 10.0
 pm_gris: 10.0
 pm_rouge: 10.0
 pm_vert: 10.0
-rouge: 0.0
-small_time_jitter: 1.0
+rouge: 0.19981474452169223
+small_time_jitter: 0.1
+src_U3O8: 0.0
+src_UF4: 0.0
+src_bleu: 0.0
+src_gris: 0.0
+src_rouge: 0.0
+src_vert: 0.0
 time_jitter: 10.0
-vert: 0.0
+vert: 4.632546185041605

analysis/etc/fc_dof.yaml

 FC_DOF:
-  U3O8: 27.3981
-  UF4: 27.285
+  U3O8: 27.39609879404094
+  UF4: 27.29551493294423
+  src_U3O8: 27.3981
+  src_UF4: 27.285
   u_U3O8: 0.005
   u_UF4: 0.005
 MC config:
-  UUID: '000000'
-  style: center
-  when: '2024-01-27 15:35:54.582813'
+  UUID: b6c84d
+  style: mc
+  when: '2024-02-02 07:24:26.599547'
 SPEED_OF_LIGHT: 0.299792458
 TNT_TS_STEP: 10.0
-uncert_FC_DOF:
-  U3O8: 0.005
-  UF4: 0.005

analysis/etc/fc_flux_factors.yaml

@@ -3,14 +3,13 @@ FC_DENSITY:
   U3O8: 9.912e-07
   UF4: 8.2978e-07
 FC_EFF:
-  U3O8: 0.776
-  UF4: 0.944
+  U3O8: 0.7808238101057202
+  UF4: 0.9391766127324924
+  src_U3O8: 0.776
+  src_UF4: 0.944
   u_U3O8: 0.04
   u_UF4: 0.021
 MC config:
-  UUID: '000000'
-  style: center
-  when: '2024-01-27 15:35:54.582813'
-u_FC_EFF:
-  U3O8: 0.04
-  UF4: 0.021
+  UUID: b6c84d
+  style: mc
+  when: '2024-02-02 07:24:26.599547'

analysis/etc/fc_flux_spect.yaml

-min_neutron_energy: 20.0
+min_neutron_energy: 10.0
 max_neutron_energy: 27000.0
 
 number_of_bins: 26990
 
-#nf_eval: 'ENDF/B-VIII.0: U-235(N,F)'
-nf_eval: 'ENDF/B-VII.1: U-235(N,F)'
+nf_eval: 'ENDF/B-VIII.0: U-235(N,F)'
+#nf_eval: 'ENDF/B-VII.1: U-235(N,F)'
 
 smoothing: 25
\ No newline at end of file

analysis/etc/ge_dof.yaml

-GE_DOF: 28.8168
+GE_DOF: 28.818582266009173
 MC config:
-  UUID: '000000'
-  style: center
-  when: '2024-01-27 15:35:54.582813'
+  UUID: b6c84d
+  style: mc
+  when: '2024-02-02 07:24:26.599547'
+src_GE_DOF: 28.8168
 u_GE_DOF: 0.005

analysis/etc/mc_source_files.d/detectors_jitters.yaml

@@ -2,7 +2,7 @@
 
 time_jitter: &B 10.0 # ns
 
-small_time_jitter: &A 1.0 # nanoseconds
+small_time_jitter: &A 0.1 # nanoseconds
 
 U3O8: 0.0
 pm_U3O8: *A

analysis/etc/mc_source_files.d/fc_dof.yaml

 # Reference file
 
 
-uncert_FC_DOF: 
-    U3O8: &A 0.005
-    UF4: &B 0.005
-    
 FC_DOF: 
     U3O8: 27.3981
-    u_U3O8: *A
+    u_U3O8: 0.005
     UF4: 27.285
-    u_UF4: *B
+    u_UF4: 0.005
 
     
 SPEED_OF_LIGHT: 0.299792458 # meters per nanoseconds

analysis/etc/mc_source_files.d/fc_flux_factors.yaml

-u_FC_EFF: 
-    U3O8: &A 0.04
-    UF4: &B 0.021
 
 FC_EFF: 
     U3O8: 0.776
-    u_U3O8: *A
+    u_U3O8: 0.04
     UF4: 0.944
-    u_UF4: *B
+    u_UF4: 0.021
     
 # Density in atoms per barns
 FC_DENSITY:

analysis/etc/neutron_loss.yaml

 MC config:
-  UUID: '000000'
-  style: center
-  when: '2024-01-27 15:35:54.582813'
-neutron loss: 0.018
+  UUID: b6c84d
+  style: mc
+  when: '2024-02-02 07:24:26.599547'
+neutron loss: 0.0180423773551037
 neutron loss uncertainty: 0.001
+src_neutron loss: 0.018
 u_neutron loss: 0.001

analysis/etc/target.yaml

 MC config:
-  UUID: '000000'
-  style: center
-  when: '2024-01-27 15:35:54.582813'
+  UUID: b6c84d
+  style: mc
+  when: '2024-02-02 07:24:26.599547'
 isotope of interest: 183W
-nuclei density: 0.00312079131
+nuclei density: 0.003206273965277562
 nuclei density uncertainty: 0.00031066
 nuclei density unit: nuclei par barn
+src_nuclei density: 0.00312079131
 u_nuclei density: 0.00031066

analysis/run_on_cc.sh

 #!/bin/bash
 
 #SBATCH --ntasks 4
-#SBATCH --mem 12000
-#SBATCH --time 0-20:00:00             
+#SBATCH --mem 10000
+#SBATCH --time 0-05:00:00
+# For MC jobs, the requirements in time and memory have been scaled
+# down (20h -> 5h, 12GB to 10) to make ressource allocation easier
 # #SBATCH --mail-user=ghenning@iphc.cnrs.fr 
 # #SBATCH --mail-type=END,FAIL
 
 
 export LC_ALL="en_US.UTF-8"
 
-echo "# [STARTING]"
+echo "# [STARTING] job: $SLURM_JOB_ID "
 date
 
 echo "# Setting up the environnement"
@@ -27,12 +29,14 @@ python --version
 
 echo -e "-*-..........-*-\n"
 
-echo $TMPDIR
+# echo $TMPDIR
 
+echo "# building C++ tool for filling into 2D histograms"
 pwd && cd src/fill_into_h2/ && make binaries && cp bin/fill_into_h2.`hostname` ../../bin/ && cd ../.. && pwd
+echo "# ... done"
 
 echo "# Running tasks"
-./run_task tasks/do_start_new_iter.py  iter=center
+./run_task tasks/do_start_new_iter.py  iter=mc
 echo -n "# Iteration UUID: "
 cat etc/uuid.txt
 #echo "#... export efficiencies"
@@ -48,8 +52,18 @@ cat etc/uuid.txt
 # echo "#... FC cut 2D and project on time"
 # ./run_task tasks/do_fc_cut_and_project.py
 echo "#... FC -> neutron flux [MC]"
-echo " XXXXXXXXX SUPRESSED FOR NOW XXXXXXXXXXXXX"
-#./run_task tasks/do_fc_to_flux.py
+./run_task tasks/do_fc_to_flux.py
+if [ $? != 0 ]; then 
+    echo "# FC to flux task failed -- that happens sometime (I/O issue ?)"; 
+    echo "# RETRYING"
+    ./run_task tasks/do_fc_to_flux.py
+    if [ $? != 0 ]; then 
+        echo "# FC to flux task failed again"; 
+        echo "# Aborting"
+        cat etc/uuid.txt >> failed.txt
+        exit 1
+    fi
+fi
 #  echo "#... ge_time_align"
 # ./run_task tasks/do_ge_timealign.py
 # echo "#... ge_calibrate"
@@ -73,6 +87,7 @@ rm -rf `hostname`_env
 
 echo "... done"
 date 
+echo "# [END] job $SLURM_JOB_ID "
 echo "..."
 echo " .."
 echo "  ."

analysis/start_chain_jobs.sh

+# Starting N jobs in chain
+
+job_to_run=$1
+Njobs=$2
+
+# rm chained_jobs.txt
+
+echo "# == Chained Jobs =="
+echo "# Will run $job_to_run $Njobs times one after the other."
+
+prev_job=$(sbatch --parsable $job_to_run)
+echo -n "# [submitting job] $job_to_run ($prev_job) : " 
+date 
+for i in $(seq $((Njobs-1))); do
+    prev_job=$(sbatch --parsable --dependency=afterok:$prev_job $job_to_run)
+    echo -n "# [submitting job] $job_to_run ($prev_job) : " 
+    date 
+done
+

analysis/tasks/do_collect_iter_results.py

@@ -34,7 +34,7 @@ def task_collect_flux():
             'targets': [this_target_file],
             'actions': [
                 (create_folder, (target_dir,)),
-                f"cp -rv {this_flux_file} {this_target_file}",
+                f"cp {this_flux_file} {this_target_file}",
                 f"./env.run scripts/Draw1Dh.py {this_target_file}",
             ]
         }
@@ -56,8 +56,8 @@ def task_collect_integral_xs():
                     'targets': [trgt_file, trgt_uncert_file],
                     'actions': [
                         (create_folder, (target_dir,)),
-                        f"cp -rv {src_file} {trgt_file}",
-                        f"cp -rv {src_uncert_file} {trgt_uncert_file}",
+                        f"cp {src_file} {trgt_file}",
+                        f"cp {src_uncert_file} {trgt_uncert_file}",
                         f"./env.run scripts/Draw1Dh.py {trgt_file}",
                     ]
                 }
@@ -73,7 +73,7 @@ def task_collect_etc():
             'file_dep': ['etc/mc_source_files.yaml'],
             'targets': [target_file],
             'actions':[
-                f"cp -rv etc/{src_file} {target_file}",
+                f"cp etc/{src_file} {target_file}",
             ],
     }
 # EOF

analysis/tasks/do_extract_transitions_gnum.py

@@ -365,6 +365,38 @@ def task_divide_by_efficiency():
                 ],
             }
     return None
+
+def task_multiply_err_by_mu():
+    '''correct errors for sum consitency'''
+    def _multiply_err_by_mu(source_err_file: str,
+                           mu_file: str,
+                           dest_err_file: str) -> str:
+        mu = max(1.0, yaml.load(open(mu_file), Loader=yaml.Loader).get('mu', 1.0))
+        return f"./env.run scripts/divide1D.py --scale={1.0/mu}  {source_err_file} > {dest_err_file}"
+    
+    for this_transition in the_transitions.keys():
+        for ge_det in Ge_detectors:
+            flavor ='clean'
+            source_err_file = f"./output/transitions/{this_transition}/{ge_det}_{flavor}.gcount_err.puscu.effcorr.txt"
+            dest_err_file = f"./output/transitions/{this_transition}/{ge_det}_{flavor}.gcount_err.puscu.effcorr.mucorr.txt"
+            mu_file = f"./output/transitions/{this_transition}/{ge_det}_{flavor}.projEg_and_fits.checksum.txt" # file is actually yaml
+            yield {
+                'name': dest_err_file,
+                'file_dep': [source_err_file,
+                             mu_file],
+                'targets': [dest_err_file],
+                'actions':[
+                     (create_folder, (f"./output/transitions/{this_transition}/",)),
+                     CmdAction((_multiply_err_by_mu, 
+                                  [], {
+                                      'source_err_file': source_err_file,
+                                      'mu_file': mu_file,
+                                      'dest_err_file': dest_err_file,
+                                  })),
+                      f"./env.run scripts/Draw1Dh.py {dest_err_file}",
+                ],
+            }
+    return None
                         
 # def task_project_transitions_signal():
 #     '''project transitions bidim according to signal'''

analysis/tasks/do_fc_to_flux.py

@@ -86,6 +86,7 @@ def task_FC_spect_to_perkeV():
         yield {
             'name': f"{FC_det} {source_file} -> {target_file}",
             'file_dep': [source_file],
+            'task_dep':['FC_time_to_en'],
             'targets': [target_file],
             'actions': [
                 (spect_to_perkeV, None, {'source_file': source_file,
@@ -109,7 +110,7 @@ def task_interpolate_perkeV():
         # interpolating
         hinterpolator = interp1d(*hsrc.xy(),
                                  kind='quadratic',
-                                 fill_value=1.0e-30)
+                                 fill_value=1.0e-30, bounds_error=False)
 
         for i, b in enumerate(htrgt):
             htrgt.bins[i].count = max(0, hinterpolator(b.center()))
@@ -150,10 +151,13 @@ def task_divide_per_sigmanf():
         evalinterpolator = interp1d(list([pts['x']*1000. for pts in the_eval_pts]),
                                     list([pts['y']*1.0 for pts in the_eval_pts]),
                                     kind='linear', #'linear'
-                                    fill_value="extrapolate")
+                                    fill_value='extrapolate', bounds_error=False)
         
         for i, b in enumerate(hsrc):
-            htrgt.bins[i].count = b.count / evalinterpolator(b.center())
+            if evalinterpolator(b.center()) >= 0:
+                htrgt.bins[i].count = b.count / evalinterpolator(b.center())
+            else:
+                htrgt.bins[i].count = 0.
         open(target_file, 'w').write(str(htrgt))
         return True
     

analysis/tasks/do_make_transitions_xs.py

@@ -45,7 +45,7 @@ def task_gcount_time_to_energy():
             for flavor in ('clean',):
                 source_file = f"./output/transitions/{this_transition}/{ge_det}_{flavor}.gcount.puscu.effcorr.txt"
                 dest_file = f"./output/transitions/{this_transition}/{ge_det}_{flavor}.gcount.puscu.effcorr.perenergy.txt"
-                source_err_file = f"./output/transitions/{this_transition}/{ge_det}_{flavor}.gcount_err.puscu.effcorr.txt"
+                source_err_file = f"./output/transitions/{this_transition}/{ge_det}_{flavor}.gcount_err.puscu.effcorr.mucorr.txt"
                 dest_err_file = f"./output/transitions/{this_transition}/{ge_det}_{flavor}.gcount_err.puscu.effcorr.perenergy.txt"
                 yield {
                     'name': source_file,