documentation, as well as correcting a mistake in neutron loss in air between...

documentation, as well as correcting a mistake in neutron loss in air between FC and target. Thankfully, since there was compensating mistakes, the result is not affected

AUTHORS

+HENNING Greg
\ No newline at end of file

README.md

-# Analysis of 183W reactions
+# Analysis code for extracting 183W(n, n' γ) cross section from Grapheme data
 
 
-## 2021-05-28
 
-I intend to extract just a few trnasitions : 1 or 2 n,n' and 1 or 2 n,2n
-
-Looking at the talys predictions, it looks like 182L02L01 and L03L02 will be the easier to look at with less conversion and higher cross section. So that will be my goal. If I manage to extrcat just these two and make a precise 1/ comaprison with model and 2/ give precise uncertainties and covariance, I will be proud of myself.
-
-As far as n, n' goes, there is the issue of the isomers. 
-Maybe the trnasition at 291 keV could be ok, also 313...
+## Requirements
 
+## `log_of_data.txt`
 
+The file `log_of_data.txt` is an extract from Ph. Dessagne's *logbook* file listing 
 **Data list** : from logs, I will keep :
 ``
    Sample is 183W #4 
@@ -24,7 +20,7 @@ Maybe the trnasition at 291 keV could be ok, also 313...
 /rawgrace12b/data-geel/2012/semaine10-w183-4
 ```
 
-Analysis with https://gitlab.in2p3.fr/gregoire.henning/pytnt-old-version/-/tree/master/ ? and a true pipeline using
+# requirements
 
 Pyhisto, numpy (for cov)
 doit, ...
@@ -36,7 +32,11 @@ in a real agile developpement provcess
  - and so on
  - cearte an environnement
  - have things ready to switch from tnt files to faster files
- 
-## Bleu gain drift a lot during semaine12.
 
-For the prelimiary part, I'll get the week (all det) out of the validated data week
\ No newline at end of file
+## Authors
+
+* **Greg Henning** - ghenning​*.at.*​iphc․cnrs․fr
+
+## License 
+
+This project is licensed under the [CeCILL-C FREE SOFTWARE LICENSE AGREEMENT](https://cecill.info/licences/Licence_CeCILL-C_V1-en.html). See [LICENSE.txt](LICENSE.txt) for more.
\ No newline at end of file

analysis/analysis log.md

-en semaine 16 : detecteur bleu et rouge donnent de muavais temps, energy, le vert et le rgis ont des soucis de temps --> je vais ignoer la semaine 16
\ No newline at end of file

analysis/etc/detectors_jitters.yaml

 MC config:
   UUID: '000000'
   style: center
-  when: '2024-03-02 18:05:25.490277'
+  when: '2024-03-16 10:54:15.019294'
 U3O8: 0.0
 UF4: 0.0
 bleu: 0.0

analysis/etc/fc_dof.yaml

@@ -6,6 +6,6 @@ FC_DOF:
 MC config:
   UUID: '000000'
   style: center
-  when: '2024-03-02 18:05:25.490277'
+  when: '2024-03-16 10:54:15.019294'
 SPEED_OF_LIGHT: 0.299792458
 TNT_TS_STEP: 10.0

analysis/etc/fc_flux_factors.yaml

-AIR_LOSS: 0.0001
+AIR_LOSS: 0.018
 FC_DENSITY:
   U3O8: 9.912e-07
   UF4: 8.2978e-07
@@ -10,4 +10,5 @@ FC_EFF:
 MC config:
   UUID: '000000'
   style: center
-  when: '2024-03-02 18:05:25.490277'
+  when: '2024-03-16 10:54:15.019294'
+u_AIR_LOSS: 0.001

analysis/etc/ge_dof.yaml

@@ -2,5 +2,5 @@ GE_DOF: 28.8168
 MC config:
   UUID: '000000'
   style: center
-  when: '2024-03-02 18:05:25.490277'
+  when: '2024-03-16 10:54:15.019294'
 u_GE_DOF: 0.005

analysis/etc/mc_source_files.d/fc_flux_factors.yaml

@@ -10,4 +10,5 @@ FC_DENSITY:
     U3O8: 9.912e-7
     UF4: 8.2978e-7
     
-AIR_LOSS: 0.0001
+AIR_LOSS: 0.018
+u_AIR_LOSS: 0.001
\ No newline at end of file

analysis/etc/mc_source_files.d/neutron_loss.yaml

-# Reference file
-
-neutron loss: 0.018
-neutron loss uncertainty: &B 0.001
-u_neutron loss: *B
\ No newline at end of file

analysis/etc/mc_source_files.yaml

@@ -2,7 +2,6 @@ files: [
     fc_dof.yaml,
     ge_dof.yaml,
     target.yaml,
-    neutron_loss.yaml,
     detectors_jitters.yaml,
     fc_flux_factors.yaml
 ]

analysis/etc/neutron_loss.yaml

-MC config:
-  UUID: '000000'
-  style: center
-  when: '2024-03-02 18:05:25.490277'
-neutron loss: 0.018
-neutron loss uncertainty: 0.001
-u_neutron loss: 0.001

analysis/etc/target.yaml

 MC config:
   UUID: '000000'
   style: center
-  when: '2024-03-02 18:05:25.490277'
+  when: '2024-03-16 10:54:15.019294'
 isotope of interest: 183W
 nuclei density: 0.00312079131
 nuclei density uncertainty: 0.00031066

analysis/run_on_cc.sh

@@ -36,9 +36,6 @@ pwd && cd src/fill_into_h2/ && make binaries && cp bin/fill_into_h2.`hostname` .
 echo "# ... done"
 
 echo "# Running tasks"
-./run_task tasks/do_start_new_iter.py  iter=center
-echo -n "# Iteration UUID: "
-cat etc/uuid.txt
 #echo "#... export efficiencies"
 #./env.run scripts/make_efficiency.py
 # echo "#... raw2histo"
@@ -51,19 +48,6 @@ cat etc/uuid.txt
 # ./run_task tasks/do_fc_pileup.py
 # echo "#... FC cut 2D and project on time"
 # ./run_task tasks/do_fc_cut_and_project.py
-echo "#... FC -> neutron flux [MC]"
-./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"
@@ -74,6 +58,22 @@ fi
 #./run_task tasks/do_ge_inel.py
 #echo "#... GE get pile up rate"
 #./run_task tasks/do_ge_pileup.py
+echo "# === Monte Carlo Loop ==="
+./run_task tasks/do_start_new_iter.py  iter=center
+echo -n "# Iteration UUID: "
+cat etc/uuid.txt
+echo "#... FC -> neutron flux [MC]"
+./run_task tasks/do_fc_to_flux.py
+# if [ $? != 0 ]; then 
+#     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 "#... getting time limits for Ge"
 ./run_task tasks/do_ge_timelimits.py
 echo "#... getting the transitions yields"
@@ -82,6 +82,9 @@ echo "#... Finishing up to get the cross section"
 ./run_task tasks/do_make_transitions_xs.py
 echo "#... Collecting ouputs of MC iteration"
 ./run_task tasks/do_collect_iter_results.py
+
+echo "# === END of Monte Carlo Loop ==="
+
 echo "#... Checking convergence"
 ./run_task tasks/do_MC_convergence_report.py
 echo "#... Making mean, std, cov and corr"

analysis/tasks/do_make_transitions_xs.py

@@ -150,15 +150,12 @@ def task_divide_gcount_per_flux():
                 }
 
 def task_multiply_by_final_factor():
-    '''divide by the number of target atoms per barns and neutron loss'''
     def multiply_by_final_factor(hfile: str,
                                  N_target_file: str,
-                                 Neutron_loss_file:str,
                                  dest_file: str):
         hsource = Histogram(fromfile=hfile)
         N_target = yaml.load(open(N_target_file), Loader=yaml.Loader)['nuclei density']
-        Neutron_loss = yaml.load(open(Neutron_loss_file), Loader=yaml.Loader)['neutron loss']
-        final_factor = 1. /(N_target * (1.0 - Neutron_loss))
+        final_factor = 1. / N_target
         
         hout= hsource.copy()
         for b in hout:
@@ -168,7 +165,6 @@ def task_multiply_by_final_factor():
         return True
     
     N_target_file = './etc/target.yaml'
-    Neutron_loss_file = 'etc/neutron_loss.yaml'
     for this_transition in the_transitions.keys():
         for this_FC in FC_detectors:
             for ge_det in Ge_detectors:
@@ -180,16 +176,14 @@ def task_multiply_by_final_factor():
                     
                 yield {
                     'name': f"{this_transition}.{this_FC}.{ge_det}.{flavor}",
-                    'file_dep': [source_file, source_err_file, N_target_file, Neutron_loss_file],
+                    'file_dep': [source_file, source_err_file, N_target_file],
                     'targets': [dest_file, dest_err_file],
                     'actions': [
                         (multiply_by_final_factor, [], {'hfile': source_file, 
                                                         'N_target_file': N_target_file,
-                                                        'Neutron_loss_file': Neutron_loss_file,
                                                         'dest_file': dest_file}),
                         (multiply_by_final_factor, [], {'hfile': source_err_file, 
                                                         'N_target_file': N_target_file,
-                                                        'Neutron_loss_file': Neutron_loss_file,
                                                         'dest_file': dest_err_file}),
                         f"./env.run scripts/Draw1Dh.py {dest_file}",
                         f"./env.run scripts/Draw1Dh.py {dest_err_file}",