Merge branch 'developing' of https://github.com/JADE-V-V/JADE into apply_corrections

Author: mcampos16

.github/workflows/pytest.yml

@@ -78,6 +78,7 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           set -o pipefail
+          git config --global http.sslBackend schannel
           source /usr/local/Modules/init/sh
           pytest --cov=. -cov-config=jade.coveragerc --cov-report xml
         env:
@@ -89,6 +90,7 @@ jobs:
       - name: Testing - Windows
         if: runner.os == 'Windows'
         run: |
+          git config --global http.sslBackend schannel
           pytest
         env:
           ACCESS_TOKEN_GITHUB: ${{ secrets.ACCESS_TOKEN_GITHUB }}

docs/source/dev/insertbenchmarks.rst

@@ -56,6 +56,8 @@ OpenMC
   `OpenMC documentation <https://docs.openmc.org/en/stable/usersguide/settings.html#compiled-sources>`_.
 - If the model uses weight windows, a weight windows file in HDF5 format should be provided.
   The file should be named ``weight_windows.h5``. This weight window will be used in simulation if it is provided.
+- If dosimetry calculations are required, the IRDFF-II data library should be used and can be implemented using an ``openmc.EnergyFunctionFilter``
+  which is outlined in this `notebook <https://nbviewer.org/gist/paulromano/842b1df9eb2003747e2fd6d95514129a>`.
 - The tallies IDs should be explicitly fixed when creating the ``tallies.xml`` file. This prevents
   OpenMC from creating them automatically and, thus, potentially changing them between different runs
   of a same benchmark. If possible, the tallies identifiers should be the same as the ones used in the

docs/source/documentation/benchdesc/ISIS-800MeV-C.rst

@@ -1,13 +1,16 @@
 ISIS Benchmark Experiment on Deep-Penetration Neutrons through Concrete and Iron Shields WITH 800 MeV PROTONS
--------
 
 .. important::
 
-    This benchmark is part of the SINBAD collection and cannot be freely distributed with JADE.
 
-The purpose of this experiment was to measure the deep-penetration neutrons through a thick bulk shield at an intense spallation neutron source facility, ISIS, of the Rutherford Appleton Laboratory (RAL), United Kingdom. 
-The experiments were performed with 800MeV protons. The protons stopped on a Tantalum target of 30cm effective thickness, located in a vacuum chamber and cooled by heavy water (D2O).  
-Different measurements were performed during the experiments to fully cover the neutron spectrum, including solid state neutron track detectors (SSNTD), thermoluminiscent dosimeters (TLD), activation detectors and an indium activation multi-moderator detector. The fast neutron flux was measured with the activation threshold detectors by using the C12(n,2n)C11, Al27(n,a)Na24 and the various threshold Bi209(n,xn)Bi210-x reactions. The activation of C12 dosimeters was measured between layers of ordinary concrete and steel located on top of the biological shield, i.e. at an emission angle of 90º relative to beam direction.
+    This benchmark is part of the SINBAD collection and cannot be freely distributed with JADE.
+
+    The purpose of this experiment was to measure the deep-penetration neutrons through a thick bulk shield at an intense spallation neutron source facility, ISIS, of the Rutherford Appleton Laboratory (RAL), United Kingdom.
+
+The experiments were performed with 800MeV protons. The protons stopped on a Tantalum target of 30cm effective thickness, located in a vacuum chamber and cooled by heavy water (D2O).
+
+Different measurements were performed during the experiments to fully cover the neutron spectrum, including solid state neutron track detectors (SSNTD), thermoluminiscent dosimeters (TLD), activation detectors and an indium activation multi-moderator detector. The fast neutron flux was measured with the activation threshold detectors by using the C12(n,2n)C11, Al27(n,a)Na24 and the various threshold Bi209(n,xn)Bi210-x reactions. The activation of C12 dosimeters was measured between layers of ordinary concrete and stell located on top of the biological shield, i.e. at an emission angle of 90º relative to beam direction.
+
 In this experiment additional shielding slabs of ordinary concrete and iron were placed upon the top center of the bulk shield just above the target, as shown in Fig. 1. 
 Figs. 2 - 4 show photos of this experiment at the top of the target station. The additional 
 concrete and iron were assembled by 119-cm-diameter by 20-cm-thick slabs of 2.36-g/cm3 

docs/source/documentation/benchdesc/fng/fng-hcpb.rst

@@ -70,6 +70,19 @@ where :math:`{\lambda}` is the decay constant, :math:`n_{tot}` is the total neut
 mass is for an individual pellet. This normalisation is included in the MCNP input file so the raw output
 can be directly compared to the measured data. 
 
+OpenMC model
+^^^^^^^^^^^^
+To allow for the simulation to run in OpenMC, vacuum boundary conditions were set for all outer surfaces of the geometry. 
+
+OpenMC tallies
+^^^^^^^^^^^^^^
+The reaction rates are calcaulated using a flux tally and an EnergyFunctionFilter, corresponding to the cross-section data for the nuclide being tallied over.  
+To make the results comparable to the experimental data, the raw output from OpenMC must be divided by the volume of the foils.
+
+The tritium production was tallied using the (n,Xt) score in OpenMC. The specific activity is then calculated in the same way as for MCNP, 
+but factors have to be folded in during post-processing. 
+
+
 Patch file
 ^^^^^^^^^^
 Coming soon... 

docs/source/documentation/benchmarks.rst

@@ -95,3 +95,5 @@ Experimental Benchmarks
 .. include:: benchdesc/rcr/rcr-ss.rst
 
 .. include:: benchdesc/rcr/rcr-fe+ni.rst
+
+.. include:: benchdesc/ISIS-800MeV-C.rst

src/jade/app/fetch.py

@@ -90,8 +90,9 @@ def fetch_from_gitlab(
     gl = gitlab.Gitlab(url=url, private_token=authorization_token, ssl_verify=False)
     try:
         gl.auth()
-    except gitlab.exceptions.GitlabAuthenticationError:
+    except gitlab.exceptions.GitlabAuthenticationError as e:
         logging.error("Gitlab authentication failed")
+        logging.error(e)
         return False
 
     # select the correct project

src/jade/resources/default_cfg/benchmarks_pp/raw/mcnp/FNG-HCPB.yaml

@@ -67,7 +67,7 @@ _cell_id_h3: &depth_h3
   16055: 28.410
   16059: 28.411
   16063: 28.412
-_cell_id_h3: &depth_h3d
+_cell_id_h3d: &depth_h3d
   16016: [9.5, 01]
   16020: [9.5,02]
   16024: [9.5,03]
@@ -127,5 +127,4 @@ Tritium activity:
 
 Tritium activity Pellet:
   concat_option: no_action
-  84: [[add_column_with_dict, {'ref_column': 'Cells', 'values': *depth_h3d, new_columns: [ 'Distance','Pellet']}],[replace, {'column': 'Cells', 'values': *depth_h3}]]
-
+  84: [[add_column_with_dict, {'ref_column': 'Cells', 'values': *depth_h3d, new_columns: [ 'Distance','Pellet']}],[replace, {'column': 'Cells', 'values': *depth_h3}]]

src/jade/resources/default_cfg/benchmarks_pp/raw/openmc/FNG-HCPB.yaml

@@ -0,0 +1,139 @@
+# Define anchors to be used in the file.
+# Use _ prefix to avoid confusing the jade parser.
+_cell_id_foils: &depth_foils
+  48001: 4.10115
+  48002: 10.40115
+  48003: 16.70115
+  48004: 23.00115
+  58001: 4.10115
+  58002: 10.40115
+  58003: 16.70115
+  58004: 23.00115
+  38001: 4.10115
+  38002: 10.40115
+  38003: 16.70115
+  38004: 23.00115
+  28000: 0.0
+  28001: 4.10115
+  28002: 10.40115
+  28003: 16.70115
+  28004: 23.00115
+_cell_id_h3: &depth_h3
+  16016: 9.501
+  16020: 9.502
+  16024: 9.503
+  16028: 9.504
+  16032: 9.505
+  16036: 9.506
+  16040: 9.507
+  16044: 9.508
+  16048: 9.509
+  16052: 9.510
+  16056: 9.511
+  16060: 9.512
+  16017: 15.801
+  16021: 15.802
+  16025: 15.803
+  16029: 15.804
+  16033: 15.805
+  16037: 15.806
+  16041: 15.807
+  16045: 15.808
+  16049: 15.809
+  16053: 15.810
+  16057: 15.811
+  16061: 15.812
+  16018: 22.101
+  16022: 22.102
+  16026: 22.103
+  16030: 22.104
+  16034: 22.105
+  16038: 22.106
+  16042: 22.107
+  16046: 22.108
+  16050: 22.109
+  16054: 22.110
+  16058: 22.111
+  16062: 22.112
+  16019: 28.401
+  16023: 28.402
+  16027: 28.403
+  16031: 28.404
+  16035: 28.405
+  16039: 28.406
+  16043: 28.407
+  16047: 28.408
+  16051: 28.409
+  16055: 28.410
+  16059: 28.411
+  16063: 28.412
+_cell_id_h3d: &depth_h3d
+  16016: [9.5, 01]
+  16020: [9.5,02]
+  16024: [9.5,03]
+  16028: [9.5,04]
+  16032: [9.5,05]
+  16036: [9.5,06]
+  16040: [9.5,07]
+  16044: [9.5,08]
+  16048: [9.5,09]
+  16052: [9.5,10]
+  16056: [9.5,11]
+  16060: [9.5,12]
+  16017: [15.8,01]
+  16021: [15.8,02]
+  16025: [15.8,03]
+  16029: [15.8,04]
+  16033: [15.8,05]
+  16037: [15.8,06]
+  16041: [15.8,07]
+  16045: [15.8,08]
+  16049: [15.8,09]
+  16053: [15.8,10]
+  16057: [15.8,11]
+  16061: [15.8,12]
+  16018: [22.1,01]
+  16022: [22.1,02]
+  16026: [22.1,03]
+  16030: [22.1,04]
+  16034: [22.1,05]
+  16038: [22.1,06]
+  16042: [22.1,07]
+  16046: [22.1,08]
+  16050: [22.1,09]
+  16054: [22.1,10]
+  16058: [22.1,11]
+  16062: [22.1,12]
+  16019: [28.4,01]
+  16023: [28.4,02]
+  16027: [28.4,03]
+  16031: [28.4,04]
+  16035: [28.4,05]
+  16039: [28.4,06]
+  16043: [28.4,07]
+  16047: [28.4,08]
+  16051: [28.4,09]
+  16055: [28.4,10]
+  16059: [28.4,11]
+  16063: [28.4,12]
+# Fluxes
+Reaction rate:
+  concat_option: no_action
+  4:  
+      - [volume, {}]
+      - [replace, {'column': 'Cells', 'values': *depth_foils}]
+
+Tritium activity:
+  concat_option: no_action
+  84: 
+      - [mass, {}]
+      - [scale, {'factor': 2.57042574E+07}]
+      - [replace, {'column': 'Cells', 'values': *depth_h3}]
+
+Tritium activity Pellet:
+  concat_option: no_action
+  84: 
+      - [mass, {}]
+      - [scale, {'factor': 2.57042574E+07}]
+      - [add_column_with_dict, {'ref_column': 'Cells', 'values': *depth_h3d, new_columns: [ 'Distance','Pellet']}]
+      - [replace, {'column': 'Cells', 'values': *depth_h3}]  

src/jade/resources/default_cfg/run_cfg.yml

@@ -239,4 +239,15 @@ IPPE-CF:
   custom_input: 
   nps: 1e8
   description: IPPE 252Cf experiment
+  only_input: false
+#
+FNG_HCPB:
+  codes:
+    d1s: []
+    mcnp: []
+    openmc: []
+    serpent: []
+  custom_input: 
+  nps: 1e8
+  description: FNG Helium Cooled Pebble Bed TBM Experiment
   only_input: false

src/jade/run/benchmark.py

@@ -113,7 +113,7 @@ def write(self, output_folder: PathLike):
             path to the output folder.
         """
         # write the input to the output folder
-        self.input._write(output_folder)
+        self.input.write(output_folder)
 
     def print_metadata(self, outpath: PathLike, metadata_file: PathLike):
         """Print the metadata of the run to the output folder.