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

Author: digiacomo4

.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 }}

README.md

@@ -1,4 +1,4 @@
-[![Testing](https://github.com/JADE-V-V/JADE/actions/workflows/pytest.yml/badge.svg?branch=master)](https://github.com/JADE-V-V/JADE/actions/workflows/pytest.yml)
+[![Testing](https://github.com/JADE-V-V/JADE/actions/workflows/pytest.yml/badge.svg?branch=developing)](https://github.com/JADE-V-V/JADE/actions/workflows/pytest.yml)
 [![Documentation Status](https://readthedocs.org/projects/jade-a-nuclear-data-libraries-vv-tool/badge/?version=latest)](https://jade-a-nuclear-data-libraries-vv-tool.readthedocs.io/en/latest/?badge=latest)
 [![codecov](https://codecov.io/gh/JADE-V-V/JADE/graph/badge.svg?token=C0Q75M9FVH)](https://codecov.io/gh/JADE-V-V/JADE)
 [![PyPi version](https://badgen.net/pypi/v/jadevv/)](https://pypi.org/project/jadevv)

docs/source/dev/insertbenchmarks.rst

@@ -54,6 +54,8 @@ OpenMC
   A compiled library file, ``libsource.so`` must be provided, which has been compiled using ``gcc`` 
   with shared libraries enabled. An example of how to compile an OpenMC source is provided in the
   `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.
 - 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
@@ -169,6 +171,8 @@ and the tallies themselves can be modified through the use of *modifiers*.
 The currently supported modifiers are:
 
 * ``no_action``: no action is taken on the tally. No arguments are expected.
+* ``volume``: a volume divisor is applied to the tally, obtained from a ``volumes.json`` file supplied with the bechmark inputs. No arguments are expected.
+* ``mass``: a mass divisor is applied to the tally, obtained from a ``volumes.json`` file supplied with the bechmark inputs, and OpenMC ``xml`` files. No arguments are expected.
 * ``scale``: the tally is scaled by a factor. The *factor* is expected as key argument and the provided value can 
   be either a float, and integer or a list (of floats or integers). 
 * ``lethargy``: a neutron flux tally is expected and converted to a neutron flux per unit lethargy.
@@ -241,6 +245,11 @@ The currently supported modifiers are:
   to be used for the cumulative sum, and *norm*, a boolean indicating whether to normalize the result with respect to the total sum (a percentage is returned).
   If no *column* argument is provided, the cumulative sum is computed on the 'Value' column by default. The argument *norm* is True by default.
 
+* ``gaussian_broadening``: applies Gaussian broadening to the 'Value' column. The optional keyarg to provide is *fwhm_frac*, 
+which specifies the fraction of the FWHM (Full Width at Half Maximum) to use for Gaussian broadening. This can be provided either 
+as a single float value, which will be applied uniformly to all energy bins, or as a list of float values with the same length as the 
+'Energy' column, allowing for a different broadening parameter for each energy bin. If not specified, the default value is 0.1 (10%).
+
 More than one modifiers can be applied in series to a single tally.
 If your benchmark requires a new modifier, please refer to :ref:`add_tally_mod`.
 
@@ -458,6 +467,13 @@ An example of plot configuration is shown below:
       shorten_x_name: 2
     select_runs: SphereSDDR_\d+_[A-Za-z]+-\d+_
 
+Update the documentation
+==============================
+
+The final step to add a new benchmark to JADE, assuming that no new functionalities are added, as detailed
+below, is to add the associated documentation. This includes a description of the benchmark as well as updating
+the overview table of implemented benchmarks in :ref:`benchmarks`.
+
 Implement new functionalities
 =============================
 

docs/source/dev/pp_gallery.rst

@@ -147,6 +147,8 @@ These are the extra ``plot_args`` that this type of plot can accept:
   in the same subplot. Default is false.
 * ``xscale``: The scale of the x-axis. Every argument that could be passed to the matplotlib function
   ``set_xscale()`` is accepted. Common ones are 'linear' or 'log'. Default is 'log'.
+* ``yscale``: The scale of the y-axis. Every argument that could be passed to the matplotlib function
+  ``set_yscale()`` is accepted. Common ones are 'linear' or 'log'. Default is 'log'.
 
 Ratio plot (ratio)
 ------------------

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

@@ -2,6 +2,7 @@ ISIS Benchmark Experiment on Deep-Penetration Neutrons through Concrete and Iron
 
 .. 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.
@@ -11,15 +12,10 @@ The experiments were performed with 800MeV protons. The protons stopped on a Tan
 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 
-
+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 
-
 density, and 119-cm-diameter by 10-cm-thick slabs of 7.8-g/cm3 density, respectively. 
-
 The concrete slabs contained iron mesh for reinforcement. 
-
 The experiment is identified as NEA-1552/38 in the SINBAD database.  
 
 Geometry and run parameters
@@ -74,16 +70,8 @@ Those quantities have been scored in a 0.1 mm thickness cylinder located at 90 d
 
 .. seealso:: **Related papers and contributions:** 
 
-OECD Nuclear Energy Agency Data Bank SINBAD, http://www.oecd-nea.org/science/wprs/shielding/sinbad/sinbadis.htm  
-
-T. Nunomiya, N. Nakao, P. Wright, T. Nakamura, E. Kim, T. Kurosawa, S. Taniguchi, M. Sasaki,, H. Iwase, Y. Uwamino, T. Shibata, S. Ito, D.R. Perry “Measurements of deep penetration of neutrons produced by 800MeV proton beam through concrete and iron at ISIS” Nuclear Instruments and Methods in Physics Research B179 (2001) 89-102. 
-
-S. Kitsos and I. Kodeli. SINBAD Compilation NEA-1552/21 “ISIS Deep-Penetration of Neutrons through Concrete and Iron shields” 
-
- 
-
-T. Nunomiya, N. Nakao, P. Wright, T. Nakamura, E. Kim, T. Kurosawa, S. Taniguchi, M. Sasaki,, H. Iwase, Y. Uwamino, T. Shibata, S. Ito, D.R. Perry. “Experimental Data of Deep Penetration Neutrons through a Concrete and Iron Shield at the ISIS Spallation Neutron Source Facility using an 800MeV Proton Beam” KEK Report 2001-24 (February 2002). 
-
- 
-
-Y. Uwamino, T Shibata, T. Ohkubo, S. Sato and D. Perry. Proceedings of SATIF-1, page 185. Arlington, Texas (1994). 
+    - OECD Nuclear Energy Agency Data Bank SINBAD, http://www.oecd-nea.org/science/wprs/shielding/sinbad/sinbadis.htm  
+    - T. Nunomiya, N. Nakao, P. Wright, T. Nakamura, E. Kim, T. Kurosawa, S. Taniguchi, M. Sasaki,, H. Iwase, Y. Uwamino, T. Shibata, S. Ito, D.R. Perry “Measurements of deep penetration of neutrons produced by 800MeV proton beam through concrete and iron at ISIS” Nuclear Instruments and Methods in Physics Research B179 (2001) 89-102. 
+    - S. Kitsos and I. Kodeli. SINBAD Compilation NEA-1552/21 “ISIS Deep-Penetration of Neutrons through Concrete and Iron shields” 
+    - T. Nunomiya, N. Nakao, P. Wright, T. Nakamura, E. Kim, T. Kurosawa, S. Taniguchi, M. Sasaki,, H. Iwase, Y. Uwamino, T. Shibata, S. Ito, D.R. Perry. “Experimental Data of Deep Penetration Neutrons through a Concrete and Iron Shield at the ISIS Spallation Neutron Source Facility using an 800MeV Proton Beam” KEK Report 2001-24 (February 2002). 
+    - Y. Uwamino, T Shibata, T. Ohkubo, S. Sato and D. Perry. Proceedings of SATIF-1, page 185. Arlington, Texas (1994). 

docs/source/documentation/benchdesc/itercylSDDR.rst

@@ -60,7 +60,7 @@ SDDR parameters
 The irradiation schedule considered for ITER Cylinder SDDR benchmark is
 reported hereafter:
 
-.. list-table:: Irradiation schedule (ITER SA2 irradiation scenario)
+.. list-table:: Irradiation schedule (Conservative ITER SA2 irradiation scenario)
     :header-rows: 1
 
     * - Source Intensity [n/s]
@@ -95,6 +95,11 @@ Two different cool-down times were considered in the photon tallies: 0s and 1e6
 That is, these are the time interval waited after the irradiation phase has finished before tallying
 the SDDR and the photon flux.
 
+.. note::
+    This scenario does not match exactly the official ITER SA2 irradiation scenario which has only 3
+    final pulses instead of 4. The results from JADE will be conservative with respect to the official
+    scenario. 
+
 The possible reactions considered during the simulation are listed in the following table:
 
 .. list-table:: List of parent-daughter couples generated by the considered reactions for the ITER Cylinder SDDR benchmark

docs/source/documentation/benchdesc/rcr/rcr-fe+ni.rst

@@ -0,0 +1,161 @@
+(RCR-Fe+Ni) RCR Iron/Nickel Sphere Experiment with 252Cf source
+------------------------------------------------------------------
+
+.. include:: /documentation/benchdesc/icbep_disclaimer.rst
+
+This benchmark was designed to evaluate fast neutron leakage spectra and neutron activation 
+from an Iron and Nickel sphere of 50cm of diameter and with a 252Cf (spontaneous fission) 
+neutron source placed in its centre. The experimental measurements were carried out in 2021 
+at the Neutron Source Laboratory (NSL) in the Research Centre Řež (RCR, Centrum Výzkumu Řež) 
+by the proton recoil method and by evaluating the reaction rates in irradiated activation foils. 
+
+The experiment is identified as ALARM-CF-Fe-SHIELD-002 in the ICSBEP database. 
+
+Benchmark structure
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The benchmark is organized into two single experimental case which just differs by the sphere material. 
+
+**Material** 
+    * Case-1: Iron 
+    * Case-2: Nickel
+**Objective**
+    #. measure the direct fast neutron leakage and its energy spectrum from the Fe sphere. 
+    #. measure the spatial distribution of neutron-induced reaction rates on the surface of the sphere. 
+**Method**
+    #. Proton recoil method using hydrogen proportional counters (HPD, 0.1-1.3 MeV neutrons) and a stilbene 
+    scintillation detector for 0.8-12 MeV neutrons, with digital pulse shape discrimination for neutron/gamma separation. 
+    #. Activation foils (58Ni(n, p)58Co, 115In(n, n')115m1) are placed at defined positions on the sphere surface and 
+    irradiated during the neutron leakage measurements. 
+
+Geometry and run parameters
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+**Sphere dimensions and materials**
+    * Case-1: 50 cm Fe sphere
+    * Case-2: 50 cm Ni Sphere
+**Density**
+    * Case-1 Iron sphere: 7.85 :math:`g/cm^3`
+    * Case-2 Nickel sphere: 8.89 :math:`g/cm^3`
+**Material**
+    Composition determined by XRF analysis:
+    * Case-1 Iron sphere: Fe 99.737%, Mn 0.075%, P 0. 025%, C 0.04%, S 0.026%, Al 0.005%, Mo 0. 01%, Cr 0.02%, Cu 0.062%. 
+    * Case-2 Nickel sphere: Ni 99.631%, Mo 0.007%, Fe 0.21%, W 8.45E-05%, Al 0.102%, Gd 7.40E-07%, Cr 0.022%, B 5.00E-06%, 
+    Mn 0.019%, Cd 8.32E-06%, Cu 0.01%.
+**Source**
+    252Cf oxide in a palladium matrix, encapsulated in double stainless-steel cladding.
+**Source position**
+    Geometric center of the sphere, placed in a 2.6 cm diameter, 28 cm deep hole drilled in a central 3 cm thick plate.
+**Experimental hall**
+    Room dimensions :math:`7.24\,\mathrm{m} \times 6.5\,\mathrm{m} \times 7.2\,\mathrm{m}` (height), sphere center 
+    2 m above floor.
+**Set-up of case**
+    It contains only the activation foils on the outside the Fe sphere (on the surface) and the neutron detectors at 
+    1 m from the sphere center. 
+
+.. figure:: /img/benchmarks/RCR-Fe+Ni_1.png
+    :width: 600
+    :align: center
+
+    Figure 1. Scheme of Iron/Nickel Sphere - Side View. Dimensions in cm.
+
+.. figure:: /img/benchmarks/RCR-Fe+Ni_2.png
+    :width: 600
+    :align: center
+
+    Figure 2. Photo of Iron Sphere with Shadow Cone and Stilbene Detector.
+
+MCNP modelling
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Two independent MCNP inputs are employed, one for each case, just with different sphere material and with the hereinafter 
+described tallies: 
+
+*Detector tallies, Fn5 MCNP type* 
+    Two detector-flux tallies have been used to collect the energy-binned neutron spectra at the same detector position 
+    with a course energy binning (F5, for the Stilbene detector) and a finer one (F15 for the hydrogen proportional 
+    counters, HPD) which matches the measurement performed. 
+*Track length flux tallies, Fn4 MCNP type*
+    A track length flux tally has been used to collect results in the cells corresponding to the activation foils in MCNP 
+    geometry. The tally has been multiplied in each input (with FM card) by the appropriate microscopic reaction cross 
+    section, to obtain results in terms of number of reactions per unit neutron from the source. Energy binning was applied 
+    to half of the tallies, while the other half recorded the total reaction rate in the same cells (see table below). Nuclear 
+    data for tally collection was taken from IRDFF-II dosimetry libraries and experimental values averaged when multiplies 
+    values where present. In the following, a list of the reactions considered for each activation foil material is reported: 
+
+.. list-table:: Tally Details
+   :header-rows: 1
+   :widths: 10 25 25 10
+
+   * - Tally No.
+     - Where
+     - Foils Reactions
+     - Energy binned
+   * - 4
+     - Outer sphere surface
+     - 58Ni(n,p)58Co
+     - Yes
+   * - 14
+     - Outer sphere surface
+     - 115In(n,n')115m1 In
+     - Yes
+   * - 24
+     - Outer sphere surface
+     - 58Ni(n,p)58Co
+     - No
+   * - 34
+     - Outer sphere surface
+     - 115In(n,n')115m1 In
+     - No
+
+Implemented broadening on Monte Carlo computed results
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Following the ICSBEP documentation, MCNP neutron spectra are broadened with a Gaussian function using a constant 10% FWHM 
+for all energy ranges for the hydrogen proportional counters while as per the table below for the stilbene scintillation detector. 
+
+.. list-table:: Energy Resolution of the Stilbene Detector for Neutron Spectra Measurement 
+   :header-rows: 1
+   :widths: 15 15
+
+   * - Elow (MeV)
+     - FWHM (%)
+   * - 17.02
+     - 1
+   * - 15.05
+     - 1.35
+   * - 13.63
+     - 1.65
+   * - 12.5
+     - 1.92
+   * - 11.42
+     - 2.23
+   * - 11.02
+     - 2.35
+   * - 10.97
+     - 2.37
+   * - 10.67
+     - 2.47
+   * - 9.96
+     - 2.73
+   * - 9.3
+     - 3.01
+   * - 8.05
+     - 3.68
+   * - 6.59
+     - 4.97
+   * - 5.91
+     - 6.07
+   * - 5.46
+     - 7.41
+   * - 5.25
+     - 8.61
+   * - 5.13
+     - 10
+
+.. seealso:: **Related papers and contributions:**
+
+    * ICSBEP, NEA/NSC/DOC/(95)03/VIII, Volume VIII, ALARM-CF-Fe-SHIELD-002. 
+    * https://www-nds.iaea.org/INDEN/  
+    * M. Schulc et al., "Measuring neutron leakage spectra using spherical benchmarks with 252Cf source in its centers",
+      Nucl. Instrum. Methods Phys. Res. A 914 (2019) 53-56. 
+    * M. Schulc et al., "Application of 252Cf neutron source for precise nuclear data experiments", Appl. Radiat. 
+      Isot. 151 (2019) 187-195.