Merge branch 'JADE-V-V:linux' into linux

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

@@ -0,0 +1,77 @@
+.. _fnghcpb:
+
+FNG Helium Cooled Pebble Bed (HCPB) Tritium Breeder Module (TBM) Mock-up
+------------------------------------------------------------------------
+
+This experiment is part of the SINBAD database (`NEA-1553/71 <hhttps://www.oecd-nea.org/science/wprs/shielding/sinbad/fng_hcpb/fnghcpb-a.htm>`_). 
+Users will need to show proof of licence and request the required input files to use this 
+benchamark in JADE.
+
+The purpose of this experiment was to validate transport through a mockup of the Helium 
+Cooled Pebble Bed (HCPB) blanket concept. This is one of the concepts anticipated for 
+the ITER test blanket module (TBM) programme and in future fusion power plants. The accurate
+prediction of the tritium production, one of the primary functions of the blanket is therefore 
+very important. The experiment was carried out at the FNG facility, described in :ref:`fngsddr`,
+in 2005.
+
+Geometry 
+^^^^^^^^
+
+The geoemtry of the mockup has external dimensions of 31.0 cm x 29.0 cm x 30.9 cm. The bulk of the 
+geometry consists of beryllium with two layers symmetric across the central plane consisting of 
+Li2CO3 containing natural Li. Stacks of 12 pellets of Li2C03 encased in Al were assemebled for measuring
+the tritium production rate. At the rear is a steel box filled with Li2CO3. 
+
+.. figure:: /img/benchmarks/fng-hcpb.jpg
+    :width: 500
+    :align: center
+
+    Layout of the FNG-HCPB experiment.
+
+Measured data
+^^^^^^^^^^^^^
+
+Activation foils were placed at increasing distance from the source through the centre of the
+geometry to measure reaction rates. The tritium production rate was measured at four different 
+depths a the locations of each of the pellet stacks above and below the central axis. 
+
+* **Reaction rates**: 197Au(n,g), 58Ni(n,g), 27Al(n,a), 93Nb(n,2n) at depths of 4.055 cm, 10.355 cm, 
+  16.655 cm and 22.955 cm from the block surface. There is an additional measurement at depth 0 cm 
+  for 93Nb(n,2n). 
+* **Tritium Activity**: Measured for each of the stacks of 12 pellets as shown in the above Figure. The 
+  tritium specific activity is available in units of Bq/g.
+
+MCNP model
+^^^^^^^^^^
+
+A single MCNP geometry is used for calculating the reaction rates and tritium activity. The 
+most recently developed SDEF source from ENEA has been used and a weight window
+is included in the input file. 
+
+All modifications necessary to the distributed input file are captured in a patch file.
+
+MCNP tallies
+^^^^^^^^^^^^^^
+
+The reaction rates are calculated using the F4 tally in MCNP and can be directly compared to 
+the experimental data set which are presented per source neutron. Tally n.4 is used in all cases. 
+The reaction MT numbers are by default assigned using the `convention for IRDFF-II <https://www-nds.iaea.org/IRDFF/IRDFF-II_ACE-LST.pdf>`_. 
+The raw output from MCNP can be compared directly the reported measured data.
+
+The tritium production is tallied for 6Li and 7Li using the reaction MT number 205 for total 
+triton production. No energy binning is required. The specific activitiy is then calculated as:
+
+.. math::
+    Specific \; activity (Bq/g) = (MCNP\_result (RR) \times \lambda (s^{-1}) \times n_{tot})/ mass (g)
+
+where :math:`{\lambda}` is the decay constant, :math:`n_{tot}` is the total neutron production and the 
+mass is for an individual pellet. 
+
+Patch file
+^^^^^^^^^^
+Coming soon... 
+
+.. seealso:: **Related papers and contributions:**
+
+    * Batistoni, P., Villari, R., TBM - HCPB Neutronics Experiments: Comparisonand Check Consistency among Results Obtained by the Different Teams Implications for ITER TBM Nuclear Design and Final Assessment, FUS-TEC–MA–NE-R-019, ENEA, Dec. 2006.
+    * Batistoni, P., Carconi, P., Villari, R., Angelone, M., Pillon, M., Zappa, G., Measurements and Analysis of Tritium Production Rate (TPR) in Ceramic Breeder and of Neutron Flux by Activation Rates in Beryllium in TBM Mock-up, FUS-TEC-MA-NE-R-014, Dec. 2005

docs/source/usage/benchdesc/fng-sic.rst

@@ -0,0 +1,80 @@
+.. _fngsic:
+
+FNG Silicon Carbide (FNG SiC)
+-----------------------------
+
+This experiment is part of the SINBAD database (`NEA-1553/56 <https://www.oecd-nea.org/science/wprs/shielding/sinbad/fng_sic/fngsic-a.htm>`_). 
+Users will need to show proof of licence and request the required input files to use this 
+benchamark in JADE.
+
+The purpose of this experiment is to validate Si and C cross sections through irradiation 
+of a monolithc sintered SiC block placed in front of the FNG source. This is in important 
+structural material that is being explored for several differnt fusion concepts.  The 
+experiment was carried out at the FNG facility, described in :ref:`fngsddr`, in 2001.
+
+Geometry 
+^^^^^^^^
+
+The SiC mock-up assembly consisted of a sintered SiC block of dimensions 45.72 cm x 
+45.72 cm x 71.12 cm located 5.3 cm from the FNG source. 
+
+.. figure:: /img/benchmarks/fng-sic.jpg
+    :width: 500
+    :align: center
+
+    Layout of FNG-SiC experiment. Figure taken from the SINBAD repository. 
+
+Measured data
+^^^^^^^^^^^^^
+
+Four experimental locations were used through the centre of the mock used to measure reaction
+rates and nuclear heating at different depths:
+
+* **Reaction rates**: 197Au(n,g), 58Ni(n,g), 27Al(n,a), 93Nb(n,2n) at depths of 10.41 cm, 25.65 cm
+  40.89 cm and 56.13 cm from the block surface. 
+* **Nuclear heating**: Measured using TLDs at depths of 14.99 cm, 30.23 cm, 40.47 cm and 60.71 cm.
+
+.. important::
+    * There was a lack of reliable data on the concentration of boron in the SiC matrix therefore 
+      it is recommended that **data related to thermal interactions are used in relative comparison
+      only between codes and cross section libraries**. This includes the nuclear heating measurements
+      and 197Au(n,g) reaction rate. 
+
+MCNP model
+^^^^^^^^^^
+
+There are two independent MCNP models in order to caputire the geoemetry of the TLD detectors. In 
+both cases the the most recently developed SDEF source from ENEA has been used and weight windows 
+are included in each input file. 
+
+Further modifications necessary to the distributed input file are captured in the patch file.
+
+MCNP tallies
+^^^^^^^^^^^^^^
+
+The total dose in the TLDs is calculated by summation of the neutron and photon dose. The neutron
+dose has an associated sensitivity coefficient that varies as a function of depth. The total dose
+is then calculated as: 
+
+D\ :sub:`t`\ = D\ :sub:`n`\ * K\ :sub:`n`\ + D\ :sub:`g`\
+
+where K\ :sub:`n`\ is the neutron sensitivity coefficient, D\ :sub:`n`\ the neutron dose and
+D\ :sub:`g`\ the photon dose.
+
+Neutron and photon energy deposition are calculated through F6 type tallies. Here, Tally n.16 is 
+used for the neutron energy deposition and Tally n. 26 for photon energy deposition. 
+
+JADE post processes the tally results by multiplying by J/MeV=1.602E-13 and g/kg=1000 to give a direct
+comparison to the experimental data given in Gy/source neutron.
+
+Reaction rates were calcualted using an F4 type tally - Tally n.4 is used in all cases. The reaction MT numbers
+are by default assigned using the `convention for IRDFF-II <https://www-nds.iaea.org/IRDFF/IRDFF-II_ACE-LST.pdf>`_. 
+The raw output from MCNP can be compared directly the reported measured data.
+
+Patch file
+^^^^^^^^^^
+Coming soon... 
+
+.. seealso:: **Related papers and contributions:**
+
+    * Angelone, M., Batistoni, P., Kodeli, I., Petrizzi, L., Pillon, M., Benchmark analysis of neutronics performances of a SIC block irradiated with 14 MeV neutrons, Fusion Engineering and Design, 63-64, 2002. 

docs/source/usage/benchmarks.rst

@@ -1,43 +1,46 @@
 ##################
 Default Benchmarks
 ##################
-This section describe more in detail all the default benchmarks
-that have been implemented in JADE dividing them between
-computational and experimental benchmarks.
+This section describes more in detail all the default benchmarks
+that have been implemented in JADE, dividing them between
+computational and experimental benchmarks. It is strongly recommended
+that the user reads this documentation carefully before using a specific 
+benchmark in JADE. 
 
 .. important::
     * Not all benchmark inputs and related files can be distributed
-      toghether with JADE due to licensing reasons. In case the user
-      provide evidence of licensing rights on specific benchmarks, the
+      together with JADE due to licensing reasons. In this case, if the user
+      provides evidence of licensing rights on specific benchmarks, the
       JADE team will provide the missing input which, once copied 
-      in the ``<JADE_root>\Benchmark inputs`` folder, allow to correctly run them.
+      in the ``<JADE_root>\Benchmark inputs`` folder, can be run in JADE. The user
+      should follow the example of distributed benchmarks for folder and naming 
+      convention.
     * For some of the benchmarks, weight windows (WW) have been produced and
-      necessary for the benchmark run. Unfortunately, these WW are often too
-      heavy for them to be distributed with Git. These files must be downloaded
-      separately and inserted in a suitable folder in ``<JADE_root>\Benchmark inputs\VRT``.  
+      necessary for the benchmark run. Unfortunately, these WW files are often too
+      heavy for them to be distributed with Git. These files must be requested 
+      and inserted in to the same folder as the corresponding input file.  
     * The benchmarks included in JADE can be also divided between
-      **transport** benchmarks (usually associated with classical
-      MCNP) and **activation** benchmarks (usually associated with
+      **transport** benchmarks and **activation** benchmarks (currently perfromed using
       D1S-UNED). It is recommended to run these two benchmarks
       categories separately, mostly because they require a different
-      input in terms of library to be assessed. If transport Benchmarks
-      expect a single library (e.g. ``31c``), activation one require
+      input in terms of the library to be assessed. If transport benchmarks
+      expect a single library (e.g. ``31c``), activation ones require
       two: an activation library and a transport one for all zaids that
       cannot be activated (e.g. ``99c-31c``).
     * In activation benchmarks, the library that is considered the assessed one
       is always the activation library (i.e. the first provided). No track
       is kept during the post-processing of which was the transport library used
-      and it is responsability of the user to make sure that comparisons between
-      activation libraries results are done in a coherent way. That is, the
-      same transport library should be always used.
+      and it is responsibility of the user to make sure that comparisons between
+      activation libraries results are done in a coherent way. That is, **the
+      same transport library should be always used**.
 
 
 Overview
 ========
-The following tables summarize the computational and experimental benchmarks
-that are included in JADE (I), the ones that are currently under developing (D), and 
-whishlisted ones (W). A more detailed description of the implemented benchmarks can
-be found in the following sections.
+The following tables summarise the computational and experimental benchmarks
+that are included in JADE **(I)**, the ones that are currently under development
+**(D)**, and a future wishlist **(W)**. A more detailed description of the implemented 
+benchmarks can be found in the following sections.
 
 **COMPUTATIONAL BENCHMARKS:**
 
@@ -85,6 +88,10 @@ Experimental Benchmarks
 
 .. include:: benchdesc/fng-w.rst
 
+.. include:: benchdesc/fng-sic.rst
+
+.. include:: benchdesc/fng-hcpb.rst
+
 .. include:: benchdesc/tud-fe.rst
 
 .. include:: benchdesc/tud-fng.rst

docs/source/usage/configuration.rst

@@ -158,7 +158,10 @@ Libraries
     :width: 400
 
 This sheet contains the paths of nuclear data library index files for the various codes.
-
+It is the users responsibility to ensure these are configured correctly, and that in 
+the case of comparisons between codes that the xsdir files are equivalent. For a more 
+detailed description of these files, refer to the appropriate documentation for each
+code
 
 .. warning::
     Do not use invalid filename characters (e.g. ``"\"``) in the names assigned to the
@@ -177,48 +180,6 @@ activation libraries. For each library a sheet needs to be added having as name
 suffix used in the xsdir file for the library. Only three columns in the table are mandatory
 and these are the **Parent**, **MT** and **Daughter** ones.
 
-.. _runconf:
-
-Benchmark run configuration
-===========================
-
-for the *Sphere Leakage* and for the *Sphere SDDR* benchmarks ad-hoc run
-configuration file are defined and can be found in the
-``<JADE_root>\Configuration\Sphere`` and ``<JADE_root>\Configuration\SphereSDDR``
-folders. These are .csv files that control for each element or typical material
-the following run parameters:
-
-NPS cut-off
-    specifies the number of particle histories to be set in the MCNP
-    STOP card.
-
-CTME cut-off
-    specifies the total computer time to be set in the MCNP STOP card.
-
-Relative Error cut-off
-    specifies a precision limit for a tally to be set in the MCNP STOP card.
-
-Density [g/cc]
-    specifies the density to be considered in the sphere for the
-    isotope/typical material.
-
-Name
-    name to be used during post-processing (e.g. Hydrogen or SS316L(N)-IG)
-
-Symbol
-    element symbol (e.g. H) or material number (e.g. M400). In case of material
-    number the id must be consistent with the ones indicated in the
-    ``<JADE_root>\Benchmarks inputs\TypicalMaterials`` file.
-
-Z
-    **[Only for elements]** element number (e.g. 1 for H).
-
-Let Override
-    If True, the general settings specified in the :ref:`mainconfig` file
-    for the STOP card are considered to have priority on the specific ones.
-    If False, the specific parameters are not ovveridden by the general ones.
-
-
 .. _ppconf:
 
 Computational benchmark post-processing configuration