Merge branch 'feature/pruning' into 'develop'

Feature/pruning

See merge request njoy/dryad!96

Author: whaeck

cmake/unit_testing.cmake

@@ -29,6 +29,8 @@ message( STATUS "Adding njoy C++ unit testing" )
 
 add_cpp_test( matrix                                                           matrix.test.cpp )
 
+# dryad tests
+
 add_cpp_test( dryad.base.UniformDistribution                                   dryad/base/UniformDistribution.test.cpp )
 
 add_cpp_test( dryad.atomic.ElectronSubshellConfiguration                       dryad/atomic/ElectronSubshellConfiguration.test.cpp )
@@ -233,3 +235,8 @@ add_cpp_test( dryad.format.gnds.createProjectileTarget                         d
 add_cpp_test( dryad.format.gnds.createProjectileTargetFromFile                 dryad/format/gnds/createProjectileTargetFromFile.test.cpp )
 add_cpp_test( dryad.format.gnds.createAtomicRelaxation                         dryad/format/gnds/createAtomicRelaxation.test.cpp )
 add_cpp_test( dryad.format.gnds.createAtomicRelaxationFromFile                 dryad/format/gnds/createAtomicRelaxationFromFile.test.cpp )
+
+# medic tests
+
+add_cpp_test( medic.pruneCrossSection                                          medic/pruneCrossSection.test.cpp )
+add_cpp_test( medic.pruneCrossSections                                         medic/pruneCrossSections.test.cpp )

cmake/unit_testing_python.cmake

@@ -96,3 +96,6 @@ add_python_test( dryad.Reaction                                        dryad/Tes
 
 add_python_test( dryad.ProjectileTarget                                dryad/Test_ProjectileTarget.py )
 add_python_test( dryad.AtomicRelaxation                                dryad/Test_AtomicRelaxation.py )
+
+add_python_test( medic.prune_cross_section                             medic/Test_prune_cross_section.py )
+add_python_test( medic.prune_cross_sections                            medic/Test_prune_cross_sections.py )

python/CMakeLists.txt

@@ -87,6 +87,9 @@ if(njoy.python)
         ${CMAKE_CURRENT_SOURCE_DIR}/src/dryad/Reaction.python.cpp
         ${CMAKE_CURRENT_SOURCE_DIR}/src/dryad/ProjectileTarget.python.cpp
         ${CMAKE_CURRENT_SOURCE_DIR}/src/dryad/AtomicRelaxation.python.cpp
+        ${CMAKE_CURRENT_SOURCE_DIR}/src/medic.python.cpp
+        ${CMAKE_CURRENT_SOURCE_DIR}/src/medic/pruneCrossSection.python.cpp
+        ${CMAKE_CURRENT_SOURCE_DIR}/src/medic/pruneCrossSections.python.cpp
     )
 
     target_link_libraries(njoy.python PRIVATE njoy)

python/src/dryad/ProjectileTarget.python.cpp

@@ -159,6 +159,24 @@ void wrapProjectileTarget( python::module& module ) {
     "    id     the reaction identifier",
     python::return_value_policy::reference_internal
   )
+  .def(
+
+    "unionise_cross_sections",
+    &Component::unioniseCrossSections,
+    python::arg( "exclude_summation" ) = false,
+    "Unionise cross section data\n\n"
+    "This function takes all cross section data and unionises the cross section\n"
+    "grids. It does not linearise the data but reevaluates the data using the\n"
+    "proper interpolation types of the cross section data.\n\n"
+    "By default, summation cross sections are included in the unionisation process.\n"
+    "unless explicitly excluded by the user. Switching on the exclusion of summation\n"
+    "cross sections may be useful when the user is going to recalculate the summation\n"
+    "cross sections after unionisation.\n\n"
+    "Arguments:\n"
+    "    self                the ProjectileTarget data\n"
+    "    exclude_summation   option to exclude summation reactions in the\n"
+    "                        unionisation (default: false)"
+  )
   .def(
 
     "calculate_summation_cross_sections",

python/src/medic.python.cpp

@@ -0,0 +1,29 @@
+// system includes
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+// local includes
+
+// namespace aliases
+namespace python = pybind11;
+
+namespace medic {
+
+  // declarations - pruning
+  void wrapPruneCrossSection( python::module& );
+  void wrapPruneCrossSections( python::module& );
+} // medic namespace
+
+void wrapMedic( python::module& module ) {
+
+  // create the submodule
+  python::module submodule = module.def_submodule(
+
+    "medic",
+    "Correcting and updating data"
+  );
+
+  // wrap components - pruning
+  medic::wrapPruneCrossSection( submodule );
+  medic::wrapPruneCrossSections( submodule );
+}

python/src/medic/pruneCrossSection.python.cpp

@@ -0,0 +1,33 @@
+// system includes
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+// local includes
+#include "njoy/medic/pruneCrossSection.hpp"
+
+// namespace aliases
+namespace python = pybind11;
+
+namespace medic {
+
+  void wrapPruneCrossSection( python::module& module ) {
+
+    // type aliases
+
+    // wrap the function
+    module
+    .def(
+
+      "prune_cross_section",
+      &njoy::medic::pruneCrossSection,
+      python::arg( "lower_energy" ),
+      python::arg( "upper_energy" ),
+      python::arg( "xs" ),
+      "Prune cross section data\n\n"
+      "Arguments:\n"
+      "    lower_energy   the new lower energy limit\n"
+      "    upper_energy   the new upper energy limit\n"
+      "    xs             the cross section table to be modified"
+    );
+  }
+} // medic namespace

python/src/medic/pruneCrossSections.python.cpp

@@ -0,0 +1,33 @@
+// system includes
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+// local includes
+#include "njoy/medic/pruneCrossSections.hpp"
+
+// namespace aliases
+namespace python = pybind11;
+
+namespace medic {
+
+  void wrapPruneCrossSections( python::module& module ) {
+
+    // type aliases
+
+    // wrap the function
+    module
+    .def(
+
+      "prune_cross_sections",
+      &njoy::medic::pruneCrossSections,
+      python::arg( "lower_energy" ),
+      python::arg( "upper_energy" ),
+      python::arg( "xs" ),
+      "Prune cross section data\n\n"
+      "Arguments:\n"
+      "    lower_energy   the new lower energy limit\n"
+      "    upper_energy   the new upper energy limit\n"
+      "    pt             the projectile-target data to be modified"
+    );
+  }
+} // medic namespace

python/src/njoy.python.cpp

@@ -10,8 +10,9 @@ namespace python = pybind11;
 // declarations - matrix functions
 void wrapMatrix( python::module& );
 
-// declarations
+// declarations - components and modules
 void wrapDryad( python::module& );
+void wrapMedic( python::module& );
 
 /**
  *  @brief njoy python bindings
@@ -26,4 +27,7 @@ PYBIND11_MODULE( njoy, module ) {
 
   // wrap dryad
   wrapDryad( module );
+
+  // wrap medic
+  wrapMedic( module );
 }

python/stubs/njoy/dryad/__init__.pyi

@@ -1014,6 +1014,24 @@ class ProjectileTarget:
             mat         the ENDF mat number to be used
             filename    the ENDF file name
         """
+    def unionise_cross_sections(self, exclude_summation: bool = False) -> None:
+        """
+        Unionise cross section data
+        
+        This function takes all cross section data and unionises the cross section
+        grids. It does not linearise the data but reevaluates the data using the
+        proper interpolation types of the cross section data.
+        
+        By default, summation cross sections are included in the unionisation process.
+        unless explicitly excluded by the user. Switching on the exclusion of summation
+        cross sections may be useful when the user is going to recalculate the summation
+        cross sections after unionisation.
+        
+        Arguments:
+            self                the ProjectileTarget data
+            exclude_summation   option to exclude summation reactions in the
+                                unionisation (default: false)
+        """
     @property
     def documentation(self) -> Documentation:
         """

python/stubs/njoy/medic.pyi

@@ -0,0 +1,24 @@
+"""
+Correcting and updating data
+"""
+from __future__ import annotations
+import njoy.dryad
+__all__: list[str] = ['prune_cross_section', 'prune_cross_sections']
+def prune_cross_section(lower_energy: float, upper_energy: float, xs: njoy.dryad.TabulatedCrossSection) -> None:
+    """
+    Prune cross section data
+    
+    Arguments:
+        lower_energy   the new lower energy limit
+        upper_energy   the new upper energy limit
+        xs             the cross section table to be modified
+    """
+def prune_cross_sections(lower_energy: float, upper_energy: float, xs: njoy.dryad.ProjectileTarget) -> None:
+    """
+    Prune cross section data
+    
+    Arguments:
+        lower_energy   the new lower energy limit
+        upper_energy   the new upper energy limit
+        pt             the projectile-target data to be modified
+    """