Merge pull request #4 from njoy/fix/review

Fix/review

CMakeLists.txt

@@ -98,7 +98,7 @@ if( NDItk.python )
       python/src/multigroup/Metadata.python.cpp
       python/src/multigroup/CrossSection.python.cpp
       python/src/multigroup/FluxWeights.python.cpp
-      python/src/multigroup/Structure.python.cpp
+      python/src/multigroup/EnergyGroupStructure.python.cpp
       python/src/multigroup/ReactionCrossSections.python.cpp
       )
 

cmake/unit_testing.cmake

@@ -33,7 +33,7 @@ add_subdirectory( src/NDItk/base/IntegerListRecord/test )
 add_subdirectory( src/NDItk/base/RealListRecord/test )
 
 add_subdirectory( src/NDItk/multigroup/Metadata/test )
-add_subdirectory( src/NDItk/multigroup/Structure/test )
+add_subdirectory( src/NDItk/multigroup/EnergyGroupStructure/test )
 add_subdirectory( src/NDItk/multigroup/FluxWeights/test )
 add_subdirectory( src/NDItk/multigroup/CrossSection/test )
 add_subdirectory( src/NDItk/multigroup/ReactionCrossSections/test )

cmake/unit_testing_python.cmake

@@ -25,8 +25,7 @@ message( STATUS "Adding NDItk Python unit testing" )
 add_python_test( multigroup.Metadata              multigroup/Test_NDItk_multigroup_Metadata.py )
 add_python_test( multigroup.CrossSection          multigroup/Test_NDItk_multigroup_CrossSection.py )
 add_python_test( multigroup.FluxWeights           multigroup/Test_NDItk_multigroup_FluxWeights.py )
-add_python_test( multigroup.Structure             multigroup/Test_NDItk_multigroup_Structure.py )
+add_python_test( multigroup.EnergyGroupStructure  multigroup/Test_NDItk_multigroup_EnergyGroupStructure.py )
 add_python_test( multigroup.ReactionCrossSections multigroup/Test_NDItk_multigroup_ReactionCrossSections.py )
 
 add_python_test( MultigroupTable   Test_NDItk_MultigroupTable.py )
-

python/src/MultigroupTable.python.cpp

@@ -15,7 +15,7 @@ void wrapMultigroupTable( python::module& module, python::module& ) {
   // type aliases
   using Table = njoy::NDItk::MultigroupTable;
   using Metadata = njoy::NDItk::multigroup::Metadata;
-  using Structure = njoy::NDItk::multigroup::Structure;
+  using EnergyGroupStructure = njoy::NDItk::multigroup::EnergyGroupStructure;
   using FluxWeights = njoy::NDItk::multigroup::FluxWeights;
   using ReactionCrossSections = njoy::NDItk::multigroup::ReactionCrossSections;
 
@@ -33,13 +33,13 @@ void wrapMultigroupTable( python::module& module, python::module& ) {
   table
   .def(
 
-    python::init< std::string, std::string, std::string, std::string, 
+    python::init< std::string, std::string, std::string, std::string,
                   double, double, double, double,
-                  Structure, FluxWeights,
+                  EnergyGroupStructure, FluxWeights,
                   ReactionCrossSections >(),
     python::arg( "zaid" ), python::arg( "libname" ), python::arg( "source" ),
     python::arg( "process" ), python::arg( "awr" ), python::arg( "weight" ),
-    python::arg( "temperature" ), python::arg( "dilution" ), 
+    python::arg( "temperature" ), python::arg( "dilution" ),
     python::arg( "structure" ), python::arg( "flux" ), python::arg( "xs" ),
     "Initialise the table\n\n"
     "Arguments:\n"

python/src/multigroup.python.cpp

@@ -13,7 +13,7 @@ namespace multigroup {
   void wrapMetadata( python::module&, python::module& );
   void wrapCrossSection( python::module&, python::module& );
   void wrapFluxWeights( python::module&, python::module& );
-  void wrapStructure( python::module&, python::module& );
+  void wrapEnergyGroupStructure( python::module&, python::module& );
   void wrapReactionCrossSections( python::module&, python::module& );
 }
 
@@ -29,6 +29,6 @@ void wrapMultigroup( python::module& module, python::module& viewmodule ) {
   multigroup::wrapMetadata( submodule, viewmodule );
   multigroup::wrapCrossSection( submodule, viewmodule );
   multigroup::wrapFluxWeights( submodule, viewmodule );
-  multigroup::wrapStructure( submodule, viewmodule );
+  multigroup::wrapEnergyGroupStructure( submodule, viewmodule );
   multigroup::wrapReactionCrossSections( submodule, viewmodule );
 }

python/src/multigroup/Structure.python.cpp → python/src/multigroup/EnergyGroupStructure.python.cpp

@@ -3,7 +3,7 @@
 #include <pybind11/stl.h>
 
 // local includes
-#include "NDItk/multigroup/Structure.hpp"
+#include "NDItk/multigroup/EnergyGroupStructure.hpp"
 #include "tools/views/views-python.hpp"
 #include "definitions.hpp"
 #include "read.hpp"
@@ -13,18 +13,18 @@ namespace python = pybind11;
 
 namespace multigroup {
 
-void wrapStructure( python::module& module, python::module& ) {
+void wrapEnergyGroupStructure( python::module& module, python::module& ) {
 
   // type aliases
-  using Record = njoy::NDItk::multigroup::Structure;
+  using Record = njoy::NDItk::multigroup::EnergyGroupStructure;
 
   // wrap views created by this record
 
   // create the record
   python::class_< Record > record(
 
     module,
-    "Structure",
+    "EnergyGroupStructure",
     "A group structure record for multigroup neutron and photon data"
   );
 

python/test/Test_NDItk_MultigroupTable.py

@@ -5,7 +5,7 @@
 
 # local imports
 from NDItk import MultigroupTable
-from NDItk.multigroup import Structure
+from NDItk.multigroup import EnergyGroupStructure
 from NDItk.multigroup import FluxWeights
 from NDItk.multigroup import ReactionCrossSections
 from NDItk.multigroup import CrossSection
@@ -33,8 +33,8 @@ def verify_chunk( self, chunk ) :
             structure = chunk.structure
             self.assertEqual( 7, structure.number_groups )
             self.assertAlmostEqual(    20, structure.boundaries[0] )
-            self.assertAlmostEqual(    18, structure.boundaries[1] )
-            self.assertAlmostEqual(    16, structure.boundaries[2] )
+            self.assertAlmostEqual(    18.123456789, structure.boundaries[1] )
+            self.assertAlmostEqual(    16.0000000000001, structure.boundaries[2] )
             self.assertAlmostEqual(    14, structure.boundaries[3] )
             self.assertAlmostEqual(    10, structure.boundaries[4] )
             self.assertAlmostEqual(     5, structure.boundaries[5] )
@@ -103,15 +103,14 @@ def verify_chunk( self, chunk ) :
         chunk = MultigroupTable( zaid = '92235.711nm', libname = 'mendf71x', source = '12/22/2011',
                                  process = '08/07/2013', awr = 233.0248, weight = 235.043937521619,
                                  temperature = 2.53e-8, dilution = 1e+10,
-                                 structure = Structure( [ 20., 18., 16., 14., 10., 5, 1, 1e-11 ] ),
+                                 structure = EnergyGroupStructure( [ 20., 18.123456789, 16.0000000000001, 14., 10., 5, 1, 1e-11 ] ),
                                  flux = FluxWeights( [ 0.1, 0.2, 0.25, 0.05, 0.15, 0.04, 0.06 ] ),
-                                 xs = ReactionCrossSections( 
-                                          xs = [ CrossSection( 2, 0., [ 10., 20., 30., 40., 50., 60., 70. ] ), 
+                                 xs = ReactionCrossSections(
+                                          xs = [ CrossSection( 2, 0., [ 10., 20., 30., 40., 50., 60., 70. ] ),
                                                  CrossSection( 16, 1.1234567, [ 1., 2., 3., 4., 5., 6., 7. ] ) ] ) )
 
         verify_chunk( self, chunk )
 
 if __name__ == '__main__' :
 
     unittest.main()
-

python/test/multigroup/Test_NDItk_multigroup_CrossSection.py

@@ -9,9 +9,9 @@
 class Test_NDItk_multigroup_CrossSection( unittest.TestCase ) :
     """Unit test for the CrossSection class."""
 
-    chunk_values = [ 2, 0, 10., 20., 30., 40., 50., 60., 70. ]
+    chunk_values = [ 2, 0, 10.0000000000001, 20., 30., 40.12345678, 50., 60., 70. ]
     chunk_string = ( '    2 0\n'
-                     '    10 20 30 40 50\n'
+                     '    10.0000000000001 20 30 40.12345678 50\n'
                      '    60 70\n' )
 
     def test_component( self ) :
@@ -22,10 +22,10 @@ def verify_chunk( self, chunk ) :
             self.assertEqual( 7, chunk.number_groups )
             self.assertEqual( 2, chunk.identifier )
             self.assertAlmostEqual( 0, chunk.qvalue )
-            self.assertAlmostEqual( 10, chunk.cross_sections[0] )
+            self.assertAlmostEqual( 10.0000000000001, chunk.cross_sections[0] )
             self.assertAlmostEqual( 20, chunk.cross_sections[1] )
             self.assertAlmostEqual( 30, chunk.cross_sections[2] )
-            self.assertAlmostEqual( 40, chunk.cross_sections[3] )
+            self.assertAlmostEqual( 40.12345678, chunk.cross_sections[3] )
             self.assertAlmostEqual( 50, chunk.cross_sections[4] )
             self.assertAlmostEqual( 60, chunk.cross_sections[5] )
             self.assertAlmostEqual( 70, chunk.cross_sections[6] )
@@ -43,7 +43,7 @@ def verify_chunk( self, chunk ) :
 
         # the data is given explicitly
         chunk = CrossSection( reaction = 2, qvalue = 0.0,
-                              values = [ 10., 20., 30., 40., 50., 60., 70. ] )
+                              values = [ 10.0000000000001, 20., 30., 40.12345678, 50., 60., 70. ] )
 
         verify_chunk( self, chunk )
 

python/test/multigroup/Test_NDItk_multigroup_Structure.py → python/test/multigroup/Test_NDItk_multigroup_EnergyGroupStructure.py

@@ -4,10 +4,10 @@
 # third party imports
 
 # local imports
-from NDItk.multigroup import Structure
+from NDItk.multigroup import EnergyGroupStructure
 
-class Test_NDItk_multigroup_Structure( unittest.TestCase ) :
-    """Unit test for the Structure class."""
+class Test_NDItk_multigroup_EnergyGroupStructure( unittest.TestCase ) :
+    """Unit test for the EnergyGroupStructure class."""
 
     chunk_values = [ 20, 18, 16, 14, 10, 5, 1, 1e-11 ]
     chunk_string = ( 'e_bounds\n'
@@ -42,12 +42,12 @@ def verify_chunk( self, chunk ) :
                 self.assertAlmostEqual( self.chunk_values[index], values[index] )
 
         # the data is given explicitly
-        chunk = Structure( boundaries = [ 20., 18., 16., 14., 10., 5, 1, 1e-11 ] )
+        chunk = EnergyGroupStructure( boundaries = [ 20., 18., 16., 14., 10., 5, 1, 1e-11 ] )
 
         verify_chunk( self, chunk )
 
         # the data is read from a string
-        chunk = Structure.from_string( self.chunk_string, 8 )
+        chunk = EnergyGroupStructure.from_string( self.chunk_string, 8 )
 
         verify_chunk( self, chunk )
 

src/NDItk/MultigroupTable.hpp

@@ -6,7 +6,7 @@
 // other includes
 #include "tools/Log.hpp"
 #include "NDItk/multigroup/Metadata.hpp"
-#include "NDItk/multigroup/Structure.hpp"
+#include "NDItk/multigroup/EnergyGroupStructure.hpp"
 #include "NDItk/multigroup/FluxWeights.hpp"
 #include "NDItk/multigroup/ReactionCrossSections.hpp"
 
@@ -21,7 +21,7 @@ class MultigroupTable {
   /* fields */
 
   multigroup::Metadata metadata_;
-  multigroup::Structure structure_;
+  multigroup::EnergyGroupStructure structure_;
   multigroup::FluxWeights weights_;
   multigroup::ReactionCrossSections xs_;
 
@@ -46,7 +46,7 @@ class MultigroupTable {
   /**
    *  @brief Return the primary group structure record
    */
-  const multigroup::Structure& structure() const { return this->structure_; }
+  const multigroup::EnergyGroupStructure& structure() const { return this->structure_; }
 
   /**
    *  @brief Return the flux weight record

src/NDItk/MultigroupTable/src/ctor.hpp

@@ -22,7 +22,7 @@ MultigroupTable() : metadata_(), structure_(), weights_(), xs_() {}
 MultigroupTable( std::string zaid, std::string libname, std::string source,
                  std::string process, double awr, double weight, double temperature,
                  double dilution,
-                 multigroup::Structure structure,
+                 multigroup::EnergyGroupStructure structure,
                  multigroup::FluxWeights weigths,
                  multigroup::ReactionCrossSections xs ) :
     metadata_( std::move( zaid ), std::move( libname ), std::move( source ),

src/NDItk/MultigroupTable/test/MultigroupTable.test.cpp

@@ -30,7 +30,8 @@ SCENARIO( "MultigroupTable" ) {
       double weight = 235.043937521619;
       double temperature = 2.53e-8;
       double dilution = 1e+10;
-      multigroup::Structure structure( { 20., 18., 16., 14., 10., 5, 1, 1e-11 } );
+      multigroup::EnergyGroupStructure structure( { 20., 18.123456789, 16.0000000000001,
+                                                    14., 10., 5, 1, 1e-11 } );
       multigroup::FluxWeights weights( { 0.1, 0.2, 0.25, 0.05, 0.15, 0.04, 0.06 } );
       multigroup::ReactionCrossSections xs( { { 2, 0.0, { 10., 20., 30., 40., 50., 60., 70. } },
                                               { 16, 1.1234567, { 1., 2., 3., 4., 5., 6., 7. } } } );
@@ -92,7 +93,7 @@ SCENARIO( "MultigroupTable" ) {
       double weight = 235.043937521619;
       double temperature = 2.53e-8;
       double dilution = 1e+10;
-      multigroup::Structure structure( { 20., 18., 16., 14., 10., 5, 1, 1e-11 } );                       // <-- 7 groups
+      multigroup::EnergyGroupStructure structure( { 20., 18., 16., 14., 10., 5, 1, 1e-11 } );            // <-- 7 groups
       multigroup::FluxWeights weights( { 0.1, 0.2, 0.25, 0.05, 0.15, 0.04 } );                           // <-- 6 groups
       multigroup::ReactionCrossSections xs( { { 2, 0.0, { 10., 20., 30., 40., 50., 60., 70., 80. } },    // <-- 8 groups
                                               { 16, 1.1234567, { 1., 2., 3., 4., 5., 6., 7., 8. } } } );
@@ -130,7 +131,7 @@ std::string chunk() {
          "num_reac\n"
          "    2\n"
          "e_bounds\n"
-         "    20 18 16 14 10\n"
+         "    20 18.123456789 16.0000000000001 14 10\n"
          "    5 1 1e-11\n"
          "wgts\n"
          "    0.1 0.2 0.25 0.05 0.15\n"
@@ -166,8 +167,8 @@ void verifyChunk( const MultigroupTable& chunk ) {
   CHECK( 8 == chunk.structure().boundaries().size() );
   CHECK( 7 == chunk.structure().numberGroups() );
   CHECK_THAT(    20, WithinRel( chunk.structure().boundaries()[0] ) );
-  CHECK_THAT(    18, WithinRel( chunk.structure().boundaries()[1] ) );
-  CHECK_THAT(    16, WithinRel( chunk.structure().boundaries()[2] ) );
+  CHECK_THAT(    18.123456789, WithinRel( chunk.structure().boundaries()[1] ) );
+  CHECK_THAT(    16.0000000000001, WithinRel( chunk.structure().boundaries()[2] ) );
   CHECK_THAT(    14, WithinRel( chunk.structure().boundaries()[3] ) );
   CHECK_THAT(    10, WithinRel( chunk.structure().boundaries()[4] ) );
   CHECK_THAT(     5, WithinRel( chunk.structure().boundaries()[5] ) );

src/NDItk/base/RealListRecord/src/write.hpp

@@ -16,11 +16,11 @@ void write( OutputIterator& iter ) const {
 
   while ( full-- ) {
 
-    buffer << "    " << x[0];
-    buffer << ' ' << x[1];
-    buffer << ' ' << x[2];
-    buffer << ' ' << x[3];
-    buffer << ' ' << x[4] << '\n';
+    buffer << "    " << std::setprecision( 15 ) << x[0];
+    buffer << ' ' << std::setprecision( 15 ) << x[1];
+    buffer << ' ' << std::setprecision( 15 ) << x[2];
+    buffer << ' ' << std::setprecision( 15 ) << x[3];
+    buffer << ' ' << std::setprecision( 15 ) << x[4] << '\n';
     x += 5;
   }
 
@@ -29,7 +29,7 @@ void write( OutputIterator& iter ) const {
     buffer << "   ";
     while ( partial-- ) {
 
-      buffer << ' ' << *x;
+      buffer << ' ' << std::setprecision( 15 ) << *x;
       ++x;
     }
      buffer << '\n';

src/NDItk/base/RealListRecord/test/RealListRecord.test.cpp

@@ -23,7 +23,7 @@ SCENARIO( "RealListRecord" ) {
 
     WHEN( "the data is given explicitly" ) {
 
-      RealListRecord chunk( "e_bounds", { 20., 18., 16., 14., 10., 5, 1, 1e-11 } );
+      RealListRecord chunk( "e_bounds", { 20.000001, 18.000000001, 16.0000000000001, 14., 10., 5, 1, 1e-11 } );
 
       THEN( "a RealListRecord can be constructed and members can "
             "be tested" ) {
@@ -69,7 +69,7 @@ SCENARIO( "RealListRecord" ) {
 std::string chunk() {
 
   return "e_bounds\n"
-         "    20 18 16 14 10\n"
+         "    20.000001 18.000000001 16.0000000000001 14 10\n"
          "    5 1 1e-11\n";
 }
 
@@ -79,9 +79,9 @@ void verifyChunk( const RealListRecord& chunk ) {
   CHECK( false == chunk.empty() );
   CHECK( 8 == chunk.size() );
   CHECK( 8 == chunk.values().size() );
-  CHECK_THAT(    20, WithinRel( chunk.values()[0] ) );
-  CHECK_THAT(    18, WithinRel( chunk.values()[1] ) );
-  CHECK_THAT(    16, WithinRel( chunk.values()[2] ) );
+  CHECK_THAT(    20.000001, WithinRel( chunk.values()[0] ) );
+  CHECK_THAT(    18.000000001, WithinRel( chunk.values()[1] ) );
+  CHECK_THAT(    16.0000000000001, WithinRel( chunk.values()[2] ) );
   CHECK_THAT(    14, WithinRel( chunk.values()[3] ) );
   CHECK_THAT(    10, WithinRel( chunk.values()[4] ) );
   CHECK_THAT(     5, WithinRel( chunk.values()[5] ) );

src/NDItk/base/SingleRealRecord.hpp

@@ -34,7 +34,7 @@ class SingleRealRecord : protected SingleValueRecord< SingleRealRecord, double >
   void write( OutputIterator& iter ) const {
 
     std::ostringstream buffer;
-    buffer << "    " << std::setprecision( 15 ) << std::right << this->data().value();
+    buffer << "    " << std::setprecision( 15 ) << this->data().value();
     for ( auto c : buffer.str() ) { *iter++ = c; }
     *iter++ = '\n';
   };

src/NDItk/fromFile.hpp

@@ -51,7 +51,7 @@ namespace NDItk {
     auto end = content.end();
 
     // read over the first line of the file
-    while ( ! *iter == '\n' ) {
+    while ( *iter != '\n' ) {
 
       ++iter;
     }

src/NDItk/multigroup/CrossSection/src/verify.hpp

@@ -3,6 +3,7 @@
  *
  *  The following verification tests are performed:
  *    - there are at least three values
+ *    - the reaction identifier looks to be an integer
  *
  *  @param[in] data    the data values in the cross section subrecord
  */
@@ -16,4 +17,11 @@ static void verify( const Range& data ) {
     Log::info( "Found {} data values", data.size() );
     throw std::exception();
   }
+
+  if ( data[0] - static_cast< int >( std::round( data[0] ) ) != 0 ) {
+
+    Log::error( "Expected an integer value for the reaction identifier" );
+    Log::info( "Found {} as the reaction identifier", data[0] );
+    throw std::exception();
+  }
 }

src/NDItk/multigroup/CrossSection/src/write.hpp

@@ -11,7 +11,8 @@ void write( OutputIterator& iter ) const {
   std::ostringstream buffer;
 
   auto x = this->begin();
-  buffer << "    " << x[0] << ' ' << std::setprecision( 15 ) << x[1] << '\n';
+  buffer << "    " << static_cast< int >( std::round( x[0] ) )
+         << ' ' << std::setprecision( 15 ) << x[1] << '\n';
   x += 2;
 
   auto full = this->numberGroups() / 5;