Merge branch 'feature/fluorescence' into 'develop'

Feature/fluorescence

See merge request njoy/dryad!116

Author: whaeck

cmake/unit_testing.cmake

@@ -154,6 +154,7 @@ add_cpp_test( dryad.format.ace.electroatomic.createAceBremsstrahlungBlock
 
 add_cpp_test( dryad.format.ace.photoatomic.createAcePrincipalCrossSectionBlock          dryad/format/ace/photoatomic/createAcePrincipalCrossSectionBlock.test.cpp )
 add_cpp_test( dryad.format.ace.photoatomic.createAcePhotoelectricCrossSectionBlock      dryad/format/ace/photoatomic/createAcePhotoelectricCrossSectionBlock.test.cpp )
+add_cpp_test( dryad.format.ace.photoatomic.createAceFluorescenceDataBlock               dryad/format/ace/photoatomic/createAceFluorescenceDataBlock.test.cpp )
 add_cpp_test( dryad.format.ace.photoatomic.createAceIncoherentScatteringFunctionBlock   dryad/format/ace/photoatomic/createAceIncoherentScatteringFunctionBlock.test.cpp )
 add_cpp_test( dryad.format.ace.photoatomic.createAceComptonProfileBlock                 dryad/format/ace/photoatomic/createAceComptonProfileBlock.test.cpp )
 add_cpp_test( dryad.format.ace.photoatomic.createAceCoherentFormFactorBlock             dryad/format/ace/photoatomic/createAceCoherentFormFactorBlock.test.cpp )

docs/src/dryad/atomic/ElectronSubshellConfiguration.rst

@@ -1,7 +1,7 @@
 .. currentmodule:: njoy.dryad.atomic
 
 
-ElectronSubshellConfiguration 
+ElectronSubshellConfiguration
 =============================
 
 General information about the concept
@@ -32,16 +32,22 @@ Read-only Attributes
 
     ~ElectronSubshellConfiguration.number_radiative_transitions
     ~ElectronSubshellConfiguration.number_non_radiative_transitions
-    ~ElectronSubshellConfiguration.number_transitions 
+    ~ElectronSubshellConfiguration.number_transitions
     ~ElectronSubshellConfiguration.has_radiative_transitions
     ~ElectronSubshellConfiguration.has_non_radiative_transitions
     ~ElectronSubshellConfiguration.has_transitions
     ~ElectronSubshellConfiguration.total_radiative_probability
     ~ElectronSubshellConfiguration.total_non_radiative_probability
+    ~ElectronSubshellConfiguration.average_radiative_energy
+    ~ElectronSubshellConfiguration.average_non_radiative_energy
 
 Methods
 ~~~~~~~
 .. autosummary::
     :toctree: generated/
 
+    ~ElectronSubshellConfiguration.has_radiative_transition
+    ~ElectronSubshellConfiguration.has_non_radiative_transition
+    ~ElectronSubshellConfiguration.radiative_transition
+    ~ElectronSubshellConfiguration.non_radiative_transition
     ~ElectronSubshellConfiguration.normalise

python/src/dryad/atomic/ElectronSubshellConfiguration.python.cpp

@@ -34,8 +34,10 @@ void wrapElectronSubshellConfiguration( python::module& module ) {
     "  - the electron population, i.e. the number of electrons in the subshell\n"
     "    when the atom is neutral (given as a floating point number)\n"
     "  - the decay modes or transitions that can fill a hole in this shell\n\n"
-    "If there are transitions defined, the transition probabilities\n"
-    "can be normalised to 1 upon construction.\n\n"
+    "If there are transitions defined, the transition probabilities can be\n"
+    "normalised to 1 upon construction. Transitions are always sorted at\n"
+    "construction time (by originating shell for radiative transitions and\n"
+    "by originating and emitting shell for non-radiative transitions).\n\n"
     "Parameters\n"
     "----------\n"
     "    id : njoy.dryad.id.ElectronSubshellID  \n"
@@ -123,6 +125,60 @@ void wrapElectronSubshellConfiguration( python::module& module ) {
     &Component::hasTransitions,
     "Flag to indicate whether or not transitions are available"
   )
+  .def(
+
+    "has_radiative_transition",
+    &Component::hasRadiativeTransition,
+    python::arg( "originating_shell" ),
+    "Return whether or not a given radiative transition is present\n\n"
+    "Parameters\n"
+    "----------\n"
+    "    originating_shell : njoy.dryad.id.ElectronSubshellID\n"
+    "         the identifier of the subshell from which the\n"
+    "         vacancy filling electron originated\n"
+  )
+  .def(
+
+    "has_non_radiative_transition",
+    &Component::hasNonRadiativeTransition,
+    python::arg( "originating_shell" ),
+    python::arg( "emitting_shell" ),
+    "Return whether or not a given non-radiative transition is present\n\n"
+    "Parameters\n"
+    "----------\n"
+    "    originating_shell : njoy.dryad.id.ElectronSubshellID\n"
+    "         the identifier of the subshell from which the\n"
+    "         vacancy filling electron originated\n"
+    "    emitting_shell : njoy.dryad.id.ElectronSubshellID\n"
+    "         the identifier of the subshell from which the emitted electron originated\n"
+  )
+  .def(
+
+    "radiative_transition",
+    &Component::radiativeTransition,
+    python::arg( "originating_shell" ),
+    "Return the requested radiative transition\n\n"
+    "Parameters\n"
+    "----------\n"
+    "    originating_shell : njoy.dryad.id.ElectronSubshellID\n"
+    "         the identifier of the subshell from which the\n"
+    "         vacancy filling electron originated\n"
+  )
+  .def(
+
+    "non_radiative_transition",
+    &Component::nonRadiativeTransition,
+    python::arg( "originating_shell" ),
+    python::arg( "emitting_shell" ),
+    "Return the requested non-radiative transition\n\n"
+    "Parameters\n"
+    "----------\n"
+    "    originating_shell : njoy.dryad.id.ElectronSubshellID\n"
+    "         the identifier of the subshell from which the\n"
+    "         vacancy filling electron originated\n"
+    "    emitting_shell : njoy.dryad.id.ElectronSubshellID\n"
+    "         the identifier of the subshell from which the emitted electron originated\n"
+  )
   .def_property(
 
     "radiative_transitions",
@@ -149,6 +205,18 @@ void wrapElectronSubshellConfiguration( python::module& module ) {
     &Component::totalNonRadiativeProbability,
     "The total non-radiative probability"
   )
+  .def_property_readonly(
+
+    "average_radiative_energy",
+    python::overload_cast<>( &Component::averageRadiativeEnergy, python::const_ ),
+    "The average radiative energy"
+  )
+  .def_property_readonly(
+
+    "average_non_radiative_energy",
+    python::overload_cast<>( &Component::averageNonRadiativeEnergy, python::const_ ),
+    "The average non-radiative energy"
+  )
   .def(
 
     "normalise",

python/src/dryad/atomic/NonRadiativeTransitionData.python.cpp

@@ -35,13 +35,13 @@ void wrapNonRadiativeTransitionData( python::module& module ) {
     "Parameters\n"
     "----------\n"
     "    originating_shell :  njoy.dryad.id.ElectronSubshellID\n"
-    "                  The identifier of the subshell from which the vacancy filling electron originated\n"
+    "        the identifier of the subshell from which the vacancy filling electron originated\n"
     "    emitting_shell : njoy.dryad.id.ElectronSubshellID\n"
-    "                   The identifier of the subshell from which the emitted electron originated\n"
+    "        the identifier of the subshell from which the emitted electron originated\n"
     "    probability : float\n"
-    "                   The probability of the transition\n"
+    "        the probability of the transition\n"
     "    energy : float, default none\n"
-    "                   The energy of the emitted electron\n\n"
+    "        the energy of the emitted electron\n\n"
   );
 
   // wrap the component

python/test/dryad/atomic/Test_ElectronSubshellConfiguration.py

@@ -21,6 +21,15 @@ def verify_chunk_without_transitions( self, chunk ) :
     self.assertEqual( False, chunk.has_non_radiative_transitions )
     self.assertEqual( False, chunk.has_transitions )
 
+    self.assertEqual( False, chunk.has_radiative_transition( ElectronSubshellID( 'L1' ) ) )
+    self.assertEqual( False, chunk.has_radiative_transition( ElectronSubshellID( 'L2' ) ) )
+    self.assertEqual( False, chunk.has_radiative_transition( ElectronSubshellID( 'L3' ) ) )
+
+    self.assertEqual( False, chunk.has_non_radiative_transition( ElectronSubshellID( 'L1' ), ElectronSubshellID( 'L1' ) ) )
+    self.assertEqual( False, chunk.has_non_radiative_transition( ElectronSubshellID( 'L1' ), ElectronSubshellID( 'L2' ) ) )
+    self.assertEqual( False, chunk.has_non_radiative_transition( ElectronSubshellID( 'L1' ), ElectronSubshellID( 'L3' ) ) )
+    self.assertEqual( False, chunk.has_non_radiative_transition( ElectronSubshellID( 'M1' ), ElectronSubshellID( 'L1' ) ) )
+
     self.assertEqual( 0, chunk.number_radiative_transitions )
     self.assertEqual( 0, chunk.number_non_radiative_transitions )
     self.assertEqual( 0, chunk.number_transitions )
@@ -29,6 +38,8 @@ def verify_chunk_without_transitions( self, chunk ) :
 
     self.assertAlmostEqual( 0, chunk.total_radiative_probability )
     self.assertAlmostEqual( 0, chunk.total_non_radiative_probability )
+    self.assertAlmostEqual( 0, chunk.average_radiative_energy )
+    self.assertAlmostEqual( 0, chunk.average_non_radiative_energy )
 
 def verify_chunk( self, chunk, normalise ) :
 
@@ -40,6 +51,15 @@ def verify_chunk( self, chunk, normalise ) :
     self.assertEqual( True, chunk.has_non_radiative_transitions )
     self.assertEqual( True, chunk.has_transitions )
 
+    self.assertEqual( False, chunk.has_radiative_transition( ElectronSubshellID( 'L1' ) ) )
+    self.assertEqual( True, chunk.has_radiative_transition( ElectronSubshellID( 'L2' ) ) )
+    self.assertEqual( True, chunk.has_radiative_transition( ElectronSubshellID( 'L3' ) ) )
+
+    self.assertEqual( True, chunk.has_non_radiative_transition( ElectronSubshellID( 'L1' ), ElectronSubshellID( 'L1' ) ) )
+    self.assertEqual( True, chunk.has_non_radiative_transition( ElectronSubshellID( 'L1' ), ElectronSubshellID( 'L2' ) ) )
+    self.assertEqual( True, chunk.has_non_radiative_transition( ElectronSubshellID( 'L1' ), ElectronSubshellID( 'L3' ) ) )
+    self.assertEqual( False, chunk.has_non_radiative_transition( ElectronSubshellID( 'M1' ), ElectronSubshellID( 'L1' ) ) )
+
     self.assertEqual( 2, chunk.number_radiative_transitions )
     self.assertEqual( 6, chunk.number_non_radiative_transitions )
     self.assertEqual( 8, chunk.number_transitions )
@@ -48,6 +68,54 @@ def verify_chunk( self, chunk, normalise ) :
 
     normalisation = 1.00000015 if normalise else 1.0
 
+    radiative0 = chunk.radiative_transition( ElectronSubshellID( 'L2' ) )
+    radiative1 = chunk.radiative_transition( ElectronSubshellID( 'L3' ) )
+    self.assertEqual( TransitionType.Radiative, radiative0.type )
+    self.assertEqual( TransitionType.Radiative, radiative1.type )
+    self.assertEqual( ElectronSubshellID( 'L2' ), radiative0.originating_shell )
+    self.assertEqual( ElectronSubshellID( 'L3' ), radiative1.originating_shell )
+    self.assertAlmostEqual( 0.00190768 / normalisation, radiative0.probability )
+    self.assertAlmostEqual( 0.00380027 / normalisation, radiative1.probability )
+    self.assertAlmostEqual( 523.09, radiative0.energy )
+    self.assertAlmostEqual( 523.13, radiative1.energy )
+
+    nonradiative0 = chunk.non_radiative_transition( ElectronSubshellID( 'L1' ), ElectronSubshellID( 'L1' ) )
+    nonradiative1 = chunk.non_radiative_transition( ElectronSubshellID( 'L1' ), ElectronSubshellID( 'L2' ) )
+    nonradiative2 = chunk.non_radiative_transition( ElectronSubshellID( 'L1' ), ElectronSubshellID( 'L3' ) )
+    nonradiative3 = chunk.non_radiative_transition( ElectronSubshellID( 'L2' ), ElectronSubshellID( 'L2' ) )
+    nonradiative4 = chunk.non_radiative_transition( ElectronSubshellID( 'L2' ), ElectronSubshellID( 'L3' ) )
+    nonradiative5 = chunk.non_radiative_transition( ElectronSubshellID( 'L3' ), ElectronSubshellID( 'L3' ) )
+    self.assertEqual( TransitionType.NonRadiative, nonradiative0.type )
+    self.assertEqual( TransitionType.NonRadiative, nonradiative1.type )
+    self.assertEqual( TransitionType.NonRadiative, nonradiative2.type )
+    self.assertEqual( TransitionType.NonRadiative, nonradiative3.type )
+    self.assertEqual( TransitionType.NonRadiative, nonradiative4.type )
+    self.assertEqual( TransitionType.NonRadiative, nonradiative5.type )
+    self.assertEqual( ElectronSubshellID( 'L1' ), nonradiative0.originating_shell )
+    self.assertEqual( ElectronSubshellID( 'L1' ), nonradiative1.originating_shell )
+    self.assertEqual( ElectronSubshellID( 'L1' ), nonradiative2.originating_shell )
+    self.assertEqual( ElectronSubshellID( 'L2' ), nonradiative3.originating_shell )
+    self.assertEqual( ElectronSubshellID( 'L2' ), nonradiative4.originating_shell )
+    self.assertEqual( ElectronSubshellID( 'L3' ), nonradiative5.originating_shell )
+    self.assertEqual( ElectronSubshellID( 'L1' ), nonradiative0.emitting_shell )
+    self.assertEqual( ElectronSubshellID( 'L2' ), nonradiative1.emitting_shell )
+    self.assertEqual( ElectronSubshellID( 'L3' ), nonradiative2.emitting_shell )
+    self.assertEqual( ElectronSubshellID( 'L2' ), nonradiative3.emitting_shell )
+    self.assertEqual( ElectronSubshellID( 'L3' ), nonradiative4.emitting_shell )
+    self.assertEqual( ElectronSubshellID( 'L3' ), nonradiative5.emitting_shell )
+    self.assertAlmostEqual( 0.178644  / normalisation, nonradiative0.probability )
+    self.assertAlmostEqual( 0.116224  / normalisation, nonradiative1.probability )
+    self.assertAlmostEqual( 0.230418  / normalisation, nonradiative2.probability )
+    self.assertAlmostEqual( 0.0110822 / normalisation, nonradiative3.probability )
+    self.assertAlmostEqual( 0.291115  / normalisation, nonradiative4.probability )
+    self.assertAlmostEqual( 0.166809  / normalisation, nonradiative5.probability )
+    self.assertAlmostEqual( 478.82, nonradiative0.energy )
+    self.assertAlmostEqual( 493.86, nonradiative1.energy )
+    self.assertAlmostEqual( 493.9 , nonradiative2.energy )
+    self.assertAlmostEqual( 508.9 , nonradiative3.energy )
+    self.assertAlmostEqual( 508.94, nonradiative4.energy )
+    self.assertAlmostEqual( 508.98, nonradiative5.energy )
+
     self.assertEqual( TransitionType.Radiative, chunk.radiative_transitions[0].type )
     self.assertEqual( TransitionType.Radiative, chunk.radiative_transitions[1].type )
     self.assertEqual( ElectronSubshellID( 'L2' ), chunk.radiative_transitions[0].originating_shell )
@@ -90,6 +158,8 @@ def verify_chunk( self, chunk, normalise ) :
 
     self.assertAlmostEqual( 0.00570795 / normalisation, chunk.total_radiative_probability )
     self.assertAlmostEqual( 0.9942922  / normalisation, chunk.total_non_radiative_probability )
+    self.assertAlmostEqual( 523.116631417584, chunk.average_radiative_energy )
+    self.assertAlmostEqual( 498.286519214372, chunk.average_non_radiative_energy )
 
 class Test_ElectronSubshellConfiguration( unittest.TestCase ) :
     """Unit test for the ElectronSubshellConfiguration class."""

src/njoy/acer/processElectronPhotonRelaxation.hpp

@@ -26,7 +26,7 @@ namespace acer {
                                                const std::string& filename ) {
 
     if ( photoatomic.interactionType() != dryad::InteractionType::Atomic ||
-         photoatomic.projectileIdentifier() != dryad::id::ParticleID::neutron() ) {
+         photoatomic.projectileIdentifier() != dryad::id::ParticleID::photon() ) {
 
       throw std::runtime_error( "The projectile-target is not photoatomic" );
     }
@@ -42,6 +42,7 @@ namespace acer {
     }
 
     //! @todo verify unionisation of the photoatomic and electroatomic data
+    //! @todo verify if binding energies of shells appear in total ionisation as jumps
     //! @todo verify normalisation?
 
     bool relativistic = true;
@@ -55,7 +56,7 @@ namespace acer {
     auto jinc = dryad::format::ace::photoatomic::createAceIncoherentScatteringFunctionBlock( photoatomic );
     auto jcoh = dryad::format::ace::photoatomic::createAceCoherentFormFactorBlock( photoatomic );
 //    auto lhnm = ;
-//    auto jflo = ;
+    auto jflo = dryad::format::ace::photoatomic::createAceFluorescenceDataBlock( photoatomic, relaxation );
     auto eps = dryad::format::ace::atomic::createAceElectronShellBlock( relativistic, relaxation );
     auto swd = dryad::format::ace::photoatomic::createAceComptonProfileBlock( photoatomic );
     auto subsh = dryad::format::ace::atomic::createAceElectronSubshellBlock( relaxation );

src/njoy/dryad/AtomicRelaxation.hpp

@@ -127,7 +127,7 @@ namespace dryad {
     bool hasSubshell( const id::ElectronSubshellID& id ) const {
 
       auto iter = this->iterator( id );
-      return iter != this->subshells().end();
+      return iter != this->subshells().end() && iter->identifier() == id;
     }
 
     /**
@@ -139,7 +139,7 @@ namespace dryad {
     subshell( const id::ElectronSubshellID& id ) const {
 
       auto iter = this->iterator( id );
-      if ( ( iter != this->subshells().end() ) && ( iter->identifier() == id ) ) {
+      if ( iter != this->subshells().end() && iter->identifier() == id ) {
 
         return *iter;
       }