refactor: Sweep through underlying AtomType-using classes (#2209)

Co-authored-by: Tristan Youngs <trisyoungs@googlemail.com>

Author: trisyoungs

benchmark/modules/angle.cpp

@@ -26,7 +26,7 @@ template <SpeciesType speciesType, SpeciesPopulation population> static void BM_
     module.keywords().set("ExcludeSameSiteAC", false);
     for (auto _ : state)
     {
-        problemDef.configuration()->incrementContentsVersion();
+        problemDef.configuration()->notifyAtomicPositionsChanged();
         module.executeProcessing(problemDef.dissolve());
     }
 }

benchmark/modules/siteRDF.cpp

@@ -18,7 +18,7 @@ template <SpeciesType speciesType, SpeciesPopulation population> static void BM_
     module.keywords().set("SiteB", sites);
     for (auto _ : state)
     {
-        problemDef.configuration()->incrementContentsVersion();
+        problemDef.configuration()->notifyAtomicPositionsChanged();
         module.executeProcessing(problemDef.dissolve());
     }
 }

benchmark/modules/voxelDensity.cpp

@@ -18,7 +18,7 @@ static void BM_Module_VoxelDensity(benchmark::State &state)
     module.keywords().setEnumeration("TargetProperty", property);
     for (auto _ : state)
     {
-        problemDef.configuration()->incrementContentsVersion();
+        problemDef.configuration()->notifyAtomicPositionsChanged();
         module.executeProcessing(problemDef.dissolve());
     }
 }

src/classes/CMakeLists.txt

@@ -4,8 +4,6 @@ add_library(
   array3DIterator.cpp
   atom.cpp
   atomType.cpp
-  atomTypeData.cpp
-  atomTypeMix.cpp
   bondFunctions.cpp
   box.cpp
   boxCubic.cpp
@@ -34,11 +32,10 @@ add_library(
   empiricalFormula.cpp
   fullPairIterator.cpp
   histogramSet.cpp
-  isotopeData.cpp
+  isotopeMix.cpp
   isotopologue.cpp
   isotopologues.cpp
   isotopologueSet.cpp
-  isotopologueWeight.cpp
   kVector.cpp
   localMolecule.cpp
   molecule.cpp
@@ -81,9 +78,7 @@ add_library(
   angleFunctions.h
   array3DIterator.h
   atom.h
-  atomTypeData.h
   atomType.h
-  atomTypeMix.h
   bondFunctions.h
   box.h
   braggReflection.h
@@ -99,11 +94,10 @@ add_library(
   empiricalFormula.h
   histogramSet.h
   interactionPotential.h
-  isotopeData.h
+  isotopeMix.h
   isotopologue.h
   isotopologues.h
   isotopologueSet.h
-  isotopologueWeight.h
   kVector.h
   localMolecule.h
   molecule.h

src/classes/atom.cpp

@@ -25,11 +25,11 @@ double Atom::y() const { return r_.y; }
 // Return z-coordinate
 double Atom::z() const { return r_.z; }
 
-// Set local AtomType index
-void Atom::setLocalTypeIndex(int id) { localTypeIndex_ = id; }
+// Set AtomType index in parent Configuration
+void Atom::setConfigurationTypeIndex(int id) { configurationTypeIndex_ = id; }
 
-// Return local AtomType index
-int Atom::localTypeIndex() const { return localTypeIndex_; }
+// Return AtomType index in parent Configuration
+int Atom::configurationTypeIndex() const { return configurationTypeIndex_; }
 
 // Set master AtomType index
 void Atom::setMasterTypeIndex(int id) { masterTypeIndex_ = id; }

src/classes/atom.h

@@ -23,7 +23,7 @@ class Atom
     // Coordinates
     Vector3 r_;
     // Assigned AtomType index, local to Configuration (for partial indexing etc.)
-    int localTypeIndex_{-1};
+    int configurationTypeIndex_{-1};
     // Assigned master AtomType index (for pair potential indexing)
     int masterTypeIndex_{-1};
 
@@ -40,10 +40,10 @@ class Atom
     double y() const;
     // Return z-coordinate
     double z() const;
-    // Set local AtomType index
-    void setLocalTypeIndex(int id);
-    // Return local AtomType index
-    int localTypeIndex() const;
+    // Set AtomType index in parent Configuration
+    void setConfigurationTypeIndex(int id);
+    // Return AtomType index in parent Configuration
+    int configurationTypeIndex() const;
     // Set master AtomType index
     void setMasterTypeIndex(int id);
     // Return master AtomType index