Changeset 03c77c

Timestamp:

Feb 24, 2011, 7:43:03 PM (14 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

6a465e

Parents:

8aba3c

git-author:

Frederik Heber <heber@…> (02/16/11 14:02:14)

git-committer:

Frederik Heber <heber@…> (02/24/11 19:43:03)

Message:

bonds::previous and ::next removed, lists.hpp deleted.

• the last of the concatenated lists has fallen to STL lists and vectors.
• greatest impact is on fragmentation functions.
• rewritten UniqueFragments::BondsPerSPList to vector<list<bond*> >.
• removed include of lists.hpp.
• removed lists.hpp from Makefile.am.

Location:

src

Files:

• ConfigFileBuffer.cpp (modified) (1 diff)
• Makefile.am (modified) (1 diff)
• atom.cpp (modified) (1 diff)
• atom_bondedparticle.cpp (modified) (2 diffs)
• bond.cpp (modified) (4 diffs)
• bond.hpp (modified) (1 diff)
• config.cpp (modified) (1 diff)
• graph.hpp (modified) (3 diffs)
• lists.hpp (deleted)
• molecule.cpp (modified) (1 diff)
• molecule.hpp (modified) (1 diff)
• molecule_fragmentation.cpp (modified) (20 diffs)
• molecule_graph.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (1 diff)
• periodentafel.cpp (modified) (1 diff)
• unittests/BondGraphUnitTest.cpp (modified) (1 diff)

src/ConfigFileBuffer.cpp

@@ -22 +22 @@
 #include "ConfigFileBuffer.hpp"
 #include "Helpers/helpers.hpp"
-#include "lists.hpp"
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"

src/Makefile.am

@@ -220 +220 @@
   graph.hpp \
   linkedcell.hpp \
-  lists.hpp \
   molecule.hpp \
   parser.hpp \

src/atom.cpp

@@ -24 +24 @@
 #include "config.hpp"
 #include "element.hpp"
-#include "lists.hpp"
 #include "parser.hpp"
 #include "LinearAlgebra/Vector.hpp"

src/atom_bondedparticle.cpp

@@ -27 +27 @@
 #include "CodePatterns/Verbose.hpp"
 #include "element.hpp"
-#include "lists.hpp"
 
 /** Constructor of class BondedParticle.
@@ -40 +39 @@
 BondedParticle::~BondedParticle()
 {
-  BondList::iterator Runner;
-  for (std::vector<BondList>::iterator iter = ListOfBonds.begin();
-      !ListOfBonds.empty();
-      iter = ListOfBonds.begin()) {
-    while (!(*iter).empty()) {
-      Runner = (*iter).begin();
-      removewithoutcheck(*Runner);
-    }
-    ListOfBonds.erase(iter);
+  const size_t max = ListOfBonds.size();
+  for (size_t i = 0; i < max; ++i) {
+    ClearBondsAtStep(i);
   }
 };

src/bond.cpp

@@ -24 +24 @@
 #include "bond.hpp"
 #include "element.hpp"
-#include "lists.hpp"
 
 
@@ -34 +33 @@
   leftatom(NULL),
   rightatom(NULL),
-  previous(NULL),
-  next(NULL),
   HydrogenBond(0),
   BondDegree(0),
@@ -53 +50 @@
   leftatom(left),
   rightatom(right),
-  previous(NULL),
-  next(NULL),
   HydrogenBond(0),
   BondDegree(degree),
@@ -79 +74 @@
   if (rightatom != NULL)
     rightatom->UnregisterBond(this);
-  unlink(this);
 };
 

src/bond.hpp

@@ -36 +36 @@
     atom *leftatom;    //!< first bond partner
     atom *rightatom;  //!< second bond partner
-    bond *previous; //!< previous atom in molecule list
-    bond *next;     //!< next atom in molecule list
     int HydrogenBond;  //!< Number of hydrogen atoms in the bond
     int BondDegree;    //!< single, double, triple, ... bond

src/config.cpp

@@ -31 +31 @@
 #include "Helpers/helpers.hpp"
 #include "CodePatterns/Info.hpp"
-#include "lists.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/toString.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
 #include "molecule.hpp"

src/graph.hpp

@@ -19 +19 @@
 #include <map>
 #include <set>
+#include <list>
 
 /****************************************** forward declarations *****************************/
@@ -61 +62 @@
  */
 struct UniqueFragments {
+  typedef std::list<bond*> BondsPerSP;
+  typedef std::vector< BondsPerSP > AllSPBonds;
+
   config *configuration;
   atom *Root;
@@ -71 +75 @@
   int *ShortestPathList;
   bool **UsedList;
-  bond **BondsPerSPList;
+  AllSPBonds BondsPerSPList;
   int *BondsPerSPCount;
 };

src/molecule.cpp

@@ -41 +41 @@
 #include "LinearAlgebra/Vector.hpp"
 #include "linkedcell.hpp"
-#include "lists.hpp"
 #include "molecule.hpp"
 #include "periodentafel.hpp"

src/molecule.hpp

@@ -261 +261 @@
   bool BuildInducedSubgraph(const molecule *Father);
   molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
-  void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
+  void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, std::vector<bond *> &BondsSet, int SetDimension, int SubOrder);
   int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
   int GuesstimateFragmentCount(int order);

src/molecule_fragmentation.cpp

@@ -28 +28 @@
 #include "element.hpp"
 #include "Helpers/helpers.hpp"
-#include "lists.hpp"
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
@@ -1105 +1104 @@
  * \param SetDimension maximum number of bits in power set
  * \param *FragmentSet snake stack to remove from
+ * \param &BondsSet set of bonds
  * \param *&TouchedList touched list
  * \param TouchedIndex currently touched
  * \return number of set bits
  */
-int AddPowersetToSnakeStack(int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, bond **BondsSet, int *&TouchedList, int &TouchedIndex)
+int AddPowersetToSnakeStack(int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, std::vector<bond *> &BondsSet, int *&TouchedList, int &TouchedIndex)
 {
   atom *OtherWalker = NULL;
@@ -1137 +1137 @@
 
 /** Counts the number of elements in a power set.
- * \param *SetFirst
- * \param *SetLast
+ * \param SetFirst begin iterator first bond
+ * \param SetLast end iterator
  * \param *&TouchedList touched list
  * \param TouchedIndex currently touched
  * \return number of elements
  */
-int CountSetMembers(bond *SetFirst, bond *SetLast, int *&TouchedList, int TouchedIndex)
+int CountSetMembers(std::list<bond *>::const_iterator SetFirst, std::list<bond *>::const_iterator SetLast, int *&TouchedList, int TouchedIndex)
 {
   int SetDimension = 0;
-  bond *Binder = SetFirst;    // start node for this level
-  while (Binder->next != SetLast) {    // compare to end node of this level
-    Binder = Binder->next;
+  for( std::list<bond *>::const_iterator Binder = SetFirst;
+      Binder != SetLast;
+      ++Binder) {
     for (int k=TouchedIndex;k--;) {
-      if (Binder->Contains(TouchedList[k]))   // if we added this very endpiece
+      if ((*Binder)->Contains(TouchedList[k]))   // if we added this very endpiece
         SetDimension++;
     }
@@ -1157 +1157 @@
 };
 
-/** Counts the number of elements in a power set.
- * \param *BondsList bonds list to fill
- * \param *SetFirst
- * \param *SetLast
+/** Fills a list of bonds from another
+ * \param *BondsList bonds array/vector to fill
+ * \param SetFirst begin iterator first bond
+ * \param SetLast end iterator
  * \param *&TouchedList touched list
  * \param TouchedIndex currently touched
  * \return number of elements
  */
-int FillBondsList(bond **BondsList, bond *SetFirst, bond *SetLast, int *&TouchedList, int TouchedIndex)
+int FillBondsList(std::vector<bond *> &BondsList, std::list<bond *>::const_iterator SetFirst, std::list<bond *>::const_iterator SetLast, int *&TouchedList, int TouchedIndex)
 {
   int SetDimension = 0;
-  bond *Binder = SetFirst;    // start node for this level
-  while (Binder->next != SetLast) {    // compare to end node of this level
-    Binder = Binder->next;
+  for( std::list<bond *>::const_iterator Binder = SetFirst;
+      Binder != SetLast;
+      ++Binder) {
     for (int k=0;k<TouchedIndex;k++) {
-      if (Binder->leftatom->nr == TouchedList[k])   // leftatom is always the close one
-        BondsList[SetDimension++] = Binder;
+      if ((*Binder)->leftatom->nr == TouchedList[k])   // leftatom is always the closer one
+        BondsList[SetDimension++] = (*Binder);
     }
   }
@@ -1210 +1210 @@
  *  -# removes all items added into the snake stack (in UniqueFragments structure) added during level (root
 distance) and current set
- * \param *out output stream for debugging
  * \param FragmentSearch UniqueFragments structure with all values needed
  * \param RootDistance current shortest path level, whose set of edges is represented by **BondsSet
+ * \param BondsSet array of bonds to check
  * \param SetDimension Number of possible bonds on this level (i.e. size of the array BondsSet[])
  * \param SubOrder remaining number of allowed vertices to add
  */
-void molecule::SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder)
+void molecule::SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, std::vector<bond *> &BondsSet, int SetDimension, int SubOrder)
 {
   int verbosity = 0; //FragmentSearch->ANOVAOrder-SubOrder;
@@ -1258 +1258 @@
 
           // first count the members in the subset
-          SubSetDimension = CountSetMembers(FragmentSearch->BondsPerSPList[2*SP], FragmentSearch->BondsPerSPList[2*SP+1], TouchedList, TouchedIndex);
+          SubSetDimension = CountSetMembers(FragmentSearch->BondsPerSPList[SP].begin(), FragmentSearch->BondsPerSPList[SP].end(), TouchedList, TouchedIndex);
 
           // then allocate and fill the list
-          bond *BondsList[SubSetDimension];
-          SubSetDimension = FillBondsList(BondsList, FragmentSearch->BondsPerSPList[2*SP], FragmentSearch->BondsPerSPList[2*SP+1], TouchedList, TouchedIndex);
+          std::vector<bond *> BondsList;
+          BondsList.resize(SubSetDimension);
+          SubSetDimension = FillBondsList(BondsList, FragmentSearch->BondsPerSPList[SP].begin(), FragmentSearch->BondsPerSPList[SP].end(), TouchedList, TouchedIndex);
 
           // then iterate
@@ -1300 +1301 @@
 void InitialiseSPList(int Order, struct UniqueFragments &FragmentSearch)
 {
-  FragmentSearch.BondsPerSPList = new bond* [Order * 2];
+  FragmentSearch.BondsPerSPList.resize(Order);
   FragmentSearch.BondsPerSPCount = new int[Order];
   for (int i=Order;i--;) {
-    FragmentSearch.BondsPerSPList[2*i] = new bond();    // start node
-    FragmentSearch.BondsPerSPList[2*i+1] = new bond();  // end node
-    FragmentSearch.BondsPerSPList[2*i]->next = FragmentSearch.BondsPerSPList[2*i+1];     // intertwine these two
-    FragmentSearch.BondsPerSPList[2*i+1]->previous = FragmentSearch.BondsPerSPList[2*i];
     FragmentSearch.BondsPerSPCount[i] = 0;
   }
@@ -1320 +1317 @@
 {
   delete[](FragmentSearch.BondsPerSPCount);
-  for (int i=Order;i--;) {
-    delete(FragmentSearch.BondsPerSPList[2*i]);
-    delete(FragmentSearch.BondsPerSPList[2*i+1]);
-  }
-  delete[](FragmentSearch.BondsPerSPList);
 };
 
@@ -1345 +1337 @@
   FragmentSearch.BondsPerSPCount[0] = 1;
   bond *Binder = new bond(FragmentSearch.Root, FragmentSearch.Root);
-  add(Binder, FragmentSearch.BondsPerSPList[1]);
+  FragmentSearch.BondsPerSPList[0].push_back(Binder);
 };
 
@@ -1356 +1348 @@
 void ResetSPList(int Order, struct UniqueFragments &FragmentSearch)
 {
-  bond *Binder = NULL;
   DoLog(0) && (Log() << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl);
   for(int i=Order;i--;) {
     DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << ": ");
-    Binder = FragmentSearch.BondsPerSPList[2*i];
-    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
-      Binder = Binder->next;
+    for (UniqueFragments::BondsPerSP::const_iterator iter = FragmentSearch.BondsPerSPList[i].begin();
+        iter != FragmentSearch.BondsPerSPList[i].end();
+        ++iter) {
       // Log() << Verbose(0) << "Removing atom " << Binder->leftatom->nr << " and " << Binder->rightatom->nr << "." << endl; // make sure numbers are local
-      FragmentSearch.ShortestPathList[Binder->leftatom->nr] = -1;
-      FragmentSearch.ShortestPathList[Binder->rightatom->nr] = -1;
+      FragmentSearch.ShortestPathList[(*iter)->leftatom->nr] = -1;
+      FragmentSearch.ShortestPathList[(*iter)->rightatom->nr] = -1;
     }
     // delete added bonds
-    cleanup(FragmentSearch.BondsPerSPList[2*i], FragmentSearch.BondsPerSPList[2*i+1]);
+    for (UniqueFragments::BondsPerSP::iterator iter = FragmentSearch.BondsPerSPList[i].begin();
+        iter != FragmentSearch.BondsPerSPList[i].end();
+        ++iter) {
+      delete(*iter);
+    }
+    FragmentSearch.BondsPerSPList[i].clear();
     // also start and end node
     DoLog(0) && (Log() << Verbose(0) << "cleaned." << endl);
@@ -1394 +1390 @@
   atom *OtherWalker = NULL;
   atom *Predecessor = NULL;
-  bond *CurrentEdge = NULL;
   bond *Binder = NULL;
   int RootKeyNr = FragmentSearch.Root->GetTrueFather()->nr;
@@ -1410 +1405 @@
 
     RemainingWalkers = FragmentSearch.BondsPerSPCount[SP];
-    CurrentEdge = FragmentSearch.BondsPerSPList[2*SP];    /// start of this SP level's list
-    while (CurrentEdge->next != FragmentSearch.BondsPerSPList[2*SP+1]) {    /// end of this SP level's list
-      CurrentEdge = CurrentEdge->next;
+    for (UniqueFragments::BondsPerSP::const_iterator CurrentEdge = FragmentSearch.BondsPerSPList[SP].begin();
+        CurrentEdge != FragmentSearch.BondsPerSPList[SP].end();
+        ++CurrentEdge) { /// start till end of this SP level's list
       RemainingWalkers--;
-      Walker = CurrentEdge->rightatom;    // rightatom is always the one more distant
-      Predecessor = CurrentEdge->leftatom;    // ... and leftatom is predecessor
+      Walker = (*CurrentEdge)->rightatom;    // rightatom is always the one more distant
+      Predecessor = (*CurrentEdge)->leftatom;    // ... and leftatom is predecessor
       AtomKeyNr = Walker->nr;
       DoLog(0) && (Log() << Verbose(0) << "Current Walker is: " << *Walker << " with nr " << Walker->nr << " and SP of " << SP << ", with " << RemainingWalkers << " remaining walkers on this level." << endl);
@@ -1438 +1433 @@
             // add the bond in between to the SP list
             Binder = new bond(Walker, OtherWalker); // create a new bond in such a manner, that bond::rightatom is always the one more distant
-            add(Binder, FragmentSearch.BondsPerSPList[2*(SP+1)+1]);
+            FragmentSearch.BondsPerSPList[SP+1].push_back(Binder);
             FragmentSearch.BondsPerSPCount[SP+1]++;
             DoLog(3) && (Log() << Verbose(3) << "Added its bond to SP list, having now " << FragmentSearch.BondsPerSPCount[SP+1] << " item(s)." << endl);
@@ -1460 +1455 @@
 void OutputSPList(int Order, struct UniqueFragments &FragmentSearch)
 {
-  bond *Binder = NULL;
   DoLog(0) && (Log() << Verbose(0) << "Printing all found lists." << endl);
   for(int i=1;i<Order;i++) {    // skip the root edge in the printing
-    Binder = FragmentSearch.BondsPerSPList[2*i];
     DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << "." << endl);
-    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
-      Binder = Binder->next;
+    for (UniqueFragments::BondsPerSP::const_iterator Binder = FragmentSearch.BondsPerSPList[i].begin();
+        Binder != FragmentSearch.BondsPerSPList[i].end();
+        ++Binder) {
       DoLog(2) && (Log() << Verbose(2) << *Binder << endl);
     }
@@ -1479 +1473 @@
 int CountNumbersInBondsList(int Order, struct UniqueFragments &FragmentSearch)
 {
-  bond *Binder = NULL;
   int SP = -1;  // the Root <-> Root edge must be subtracted!
   for(int i=Order;i--;) { // sum up all found edges
-    Binder = FragmentSearch.BondsPerSPList[2*i];
-    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
-      Binder = Binder->next;
+    for (UniqueFragments::BondsPerSP::const_iterator Binder = FragmentSearch.BondsPerSPList[i].begin();
+        Binder != FragmentSearch.BondsPerSPList[i].end();
+        ++Binder) {
       SP++;
     }
@@ -1531 +1524 @@
 
     // prepare the subset and call the generator
-    bond* BondsList[FragmentSearch.BondsPerSPCount[0]];
-    for(int i=0;i<FragmentSearch.BondsPerSPCount[0];i++)
-      BondsList[i] = NULL;
-    BondsList[0] = FragmentSearch.BondsPerSPList[0]->next;  // on SP level 0 there's only the root bond
+    std::vector<bond*> BondsList;
+    BondsList.resize(FragmentSearch.BondsPerSPCount[0]);
+    ASSERT(FragmentSearch.BondsPerSPList[0].size() != 0,
+        "molecule::PowerSetGenerator() - FragmentSearch.BondsPerSPList[0] contains no root bond.");
+    BondsList[0] = (*FragmentSearch.BondsPerSPList[0].begin());  // on SP level 0 there's only the root bond
 
     SPFragmentGenerator(&FragmentSearch, 0, BondsList, FragmentSearch.BondsPerSPCount[0], Order);
@@ -1797 +1791 @@
 {
   bond *Binder = NULL;
-  bond *OtherBinder = NULL;
+  //bond *OtherBinder = NULL;
   atom *Walker = NULL;
   atom *OtherWalker = NULL;
@@ -1803 +1797 @@
   enum Shading *ColorList = NULL;
   double tmp;
-  bool LastBond = true; // only needed to due list construct
+  //bool LastBond = true; // only needed to due list construct
   Vector Translationvector;
   //std::deque<atom *> *CompStack = NULL;
@@ -1829 +1823 @@
           //Log() << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl;
           if (tmp > BondDistance) {
-//            OtherBinder = Binder->next; // note down binding partner for later re-insertion
-//            if (OtherBinder != NULL) {
-//              LastBond = false;
-//            } else {
-//              OtherBinder = Binder->previous;
-//              LastBond = true;
-//            }
-//            unlink(Binder);   // unlink bond
             DoLog(2) && (Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl);
             flag = true;
@@ -1877 +1863 @@
         }
       }
-      // re-add bond
-      if (OtherBinder == NULL) { // is the only bond?
-        //Do nothing
-      } else {
-        if (!LastBond) {
-          link(Binder, OtherBinder);
-        } else {
-          link(OtherBinder, Binder);
-        }
-      }
+//      // re-add bond
+//      if (OtherBinder == NULL) { // is the only bond?
+//        //Do nothing
+//      } else {
+//        if (!LastBond) {
+//          link(Binder, OtherBinder); // no more implemented bond::previous ...
+//        } else {
+//          link(OtherBinder, Binder); // no more implemented bond::previous ...
+//        }
+//      }
     } else {
       DoLog(3) && (Log() << Verbose(3) << "No corrections for this fragment." << endl);

src/molecule_graph.cpp

@@ -32 +32 @@
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "linkedcell.hpp"
-#include "lists.hpp"
 #include "molecule.hpp"
 #include "World.hpp"

src/moleculelist.cpp

@@ -38 +38 @@
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "linkedcell.hpp"
-#include "lists.hpp"
 #include "molecule.hpp"
 #include "periodentafel.hpp"

src/periodentafel.cpp

@@ -29 +29 @@
 #include "Helpers/helpers.hpp"
 #include "CodePatterns/Log.hpp"
-//#include "lists.hpp"
 #include "periodentafel.hpp"
 #include "CodePatterns/Verbose.hpp"

src/unittests/BondGraphUnitTest.cpp

@@ -156 +156 @@
 {
 
-  //atom *Walker = TestMolecule->start->next;
-  //atom *Runner = TestMolecule->end->previous;
-  //CPPUNIT_ASSERT( TestMolecule->end != Walker );
   CPPUNIT_ASSERT_EQUAL( false , BG->LoadBondLengthTable(dummy) );
   CPPUNIT_ASSERT_EQUAL( true , BG->ConstructBondGraph(TestMolecule) );