Changes in src/World.cpp [388ddd:09f615]

File:

• src/World.cpp (modified) (3 diffs)

src/World.cpp

@@ -194 +194 @@
 }
 
-bool areBondsPresent(const unsigned int _step)
-{
-  bool status = false;
-
-  for (World::AtomConstIterator iter = const_cast<const World &>(World::getInstance()).getAtomIter();
-      (!status) && (iter != const_cast<const World &>(World::getInstance()).atomEnd()); ++iter) {
-    const atom * const Walker = *iter;
-    status |= !Walker->getListOfBondsAtStep(_step).empty();
-  }
-
-  return status;
-}
-
-void copyBondgraph(const unsigned int _srcstep, const unsigned int _deststep)
-{
-  // gather all bonds from _srcstep
-  std::set<bond *> SetOfBonds;
-  for (World::AtomConstIterator iter = const_cast<const World &>(World::getInstance()).getAtomIter();
-      iter != const_cast<const World &>(World::getInstance()).atomEnd(); ++iter) {
-    const atom * const Walker = *iter;
-    const BondList bonds = Walker->getListOfBondsAtStep(_srcstep);
-    BOOST_FOREACH( bond::ptr bondptr, bonds) {
-      SetOfBonds.insert(bondptr.get());
-    }
-  }
-  LOG(4, "DEBUG: We gathered " << SetOfBonds.size() << " bonds in total.");
-
-  // copy bond to new time step
-  for (std::set<bond *>::const_iterator bonditer = SetOfBonds.begin();
-      bonditer != SetOfBonds.end(); ++bonditer) {
-    const atom * const Walker = (*bonditer)->leftatom;
-    const atom * const OtherWalker = (*bonditer)->rightatom;
-    const_cast<atom *>(Walker)->addBond(_deststep, const_cast<atom *>(OtherWalker));
-  }
-}
-
 void World::setTime(const unsigned int _step)
 {
   if (_step != WorldTime::getTime()) {
-    const unsigned int oldstep = WorldTime::getTime();
     // set new time
     WorldTime::getInstance().setTime(_step);
@@ -244 +207 @@
       destroyMolecule(*iter);
     }
-    // 2. copy bond graph
-    if (!areBondsPresent(_step)) {
-//      AtomComposite Set = getAllAtoms();
-//      BG->cleanAdjacencyList(Set);
-      copyBondgraph(oldstep, _step);
-    }
+    // 2. (re-)create bondgraph
+    AtomComposite Set = getAllAtoms();
+    BG->CreateAdjacency(Set);
 
     // 3. scan for connected subgraphs => molecules
@@ -879 +839 @@
   delete configuration;
   delete Thermostats;
+  delete homologies;
 }