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

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);
@@ -207 +244 @@
       destroyMolecule(*iter);
     }
-    // 2. (re-)create bondgraph
-    AtomComposite Set = getAllAtoms();
-    BG->CreateAdjacency(Set);
+    // 2. copy bond graph
+    if (!areBondsPresent(_step)) {
+//      AtomComposite Set = getAllAtoms();
+//      BG->cleanAdjacencyList(Set);
+      copyBondgraph(oldstep, _step);
+    }
 
     // 3. scan for connected subgraphs => molecules
@@ -839 +879 @@
   delete configuration;
   delete Thermostats;
-  delete homologies;
 }